From 86e827ef546042fb1ec2a48806550ae04b382941 Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 27 Jan 2022 18:15:24 +0100 Subject: [PATCH 01/27] draft add_workflow_run function --- notebooks/ROcrate-example.ipynb | 160 ++++++++++++++++++++++++++++++++ rocrate/rocrate.py | 33 +++++++ rocrate/rocrate_api.py | 22 +++++ 3 files changed, 215 insertions(+) create mode 100644 notebooks/ROcrate-example.ipynb diff --git a/notebooks/ROcrate-example.ipynb b/notebooks/ROcrate-example.ipynb new file mode 100644 index 00000000..ca290661 --- /dev/null +++ b/notebooks/ROcrate-example.ipynb @@ -0,0 +1,160 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "sys.path.append('/home/padge/Elixir/workflow-export/ro-crate-py/')\n", + "import os\n", + "from rocrate.rocrate import ROCrate\n", + "base_path = '/home/padge/Elixir/workflow-export/'" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'/home/padge/Elixir/workflow-export/ro-crate-py/notebooks'" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "os.getcwd()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# adding a Dataset\n", + "crate = ROCrate()\n", + "os.makedirs(\"tmp3\", exist_ok=True)\n", + "open('tmp3/empty_file', 'w').close()\n", + "dataset_entity = crate.add_directory(source=\"tmpd3\", dest_path=\"new_tmp\")\n", + "crate.write(\"./new_crate4\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from IPython.core.debugger import set_trace;set_trace()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "SRR10903401\n", + "FooBar\n" + ] + } + ], + "source": [ + "shutil.rmtree(\"/home/padge/Downloads/Elixir/ro-crate-py/tmp/crate\")\n", + "shutil.copytree(\"/home/padge/Downloads/Elixir/ro-crate-py/test/test-data/read_crate\", \"/home/padge/Downloads/Elixir/ro-crate-py/tmp/crate\")\n", + "crate = ROCrate(\"/home/padge/Downloads/Elixir/ro-crate-py/tmp/crate\")\n", + "readme = crate.dereference(\"test_file_galaxy.txt\")\n", + "with open(readme.source, \"rt\") as f:\n", + " print(f.readline().strip())\n", + "new_source = \"/home/padge/Downloads/Elixir/ro-crate-py/tmp/foobar.txt\"\n", + "with open(new_source, \"wt\") as f:\n", + " f.write(\"FooBar\\n\")\n", + "crate.delete(readme)\n", + "crate.add_file(new_source, \"test_file_galaxy.txt\")\n", + "crate.write(\"/home/padge/Downloads/Elixir/ro-crate-py/tmp/crate\")\n", + "with open(readme.source, \"rt\") as f:\n", + " print(f.readline().strip())\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# import pdb\n", + "from IPython.core.debugger import set_trace\n", + "set_trace()\n", + "\n", + "# adding a Dataset\n", + "crate = ROCrate(\"/home/padge/Downloads/Elixir/ro-crate-py/tmp/crate/\")\n", + "sample_dir = '/home/padge/Downloads/Elixir/ro-crate-py/tmp/examples2/'\n", + "dataset_entity = crate.add_directory(sample_dir, \"new_dir\")\n", + "crate.write(\"/home/padge/Downloads/Elixir/ro-crate-py/tmp/crate2\")\n" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "from rocrate import rocrate_api\n", + "\n", + "wf_path = base_path + \"example-history-export3.ga\"\n", + "dataset_path = base_path + \"example-history-export3/datasets/\"\n", + "files_list = os.listdir(dataset_path)\n", + "files_list = [dataset_path + f for f in files_list]\n", + "\n", + "# Create base package\n", + "wf_crate = rocrate_api.make_workflow_rocrate(workflow_path=wf_path,wf_type=\"Galaxy\",include_files=files_list)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [], + "source": [ + "# write crate to disk\n", + "out_path = base_path + \"example-history-export3-crate\"\n", + "wf_crate.write(out_path)" + ] + } + ], + "metadata": { + "interpreter": { + "hash": "bcc799c17010608b26cede4750872a7cf236af662c7ba3d883e539f7db8da28c" + }, + "kernelspec": { + "display_name": "Python 3.9.5 64-bit ('base': conda)", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.5" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py index 8d5befc7..091e7fbc 100644 --- a/rocrate/rocrate.py +++ b/rocrate/rocrate.py @@ -522,6 +522,39 @@ def add_workflow( workflow.subjectOf = cwl_workflow return workflow + def add_workflow_run( + self, source=None, dest_path=None, fetch_remote=False, validate_url=True, properties=None, + main=False, lang="cwl", lang_version=None, gen_cwl=False, cls=ComputationalWorkflow + ): + workflow_run = self.add(cls( + self, source=source, dest_path=dest_path, fetch_remote=fetch_remote, + validate_url=validate_url, properties=properties + )) + if isinstance(lang, ComputerLanguage): + assert lang.crate is self + else: + kwargs = {"version": lang_version} if lang_version else {} + lang = get_lang(self, lang, **kwargs) + self.add(lang) + lang_str = lang.id.rsplit("#", 1)[1] + workflow_run.lang = lang + if main: + self.mainEntity = workflow_run + profiles = set(_.rstrip("/") for _ in get_norm_value(self.metadata, "conformsTo")) + profiles.add(WORKFLOW_PROFILE) + self.metadata["conformsTo"] = [{"@id": _} for _ in sorted(profiles)] + if gen_cwl and lang_str != "cwl": + if lang_str != "galaxy": + raise ValueError(f"conversion from {lang.name} to abstract CWL not supported") + cwl_source = galaxy_to_abstract_cwl(source) + cwl_dest_path = Path(source).with_suffix(".cwl").name + cwl_workflow = self.add_workflow_run( + source=cwl_source, dest_path=cwl_dest_path, fetch_remote=fetch_remote, properties=properties, + main=False, lang="cwl", gen_cwl=False, cls=WorkflowDescription + ) + workflow_run.subjectOf = cwl_workflow + return workflow_run + def add_test_suite(self, identifier=None, name=None, main_entity=None): test_ref_prop = "mentions" if not main_entity: diff --git a/rocrate/rocrate_api.py b/rocrate/rocrate_api.py index 31100d46..308fa5b1 100644 --- a/rocrate/rocrate_api.py +++ b/rocrate/rocrate_api.py @@ -76,3 +76,25 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], wf_crate.add_file(file_entry) return wf_crate + +def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata, author=None, include_files=[], + fetch_remote=False, cwl=None, diagram=None): + + wfr_crate = roc.ROCrate() + workflow_path = Path(workflow_path) + wf_file = wfr_crate.add_workflow( + workflow_path, workflow_path.name, fetch_remote=fetch_remote, + main=True, lang=wf_type, gen_cwl=(cwl is None) + ) + + # if the source is a remote URL then add https://schema.org/codeRepository + # property to it this can be checked by checking if the source is a URL + # instead of a local path + if 'url' in wf_file.properties(): + wf_file['codeRepository'] = wf_file['url'] + + # add extra files + for file_entry in include_files: + wfr_crate.add_file(file_entry) + + return wfr_crate \ No newline at end of file From 5d291a45481e35998a41e58167b9e72ac048bc5d Mon Sep 17 00:00:00 2001 From: pauldg Date: Tue, 22 Feb 2022 18:32:40 +0100 Subject: [PATCH 02/27] first functions and tests for parsing a galaxy export and extracting prov from it --- rocrate/provenance_constants.py | 55 ++ rocrate/provenance_profile.py | 749 ++++++++++++++++++ rocrate/rocrate_api.py | 2 +- .../collections_attrs.txt | 1 + ...tenate_datasets_on_data_2_and_data_1_3.txt | 4 + .../datasets/dataset1.txt_2.txt | 2 + .../datasets/dataset2.txt_1.txt | 2 + .../datasets/tutorial_output.txt_4.txt | 3 + .../test_ga_history_export/datasets_attrs.txt | 101 +++ .../datasets_attrs.txt.provenance | 1 + .../test_ga_history_export/export_attrs.txt | 1 + .../test_ga_history_export/history_attrs.txt | 11 + .../implicit_collection_jobs_attrs.txt | 1 + .../test_ga_history_export/jobs_attrs.txt | 165 ++++ .../libraries_attrs.txt | 1 + .../ro-crate-metadata.json | 92 +++ test/test_parse_ga_export.py | 20 + tools/parse_ga_export.py | 18 + 18 files changed, 1228 insertions(+), 1 deletion(-) create mode 100644 rocrate/provenance_constants.py create mode 100644 rocrate/provenance_profile.py create mode 100644 test/test-data/test_ga_history_export/collections_attrs.txt create mode 100644 test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt create mode 100644 test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt create mode 100644 test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt create mode 100644 test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt create mode 100644 test/test-data/test_ga_history_export/datasets_attrs.txt create mode 100644 test/test-data/test_ga_history_export/datasets_attrs.txt.provenance create mode 100644 test/test-data/test_ga_history_export/export_attrs.txt create mode 100644 test/test-data/test_ga_history_export/history_attrs.txt create mode 100644 test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt create mode 100644 test/test-data/test_ga_history_export/jobs_attrs.txt create mode 100644 test/test-data/test_ga_history_export/libraries_attrs.txt create mode 100644 test/test-data/test_ga_history_export/ro-crate-metadata.json create mode 100644 test/test_parse_ga_export.py create mode 100644 tools/parse_ga_export.py diff --git a/rocrate/provenance_constants.py b/rocrate/provenance_constants.py new file mode 100644 index 00000000..0e4956c4 --- /dev/null +++ b/rocrate/provenance_constants.py @@ -0,0 +1,55 @@ +import hashlib +import os +import uuid + +from prov.identifier import Namespace + +__citation__ = "https://doi.org/10.5281/zenodo.1208477" + +# NOTE: Semantic versioning of the CWLProv Research Object +# **and** the cwlprov files +# +# Rough guide (major.minor.patch): +# 1. Bump major number if removing/"breaking" resources or PROV statements +# 2. Bump minor number if adding resources or PROV statements +# 3. Bump patch number for non-breaking non-adding changes, +# e.g. fixing broken relative paths +CWLPROV_VERSION = "https://w3id.org/cwl/prov/0.6.0" + +# Research Object folders +METADATA = "metadata" +DATA = "data" +WORKFLOW = "workflow" +SNAPSHOT = "snapshot" +# sub-folders +MAIN = os.path.join(WORKFLOW, "main") +PROVENANCE = os.path.join(METADATA, "provenance") +LOGS = os.path.join(METADATA, "logs") +WFDESC = Namespace("wfdesc", "http://purl.org/wf4ever/wfdesc#") +WFPROV = Namespace("wfprov", "http://purl.org/wf4ever/wfprov#") +WF4EVER = Namespace("wf4ever", "http://purl.org/wf4ever/wf4ever#") +RO = Namespace("ro", "http://purl.org/wf4ever/ro#") +ORE = Namespace("ore", "http://www.openarchives.org/ore/terms/") +FOAF = Namespace("foaf", "http://xmlns.com/foaf/0.1/") +SCHEMA = Namespace("schema", "http://schema.org/") +CWLPROV = Namespace("cwlprov", "https://w3id.org/cwl/prov#") +ORCID = Namespace("orcid", "https://orcid.org/") +UUID = Namespace("id", "urn:uuid:") + +# BagIt and YAML always use UTF-8 +ENCODING = "UTF-8" +TEXT_PLAIN = 'text/plain; charset="%s"' % ENCODING + +# sha1, compatible with the File type's "checksum" field +# e.g. "checksum" = "sha1$47a013e660d408619d894b20806b1d5086aab03b" +# See ./cwltool/schemas/v1.0/Process.yml +Hasher = hashlib.sha1 +SHA1 = "sha1" +SHA256 = "sha256" +SHA512 = "sha512" + +# TODO: Better identifiers for user, at least +# these should be preserved in ~/.config/cwl for every execution +# on this host +USER_UUID = uuid.uuid4().urn +ACCOUNT_UUID = uuid.uuid4().urn diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py new file mode 100644 index 00000000..bda49007 --- /dev/null +++ b/rocrate/provenance_profile.py @@ -0,0 +1,749 @@ +import copy +import datetime +import logging +import urllib +import uuid +from io import BytesIO +from pathlib import PurePath, PurePosixPath +from socket import getfqdn +from typing import ( + Any, + Dict, + List, + MutableMapping, + MutableSequence, + Optional, + Tuple, + Union, + cast, +) + +from prov.identifier import Identifier +from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity +from schema_salad.sourceline import SourceLine +from typing_extensions import TYPE_CHECKING + +# from .errors import WorkflowException +# from .job import CommandLineJob, JobBase +# from .loghandler import #_logger +# from .process import Process, shortname +from rocrate.provenance_constants import ( + ACCOUNT_UUID, + CWLPROV, + ENCODING, + FOAF, + METADATA, + ORE, + PROVENANCE, + RO, + SCHEMA, + SHA1, + SHA256, + TEXT_PLAIN, + UUID, + WF4EVER, + WFDESC, + WFPROV, +) +# from .stdfsaccess import StdFsAccess +from rocrate.utils_cwl import CWLObjectType, JobsType, get_listing, posix_path, versionstring +# from .workflow_job import WorkflowJob + +# if TYPE_CHECKING: +# from rocrate.provenance import ResearchObject + +from pathlib import Path +import rocrate.rocrate as roc + + +class ProvenanceProfile: + """ + Provenance profile. + + Populated from a galaxy workflow export. + """ + + def __init__( + self, + ga_export: Dict, #"ResearchObject", #should be changed to ro_crate? + full_name: str, + orcid: str, + # fsaccess: StdFsAccess, + run_uuid: Optional[uuid.UUID] = None, + ) -> None: + """ + Initialize the provenance profile. + Keyword arguments: + research_object -- the research object or ro-crate + full_name -- author name + orcid -- orcid (optional) + fsaccess -- file system access to create RO + run_uuid -- uuid for the workflow run + """ + # self.fsaccess = fsaccess + self.orcid = orcid + self.ga_export = ga_export + # self.research_object = research_object + # self.folder = self.research_object.folder + self.ro_uuid = uuid.uuid4() + # TODO: should be connected to a ro_crate? + self.base_uri = "arcp://uuid,%s/" % self.ro_uuid + self.document = ProvDocument() + # TODO extract engine_uuid from galaxy, type: str + self.engine_uuid = "urn:uuid:%s" % uuid.uuid4() #type: str + # self.add_to_manifest = self.research_object.add_to_manifest + self.full_name = full_name + self.workflow_run_uuid = run_uuid or uuid.uuid4() + self.workflow_run_uri = self.workflow_run_uuid.urn # type: str + self.generate_prov_doc() + + def __str__(self) -> str: + """Represent this Provenvance profile as a string.""" + return "ProvenanceProfile <{}>".format( + self.workflow_run_uri, + # self.research_object, #? + ) + + def generate_prov_doc(self) -> Tuple[str, ProvDocument]: + """Add basic namespaces.""" + # TODO: + # can we identify a host where the workflow was executed? + # should OnlineAccount be used to describe a galaxy user? + # PROV_TYPE: FOAF["OnlineAccount"], + + # TODO: + # need to check how to get the exact galaxy version + self.galaxy_version = "galaxy" #%s" % versionstring().split()[-1] + # TODO: change notation to already imported namespaces? + self.document.add_namespace("wfprov", "http://purl.org/wf4ever/wfprov#") + # document.add_namespace('prov', 'http://www.w3.org/ns/prov#') + self.document.add_namespace("wfdesc", "http://purl.org/wf4ever/wfdesc#") + # TODO: Make this ontology. For now only has cwlprov:image + self.document.add_namespace("cwlprov", "https://w3id.org/cwl/prov#") + self.document.add_namespace("foaf", "http://xmlns.com/foaf/0.1/") + self.document.add_namespace("schema", "http://schema.org/") + self.document.add_namespace("orcid", "https://orcid.org/") + self.document.add_namespace("id", "urn:uuid:") + # NOTE: Internet draft expired 2004-03-04 (!) + # https://tools.ietf.org/html/draft-thiemann-hash-urn-01 + # TODO: Change to nih:sha-256; hashes + # https://tools.ietf.org/html/rfc6920#section-7 + self.document.add_namespace("data", "urn:hash::sha1:") + # Also needed for docker images + # self.document.add_namespace(SHA256, "nih:sha-256;") + + # info only, won't really be used by prov as sub-resources use + # annotations + # self.document.add_namespace("researchobject", self.research_object.base_uri) + # self.metadata_ns = self.document.add_namespace( + # "metadata", self.research_object.base_uri + METADATA + "/" + # ) + # Pre-register provenance directory so we can refer to its files + self.provenance_ns = self.document.add_namespace( + "provenance", self.base_uri + posix_path(PROVENANCE) + "/" + ) + # TODO: use appropriate refs for ga_export and related inputs + ro_identifier_workflow = self.base_uri + "ga_export" + self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow) + ro_identifier_input = ( + self.base_uri + "ga_export/datasets#" + ) + self.document.add_namespace("input", ro_identifier_input) + + # More info about the account (e.g. username, fullname) + # TODO: extract this info from galaxy somehow, probably only a username + account = self.document.agent(ACCOUNT_UUID) + if self.orcid or self.full_name: + person = {PROV_TYPE: PROV["Person"], "prov:type": SCHEMA["Person"]} + if self.full_name: + person["prov:label"] = self.full_name + person["foaf:name"] = self.full_name + person["schema:name"] = self.full_name + else: + # TODO: Look up name from ORCID API? + pass + # print(self.orcid or uuid.uuid4().urn) + agent = self.document.agent(self.orcid or uuid.uuid4().urn, person) + self.document.actedOnBehalfOf(account, agent) + + # The engine that executed the workflow + wfengine = self.document.agent( + self.engine_uuid, + { + PROV_TYPE: PROV["SoftwareAgent"], + "prov:type": WFPROV["WorkflowEngine"], + # TODO: get galaxy version + "prov:label": "galaxy_version_placeholder", + }, + ) + # FIXME: This datetime will be a bit too delayed, we should + # capture when cwltool.py earliest started? + self.document.wasStartedBy(wfengine, None, account, datetime.datetime.now()) + # define workflow run level activity + self.document.activity( + self.workflow_run_uri, + datetime.datetime.now(), + None, + { + PROV_TYPE: WFPROV["WorkflowRun"], + "prov:label": "Run of galaxy workflow", + }, + ) + # association between SoftwareAgent and WorkflowRun + main_workflow = "wf:main" + # print(self.workflow_run_uri, self.engine_uuid, main_workflow) + self.document.wasAssociatedWith( + self.workflow_run_uri, self.engine_uuid, main_workflow + ) + self.document.wasStartedBy( + self.workflow_run_uri, None, self.engine_uuid, datetime.datetime.now() + ) + return (self.workflow_run_uri, self.document) + + # def evaluate( + # self, + # process: Process, + # job: JobsType, + # job_order_object: CWLObjectType, + # research_obj: "ResearchObject", + # ) -> None: + # """Evaluate the nature of job.""" + # if not hasattr(process, "steps"): + # # record provenance of independent commandline tool executions + # self.prospective_prov(job) + # customised_job = copy_job_order(job, job_order_object) + # self.used_artefacts(customised_job, self.workflow_run_uri) + # research_obj.create_job(customised_job) + # elif hasattr(job, "workflow"): + # # record provenance of workflow executions + # self.prospective_prov(job) + # customised_job = copy_job_order(job, job_order_object) + # self.used_artefacts(customised_job, self.workflow_run_uri) + + def declare_process( + self, + process_name: str, + ga_export_jobs_attrs: list, + when: datetime.datetime, + process_run_id: Optional[str] = None, + ) -> str: + """Record the start of each Process.""" + if process_run_id is None: + process_run_id = uuid.uuid4().urn + prov_label = "Run of ga_export/jobs_attrs.txt#" + process_name + self.document.activity( + process_run_id, + None, + None, + {PROV_TYPE: WFPROV["ProcessRun"], PROV_LABEL: prov_label}, + ) + self.document.wasAssociatedWith( + process_run_id, self.engine_uuid, str("wf:main/" + process_name) + ) + self.document.wasStartedBy( + process_run_id, None, self.workflow_run_uri, when, None, None + ) + return process_run_id + + def record_process_end( + self, + process_name: str, + process_run_id: str, + outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None], + when: datetime.datetime, + ) -> None: + self.generate_output_prov(outputs, process_run_id, process_name) + self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when) + + def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, str]: + if value["class"] != "File": + raise ValueError("Must have class:File: %s" % value) + # Need to determine file hash aka RO filename + entity = None # type: Optional[ProvEntity] + checksum = None + if "checksum" in value: + csum = cast(str, value["checksum"]) + (method, checksum) = csum.split("$", 1) + if method == SHA1: # and self.research_object.has_data_file(checksum): + entity = self.document.entity("data:" + checksum) + + if not entity and "location" in value: + location = str(value["location"]) + # If we made it here, we'll have to add it to the RO + with self.fsaccess.open(location, "rb") as fhandle: + relative_path = self.research_object.add_data_file(fhandle) + # FIXME: This naively relies on add_data_file setting hash as filename + checksum = PurePath(relative_path).name + entity = self.document.entity( + "data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]} + ) + if "checksum" not in value: + value["checksum"] = f"{SHA1}${checksum}" + + if not entity and "contents" in value: + # Anonymous file, add content as string + entity, checksum = self.declare_string(cast(str, value["contents"])) + + # By here one of them should have worked! + if not entity or not checksum: + raise ValueError( + "class:File but missing checksum/location/content: %r" % value + ) + + # Track filename and extension, this is generally useful only for + # secondaryFiles. Note that multiple uses of a file might thus record + # different names for the same entity, so we'll + # make/track a specialized entity by UUID + file_id = value.setdefault("@id", uuid.uuid4().urn) + # A specialized entity that has just these names + file_entity = self.document.entity( + file_id, + [(PROV_TYPE, WFPROV["Artifact"]), (PROV_TYPE, WF4EVER["File"])], + ) # type: ProvEntity + + if "basename" in value: + file_entity.add_attributes({CWLPROV["basename"]: value["basename"]}) + if "nameroot" in value: + file_entity.add_attributes({CWLPROV["nameroot"]: value["nameroot"]}) + if "nameext" in value: + file_entity.add_attributes({CWLPROV["nameext"]: value["nameext"]}) + self.document.specializationOf(file_entity, entity) + + # Check for secondaries + for sec in cast( + MutableSequence[CWLObjectType], value.get("secondaryFiles", []) + ): + # TODO: Record these in a specializationOf entity with UUID? + if sec["class"] == "File": + (sec_entity, _, _) = self.declare_file(sec) + elif sec["class"] == "Directory": + sec_entity = self.declare_directory(sec) + else: + raise ValueError(f"Got unexpected secondaryFiles value: {sec}") + # We don't know how/when/where the secondary file was generated, + # but CWL convention is a kind of summary/index derived + # from the original file. As its generally in a different format + # then prov:Quotation is not appropriate. + self.document.derivation( + sec_entity, + file_entity, + other_attributes={PROV["type"]: CWLPROV["SecondaryFile"]}, + ) + + return file_entity, entity, checksum + + def declare_directory(self, value: CWLObjectType) -> ProvEntity: + """Register any nested files/directories.""" + # FIXME: Calculate a hash-like identifier for directory + # so we get same value if it's the same filenames/hashes + # in a different location. + # For now, mint a new UUID to identify this directory, but + # attempt to keep it inside the value dictionary + dir_id = cast(str, value.setdefault("@id", uuid.uuid4().urn)) + + # New annotation file to keep the ORE Folder listing + ore_doc_fn = dir_id.replace("urn:uuid:", "directory-") + ".ttl" + dir_bundle = self.document.bundle(self.metadata_ns[ore_doc_fn]) + + coll = self.document.entity( + dir_id, + [ + (PROV_TYPE, WFPROV["Artifact"]), + (PROV_TYPE, PROV["Collection"]), + (PROV_TYPE, PROV["Dictionary"]), + (PROV_TYPE, RO["Folder"]), + ], + ) + # ORE description of ro:Folder, saved separately + coll_b = dir_bundle.entity( + dir_id, + [(PROV_TYPE, RO["Folder"]), (PROV_TYPE, ORE["Aggregation"])], + ) + self.document.mentionOf(dir_id + "#ore", dir_id, dir_bundle.identifier) + + # dir_manifest = dir_bundle.entity( + # dir_bundle.identifier, {PROV["type"]: ORE["ResourceMap"], + # ORE["describes"]: coll_b.identifier}) + + coll_attribs = [(ORE["isDescribedBy"], dir_bundle.identifier)] + coll_b_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] + + # FIXME: .listing might not be populated yet - hopefully + # a later call to this method will sort that + is_empty = True + + if "listing" not in value: + get_listing(self.fsaccess, value) + for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])): + is_empty = False + # Declare child-artifacts + entity = self.declare_artefact(entry) + self.document.membership(coll, entity) + # Membership relation aka our ORE Proxy + m_id = uuid.uuid4().urn + m_entity = self.document.entity(m_id) + m_b = dir_bundle.entity(m_id) + + # PROV-O style Dictionary + # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition + # ..as prov.py do not currently allow PROV-N extensions + # like hadDictionaryMember(..) + m_entity.add_asserted_type(PROV["KeyEntityPair"]) + + m_entity.add_attributes( + { + PROV["pairKey"]: entry["basename"], + PROV["pairEntity"]: entity, + } + ) + + # As well as a being a + # http://wf4ever.github.io/ro/2016-01-28/ro/#FolderEntry + m_b.add_asserted_type(RO["FolderEntry"]) + m_b.add_asserted_type(ORE["Proxy"]) + m_b.add_attributes( + { + RO["entryName"]: entry["basename"], + ORE["proxyIn"]: coll, + ORE["proxyFor"]: entity, + } + ) + coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) + coll_b_attribs.append((ORE["aggregates"], m_b)) + + coll.add_attributes(coll_attribs) + coll_b.add_attributes(coll_b_attribs) + + # Also Save ORE Folder as annotation metadata + ore_doc = ProvDocument() + ore_doc.add_namespace(ORE) + ore_doc.add_namespace(RO) + ore_doc.add_namespace(UUID) + ore_doc.add_bundle(dir_bundle) + ore_doc = ore_doc.flattened() + ore_doc_path = str(PurePosixPath(METADATA, ore_doc_fn)) + with self.research_object.write_bag_file(ore_doc_path) as provenance_file: + ore_doc.serialize(provenance_file, format="rdf", rdf_format="turtle") + self.research_object.add_annotation( + dir_id, [ore_doc_fn], ORE["isDescribedBy"].uri + ) + + if is_empty: + # Empty directory + coll.add_asserted_type(PROV["EmptyCollection"]) + coll.add_asserted_type(PROV["EmptyDictionary"]) + self.research_object.add_uri(coll.identifier.uri) + return coll + + def declare_string(self, value: str) -> Tuple[ProvEntity, str]: + """Save as string in UTF-8.""" + byte_s = BytesIO(str(value).encode(ENCODING)) + data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN) + checksum = PurePosixPath(data_file).name + # FIXME: Don't naively assume add_data_file uses hash in filename! + data_id = "data:%s" % PurePosixPath(data_file).stem + entity = self.document.entity( + data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)} + ) # type: ProvEntity + return entity, checksum + + def declare_artefact(self, value: Any) -> ProvEntity: + """Create data artefact entities for all file objects.""" + if value is None: + # FIXME: If this can happen in CWL, we'll + # need a better way to represent this in PROV + return self.document.entity(CWLPROV["None"], {PROV_LABEL: "None"}) + + if isinstance(value, (bool, int, float)): + # Typically used in job documents for flags + + # FIXME: Make consistent hash URIs for these + # that somehow include the type + # (so "1" != 1 != "1.0" != true) + entity = self.document.entity(uuid.uuid4().urn, {PROV_VALUE: value}) + self.research_object.add_uri(entity.identifier.uri) + return entity + + if isinstance(value, (str, str)): + (entity, _) = self.declare_string(value) + return entity + + if isinstance(value, bytes): + # If we got here then we must be in Python 3 + byte_s = BytesIO(value) + data_file = self.research_object.add_data_file(byte_s) + # FIXME: Don't naively assume add_data_file uses hash in filename! + data_id = "data:%s" % PurePosixPath(data_file).stem + return self.document.entity( + data_id, + {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)}, + ) + + if isinstance(value, MutableMapping): + if "@id" in value: + # Already processed this value, but it might not be in this PROV + entities = self.document.get_record(value["@id"]) + if entities: + return entities[0] + # else, unknown in PROV, re-add below as if it's fresh + + # Base case - we found a File we need to update + if value.get("class") == "File": + (entity, _, _) = self.declare_file(value) + value["@id"] = entity.identifier.uri + return entity + + if value.get("class") == "Directory": + entity = self.declare_directory(value) + value["@id"] = entity.identifier.uri + return entity + coll_id = value.setdefault("@id", uuid.uuid4().urn) + # some other kind of dictionary? + # TODO: also Save as JSON + coll = self.document.entity( + coll_id, + [ + (PROV_TYPE, WFPROV["Artifact"]), + (PROV_TYPE, PROV["Collection"]), + (PROV_TYPE, PROV["Dictionary"]), + ], + ) + + if value.get("class"): + #_logger.warning("Unknown data class %s.", value["class"]) + # FIXME: The class might be "http://example.com/somethingelse" + coll.add_asserted_type(CWLPROV[value["class"]]) + + # Let's iterate and recurse + coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] + for (key, val) in value.items(): + v_ent = self.declare_artefact(val) + self.document.membership(coll, v_ent) + m_entity = self.document.entity(uuid.uuid4().urn) + # Note: only support PROV-O style dictionary + # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition + # as prov.py do not easily allow PROV-N extensions + m_entity.add_asserted_type(PROV["KeyEntityPair"]) + m_entity.add_attributes( + {PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent} + ) + coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) + coll.add_attributes(coll_attribs) + self.research_object.add_uri(coll.identifier.uri) + return coll + + # some other kind of Collection? + # TODO: also save as JSON + try: + members = [] + for each_input_obj in iter(value): + # Recurse and register any nested objects + e = self.declare_artefact(each_input_obj) + members.append(e) + + # If we reached this, then we were allowed to iterate + coll = self.document.entity( + uuid.uuid4().urn, + [ + (PROV_TYPE, WFPROV["Artifact"]), + (PROV_TYPE, PROV["Collection"]), + ], + ) + if not members: + coll.add_asserted_type(PROV["EmptyCollection"]) + else: + for member in members: + # FIXME: This won't preserve order, for that + # we would need to use PROV.Dictionary + # with numeric keys + self.document.membership(coll, member) + self.research_object.add_uri(coll.identifier.uri) + # FIXME: list value does not support adding "@id" + return coll + except TypeError: + #_logger.warning("Unrecognized type %s of %r", type(value), value) + # Let's just fall back to Python repr() + entity = self.document.entity(uuid.uuid4().urn, {PROV_LABEL: repr(value)}) + self.research_object.add_uri(entity.identifier.uri) + return entity + + def used_artefacts( + self, + job_order: Union[CWLObjectType, List[CWLObjectType]], + process_run_id: str, + name: Optional[str] = None, + ) -> None: + """Add used() for each data artefact.""" + if isinstance(job_order, list): + for entry in job_order: + self.used_artefacts(entry, process_run_id, name) + else: + # FIXME: Use workflow name in packed.cwl, "main" is wrong for nested workflows + base = "main" + if name is not None: + base += "/" + name + for key, value in job_order.items(): + prov_role = self.wf_ns[f"{base}/{key}"] + try: + entity = self.declare_artefact(value) + self.document.used( + process_run_id, + entity, + datetime.datetime.now(), + None, + {"prov:role": prov_role}, + ) + except OSError: + pass + + def generate_output_prov( + self, + final_output: Union[CWLObjectType, MutableSequence[CWLObjectType], None], + process_run_id: Optional[str], + name: Optional[str], + ) -> None: + """Call wasGeneratedBy() for each output,copy the files into the RO.""" + if isinstance(final_output, MutableSequence): + for entry in final_output: + self.generate_output_prov(entry, process_run_id, name) + elif final_output is not None: + # Timestamp should be created at the earliest + timestamp = datetime.datetime.now() + + # For each output, find/register the corresponding + # entity (UUID) and document it as generated in + # a role corresponding to the output + for output, value in final_output.items(): + entity = self.declare_artefact(value) + if name is not None: + name = urllib.parse.quote(str(name), safe=":/,#") + # FIXME: Probably not "main" in nested workflows + role = self.wf_ns[f"main/{name}/{output}"] + else: + role = self.wf_ns["main/%s" % output] + + if not process_run_id: + process_run_id = self.workflow_run_uri + + self.document.wasGeneratedBy( + entity, process_run_id, timestamp, None, {"prov:role": role} + ) + + def prospective_prov(self, job: JobsType) -> None: + """Create prospective prov recording as wfdesc prov:Plan.""" + if not isinstance(job, WorkflowJob): + # direct command line tool execution + self.document.entity( + "wf:main", + { + PROV_TYPE: WFDESC["Process"], + "prov:type": PROV["Plan"], + "prov:label": "Prospective provenance", + }, + ) + return + + self.document.entity( + "wf:main", + { + PROV_TYPE: WFDESC["Workflow"], + "prov:type": PROV["Plan"], + "prov:label": "Prospective provenance", + }, + ) + + for step in job.steps: + stepnametemp = "wf:main/" + str(step.name)[5:] + stepname = urllib.parse.quote(stepnametemp, safe=":/,#") + provstep = self.document.entity( + stepname, + {PROV_TYPE: WFDESC["Process"], "prov:type": PROV["Plan"]}, + ) + self.document.entity( + "wf:main", + { + "wfdesc:hasSubProcess": provstep, + "prov:label": "Prospective provenance", + }, + ) + # TODO: Declare roles/parameters as well + + def activity_has_provenance(self, activity, prov_ids): + # type: (str, List[Identifier]) -> None + """Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files.""" + # NOTE: The below will only work if the corresponding metadata/provenance arcp URI + # is a pre-registered namespace in the PROV Document + attribs = [(PROV["has_provenance"], prov_id) for prov_id in prov_ids] + self.document.activity(activity, other_attributes=attribs) + # Tip: we can't use https://www.w3.org/TR/prov-links/#term-mention + # as prov:mentionOf() is only for entities, not activities + uris = [i.uri for i in prov_ids] + self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) + + def finalize_prov_profile(self, name): + # type: (Optional[str]) -> List[Identifier] + """Transfer the provenance related files to the RO.""" + # NOTE: Relative posix path + if name is None: + # main workflow, fixed filenames + filename = "primary.cwlprov" + else: + # ASCII-friendly filename, avoiding % as we don't want %2520 in manifest.json + wf_name = urllib.parse.quote(str(name), safe="").replace("%", "_") + # Note that the above could cause overlaps for similarly named + # workflows, but that's OK as we'll also include run uuid + # which also covers thhe case of this step being run in + # multiple places or iterations + filename = f"{wf_name}.{self.workflow_run_uuid}.cwlprov" + + basename = str(PurePosixPath(PROVENANCE) / filename) + + # TODO: Also support other profiles than CWLProv, e.g. ProvOne + + # list of prov identifiers of provenance files + prov_ids = [] + + # https://www.w3.org/TR/prov-xml/ + with self.research_object.write_bag_file(basename + ".xml") as provenance_file: + self.document.serialize(provenance_file, format="xml", indent=4) + prov_ids.append(self.provenance_ns[filename + ".xml"]) + + # https://www.w3.org/TR/prov-n/ + with self.research_object.write_bag_file( + basename + ".provn" + ) as provenance_file: + self.document.serialize(provenance_file, format="provn", indent=2) + prov_ids.append(self.provenance_ns[filename + ".provn"]) + + # https://www.w3.org/Submission/prov-json/ + with self.research_object.write_bag_file(basename + ".json") as provenance_file: + self.document.serialize(provenance_file, format="json", indent=2) + prov_ids.append(self.provenance_ns[filename + ".json"]) + + # "rdf" aka https://www.w3.org/TR/prov-o/ + # which can be serialized to ttl/nt/jsonld (and more!) + + # https://www.w3.org/TR/turtle/ + with self.research_object.write_bag_file(basename + ".ttl") as provenance_file: + self.document.serialize(provenance_file, format="rdf", rdf_format="turtle") + prov_ids.append(self.provenance_ns[filename + ".ttl"]) + + # https://www.w3.org/TR/n-triples/ + with self.research_object.write_bag_file(basename + ".nt") as provenance_file: + self.document.serialize( + provenance_file, format="rdf", rdf_format="ntriples" + ) + prov_ids.append(self.provenance_ns[filename + ".nt"]) + + # https://www.w3.org/TR/json-ld/ + # TODO: Use a nice JSON-LD context + # see also https://eprints.soton.ac.uk/395985/ + # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld :( + with self.research_object.write_bag_file( + basename + ".jsonld" + ) as provenance_file: + self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") + prov_ids.append(self.provenance_ns[filename + ".jsonld"]) + + #_logger.debug("[provenance] added provenance: %s", prov_ids) + return prov_ids diff --git a/rocrate/rocrate_api.py b/rocrate/rocrate_api.py index 308fa5b1..c944a3ee 100644 --- a/rocrate/rocrate_api.py +++ b/rocrate/rocrate_api.py @@ -78,7 +78,7 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], return wf_crate def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata, author=None, include_files=[], - fetch_remote=False, cwl=None, diagram=None): + fetch_remote=False, cwl=None, diagram=None): wfr_crate = roc.ROCrate() workflow_path = Path(workflow_path) diff --git a/test/test-data/test_ga_history_export/collections_attrs.txt b/test/test-data/test_ga_history_export/collections_attrs.txt new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/collections_attrs.txt @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt b/test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt new file mode 100644 index 00000000..8b3f00b0 --- /dev/null +++ b/test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt @@ -0,0 +1,4 @@ +hello +universe! +hello +world diff --git a/test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt b/test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt new file mode 100644 index 00000000..94954abd --- /dev/null +++ b/test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt @@ -0,0 +1,2 @@ +hello +world diff --git a/test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt b/test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt new file mode 100644 index 00000000..718e715c --- /dev/null +++ b/test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt @@ -0,0 +1,2 @@ +hello +universe! diff --git a/test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt b/test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt new file mode 100644 index 00000000..f631dd54 --- /dev/null +++ b/test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt @@ -0,0 +1,3 @@ +hello +universe! +world diff --git a/test/test-data/test_ga_history_export/datasets_attrs.txt b/test/test-data/test_ga_history_export/datasets_attrs.txt new file mode 100644 index 00000000..2a1cf10b --- /dev/null +++ b/test/test-data/test_ga_history_export/datasets_attrs.txt @@ -0,0 +1,101 @@ +[{ + "annotation": null, + "blurb": "2 lines", + "copied_from_history_dataset_association_id_chain": ["2524d3d3b68ad39a"], + "create_time": "2021-06-23 10:46:27.112621", + "dataset_uuid": "18e78952-9447-4215-942c-542c35250d20", + "deleted": false, + "designation": null, + "encoded_id": "7ca3de8f49293d1a", + "extension": "txt", + "file_name": "datasets/dataset2.txt_1.txt", + "hid": 1, + "history_encoded_id": "a9eae7b6d5994701", + "info": "", + "metadata": { + "data_lines": 2, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "dataset2.txt", + "peek": "hello\nuniverse!\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:46:28.363987", + "visible": true +}, { + "annotation": null, + "blurb": "2 lines", + "copied_from_history_dataset_association_id_chain": ["7c1d8e3101dbcdba"], + "create_time": "2021-06-23 10:46:27.185496", + "dataset_uuid": "6b0af26e-574c-475a-bb6d-1b4df9f137d8", + "deleted": false, + "designation": null, + "encoded_id": "2e789aae2475b7da", + "extension": "txt", + "file_name": "datasets/dataset1.txt_2.txt", + "hid": 2, + "history_encoded_id": "a9eae7b6d5994701", + "info": "", + "metadata": { + "data_lines": 2, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "dataset1.txt", + "peek": "hello\nworld\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:46:28.363991", + "visible": true +}, { + "annotation": null, + "blurb": "4 lines", + "copied_from_history_dataset_association_id_chain": [], + "create_time": "2021-06-23 10:46:28.365628", + "dataset_uuid": "cf936245-b1d6-4840-b79d-2e20af74b921", + "deleted": false, + "designation": "out_file1", + "encoded_id": "fd7fec473f1e6c6b", + "extension": "txt", + "file_name": "datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt", + "hid": 3, + "history_encoded_id": "a9eae7b6d5994701", + "info": "", + "metadata": { + "data_lines": 4, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "Concatenate datasets on data 2 and data 1", + "peek": "hello\nuniverse!\nhello\nworld\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:46:44.644667", + "visible": true +}, { + "annotation": null, + "blurb": "3 lines", + "copied_from_history_dataset_association_id_chain": [], + "create_time": "2021-06-23 10:46:28.531348", + "dataset_uuid": "d9b5abdc-2a54-4fb7-b3df-1f05e9f2399a", + "deleted": false, + "designation": "out_file1", + "encoded_id": "775bc9b3c1750167", + "extension": "txt", + "file_name": "datasets/tutorial_output.txt_4.txt", + "hid": 4, + "history_encoded_id": "a9eae7b6d5994701", + "info": "\nKept 3 of 4 total lines.\nUsed random seed of \"0\".", + "metadata": { + "data_lines": 3, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "tutorial_output.txt", + "peek": "hello\nuniverse!\nworld\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:47:04.750978", + "visible": true +}] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/datasets_attrs.txt.provenance b/test/test-data/test_ga_history_export/datasets_attrs.txt.provenance new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/datasets_attrs.txt.provenance @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/export_attrs.txt b/test/test-data/test_ga_history_export/export_attrs.txt new file mode 100644 index 00000000..a2100763 --- /dev/null +++ b/test/test-data/test_ga_history_export/export_attrs.txt @@ -0,0 +1 @@ +{"galaxy_export_version": "2"} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_attrs.txt b/test/test-data/test_ga_history_export/history_attrs.txt new file mode 100644 index 00000000..53de783c --- /dev/null +++ b/test/test-data/test_ga_history_export/history_attrs.txt @@ -0,0 +1,11 @@ +{ + "model_class": "History", + "create_time": "2021-06-23 10:46:26.457161", + "update_time": "2022-01-06 17:05:06.816140", + "name": "Minimal-history", + "hid_counter": 5, + "genome_build": "?", + "annotation": null, + "tags": ["planemo-tutorial"], + "encoded_id": "a9eae7b6d5994701" +} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt b/test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/jobs_attrs.txt b/test/test-data/test_ga_history_export/jobs_attrs.txt new file mode 100644 index 00000000..1e2a84f0 --- /dev/null +++ b/test/test-data/test_ga_history_export/jobs_attrs.txt @@ -0,0 +1,165 @@ +[{ + "command_line": "python '/srv/galaxy/shared/src/lib/galaxy/tools/data_fetch.py' --galaxy-root '/srv/galaxy/shared/src' --datatypes-registry '/srv/galaxy/shared/etc/tmpdir/jwd/079/79718/registry.xml' --request-version '1' --request '/srv/galaxy/shared/etc/tmpdir/jwd/079/79718/configs/tmpjgi6b5_u'", + "create_time": "2021-06-23T10:20:22.770291", + "encoded_id": "7b69c80a9f428343", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": {}, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "output0": ["2524d3d3b68ad39a"] + }, + "params": { + "file_count": "1", + "files": [{ + "__index__": 0, + "file_data": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" + }], + "paramfile": null, + "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"ext\": \"auto\", \"dbkey\": \"?\", \"to_posix_lines\": true, \"src\": \"path\", \"name\": \"dataset2.txt\", \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2\", \"object_id\": 155708}], \"auto_decompress\": false}], \"check_content\": true}", + "request_version": "1" + }, + "state": "ok", + "tool_id": "__DATA_FETCH__", + "tool_stderr": "", + "tool_stdout": "", + "tool_version": "0.1.0", + "traceback": null, + "update_time": "2021-06-23T10:20:42.041319" +}, { + "command_line": "python '/srv/galaxy/shared/src/lib/galaxy/tools/data_fetch.py' --galaxy-root '/srv/galaxy/shared/src' --datatypes-registry '/srv/galaxy/shared/etc/tmpdir/jwd/079/79717/registry.xml' --request-version '1' --request '/srv/galaxy/shared/etc/tmpdir/jwd/079/79717/configs/tmpmod1j0bw'", + "create_time": "2021-06-23T10:20:00.981702", + "encoded_id": "77dd7a937748a715", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": {}, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "output0": ["7c1d8e3101dbcdba"] + }, + "params": { + "file_count": "1", + "files": [{ + "__index__": 0, + "file_data": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a" + }], + "paramfile": null, + "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"ext\": \"auto\", \"dbkey\": \"?\", \"to_posix_lines\": true, \"src\": \"path\", \"name\": \"dataset1.txt\", \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a\", \"object_id\": 155707}], \"auto_decompress\": false}], \"check_content\": true}", + "request_version": "1" + }, + "state": "ok", + "tool_id": "__DATA_FETCH__", + "tool_stderr": "", + "tool_stdout": "", + "tool_version": "0.1.0", + "traceback": null, + "update_time": "2021-06-23T10:20:22.202678" +}, { + "command_line": "python /srv/galaxy/shared/src/tools/filters/catWrapper.py '/srv/galaxy/shared/etc/tmpdir/jwd/079/79726/outputs/galaxy_dataset_cf936245-b1d6-4840-b79d-2e20af74b921.dat' '/srv/galaxy/shared/database/files/000/134/dataset_134410.dat' '/srv/galaxy/shared/database/files/000/134/dataset_134409.dat'", + "create_time": "2021-06-23T10:46:28.351123", + "encoded_id": "77cf44871c57dd95", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": { + "input1": ["7ca3de8f49293d1a"], + "queries_0|input2": ["2e789aae2475b7da"] + }, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "out_file1": ["fd7fec473f1e6c6b"] + }, + "params": { + "__input_ext": "txt", + "__workflow_invocation_uuid__": "42f21c0ad41011eb87defa163eba836f", + "chromInfo": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "dbkey": "?", + "input1": { + "values": [{ + "id": "7ca3de8f49293d1a", + "src": "hda" + }] + }, + "queries": [{ + "__index__": 0, + "input2": { + "values": [{ + "id": "2e789aae2475b7da", + "src": "hda" + }] + } + }] + }, + "state": "ok", + "tool_id": "cat1", + "tool_stderr": "", + "tool_stdout": "", + "tool_version": "1.0.0", + "traceback": null, + "update_time": "2021-06-23T10:46:44.738703" +}, { + "command_line": "python '/srv/galaxy/shared/src/tools/filters/random_lines_two_pass.py' '/srv/galaxy/shared/database/files/000/134/dataset_134423.dat' '/srv/galaxy/shared/etc/tmpdir/jwd/079/79727/outputs/galaxy_dataset_d9b5abdc-2a54-4fb7-b3df-1f05e9f2399a.dat' '3' --seed '0'", + "create_time": "2021-06-23T10:46:28.526901", + "encoded_id": "ea1a7696fd6484de", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": { + "input": ["fd7fec473f1e6c6b"] + }, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "out_file1": ["775bc9b3c1750167"] + }, + "params": { + "__input_ext": "txt", + "__workflow_invocation_uuid__": "42f21c0ad41011eb87defa163eba836f", + "chromInfo": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "dbkey": "?", + "input": { + "values": [{ + "id": "fd7fec473f1e6c6b", + "src": "hda" + }] + }, + "num_lines": "3", + "seed_source": { + "__current_case__": 1, + "seed": "0", + "seed_source_selector": "set_seed" + } + }, + "state": "ok", + "tool_id": "random_lines1", + "tool_stderr": "", + "tool_stdout": "Kept 3 of 4 total lines.\nUsed random seed of \"0\".\n", + "tool_version": "2.0.2", + "traceback": null, + "update_time": "2021-06-23T10:47:04.837750" +}] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/libraries_attrs.txt b/test/test-data/test_ga_history_export/libraries_attrs.txt new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/libraries_attrs.txt @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/ro-crate-metadata.json b/test/test-data/test_ga_history_export/ro-crate-metadata.json new file mode 100644 index 00000000..ff182bec --- /dev/null +++ b/test/test-data/test_ga_history_export/ro-crate-metadata.json @@ -0,0 +1,92 @@ +{ + "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "datePublished": "2021-11-29T18:48:54+00:00", + "hasPart": [ + { + "@id": "datasets/" + }, + { + "@id": "implicit_collection_jobs_attrs.txt" + }, + { + "@id": "jobs_attrs.txt" + }, + { + "@id": "libraries_attrs.txt" + }, + { + "@id": "history_attrs.txt" + }, + { + "@id": "datasets_attrs.txt" + }, + { + "@id": "collections_attrs.txt" + }, + { + "@id": "datasets_attrs.txt.provenance" + }, + { + "@id": "export_attrs.txt" + }, + { + "@id": "datasets/a.tab_1.tabular" + } + ] + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": { + "@id": "https://w3id.org/ro/crate/1.1" + } + }, + { + "@id": "datasets/", + "@type": "Dataset" + }, + { + "@id": "implicit_collection_jobs_attrs.txt", + "@type": "File" + }, + { + "@id": "jobs_attrs.txt", + "@type": "File" + }, + { + "@id": "libraries_attrs.txt", + "@type": "File" + }, + { + "@id": "history_attrs.txt", + "@type": "File" + }, + { + "@id": "datasets_attrs.txt", + "@type": "File" + }, + { + "@id": "collections_attrs.txt", + "@type": "File" + }, + { + "@id": "datasets_attrs.txt.provenance", + "@type": "File" + }, + { + "@id": "export_attrs.txt", + "@type": "File" + }, + { + "@id": "datasets/a.tab_1.tabular", + "@type": "File" + } + ] +} \ No newline at end of file diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py new file mode 100644 index 00000000..5417da6c --- /dev/null +++ b/test/test_parse_ga_export.py @@ -0,0 +1,20 @@ +import sys +import pytest +from typing import ( + Tuple, +) +from prov.model import ProvDocument +sys.path.append('./ro-crate-py') +from rocrate.rocrate import ROCrate +from tools import parse_ga_export +from rocrate.provenance_profile import ProvenanceProfile + +def test_ga_history_parsing(test_data_dir, tmpdir, helpers): + export_dir = "test_ga_history_export" + export_path = test_data_dir / export_dir + + metadata_export = parse_ga_export.ga_history_export(export_path) + prov = ProvenanceProfile(metadata_export, "PDG", "https://orcid.org/0000-0002-8940-4946") + print(len(metadata_export['jobs_attrs'])) + # print(prov.document.serialize(format="rdf", rdf_format="turtle")) + assert isinstance(prov, ProvenanceProfile) \ No newline at end of file diff --git a/tools/parse_ga_export.py b/tools/parse_ga_export.py new file mode 100644 index 00000000..52e5553d --- /dev/null +++ b/tools/parse_ga_export.py @@ -0,0 +1,18 @@ +import json +import os +import re + +def ga_history_export(export_dir): + fn_list = os.listdir(export_dir) + + export_metadata = {} + for f in fn_list : + export_dir_path = os.path.join(export_dir,f) + if os.path.isfile(export_dir_path): + with open(export_dir_path,"r") as fh: + # create keys for metadata files, removes '.' and 'txt' from fn + key = '_'.join(list(filter(None, re.split('\.|txt',f)))) + export_metadata[key] = json.loads(fh.read()) + + + return export_metadata \ No newline at end of file From c4378f46eba385a7c411ae4367a58d6c721847aa Mon Sep 17 00:00:00 2001 From: pauldg Date: Tue, 22 Feb 2022 18:49:13 +0100 Subject: [PATCH 03/27] add process parsing functionc --- rocrate/provenance_profile.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index bda49007..763a7a26 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -222,19 +222,26 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: def declare_process( self, - process_name: str, - ga_export_jobs_attrs: list, + # process_name: str, + ga_export_jobs_attrs: dict, when: datetime.datetime, process_run_id: Optional[str] = None, ) -> str: """Record the start of each Process.""" if process_run_id is None: process_run_id = uuid.uuid4().urn + + cmd = ga_export_jobs_attrs["command_line"] + process_name = ga_export_jobs_attrs["tool_id"] + tool_version = ga_export_jobs_attrs["tool_version"] prov_label = "Run of ga_export/jobs_attrs.txt#" + process_name + start_time = ga_export_jobs_attrs["create_time"] + end_time = ga_export_jobs_attrs["update_time"] + self.document.activity( process_run_id, - None, - None, + start_time, + end_time, {PROV_TYPE: WFPROV["ProcessRun"], PROV_LABEL: prov_label}, ) self.document.wasAssociatedWith( From df026556c2a61c45bb473d50e06ca6f742135ca6 Mon Sep 17 00:00:00 2001 From: pauldg Date: Wed, 23 Feb 2022 20:44:11 +0100 Subject: [PATCH 04/27] added functions for parsing history export --- rocrate/provenance_profile.py | 44 +++-- .../history_export/collections_attrs.txt | 1 + ...tenate_datasets_on_data_2_and_data_1_3.txt | 4 + .../datasets/dataset1.txt_2.txt | 2 + .../datasets/dataset2.txt_1.txt | 2 + .../datasets/tutorial_output.txt_4.txt | 3 + .../history_export/datasets_attrs.txt | 101 +++++++++++ .../datasets_attrs.txt.provenance | 1 + .../history_export/export_attrs.txt | 1 + .../history_export/history_attrs.txt | 11 ++ .../implicit_collection_jobs_attrs.txt | 1 + .../history_export/jobs_attrs.txt | 165 ++++++++++++++++++ .../history_export/libraries_attrs.txt | 1 + .../test_ga_history_export/wf_definition.ga | 131 ++++++++++++++ test/test_parse_ga_export.py | 51 +++++- tools/parse_ga_export.py | 3 +- 16 files changed, 502 insertions(+), 20 deletions(-) create mode 100644 test/test-data/test_ga_history_export/history_export/collections_attrs.txt create mode 100644 test/test-data/test_ga_history_export/history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt create mode 100644 test/test-data/test_ga_history_export/history_export/datasets/dataset1.txt_2.txt create mode 100644 test/test-data/test_ga_history_export/history_export/datasets/dataset2.txt_1.txt create mode 100644 test/test-data/test_ga_history_export/history_export/datasets/tutorial_output.txt_4.txt create mode 100644 test/test-data/test_ga_history_export/history_export/datasets_attrs.txt create mode 100644 test/test-data/test_ga_history_export/history_export/datasets_attrs.txt.provenance create mode 100644 test/test-data/test_ga_history_export/history_export/export_attrs.txt create mode 100644 test/test-data/test_ga_history_export/history_export/history_attrs.txt create mode 100644 test/test-data/test_ga_history_export/history_export/implicit_collection_jobs_attrs.txt create mode 100644 test/test-data/test_ga_history_export/history_export/jobs_attrs.txt create mode 100644 test/test-data/test_ga_history_export/history_export/libraries_attrs.txt create mode 100644 test/test-data/test_ga_history_export/wf_definition.ga diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 763a7a26..c6e711db 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -55,6 +55,9 @@ from pathlib import Path import rocrate.rocrate as roc +def posix_path(local_path: str) -> str: + return str(PurePosixPath(Path(local_path))) + class ProvenanceProfile: """ @@ -96,6 +99,8 @@ def __init__( self.workflow_run_uuid = run_uuid or uuid.uuid4() self.workflow_run_uri = self.workflow_run_uuid.urn # type: str self.generate_prov_doc() + for job in ga_export["jobs_attrs"]: + self.declare_process(job) def __str__(self) -> str: """Represent this Provenvance profile as a string.""" @@ -224,7 +229,7 @@ def declare_process( self, # process_name: str, ga_export_jobs_attrs: dict, - when: datetime.datetime, + # when: datetime.datetime, process_run_id: Optional[str] = None, ) -> str: """Record the start of each Process.""" @@ -238,17 +243,27 @@ def declare_process( start_time = ga_export_jobs_attrs["create_time"] end_time = ga_export_jobs_attrs["update_time"] + # cmd = self.document.entity( + # uuid.uuid4().urn, + # {PROV_TYPE: WFPROV["Artifact"], PROV_LABEL: ga_export_jobs_attrs["command_line"]} + # ) + self.document.activity( process_run_id, start_time, end_time, - {PROV_TYPE: WFPROV["ProcessRun"], PROV_LABEL: prov_label}, + { + PROV_TYPE: WFPROV["ProcessRun"], + PROV_LABEL: prov_label, + # Find out how to include commandline as a string + # PROV_LABEL: cmd + }, ) self.document.wasAssociatedWith( process_run_id, self.engine_uuid, str("wf:main/" + process_name) ) self.document.wasStartedBy( - process_run_id, None, self.workflow_run_uri, when, None, None + process_run_id, None, self.workflow_run_uri, start_time, None, None ) return process_run_id @@ -256,13 +271,13 @@ def record_process_end( self, process_name: str, process_run_id: str, - outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None], + # outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None], when: datetime.datetime, ) -> None: self.generate_output_prov(outputs, process_run_id, process_name) self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when) - def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, str]: + def declare_file(self) -> Tuple[ProvEntity, ProvEntity, str]: if value["class"] != "File": raise ValueError("Must have class:File: %s" % value) # Need to determine file hash aka RO filename @@ -318,7 +333,8 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st # Check for secondaries for sec in cast( - MutableSequence[CWLObjectType], value.get("secondaryFiles", []) + # MutableSequence[CWLObjectType], + value.get("secondaryFiles", []) ): # TODO: Record these in a specializationOf entity with UUID? if sec["class"] == "File": @@ -339,7 +355,9 @@ def declare_file(self, value: CWLObjectType) -> Tuple[ProvEntity, ProvEntity, st return file_entity, entity, checksum - def declare_directory(self, value: CWLObjectType) -> ProvEntity: + def declare_directory(self + # , value: CWLObjectType + ) -> ProvEntity: """Register any nested files/directories.""" # FIXME: Calculate a hash-like identifier for directory # so we get same value if it's the same filenames/hashes @@ -444,15 +462,15 @@ def declare_directory(self, value: CWLObjectType) -> ProvEntity: def declare_string(self, value: str) -> Tuple[ProvEntity, str]: """Save as string in UTF-8.""" - byte_s = BytesIO(str(value).encode(ENCODING)) - data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN) - checksum = PurePosixPath(data_file).name + # byte_s = BytesIO(str(value).encode(ENCODING)) + # data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN) + # checksum = PurePosixPath(data_file).name # FIXME: Don't naively assume add_data_file uses hash in filename! data_id = "data:%s" % PurePosixPath(data_file).stem entity = self.document.entity( data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)} ) # type: ProvEntity - return entity, checksum + return entity #, checksum def declare_artefact(self, value: Any) -> ProvEntity: """Create data artefact entities for all file objects.""" @@ -689,11 +707,11 @@ def activity_has_provenance(self, activity, prov_ids): def finalize_prov_profile(self, name): # type: (Optional[str]) -> List[Identifier] - """Transfer the provenance related files to the RO.""" + """Transfer the provenance related files to the RO-crate""" # NOTE: Relative posix path if name is None: # main workflow, fixed filenames - filename = "primary.cwlprov" + filename = "ga_export.cwlprov" else: # ASCII-friendly filename, avoiding % as we don't want %2520 in manifest.json wf_name = urllib.parse.quote(str(name), safe="").replace("%", "_") diff --git a/test/test-data/test_ga_history_export/history_export/collections_attrs.txt b/test/test-data/test_ga_history_export/history_export/collections_attrs.txt new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/collections_attrs.txt @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt b/test/test-data/test_ga_history_export/history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt new file mode 100644 index 00000000..8b3f00b0 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt @@ -0,0 +1,4 @@ +hello +universe! +hello +world diff --git a/test/test-data/test_ga_history_export/history_export/datasets/dataset1.txt_2.txt b/test/test-data/test_ga_history_export/history_export/datasets/dataset1.txt_2.txt new file mode 100644 index 00000000..94954abd --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/datasets/dataset1.txt_2.txt @@ -0,0 +1,2 @@ +hello +world diff --git a/test/test-data/test_ga_history_export/history_export/datasets/dataset2.txt_1.txt b/test/test-data/test_ga_history_export/history_export/datasets/dataset2.txt_1.txt new file mode 100644 index 00000000..718e715c --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/datasets/dataset2.txt_1.txt @@ -0,0 +1,2 @@ +hello +universe! diff --git a/test/test-data/test_ga_history_export/history_export/datasets/tutorial_output.txt_4.txt b/test/test-data/test_ga_history_export/history_export/datasets/tutorial_output.txt_4.txt new file mode 100644 index 00000000..f631dd54 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/datasets/tutorial_output.txt_4.txt @@ -0,0 +1,3 @@ +hello +universe! +world diff --git a/test/test-data/test_ga_history_export/history_export/datasets_attrs.txt b/test/test-data/test_ga_history_export/history_export/datasets_attrs.txt new file mode 100644 index 00000000..2a1cf10b --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/datasets_attrs.txt @@ -0,0 +1,101 @@ +[{ + "annotation": null, + "blurb": "2 lines", + "copied_from_history_dataset_association_id_chain": ["2524d3d3b68ad39a"], + "create_time": "2021-06-23 10:46:27.112621", + "dataset_uuid": "18e78952-9447-4215-942c-542c35250d20", + "deleted": false, + "designation": null, + "encoded_id": "7ca3de8f49293d1a", + "extension": "txt", + "file_name": "datasets/dataset2.txt_1.txt", + "hid": 1, + "history_encoded_id": "a9eae7b6d5994701", + "info": "", + "metadata": { + "data_lines": 2, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "dataset2.txt", + "peek": "hello\nuniverse!\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:46:28.363987", + "visible": true +}, { + "annotation": null, + "blurb": "2 lines", + "copied_from_history_dataset_association_id_chain": ["7c1d8e3101dbcdba"], + "create_time": "2021-06-23 10:46:27.185496", + "dataset_uuid": "6b0af26e-574c-475a-bb6d-1b4df9f137d8", + "deleted": false, + "designation": null, + "encoded_id": "2e789aae2475b7da", + "extension": "txt", + "file_name": "datasets/dataset1.txt_2.txt", + "hid": 2, + "history_encoded_id": "a9eae7b6d5994701", + "info": "", + "metadata": { + "data_lines": 2, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "dataset1.txt", + "peek": "hello\nworld\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:46:28.363991", + "visible": true +}, { + "annotation": null, + "blurb": "4 lines", + "copied_from_history_dataset_association_id_chain": [], + "create_time": "2021-06-23 10:46:28.365628", + "dataset_uuid": "cf936245-b1d6-4840-b79d-2e20af74b921", + "deleted": false, + "designation": "out_file1", + "encoded_id": "fd7fec473f1e6c6b", + "extension": "txt", + "file_name": "datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt", + "hid": 3, + "history_encoded_id": "a9eae7b6d5994701", + "info": "", + "metadata": { + "data_lines": 4, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "Concatenate datasets on data 2 and data 1", + "peek": "hello\nuniverse!\nhello\nworld\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:46:44.644667", + "visible": true +}, { + "annotation": null, + "blurb": "3 lines", + "copied_from_history_dataset_association_id_chain": [], + "create_time": "2021-06-23 10:46:28.531348", + "dataset_uuid": "d9b5abdc-2a54-4fb7-b3df-1f05e9f2399a", + "deleted": false, + "designation": "out_file1", + "encoded_id": "775bc9b3c1750167", + "extension": "txt", + "file_name": "datasets/tutorial_output.txt_4.txt", + "hid": 4, + "history_encoded_id": "a9eae7b6d5994701", + "info": "\nKept 3 of 4 total lines.\nUsed random seed of \"0\".", + "metadata": { + "data_lines": 3, + "dbkey": "?" + }, + "model_class": "HistoryDatasetAssociation", + "name": "tutorial_output.txt", + "peek": "hello\nuniverse!\nworld\n", + "state": "ok", + "tags": [], + "update_time": "2021-06-23 10:47:04.750978", + "visible": true +}] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/datasets_attrs.txt.provenance b/test/test-data/test_ga_history_export/history_export/datasets_attrs.txt.provenance new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/datasets_attrs.txt.provenance @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/export_attrs.txt b/test/test-data/test_ga_history_export/history_export/export_attrs.txt new file mode 100644 index 00000000..a2100763 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/export_attrs.txt @@ -0,0 +1 @@ +{"galaxy_export_version": "2"} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/history_attrs.txt b/test/test-data/test_ga_history_export/history_export/history_attrs.txt new file mode 100644 index 00000000..53de783c --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/history_attrs.txt @@ -0,0 +1,11 @@ +{ + "model_class": "History", + "create_time": "2021-06-23 10:46:26.457161", + "update_time": "2022-01-06 17:05:06.816140", + "name": "Minimal-history", + "hid_counter": 5, + "genome_build": "?", + "annotation": null, + "tags": ["planemo-tutorial"], + "encoded_id": "a9eae7b6d5994701" +} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/implicit_collection_jobs_attrs.txt b/test/test-data/test_ga_history_export/history_export/implicit_collection_jobs_attrs.txt new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/implicit_collection_jobs_attrs.txt @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/jobs_attrs.txt b/test/test-data/test_ga_history_export/history_export/jobs_attrs.txt new file mode 100644 index 00000000..1e2a84f0 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/jobs_attrs.txt @@ -0,0 +1,165 @@ +[{ + "command_line": "python '/srv/galaxy/shared/src/lib/galaxy/tools/data_fetch.py' --galaxy-root '/srv/galaxy/shared/src' --datatypes-registry '/srv/galaxy/shared/etc/tmpdir/jwd/079/79718/registry.xml' --request-version '1' --request '/srv/galaxy/shared/etc/tmpdir/jwd/079/79718/configs/tmpjgi6b5_u'", + "create_time": "2021-06-23T10:20:22.770291", + "encoded_id": "7b69c80a9f428343", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": {}, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "output0": ["2524d3d3b68ad39a"] + }, + "params": { + "file_count": "1", + "files": [{ + "__index__": 0, + "file_data": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" + }], + "paramfile": null, + "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"ext\": \"auto\", \"dbkey\": \"?\", \"to_posix_lines\": true, \"src\": \"path\", \"name\": \"dataset2.txt\", \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2\", \"object_id\": 155708}], \"auto_decompress\": false}], \"check_content\": true}", + "request_version": "1" + }, + "state": "ok", + "tool_id": "__DATA_FETCH__", + "tool_stderr": "", + "tool_stdout": "", + "tool_version": "0.1.0", + "traceback": null, + "update_time": "2021-06-23T10:20:42.041319" +}, { + "command_line": "python '/srv/galaxy/shared/src/lib/galaxy/tools/data_fetch.py' --galaxy-root '/srv/galaxy/shared/src' --datatypes-registry '/srv/galaxy/shared/etc/tmpdir/jwd/079/79717/registry.xml' --request-version '1' --request '/srv/galaxy/shared/etc/tmpdir/jwd/079/79717/configs/tmpmod1j0bw'", + "create_time": "2021-06-23T10:20:00.981702", + "encoded_id": "77dd7a937748a715", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": {}, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "output0": ["7c1d8e3101dbcdba"] + }, + "params": { + "file_count": "1", + "files": [{ + "__index__": 0, + "file_data": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a" + }], + "paramfile": null, + "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"ext\": \"auto\", \"dbkey\": \"?\", \"to_posix_lines\": true, \"src\": \"path\", \"name\": \"dataset1.txt\", \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a\", \"object_id\": 155707}], \"auto_decompress\": false}], \"check_content\": true}", + "request_version": "1" + }, + "state": "ok", + "tool_id": "__DATA_FETCH__", + "tool_stderr": "", + "tool_stdout": "", + "tool_version": "0.1.0", + "traceback": null, + "update_time": "2021-06-23T10:20:22.202678" +}, { + "command_line": "python /srv/galaxy/shared/src/tools/filters/catWrapper.py '/srv/galaxy/shared/etc/tmpdir/jwd/079/79726/outputs/galaxy_dataset_cf936245-b1d6-4840-b79d-2e20af74b921.dat' '/srv/galaxy/shared/database/files/000/134/dataset_134410.dat' '/srv/galaxy/shared/database/files/000/134/dataset_134409.dat'", + "create_time": "2021-06-23T10:46:28.351123", + "encoded_id": "77cf44871c57dd95", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": { + "input1": ["7ca3de8f49293d1a"], + "queries_0|input2": ["2e789aae2475b7da"] + }, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "out_file1": ["fd7fec473f1e6c6b"] + }, + "params": { + "__input_ext": "txt", + "__workflow_invocation_uuid__": "42f21c0ad41011eb87defa163eba836f", + "chromInfo": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "dbkey": "?", + "input1": { + "values": [{ + "id": "7ca3de8f49293d1a", + "src": "hda" + }] + }, + "queries": [{ + "__index__": 0, + "input2": { + "values": [{ + "id": "2e789aae2475b7da", + "src": "hda" + }] + } + }] + }, + "state": "ok", + "tool_id": "cat1", + "tool_stderr": "", + "tool_stdout": "", + "tool_version": "1.0.0", + "traceback": null, + "update_time": "2021-06-23T10:46:44.738703" +}, { + "command_line": "python '/srv/galaxy/shared/src/tools/filters/random_lines_two_pass.py' '/srv/galaxy/shared/database/files/000/134/dataset_134423.dat' '/srv/galaxy/shared/etc/tmpdir/jwd/079/79727/outputs/galaxy_dataset_d9b5abdc-2a54-4fb7-b3df-1f05e9f2399a.dat' '3' --seed '0'", + "create_time": "2021-06-23T10:46:28.526901", + "encoded_id": "ea1a7696fd6484de", + "exit_code": 0, + "galaxy_version": "21.01", + "implicit_output_dataset_collection_mapping": {}, + "info": null, + "input_dataset_collection_element_mapping": {}, + "input_dataset_collection_mapping": {}, + "input_dataset_mapping": { + "input": ["fd7fec473f1e6c6b"] + }, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_dataset_collection_mapping": {}, + "output_dataset_mapping": { + "out_file1": ["775bc9b3c1750167"] + }, + "params": { + "__input_ext": "txt", + "__workflow_invocation_uuid__": "42f21c0ad41011eb87defa163eba836f", + "chromInfo": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", + "dbkey": "?", + "input": { + "values": [{ + "id": "fd7fec473f1e6c6b", + "src": "hda" + }] + }, + "num_lines": "3", + "seed_source": { + "__current_case__": 1, + "seed": "0", + "seed_source_selector": "set_seed" + } + }, + "state": "ok", + "tool_id": "random_lines1", + "tool_stderr": "", + "tool_stdout": "Kept 3 of 4 total lines.\nUsed random seed of \"0\".\n", + "tool_version": "2.0.2", + "traceback": null, + "update_time": "2021-06-23T10:47:04.837750" +}] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/libraries_attrs.txt b/test/test-data/test_ga_history_export/history_export/libraries_attrs.txt new file mode 100644 index 00000000..0637a088 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/libraries_attrs.txt @@ -0,0 +1 @@ +[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/wf_definition.ga b/test/test-data/test_ga_history_export/wf_definition.ga new file mode 100644 index 00000000..28194ed4 --- /dev/null +++ b/test/test-data/test_ga_history_export/wf_definition.ga @@ -0,0 +1,131 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Workflow constructed from history 'Minimal-history'", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "dataset2.txt" + } + ], + "label": "dataset2.txt", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 10, + "top": 10 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "8dfb1a60-ac90-4125-b1a4-c674a084bf37", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "dataset1.txt" + } + ], + "label": "dataset1.txt", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 10, + "top": 130 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "104d6198-2f2e-46f1-8006-1c594f1f091c", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "cat1", + "errors": null, + "id": 2, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "queries_0|input2": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 230, + "top": 10 + }, + "post_job_actions": {}, + "tool_id": "cat1", + "tool_state": "{\"__input_ext\": \"txt\", \"__workflow_invocation_uuid__\": \"42f21c0ad41011eb87defa163eba836f\", \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input1\": null, \"queries\": [{\"__index__\": 0, \"input2\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "821567a8-1edd-4f35-9430-596fd6801ca1", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "random_lines1", + "errors": null, + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Select random lines", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 450, + "top": 10 + }, + "post_job_actions": {}, + "tool_id": "random_lines1", + "tool_state": "{\"__input_ext\": \"txt\", \"__workflow_invocation_uuid__\": \"42f21c0ad41011eb87defa163eba836f\", \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": null, \"num_lines\": \"3\", \"seed_source\": {\"seed_source_selector\": \"set_seed\", \"__current_case__\": 1, \"seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0.2", + "type": "tool", + "uuid": "a6b4dc53-9a0f-4a5c-9311-f9f03238f9dc", + "workflow_outputs": [] + } + }, + "tags": [], + "uuid": "de90339e-0497-49da-a1ce-f7e2dd3080c6", + "version": 0 +} \ No newline at end of file diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index 5417da6c..8246b5d8 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -6,15 +6,56 @@ from prov.model import ProvDocument sys.path.append('./ro-crate-py') from rocrate.rocrate import ROCrate -from tools import parse_ga_export +from rocrate import rocrate_api as roc_api +from rocrate.model.computerlanguage import CWL_DEFAULT_VERSION, GALAXY_DEFAULT_VERSION from rocrate.provenance_profile import ProvenanceProfile +WF_CRATE = "https://w3id.org/workflowhub/workflow-ro-crate" +from tools import parse_ga_export + + def test_ga_history_parsing(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" - export_path = test_data_dir / export_dir + export_path = test_data_dir / export_dir / "history_export" - metadata_export = parse_ga_export.ga_history_export(export_path) + metadata_export = parse_ga_export.load_ga_history_export(export_path) prov = ProvenanceProfile(metadata_export, "PDG", "https://orcid.org/0000-0002-8940-4946") - print(len(metadata_export['jobs_attrs'])) + # print(len(metadata_export['jobs_attrs'])) # print(prov.document.serialize(format="rdf", rdf_format="turtle")) - assert isinstance(prov, ProvenanceProfile) \ No newline at end of file + assert isinstance(prov, ProvenanceProfile) + + +def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): + wf_id = 'test_galaxy_wf.ga' + wf_path = test_data_dir / wf_id + wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy') + assert isinstance(wf_crate, ROCrate) + + wf = wf_crate.dereference(wf_id) + assert wf._default_type == "ComputationalWorkflow" + assert wf_crate.mainEntity is wf + lang = wf_crate.dereference(f"{WF_CRATE}#galaxy") + assert hasattr(lang, "name") + assert lang.version == GALAXY_DEFAULT_VERSION + assert wf.get("programmingLanguage") is lang + assert wf.get("subjectOf") is not None + assert helpers.WORKFLOW_DESC_TYPES.issubset(wf["subjectOf"].type) + + out_path = tmpdir / 'ro_crate_out' + out_path.mkdir() + wf_crate.write(out_path) + json_entities = helpers.read_json_entities(out_path) + helpers.check_wf_crate(json_entities, wf_id) + wf_entity = json_entities[wf_id] + assert "subjectOf" in wf_entity + abstract_wf_id = wf_entity["subjectOf"]["@id"] + abstract_wf_entity = json_entities[abstract_wf_id] + assert helpers.WORKFLOW_DESC_TYPES.issubset(abstract_wf_entity["@type"]) + + wf_out_path = out_path / wf_id + assert wf_out_path.exists() + with open(wf_path) as f1, open(wf_out_path) as f2: + assert f1.read() == f2.read() + + abstract_wf_out_path = out_path / abstract_wf_id + assert abstract_wf_out_path.exists() \ No newline at end of file diff --git a/tools/parse_ga_export.py b/tools/parse_ga_export.py index 52e5553d..381c7072 100644 --- a/tools/parse_ga_export.py +++ b/tools/parse_ga_export.py @@ -2,7 +2,7 @@ import os import re -def ga_history_export(export_dir): +def load_ga_history_export(export_dir): fn_list = os.listdir(export_dir) export_metadata = {} @@ -14,5 +14,4 @@ def ga_history_export(export_dir): key = '_'.join(list(filter(None, re.split('\.|txt',f)))) export_metadata[key] = json.loads(fh.read()) - return export_metadata \ No newline at end of file From 5bc6856f72278e74dbacfc0d66236e4f89c17908 Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 3 Mar 2022 12:00:43 +0100 Subject: [PATCH 05/27] added tests and improved prov extraction --- rocrate/provenance_profile.py | 395 +++++++++--------- .../collections_attrs.txt | 1 - ...tenate_datasets_on_data_2_and_data_1_3.txt | 4 - .../datasets/dataset1.txt_2.txt | 2 - .../datasets/dataset2.txt_1.txt | 2 - .../datasets/tutorial_output.txt_4.txt | 3 - .../test_ga_history_export/datasets_attrs.txt | 101 ----- .../datasets_attrs.txt.provenance | 1 - .../test_ga_history_export/export_attrs.txt | 1 - .../test_ga_history_export/history_attrs.txt | 11 - .../implicit_collection_jobs_attrs.txt | 1 - .../test_ga_history_export/jobs_attrs.txt | 165 -------- .../libraries_attrs.txt | 1 - .../ro-crate-metadata.json | 92 ---- test/test_parse_ga_export.py | 20 +- tools/load_ga_export.py | 78 ++++ tools/parse_ga_export.py | 17 - 17 files changed, 289 insertions(+), 606 deletions(-) delete mode 100644 test/test-data/test_ga_history_export/collections_attrs.txt delete mode 100644 test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt delete mode 100644 test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt delete mode 100644 test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt delete mode 100644 test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt delete mode 100644 test/test-data/test_ga_history_export/datasets_attrs.txt delete mode 100644 test/test-data/test_ga_history_export/datasets_attrs.txt.provenance delete mode 100644 test/test-data/test_ga_history_export/export_attrs.txt delete mode 100644 test/test-data/test_ga_history_export/history_attrs.txt delete mode 100644 test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt delete mode 100644 test/test-data/test_ga_history_export/jobs_attrs.txt delete mode 100644 test/test-data/test_ga_history_export/libraries_attrs.txt delete mode 100644 test/test-data/test_ga_history_export/ro-crate-metadata.json create mode 100644 tools/load_ga_export.py delete mode 100644 tools/parse_ga_export.py diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index c6e711db..0d78add3 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -9,6 +9,7 @@ from typing import ( Any, Dict, + Iterable, List, MutableMapping, MutableSequence, @@ -22,6 +23,7 @@ from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity from schema_salad.sourceline import SourceLine from typing_extensions import TYPE_CHECKING +from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset # from .errors import WorkflowException # from .job import CommandLineJob, JobBase @@ -58,6 +60,11 @@ def posix_path(local_path: str) -> str: return str(PurePosixPath(Path(local_path))) +def remove_escapes(s): + escapes = ''.join([chr(char) for char in range(1, 32)]) + translator = str.maketrans('', '', escapes) + t = s.translate(translator) + class ProvenanceProfile: """ @@ -68,7 +75,7 @@ class ProvenanceProfile: def __init__( self, - ga_export: Dict, #"ResearchObject", #should be changed to ro_crate? + ga_export: Dict, full_name: str, orcid: str, # fsaccess: StdFsAccess, @@ -77,30 +84,35 @@ def __init__( """ Initialize the provenance profile. Keyword arguments: - research_object -- the research object or ro-crate + ga_export -- the galaxy metadata export (Dict) full_name -- author name orcid -- orcid (optional) - fsaccess -- file system access to create RO run_uuid -- uuid for the workflow run """ # self.fsaccess = fsaccess self.orcid = orcid self.ga_export = ga_export - # self.research_object = research_object - # self.folder = self.research_object.folder self.ro_uuid = uuid.uuid4() # TODO: should be connected to a ro_crate? self.base_uri = "arcp://uuid,%s/" % self.ro_uuid self.document = ProvDocument() # TODO extract engine_uuid from galaxy, type: str self.engine_uuid = "urn:uuid:%s" % uuid.uuid4() #type: str - # self.add_to_manifest = self.research_object.add_to_manifest self.full_name = full_name self.workflow_run_uuid = run_uuid or uuid.uuid4() self.workflow_run_uri = self.workflow_run_uuid.urn # type: str + + metadata_export = load_ga_history_export(ga_export) self.generate_prov_doc() - for job in ga_export["jobs_attrs"]: - self.declare_process(job) + self.jobs = [] + # print(metadata_export["jobs_attrs"][0]["params"]) + for job in metadata_export["jobs_attrs"]: + job_attrs = GalaxyJob() + job_attrs.parse_ga_jobs_attrs(job) + self.jobs.append(job_attrs.attributes) + self.declare_process(job_attrs.attributes) + + # print(self.document.serialize(format="rdf", rdf_format="turtle")) def __str__(self) -> str: """Represent this Provenvance profile as a string.""" @@ -115,10 +127,8 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: # can we identify a host where the workflow was executed? # should OnlineAccount be used to describe a galaxy user? # PROV_TYPE: FOAF["OnlineAccount"], - - # TODO: - # need to check how to get the exact galaxy version - self.galaxy_version = "galaxy" #%s" % versionstring().split()[-1] + # TODO: change how we register galaxy version, probably a declare_version func + # self.galaxy_version = self.ga_export["jobs_attrs"][0]["galaxy_version"] # TODO: change notation to already imported namespaces? self.document.add_namespace("wfprov", "http://purl.org/wf4ever/wfprov#") # document.add_namespace('prov', 'http://www.w3.org/ns/prov#') @@ -137,12 +147,6 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: # Also needed for docker images # self.document.add_namespace(SHA256, "nih:sha-256;") - # info only, won't really be used by prov as sub-resources use - # annotations - # self.document.add_namespace("researchobject", self.research_object.base_uri) - # self.metadata_ns = self.document.add_namespace( - # "metadata", self.research_object.base_uri + METADATA + "/" - # ) # Pre-register provenance directory so we can refer to its files self.provenance_ns = self.document.add_namespace( "provenance", self.base_uri + posix_path(PROVENANCE) + "/" @@ -167,7 +171,7 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: else: # TODO: Look up name from ORCID API? pass - # print(self.orcid or uuid.uuid4().urn) + agent = self.document.agent(self.orcid or uuid.uuid4().urn, person) self.document.actedOnBehalfOf(account, agent) @@ -181,8 +185,6 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: "prov:label": "galaxy_version_placeholder", }, ) - # FIXME: This datetime will be a bit too delayed, we should - # capture when cwltool.py earliest started? self.document.wasStartedBy(wfengine, None, account, datetime.datetime.now()) # define workflow run level activity self.document.activity( @@ -196,7 +198,6 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: ) # association between SoftwareAgent and WorkflowRun main_workflow = "wf:main" - # print(self.workflow_run_uri, self.engine_uuid, main_workflow) self.document.wasAssociatedWith( self.workflow_run_uri, self.engine_uuid, main_workflow ) @@ -205,26 +206,6 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: ) return (self.workflow_run_uri, self.document) - # def evaluate( - # self, - # process: Process, - # job: JobsType, - # job_order_object: CWLObjectType, - # research_obj: "ResearchObject", - # ) -> None: - # """Evaluate the nature of job.""" - # if not hasattr(process, "steps"): - # # record provenance of independent commandline tool executions - # self.prospective_prov(job) - # customised_job = copy_job_order(job, job_order_object) - # self.used_artefacts(customised_job, self.workflow_run_uri) - # research_obj.create_job(customised_job) - # elif hasattr(job, "workflow"): - # # record provenance of workflow executions - # self.prospective_prov(job) - # customised_job = copy_job_order(job, job_order_object) - # self.used_artefacts(customised_job, self.workflow_run_uri) - def declare_process( self, # process_name: str, @@ -243,6 +224,7 @@ def declare_process( start_time = ga_export_jobs_attrs["create_time"] end_time = ga_export_jobs_attrs["update_time"] + #TODO: Find out how to include commandline as a string # cmd = self.document.entity( # uuid.uuid4().urn, # {PROV_TYPE: WFPROV["Artifact"], PROV_LABEL: ga_export_jobs_attrs["command_line"]} @@ -255,7 +237,7 @@ def declare_process( { PROV_TYPE: WFPROV["ProcessRun"], PROV_LABEL: prov_label, - # Find out how to include commandline as a string + #TODO: Find out how to include commandline as a string # PROV_LABEL: cmd }, ) @@ -265,19 +247,178 @@ def declare_process( self.document.wasStartedBy( process_run_id, None, self.workflow_run_uri, start_time, None, None ) + self.used_artefacts(process_run_id, ga_export_jobs_attrs) + # self.generate_output_prov(outputs, process_run_id, process_name) + # self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when) return process_run_id - def record_process_end( + def used_artefacts( self, - process_name: str, process_run_id: str, - # outputs: Union[CWLObjectType, MutableSequence[CWLObjectType], None], - when: datetime.datetime, + process_metadata: dict, + process_name: Optional[str] = None, ) -> None: - self.generate_output_prov(outputs, process_run_id, process_name) - self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when) + """Add used() for each data artefact.""" + # FIXME: Use workflow name if available, "main" is wrong for nested workflows + base = "main" + if process_name is not None: + base += "/" + process_name + tool_id = process_metadata["tool_id"] + base += "/" + tool_id + items = ["inputs","outputs","parameters"] + # print(process_metadata["params"]) + for item in items: + # print(item) + # print("-----------") + # print(process_metadata[item]) + + for key, value in process_metadata[item].items(): + prov_role = self.wf_ns[f"{base}/{key}"] + + print("key : ",key) + print("-----------") + print("value: ",value) + print("-----------") + print("type : ",type(value)) + if not value: + value = "" + # if value and isinstance(value, str): + # value = remove_escapes(value) + + for artefact in value: + try: + # print(artefact) + entity = self.declare_artefact(artefact) + self.document.used( + process_run_id, + entity, + datetime.datetime.now(), + None, + {"prov:role": prov_role}, + ) + except OSError: + pass + + def declare_artefact(self, value: Any) -> ProvEntity: + """Create data artefact entities for all file objects.""" + if value is None: + # FIXME: If this can happen we'll need a better way to represent this in PROV + return self.document.entity(CWLPROV["None"], {PROV_LABEL: "None"}) + + if isinstance(value, (bool, int, float)): + # Typically used in job documents for flags + + # FIXME: Make consistent hash URIs for these + # that somehow include the type + # (so "1" != 1 != "1.0" != true) + entity = self.document.entity(uuid.uuid4().urn, {PROV_VALUE: value}) + # self.research_object.add_uri(entity.identifier.uri) + return entity + + if isinstance(value, (str)): + entity = self.declare_string(value) + return entity + + if isinstance(value, bytes): + # If we got here then we must be in Python 3 + byte_s = BytesIO(value) + # data_file = self.research_object.add_data_file(byte_s) + # FIXME: Don't naively assume add_data_file uses hash in filename! + data_id = "data:%s" % str(value) #PurePosixPath(data_file).stem + return self.document.entity( + data_id, + {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)}, + ) + + if isinstance(value, Dict): + if "@id" in value: + # Already processed this value, but it might not be in this PROV + entities = self.document.get_record(value["@id"]) + if entities: + return entities[0] + # else, unknown in PROV, re-add below as if it's fresh + + # Base case - we found a File we need to update + if value.get("class") == "File": + (entity, _, _) = self.declare_file(value) + value["@id"] = entity.identifier.uri + return entity + + if value.get("class") == "Directory": + entity = self.declare_directory(value) + value["@id"] = entity.identifier.uri + return entity + coll_id = value.setdefault("@id", uuid.uuid4().urn) + # some other kind of dictionary? + # TODO: also Save as JSON + coll = self.document.entity( + coll_id, + [ + (PROV_TYPE, WFPROV["Artifact"]), + (PROV_TYPE, PROV["Collection"]), + (PROV_TYPE, PROV["Dictionary"]), + ], + ) + + if value.get("class"): + #_logger.warning("Unknown data class %s.", value["class"]) + # FIXME: The class might be "http://example.com/somethingelse" + coll.add_asserted_type(CWLPROV[value["class"]]) + + # Let's iterate and recurse + coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] + for (key, val) in value.items(): + v_ent = self.declare_artefact(val) + self.document.membership(coll, v_ent) + m_entity = self.document.entity(uuid.uuid4().urn) + # Note: only support PROV-O style dictionary + # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition + # as prov.py do not easily allow PROV-N extensions + m_entity.add_asserted_type(PROV["KeyEntityPair"]) + m_entity.add_attributes( + {PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent} + ) + coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) + coll.add_attributes(coll_attribs) + # self.research_object.add_uri(coll.identifier.uri) + return coll - def declare_file(self) -> Tuple[ProvEntity, ProvEntity, str]: + # some other kind of Collection? + # TODO: also save as JSON + try: + members = [] + for each_input_obj in iter(value): + # Recurse and register any nested objects + e = self.declare_artefact(each_input_obj) + members.append(e) + + # If we reached this, then we were allowed to iterate + coll = self.document.entity( + uuid.uuid4().urn, + [ + (PROV_TYPE, WFPROV["Artifact"]), + (PROV_TYPE, PROV["Collection"]), + ], + ) + if not members: + coll.add_asserted_type(PROV["EmptyCollection"]) + else: + for member in members: + # FIXME: This won't preserve order, for that + # we would need to use PROV.Dictionary + # with numeric keys + self.document.membership(coll, member) + # self.research_object.add_uri(coll.identifier.uri) + # FIXME: list value does not support adding "@id" + return coll + except TypeError: + #_logger.warning("Unrecognized type %s of %r", type(value), value) + # Let's just fall back to Python repr() + entity = self.document.entity(uuid.uuid4().urn, {PROV_LABEL: repr(value)}) + # self.research_object.add_uri(entity.identifier.uri) + return entity + + def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: if value["class"] != "File": raise ValueError("Must have class:File: %s" % value) # Need to determine file hash aka RO filename @@ -457,7 +598,7 @@ def declare_directory(self # Empty directory coll.add_asserted_type(PROV["EmptyCollection"]) coll.add_asserted_type(PROV["EmptyDictionary"]) - self.research_object.add_uri(coll.identifier.uri) + # self.research_object.add_uri(coll.identifier.uri) return coll def declare_string(self, value: str) -> Tuple[ProvEntity, str]: @@ -466,160 +607,12 @@ def declare_string(self, value: str) -> Tuple[ProvEntity, str]: # data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN) # checksum = PurePosixPath(data_file).name # FIXME: Don't naively assume add_data_file uses hash in filename! - data_id = "data:%s" % PurePosixPath(data_file).stem + data_id = "data:%s" % str(value) #PurePosixPath(data_file).stem entity = self.document.entity( data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)} ) # type: ProvEntity return entity #, checksum - def declare_artefact(self, value: Any) -> ProvEntity: - """Create data artefact entities for all file objects.""" - if value is None: - # FIXME: If this can happen in CWL, we'll - # need a better way to represent this in PROV - return self.document.entity(CWLPROV["None"], {PROV_LABEL: "None"}) - - if isinstance(value, (bool, int, float)): - # Typically used in job documents for flags - - # FIXME: Make consistent hash URIs for these - # that somehow include the type - # (so "1" != 1 != "1.0" != true) - entity = self.document.entity(uuid.uuid4().urn, {PROV_VALUE: value}) - self.research_object.add_uri(entity.identifier.uri) - return entity - - if isinstance(value, (str, str)): - (entity, _) = self.declare_string(value) - return entity - - if isinstance(value, bytes): - # If we got here then we must be in Python 3 - byte_s = BytesIO(value) - data_file = self.research_object.add_data_file(byte_s) - # FIXME: Don't naively assume add_data_file uses hash in filename! - data_id = "data:%s" % PurePosixPath(data_file).stem - return self.document.entity( - data_id, - {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)}, - ) - - if isinstance(value, MutableMapping): - if "@id" in value: - # Already processed this value, but it might not be in this PROV - entities = self.document.get_record(value["@id"]) - if entities: - return entities[0] - # else, unknown in PROV, re-add below as if it's fresh - - # Base case - we found a File we need to update - if value.get("class") == "File": - (entity, _, _) = self.declare_file(value) - value["@id"] = entity.identifier.uri - return entity - - if value.get("class") == "Directory": - entity = self.declare_directory(value) - value["@id"] = entity.identifier.uri - return entity - coll_id = value.setdefault("@id", uuid.uuid4().urn) - # some other kind of dictionary? - # TODO: also Save as JSON - coll = self.document.entity( - coll_id, - [ - (PROV_TYPE, WFPROV["Artifact"]), - (PROV_TYPE, PROV["Collection"]), - (PROV_TYPE, PROV["Dictionary"]), - ], - ) - - if value.get("class"): - #_logger.warning("Unknown data class %s.", value["class"]) - # FIXME: The class might be "http://example.com/somethingelse" - coll.add_asserted_type(CWLPROV[value["class"]]) - - # Let's iterate and recurse - coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] - for (key, val) in value.items(): - v_ent = self.declare_artefact(val) - self.document.membership(coll, v_ent) - m_entity = self.document.entity(uuid.uuid4().urn) - # Note: only support PROV-O style dictionary - # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition - # as prov.py do not easily allow PROV-N extensions - m_entity.add_asserted_type(PROV["KeyEntityPair"]) - m_entity.add_attributes( - {PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent} - ) - coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) - coll.add_attributes(coll_attribs) - self.research_object.add_uri(coll.identifier.uri) - return coll - - # some other kind of Collection? - # TODO: also save as JSON - try: - members = [] - for each_input_obj in iter(value): - # Recurse and register any nested objects - e = self.declare_artefact(each_input_obj) - members.append(e) - - # If we reached this, then we were allowed to iterate - coll = self.document.entity( - uuid.uuid4().urn, - [ - (PROV_TYPE, WFPROV["Artifact"]), - (PROV_TYPE, PROV["Collection"]), - ], - ) - if not members: - coll.add_asserted_type(PROV["EmptyCollection"]) - else: - for member in members: - # FIXME: This won't preserve order, for that - # we would need to use PROV.Dictionary - # with numeric keys - self.document.membership(coll, member) - self.research_object.add_uri(coll.identifier.uri) - # FIXME: list value does not support adding "@id" - return coll - except TypeError: - #_logger.warning("Unrecognized type %s of %r", type(value), value) - # Let's just fall back to Python repr() - entity = self.document.entity(uuid.uuid4().urn, {PROV_LABEL: repr(value)}) - self.research_object.add_uri(entity.identifier.uri) - return entity - - def used_artefacts( - self, - job_order: Union[CWLObjectType, List[CWLObjectType]], - process_run_id: str, - name: Optional[str] = None, - ) -> None: - """Add used() for each data artefact.""" - if isinstance(job_order, list): - for entry in job_order: - self.used_artefacts(entry, process_run_id, name) - else: - # FIXME: Use workflow name in packed.cwl, "main" is wrong for nested workflows - base = "main" - if name is not None: - base += "/" + name - for key, value in job_order.items(): - prov_role = self.wf_ns[f"{base}/{key}"] - try: - entity = self.declare_artefact(value) - self.document.used( - process_run_id, - entity, - datetime.datetime.now(), - None, - {"prov:role": prov_role}, - ) - except OSError: - pass def generate_output_prov( self, @@ -703,7 +696,7 @@ def activity_has_provenance(self, activity, prov_ids): # Tip: we can't use https://www.w3.org/TR/prov-links/#term-mention # as prov:mentionOf() is only for entities, not activities uris = [i.uri for i in prov_ids] - self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) + # self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) def finalize_prov_profile(self, name): # type: (Optional[str]) -> List[Identifier] diff --git a/test/test-data/test_ga_history_export/collections_attrs.txt b/test/test-data/test_ga_history_export/collections_attrs.txt deleted file mode 100644 index 0637a088..00000000 --- a/test/test-data/test_ga_history_export/collections_attrs.txt +++ /dev/null @@ -1 +0,0 @@ -[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt b/test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt deleted file mode 100644 index 8b3f00b0..00000000 --- a/test/test-data/test_ga_history_export/datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt +++ /dev/null @@ -1,4 +0,0 @@ -hello -universe! -hello -world diff --git a/test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt b/test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt deleted file mode 100644 index 94954abd..00000000 --- a/test/test-data/test_ga_history_export/datasets/dataset1.txt_2.txt +++ /dev/null @@ -1,2 +0,0 @@ -hello -world diff --git a/test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt b/test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt deleted file mode 100644 index 718e715c..00000000 --- a/test/test-data/test_ga_history_export/datasets/dataset2.txt_1.txt +++ /dev/null @@ -1,2 +0,0 @@ -hello -universe! diff --git a/test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt b/test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt deleted file mode 100644 index f631dd54..00000000 --- a/test/test-data/test_ga_history_export/datasets/tutorial_output.txt_4.txt +++ /dev/null @@ -1,3 +0,0 @@ -hello -universe! -world diff --git a/test/test-data/test_ga_history_export/datasets_attrs.txt b/test/test-data/test_ga_history_export/datasets_attrs.txt deleted file mode 100644 index 2a1cf10b..00000000 --- a/test/test-data/test_ga_history_export/datasets_attrs.txt +++ /dev/null @@ -1,101 +0,0 @@ -[{ - "annotation": null, - "blurb": "2 lines", - "copied_from_history_dataset_association_id_chain": ["2524d3d3b68ad39a"], - "create_time": "2021-06-23 10:46:27.112621", - "dataset_uuid": "18e78952-9447-4215-942c-542c35250d20", - "deleted": false, - "designation": null, - "encoded_id": "7ca3de8f49293d1a", - "extension": "txt", - "file_name": "datasets/dataset2.txt_1.txt", - "hid": 1, - "history_encoded_id": "a9eae7b6d5994701", - "info": "", - "metadata": { - "data_lines": 2, - "dbkey": "?" - }, - "model_class": "HistoryDatasetAssociation", - "name": "dataset2.txt", - "peek": "hello\nuniverse!\n", - "state": "ok", - "tags": [], - "update_time": "2021-06-23 10:46:28.363987", - "visible": true -}, { - "annotation": null, - "blurb": "2 lines", - "copied_from_history_dataset_association_id_chain": ["7c1d8e3101dbcdba"], - "create_time": "2021-06-23 10:46:27.185496", - "dataset_uuid": "6b0af26e-574c-475a-bb6d-1b4df9f137d8", - "deleted": false, - "designation": null, - "encoded_id": "2e789aae2475b7da", - "extension": "txt", - "file_name": "datasets/dataset1.txt_2.txt", - "hid": 2, - "history_encoded_id": "a9eae7b6d5994701", - "info": "", - "metadata": { - "data_lines": 2, - "dbkey": "?" - }, - "model_class": "HistoryDatasetAssociation", - "name": "dataset1.txt", - "peek": "hello\nworld\n", - "state": "ok", - "tags": [], - "update_time": "2021-06-23 10:46:28.363991", - "visible": true -}, { - "annotation": null, - "blurb": "4 lines", - "copied_from_history_dataset_association_id_chain": [], - "create_time": "2021-06-23 10:46:28.365628", - "dataset_uuid": "cf936245-b1d6-4840-b79d-2e20af74b921", - "deleted": false, - "designation": "out_file1", - "encoded_id": "fd7fec473f1e6c6b", - "extension": "txt", - "file_name": "datasets/Concatenate_datasets_on_data_2_and_data_1_3.txt", - "hid": 3, - "history_encoded_id": "a9eae7b6d5994701", - "info": "", - "metadata": { - "data_lines": 4, - "dbkey": "?" - }, - "model_class": "HistoryDatasetAssociation", - "name": "Concatenate datasets on data 2 and data 1", - "peek": "hello\nuniverse!\nhello\nworld\n", - "state": "ok", - "tags": [], - "update_time": "2021-06-23 10:46:44.644667", - "visible": true -}, { - "annotation": null, - "blurb": "3 lines", - "copied_from_history_dataset_association_id_chain": [], - "create_time": "2021-06-23 10:46:28.531348", - "dataset_uuid": "d9b5abdc-2a54-4fb7-b3df-1f05e9f2399a", - "deleted": false, - "designation": "out_file1", - "encoded_id": "775bc9b3c1750167", - "extension": "txt", - "file_name": "datasets/tutorial_output.txt_4.txt", - "hid": 4, - "history_encoded_id": "a9eae7b6d5994701", - "info": "\nKept 3 of 4 total lines.\nUsed random seed of \"0\".", - "metadata": { - "data_lines": 3, - "dbkey": "?" - }, - "model_class": "HistoryDatasetAssociation", - "name": "tutorial_output.txt", - "peek": "hello\nuniverse!\nworld\n", - "state": "ok", - "tags": [], - "update_time": "2021-06-23 10:47:04.750978", - "visible": true -}] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/datasets_attrs.txt.provenance b/test/test-data/test_ga_history_export/datasets_attrs.txt.provenance deleted file mode 100644 index 0637a088..00000000 --- a/test/test-data/test_ga_history_export/datasets_attrs.txt.provenance +++ /dev/null @@ -1 +0,0 @@ -[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/export_attrs.txt b/test/test-data/test_ga_history_export/export_attrs.txt deleted file mode 100644 index a2100763..00000000 --- a/test/test-data/test_ga_history_export/export_attrs.txt +++ /dev/null @@ -1 +0,0 @@ -{"galaxy_export_version": "2"} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_attrs.txt b/test/test-data/test_ga_history_export/history_attrs.txt deleted file mode 100644 index 53de783c..00000000 --- a/test/test-data/test_ga_history_export/history_attrs.txt +++ /dev/null @@ -1,11 +0,0 @@ -{ - "model_class": "History", - "create_time": "2021-06-23 10:46:26.457161", - "update_time": "2022-01-06 17:05:06.816140", - "name": "Minimal-history", - "hid_counter": 5, - "genome_build": "?", - "annotation": null, - "tags": ["planemo-tutorial"], - "encoded_id": "a9eae7b6d5994701" -} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt b/test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt deleted file mode 100644 index 0637a088..00000000 --- a/test/test-data/test_ga_history_export/implicit_collection_jobs_attrs.txt +++ /dev/null @@ -1 +0,0 @@ -[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/jobs_attrs.txt b/test/test-data/test_ga_history_export/jobs_attrs.txt deleted file mode 100644 index 1e2a84f0..00000000 --- a/test/test-data/test_ga_history_export/jobs_attrs.txt +++ /dev/null @@ -1,165 +0,0 @@ -[{ - "command_line": "python '/srv/galaxy/shared/src/lib/galaxy/tools/data_fetch.py' --galaxy-root '/srv/galaxy/shared/src' --datatypes-registry '/srv/galaxy/shared/etc/tmpdir/jwd/079/79718/registry.xml' --request-version '1' --request '/srv/galaxy/shared/etc/tmpdir/jwd/079/79718/configs/tmpjgi6b5_u'", - "create_time": "2021-06-23T10:20:22.770291", - "encoded_id": "7b69c80a9f428343", - "exit_code": 0, - "galaxy_version": "21.01", - "implicit_output_dataset_collection_mapping": {}, - "info": null, - "input_dataset_collection_element_mapping": {}, - "input_dataset_collection_mapping": {}, - "input_dataset_mapping": {}, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_dataset_collection_mapping": {}, - "output_dataset_mapping": { - "output0": ["2524d3d3b68ad39a"] - }, - "params": { - "file_count": "1", - "files": [{ - "__index__": 0, - "file_data": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" - }], - "paramfile": null, - "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"ext\": \"auto\", \"dbkey\": \"?\", \"to_posix_lines\": true, \"src\": \"path\", \"name\": \"dataset2.txt\", \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2\", \"object_id\": 155708}], \"auto_decompress\": false}], \"check_content\": true}", - "request_version": "1" - }, - "state": "ok", - "tool_id": "__DATA_FETCH__", - "tool_stderr": "", - "tool_stdout": "", - "tool_version": "0.1.0", - "traceback": null, - "update_time": "2021-06-23T10:20:42.041319" -}, { - "command_line": "python '/srv/galaxy/shared/src/lib/galaxy/tools/data_fetch.py' --galaxy-root '/srv/galaxy/shared/src' --datatypes-registry '/srv/galaxy/shared/etc/tmpdir/jwd/079/79717/registry.xml' --request-version '1' --request '/srv/galaxy/shared/etc/tmpdir/jwd/079/79717/configs/tmpmod1j0bw'", - "create_time": "2021-06-23T10:20:00.981702", - "encoded_id": "77dd7a937748a715", - "exit_code": 0, - "galaxy_version": "21.01", - "implicit_output_dataset_collection_mapping": {}, - "info": null, - "input_dataset_collection_element_mapping": {}, - "input_dataset_collection_mapping": {}, - "input_dataset_mapping": {}, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_dataset_collection_mapping": {}, - "output_dataset_mapping": { - "output0": ["7c1d8e3101dbcdba"] - }, - "params": { - "file_count": "1", - "files": [{ - "__index__": 0, - "file_data": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a" - }], - "paramfile": null, - "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"ext\": \"auto\", \"dbkey\": \"?\", \"to_posix_lines\": true, \"src\": \"path\", \"name\": \"dataset1.txt\", \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a\", \"object_id\": 155707}], \"auto_decompress\": false}], \"check_content\": true}", - "request_version": "1" - }, - "state": "ok", - "tool_id": "__DATA_FETCH__", - "tool_stderr": "", - "tool_stdout": "", - "tool_version": "0.1.0", - "traceback": null, - "update_time": "2021-06-23T10:20:22.202678" -}, { - "command_line": "python /srv/galaxy/shared/src/tools/filters/catWrapper.py '/srv/galaxy/shared/etc/tmpdir/jwd/079/79726/outputs/galaxy_dataset_cf936245-b1d6-4840-b79d-2e20af74b921.dat' '/srv/galaxy/shared/database/files/000/134/dataset_134410.dat' '/srv/galaxy/shared/database/files/000/134/dataset_134409.dat'", - "create_time": "2021-06-23T10:46:28.351123", - "encoded_id": "77cf44871c57dd95", - "exit_code": 0, - "galaxy_version": "21.01", - "implicit_output_dataset_collection_mapping": {}, - "info": null, - "input_dataset_collection_element_mapping": {}, - "input_dataset_collection_mapping": {}, - "input_dataset_mapping": { - "input1": ["7ca3de8f49293d1a"], - "queries_0|input2": ["2e789aae2475b7da"] - }, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_dataset_collection_mapping": {}, - "output_dataset_mapping": { - "out_file1": ["fd7fec473f1e6c6b"] - }, - "params": { - "__input_ext": "txt", - "__workflow_invocation_uuid__": "42f21c0ad41011eb87defa163eba836f", - "chromInfo": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "dbkey": "?", - "input1": { - "values": [{ - "id": "7ca3de8f49293d1a", - "src": "hda" - }] - }, - "queries": [{ - "__index__": 0, - "input2": { - "values": [{ - "id": "2e789aae2475b7da", - "src": "hda" - }] - } - }] - }, - "state": "ok", - "tool_id": "cat1", - "tool_stderr": "", - "tool_stdout": "", - "tool_version": "1.0.0", - "traceback": null, - "update_time": "2021-06-23T10:46:44.738703" -}, { - "command_line": "python '/srv/galaxy/shared/src/tools/filters/random_lines_two_pass.py' '/srv/galaxy/shared/database/files/000/134/dataset_134423.dat' '/srv/galaxy/shared/etc/tmpdir/jwd/079/79727/outputs/galaxy_dataset_d9b5abdc-2a54-4fb7-b3df-1f05e9f2399a.dat' '3' --seed '0'", - "create_time": "2021-06-23T10:46:28.526901", - "encoded_id": "ea1a7696fd6484de", - "exit_code": 0, - "galaxy_version": "21.01", - "implicit_output_dataset_collection_mapping": {}, - "info": null, - "input_dataset_collection_element_mapping": {}, - "input_dataset_collection_mapping": {}, - "input_dataset_mapping": { - "input": ["fd7fec473f1e6c6b"] - }, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_dataset_collection_mapping": {}, - "output_dataset_mapping": { - "out_file1": ["775bc9b3c1750167"] - }, - "params": { - "__input_ext": "txt", - "__workflow_invocation_uuid__": "42f21c0ad41011eb87defa163eba836f", - "chromInfo": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len", - "dbkey": "?", - "input": { - "values": [{ - "id": "fd7fec473f1e6c6b", - "src": "hda" - }] - }, - "num_lines": "3", - "seed_source": { - "__current_case__": 1, - "seed": "0", - "seed_source_selector": "set_seed" - } - }, - "state": "ok", - "tool_id": "random_lines1", - "tool_stderr": "", - "tool_stdout": "Kept 3 of 4 total lines.\nUsed random seed of \"0\".\n", - "tool_version": "2.0.2", - "traceback": null, - "update_time": "2021-06-23T10:47:04.837750" -}] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/libraries_attrs.txt b/test/test-data/test_ga_history_export/libraries_attrs.txt deleted file mode 100644 index 0637a088..00000000 --- a/test/test-data/test_ga_history_export/libraries_attrs.txt +++ /dev/null @@ -1 +0,0 @@ -[] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/ro-crate-metadata.json b/test/test-data/test_ga_history_export/ro-crate-metadata.json deleted file mode 100644 index ff182bec..00000000 --- a/test/test-data/test_ga_history_export/ro-crate-metadata.json +++ /dev/null @@ -1,92 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.1/context", - "@graph": [ - { - "@id": "./", - "@type": "Dataset", - "datePublished": "2021-11-29T18:48:54+00:00", - "hasPart": [ - { - "@id": "datasets/" - }, - { - "@id": "implicit_collection_jobs_attrs.txt" - }, - { - "@id": "jobs_attrs.txt" - }, - { - "@id": "libraries_attrs.txt" - }, - { - "@id": "history_attrs.txt" - }, - { - "@id": "datasets_attrs.txt" - }, - { - "@id": "collections_attrs.txt" - }, - { - "@id": "datasets_attrs.txt.provenance" - }, - { - "@id": "export_attrs.txt" - }, - { - "@id": "datasets/a.tab_1.tabular" - } - ] - }, - { - "@id": "ro-crate-metadata.json", - "@type": "CreativeWork", - "about": { - "@id": "./" - }, - "conformsTo": { - "@id": "https://w3id.org/ro/crate/1.1" - } - }, - { - "@id": "datasets/", - "@type": "Dataset" - }, - { - "@id": "implicit_collection_jobs_attrs.txt", - "@type": "File" - }, - { - "@id": "jobs_attrs.txt", - "@type": "File" - }, - { - "@id": "libraries_attrs.txt", - "@type": "File" - }, - { - "@id": "history_attrs.txt", - "@type": "File" - }, - { - "@id": "datasets_attrs.txt", - "@type": "File" - }, - { - "@id": "collections_attrs.txt", - "@type": "File" - }, - { - "@id": "datasets_attrs.txt.provenance", - "@type": "File" - }, - { - "@id": "export_attrs.txt", - "@type": "File" - }, - { - "@id": "datasets/a.tab_1.tabular", - "@type": "File" - } - ] -} \ No newline at end of file diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index 8246b5d8..d5874595 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -11,15 +11,29 @@ from rocrate.provenance_profile import ProvenanceProfile WF_CRATE = "https://w3id.org/workflowhub/workflow-ro-crate" -from tools import parse_ga_export +from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset +def test_ga_history_loading(test_data_dir, tmpdir, helpers): + export_dir = "test_ga_history_export" + export_path = test_data_dir / export_dir / "history_export" + + metadata_export = load_ga_history_export(export_path) + jobs = [] + for job in metadata_export["jobs_attrs"]: + job_attrs = GalaxyJob() + job_attrs.parse_ga_jobs_attrs(job) + jobs.append(job_attrs.attributes) + + assert isinstance(job_attrs, GalaxyJob) + print(jobs[0]) + assert len(jobs) == 4 def test_ga_history_parsing(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" export_path = test_data_dir / export_dir / "history_export" - metadata_export = parse_ga_export.load_ga_history_export(export_path) - prov = ProvenanceProfile(metadata_export, "PDG", "https://orcid.org/0000-0002-8940-4946") + # metadata_export = load_ga_history_export(export_path) + prov = ProvenanceProfile(export_path, "PDG", "https://orcid.org/0000-0002-8940-4946") # print(len(metadata_export['jobs_attrs'])) # print(prov.document.serialize(format="rdf", rdf_format="turtle")) assert isinstance(prov, ProvenanceProfile) diff --git a/tools/load_ga_export.py b/tools/load_ga_export.py new file mode 100644 index 00000000..b608c7fa --- /dev/null +++ b/tools/load_ga_export.py @@ -0,0 +1,78 @@ +import json +import os +import re +from typing import ( + IO, + Any, + Callable, + Dict, + Generator, + Iterable, + List, + MutableMapping, + MutableSequence, + NamedTuple, + Optional, + Set, + Tuple, + Union, + cast, +) + +def load_ga_history_export(export_dir): + fn_list = os.listdir(export_dir) + export_metadata = {} + for f in fn_list : + export_dir_path = os.path.join(export_dir,f) + if os.path.isfile(export_dir_path): + with open(export_dir_path,"r") as fh: + # create keys for metadata files, removes '.' and 'txt' from fn + key = '_'.join(list(filter(None, re.split('\.|txt',f)))) + export_metadata[key] = json.loads(fh.read()) + return export_metadata + +class GalaxyJob(Dict): + def __init__(self): + """ + Initialize the GalaxyJob object. + """ + self.attributes = {} + self.attributes["inputs"] = {} + self.attributes["outputs"] = {} + self.attributes["parameters"] = {} + + def parse_ga_jobs_attrs(self, job_attrs): + + for key, value in job_attrs.items(): + if not isinstance(value, dict): + self.attributes[key] = value + else: + if len(value) == 0: + pass + else: + if "input" in key: + self.attributes["inputs"].update(job_attrs[key]) + if "output" in key: + self.attributes["outputs"].update(job_attrs[key]) + if "params" in key: + self.attributes["parameters"].update(job_attrs[key]) + +class GalaxyDataset(Dict): + def __init__(self, ga_export_dataset_attrs): + """ + Initialize the GalaxyDataset object. + """ + self.attributes = {} + self.attributes["metadata"] = {} + + def parse_ga_dataset_attrs(self, job_attrs): + + for key, value in job_attrs.items(): + if not isinstance(value, dict): + self.attributes[key] = value + else: + if len(value) == 0: + pass + else: + if "metadata" in key: + self.attributes["metadata"].update(job_attrs[key]) \ No newline at end of file diff --git a/tools/parse_ga_export.py b/tools/parse_ga_export.py deleted file mode 100644 index 381c7072..00000000 --- a/tools/parse_ga_export.py +++ /dev/null @@ -1,17 +0,0 @@ -import json -import os -import re - -def load_ga_history_export(export_dir): - fn_list = os.listdir(export_dir) - - export_metadata = {} - for f in fn_list : - export_dir_path = os.path.join(export_dir,f) - if os.path.isfile(export_dir_path): - with open(export_dir_path,"r") as fh: - # create keys for metadata files, removes '.' and 'txt' from fn - key = '_'.join(list(filter(None, re.split('\.|txt',f)))) - export_metadata[key] = json.loads(fh.read()) - - return export_metadata \ No newline at end of file From 2a2f0c3629ef575592453bd52ad1c8100525537e Mon Sep 17 00:00:00 2001 From: pauldg Date: Mon, 7 Mar 2022 11:12:43 +0100 Subject: [PATCH 06/27] changes --- requirements.txt | 2 + rocrate/provenance_profile.py | 79 ++++++++++++++++++++++------------- test/test_parse_ga_export.py | 2 +- 3 files changed, 53 insertions(+), 30 deletions(-) diff --git a/requirements.txt b/requirements.txt index 69b84474..d473ab3d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,3 +4,5 @@ galaxy2cwl jinja2 python-dateutil click +prov +schema_salad \ No newline at end of file diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 0d78add3..f9d9980b 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -1,8 +1,10 @@ import copy +import pdb import datetime import logging import urllib import uuid +import json from io import BytesIO from pathlib import PurePath, PurePosixPath from socket import getfqdn @@ -24,6 +26,7 @@ from schema_salad.sourceline import SourceLine from typing_extensions import TYPE_CHECKING from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset +from ast import literal_eval # from .errors import WorkflowException # from .job import CommandLineJob, JobBase @@ -48,7 +51,7 @@ WFPROV, ) # from .stdfsaccess import StdFsAccess -from rocrate.utils_cwl import CWLObjectType, JobsType, get_listing, posix_path, versionstring +# from rocrate.utils_cwl import CWLObjectType, JobsType, get_listing, posix_path, versionstring # from .workflow_job import WorkflowJob # if TYPE_CHECKING: @@ -65,6 +68,14 @@ def remove_escapes(s): translator = str.maketrans('', '', escapes) t = s.translate(translator) +def reassign(d): + for k, v in d.items(): + try: + evald = literal_eval(v) + if isinstance(evald, dict): + d[k] = evald + except ValueError: + pass class ProvenanceProfile: """ @@ -274,30 +285,32 @@ def used_artefacts( for key, value in process_metadata[item].items(): prov_role = self.wf_ns[f"{base}/{key}"] - - print("key : ",key) - print("-----------") - print("value: ",value) - print("-----------") - print("type : ",type(value)) + if not value: value = "" - # if value and isinstance(value, str): - # value = remove_escapes(value) - - for artefact in value: - try: - # print(artefact) - entity = self.declare_artefact(artefact) - self.document.used( - process_run_id, - entity, - datetime.datetime.now(), - None, - {"prov:role": prov_role}, - ) - except OSError: - pass + if "json" in key: + value = json.loads(value) + + # print("key : ",key) + # print("-----------") + # print("value: ",value) + # print("-----------") + # print("type : ",type(value)) + # print("-----------") + + # for artefact in value: + try: + pdb.set_trace() + entity = self.declare_artefact(value) + self.document.used( + process_run_id, + entity, + datetime.datetime.now(), + None, + {"prov:role": prov_role}, + ) + except OSError: + pass def declare_artefact(self, value: Any) -> ProvEntity: """Create data artefact entities for all file objects.""" @@ -316,6 +329,8 @@ def declare_artefact(self, value: Any) -> ProvEntity: return entity if isinstance(value, (str)): + # clean up unwanted characters + value = value.replace("|", "_") entity = self.declare_string(value) return entity @@ -368,6 +383,12 @@ def declare_artefact(self, value: Any) -> ProvEntity: # Let's iterate and recurse coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] for (key, val) in value.items(): + # clean up unwanted characters + if isinstance(key, str): + key = key.replace("|", "_") + if isinstance(val, str): + val = val.replace("|", "_") + v_ent = self.declare_artefact(val) self.document.membership(coll, v_ent) m_entity = self.document.entity(uuid.uuid4().urn) @@ -538,9 +559,9 @@ def declare_directory(self # a later call to this method will sort that is_empty = True - if "listing" not in value: - get_listing(self.fsaccess, value) - for entry in cast(MutableSequence[CWLObjectType], value.get("listing", [])): + # if "listing" not in value: + # get_listing(self.fsaccess, value) + for entry in cast(Dict, value.get("listing", [])): is_empty = False # Declare child-artifacts entity = self.declare_artefact(entry) @@ -616,7 +637,7 @@ def declare_string(self, value: str) -> Tuple[ProvEntity, str]: def generate_output_prov( self, - final_output: Union[CWLObjectType, MutableSequence[CWLObjectType], None], + final_output: Union[Dict, None], process_run_id: Optional[str], name: Optional[str], ) -> None: @@ -647,9 +668,9 @@ def generate_output_prov( entity, process_run_id, timestamp, None, {"prov:role": role} ) - def prospective_prov(self, job: JobsType) -> None: + def prospective_prov(self, job: GalaxyJob) -> None: """Create prospective prov recording as wfdesc prov:Plan.""" - if not isinstance(job, WorkflowJob): + if not isinstance(job, GalaxyJob): # direct command line tool execution self.document.entity( "wf:main", diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index d5874595..71532868 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -35,7 +35,7 @@ def test_ga_history_parsing(test_data_dir, tmpdir, helpers): # metadata_export = load_ga_history_export(export_path) prov = ProvenanceProfile(export_path, "PDG", "https://orcid.org/0000-0002-8940-4946") # print(len(metadata_export['jobs_attrs'])) - # print(prov.document.serialize(format="rdf", rdf_format="turtle")) + print(prov.document.serialize(format="rdf", rdf_format="turtle")) assert isinstance(prov, ProvenanceProfile) From efcbb9511389a3110eb8ad28fcf381f921de7c6f Mon Sep 17 00:00:00 2001 From: pauldg Date: Tue, 29 Mar 2022 18:31:02 +0200 Subject: [PATCH 07/27] updated provenance_profile.py --- rocrate/provenance_profile.py | 15 +- test/test_parse_ga_export.py | 2 + test/test_prov.ttl | 1081 +++++++++++++++++++++++++++++++++ 3 files changed, 1093 insertions(+), 5 deletions(-) create mode 100644 test/test_prov.ttl diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index f9d9980b..f69e9df9 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -163,7 +163,7 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: "provenance", self.base_uri + posix_path(PROVENANCE) + "/" ) # TODO: use appropriate refs for ga_export and related inputs - ro_identifier_workflow = self.base_uri + "ga_export" + ro_identifier_workflow = self.base_uri + "ga_export" + "/" self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow) ro_identifier_input = ( self.base_uri + "ga_export/datasets#" @@ -284,12 +284,16 @@ def used_artefacts( # print(process_metadata[item]) for key, value in process_metadata[item].items(): - prov_role = self.wf_ns[f"{base}/{key}"] - if not value: value = "" if "json" in key: value = json.loads(value) + if isinstance(key, str): + key = key.replace("|", "_") + if isinstance(value, str): + val = value.replace("|", "_") + + prov_role = self.wf_ns[f"{base}/{key}"] # print("key : ",key) # print("-----------") @@ -300,7 +304,7 @@ def used_artefacts( # for artefact in value: try: - pdb.set_trace() + # pdb.set_trace() entity = self.declare_artefact(value) self.document.used( process_run_id, @@ -336,7 +340,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: if isinstance(value, bytes): # If we got here then we must be in Python 3 - byte_s = BytesIO(value) + # byte_s = BytesIO(value) # data_file = self.research_object.add_data_file(byte_s) # FIXME: Don't naively assume add_data_file uses hash in filename! data_id = "data:%s" % str(value) #PurePosixPath(data_file).stem @@ -628,6 +632,7 @@ def declare_string(self, value: str) -> Tuple[ProvEntity, str]: # data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN) # checksum = PurePosixPath(data_file).name # FIXME: Don't naively assume add_data_file uses hash in filename! + value = str(value).replace("|", "_") data_id = "data:%s" % str(value) #PurePosixPath(data_file).stem entity = self.document.entity( data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)} diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index 71532868..12d9c2e2 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -36,6 +36,8 @@ def test_ga_history_parsing(test_data_dir, tmpdir, helpers): prov = ProvenanceProfile(export_path, "PDG", "https://orcid.org/0000-0002-8940-4946") # print(len(metadata_export['jobs_attrs'])) print(prov.document.serialize(format="rdf", rdf_format="turtle")) + with open("test_prov.ttl","w") as provenance_file: + prov.document.serialize(provenance_file,format="rdf", rdf_format="turtle") assert isinstance(prov, ProvenanceProfile) diff --git a/test/test_prov.ttl b/test/test_prov.ttl new file mode 100644 index 00000000..c2cdbc40 --- /dev/null +++ b/test/test_prov.ttl @@ -0,0 +1,1081 @@ +@prefix data: . +@prefix foaf: . +@prefix id: . +@prefix orcid: . +@prefix prov: . +@prefix rdfs: . +@prefix schema: . +@prefix wf: . +@prefix wfprov: . +@prefix xsd: . + +id:2d74b09c-b2a3-4db2-9569-0ed8fb27b36a a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:hadActivity id:20e49739-c446-4fa8-b564-c002a6762af8 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.036989"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.038601"^^xsd:dateTime ; + prov:entity id:cfa5924e-df83-482f-9986-1126f46a08fb ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.036616"^^xsd:dateTime ; + prov:entity id:b2c2277d-6021-4112-850d-e6919b16ffe2 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.037115"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.037050"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.037174"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.036920"^^xsd:dateTime ; + prov:entity id:d2fd94f5-3b74-4275-b2e6-9a740901bd12 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.037723"^^xsd:dateTime ; + prov:entity id:4211e9db-3e4c-4c72-b40b-5cd61e509919 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.036738"^^xsd:dateTime ; + prov:entity id:e00df3b8-b936-45aa-931b-e55aa48d5845 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:wasAssociatedWith id:e1515807-7299-444b-a8ff-366789285b60 . + +id:799e5218-7301-43c2-851d-fa3da27b83d8 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:hadActivity id:20e49739-c446-4fa8-b564-c002a6762af8 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.040067"^^xsd:dateTime ; + prov:entity id:16a9f31d-a9fd-410b-ab7e-4a3c2f6902e0 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.039459"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.040589"^^xsd:dateTime ; + prov:entity id:789f87ee-4c9e-410a-8e0d-d56b88ff8894 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.039328"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.039150"^^xsd:dateTime ; + prov:entity id:75614749-0504-46e7-918c-d552b6ef6873 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.039270"^^xsd:dateTime ; + prov:entity id:858bcf6c-d3e9-4cbb-98db-e3e23a10b56e ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.039398"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.039514"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.040182"^^xsd:dateTime ; + prov:entity data:3 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:wasAssociatedWith id:e1515807-7299-444b-a8ff-366789285b60 . + +id:e6c6a259-caa6-4637-873f-c91a4787cc6d a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:hadActivity id:20e49739-c446-4fa8-b564-c002a6762af8 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.035999"^^xsd:dateTime ; + prov:entity id:7eaadbec-4494-4367-82b6-0cd14b4fffc4 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.033953"^^xsd:dateTime ; + prov:entity id:e3e5c826-43a9-44c6-905c-a8a4a1105eff ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.034038"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.036060"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.033411"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.033343"^^xsd:dateTime ; + prov:entity id:4f87d9db-d488-4386-be6e-1d7a65449be4 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:wasAssociatedWith id:e1515807-7299-444b-a8ff-366789285b60 . + +id:f6db7670-04d7-4035-986b-204226451914 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:hadActivity id:20e49739-c446-4fa8-b564-c002a6762af8 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.029123"^^xsd:dateTime ; + prov:entity id:0926faad-cc2b-437d-8ba7-5a1b7cbcc1cd ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.029205"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.029703"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.032326"^^xsd:dateTime ; + prov:entity id:0d405ad5-5e6f-409f-9ed8-6d6e0f6305e4 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.032449"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-07T12:43:03.029636"^^xsd:dateTime ; + prov:entity id:bdde3981-0ad0-49f9-b228-60858920e96d ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:wasAssociatedWith id:e1515807-7299-444b-a8ff-366789285b60 . + +orcid:0000-0002-8940-4946 a schema:Person, + prov:Agent, + prov:Person ; + rdfs:label "PDG"^^xsd:string ; + schema:name "PDG"^^xsd:string ; + foaf:name "PDG"^^xsd:string . + +data:2524d3d3b68ad39a a wfprov:Artifact, + prov:Entity ; + prov:value "2524d3d3b68ad39a"^^xsd:string . + +data:3 a wfprov:Artifact, + prov:Entity ; + prov:value "3"^^xsd:string . + +data:775bc9b3c1750167 a wfprov:Artifact, + prov:Entity ; + prov:value "775bc9b3c1750167"^^xsd:string . + +data:7c1d8e3101dbcdba a wfprov:Artifact, + prov:Entity ; + prov:value "7c1d8e3101dbcdba"^^xsd:string . + +id:01747b41-76b6-4ee3-8baa-f2a38ef2588b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:14e7c198-8f10-4656-94e4-e6afb569d09c ; + prov:pairKey "object_id"^^xsd:string . + +id:06c1a25c-0fb4-4cbf-8058-d088ca1ff260 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:7ca3de8f49293d1a ; + prov:pairKey "id"^^xsd:string . + +id:08561888-4226-440a-8346-d02fa58d7124 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:0926faad-cc2b-437d-8ba7-5a1b7cbcc1cd a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2524d3d3b68ad39a . + +id:0d405ad5-5e6f-409f-9ed8-6d6e0f6305e4 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:3e45e45e-5272-4108-b43a-d6847917fe76, + id:471fc2ea-17d6-4c4d-95b5-c33e8afdafc3, + id:4c0932b4-50d9-4463-a555-b97101ccd38d ; + prov:hadMember , + id:c306ccbe-5c38-409f-8e8c-d07b90071064, + id:e539820a-376d-4d6b-9b76-83fd6b45fc06 . + +id:12aeb197-393c-474f-8c02-2a646dd3ff45 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:set_seed ; + prov:pairKey "seed_source_selector"^^xsd:string . + +id:135c7d70-dce8-4495-b383-c205f7a09377 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:1616545c-1b7b-431d-a266-d1548fbcf1c7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:f8b6a64b-c2a7-4379-9332-e56cd20a5205 ; + prov:pairKey "in_place"^^xsd:string . + +id:16a9f31d-a9fd-410b-ab7e-4a3c2f6902e0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:a42768b7-eb03-4adf-9acf-d3f246ec1180, + id:eae74a98-c429-4feb-b5ec-f4337ecd310a ; + prov:hadMember , + id:5c7939ed-17c6-4258-97a2-cbddf4e53571 . + +id:19c2fef7-4841-43bb-9e84-5578ec8c0fe1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:1c646195-e527-49d4-add9-57d75b59f28f a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:bdd9651f-565b-4f01-9b44-ecab0f8d03cc ; + prov:pairKey "destination"^^xsd:string . + +id:1dde2384-f621-4430-ad69-7b882879ec12 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:2034fd0b-8758-4122-ac5a-2da3b99d9601 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:2a5c2479-5e36-4f56-b5e1-c4bb157d8c1f a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:0 ; + prov:pairKey "seed"^^xsd:string . + +id:2d340838-6c11-4b9b-8efb-a3cdd1daf03e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:56995ae6-a9bf-446a-8ff2-a3f6b6e4c3d9 ; + prov:pairKey "values"^^xsd:string . + +id:35336b14-07be-4324-a3e2-b1ae386ec383 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:06c1a25c-0fb4-4cbf-8058-d088ca1ff260, + id:d78b7d83-0649-4480-88c3-d5031257914a, + id:f718bf7a-9772-4df8-a79b-065ac0f48060 ; + prov:hadMember data:7ca3de8f49293d1a, + data:hda, + . + +id:3cb906bd-a339-4dce-9f10-8830e77064dd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:aba904a4-c936-440b-8a8e-f0c785e5d6f6 ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:3e45e45e-5272-4108-b43a-d6847917fe76 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:c306ccbe-5c38-409f-8e8c-d07b90071064 ; + prov:pairKey "targets"^^xsd:string . + +id:3e80874d-b085-4be6-b7e6-6752a504df15 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:434fa725-7662-4a38-a6b6-0c5b7a046a6d, + id:4ca631fe-a3c3-40cf-a2f1-c35c216fc4c3, + id:ae22b859-366d-4823-8dc3-8246dde1d038 ; + prov:hadMember data:fd7fec473f1e6c6b, + data:hda, + . + +id:411b4b64-efa0-498b-831b-e1a811b533fc a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:4211e9db-3e4c-4c72-b40b-5cd61e509919 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:848b21af-2337-43b4-88d3-556edb65da6d, + id:9ff8d7db-bc2e-4c36-96a9-ba9b0acc5d66 ; + prov:hadMember , + id:fcc931f3-252e-4db0-81ae-44745d02e60b . + +id:434fa725-7662-4a38-a6b6-0c5b7a046a6d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:fd7fec473f1e6c6b ; + prov:pairKey "id"^^xsd:string . + +id:435fe41f-0b33-476d-ac9e-0ae09aa868aa a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:c9e82030-9dc0-4ecb-b5e2-1080e851476b, + id:e38a5ee3-57ea-4bd2-98ed-ae29ba42f819, + id:f2a08bca-e609-45bb-a7e2-461ffd56a888 ; + prov:hadMember data:2e789aae2475b7da, + data:hda, + . + +id:458ba136-e386-4887-81d2-0dc58f05d613 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1616545c-1b7b-431d-a266-d1548fbcf1c7, + id:2034fd0b-8758-4122-ac5a-2da3b99d9601, + id:411b4b64-efa0-498b-831b-e1a811b533fc, + id:4d9d83e8-2b4a-4da1-a733-0bc97c7a4fba, + id:61c482a1-fcb0-4e6c-a464-5ee8e731bbce, + id:7eb26f31-0568-4a19-8bd6-250d198af74f, + id:92ea61f0-9411-4237-afe1-124e9a791e0c, + id:a865a7ee-e00a-4a5f-9e9d-e38d4e9c7ff2, + id:b42d5b13-379e-4dba-8280-37e5e1ad9bfe, + id:d9b124d2-3709-42e8-a9d6-46741deaedcd, + id:f81db514-cf8d-496e-8a20-2124f9ec7106 ; + prov:hadMember , + , + data:auto, + data:dataset2.txt, + data:path, + , + id:20e2d794-4254-4633-aae0-ec5e89a26cf7, + id:331b5070-e37d-4cc2-a1d2-42fa8a860fcc, + id:a0d80900-bfe5-430d-8b2a-d84f1e30819b, + id:d26ae8a8-25ea-44f6-b525-60c07c6d5a26, + id:f8b6a64b-c2a7-4379-9332-e56cd20a5205 . + +id:471fc2ea-17d6-4c4d-95b5-c33e8afdafc3 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:4886ee12-8a4c-4ace-9612-a99c59d60862 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:4c0932b4-50d9-4463-a555-b97101ccd38d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e539820a-376d-4d6b-9b76-83fd6b45fc06 ; + prov:pairKey "check_content"^^xsd:string . + +id:4ca631fe-a3c3-40cf-a2f1-c35c216fc4c3 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:4d9d83e8-2b4a-4da1-a733-0bc97c7a4fba a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:4e9f2201-16ee-411e-b0b5-6b721a31961b a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1c646195-e527-49d4-add9-57d75b59f28f, + id:7e9d3f8d-26fa-4a75-a7be-8bf19a988a22, + id:98ab820f-380b-4de0-921b-3e5eefa05895, + id:d71b0844-dcb3-4f95-8ef4-a123c1fda9ab ; + prov:hadMember , + id:2699f676-0e8d-45f9-83e4-e18d42c8ea37, + id:47576d8c-0376-4b0a-b92a-62986ff6d530, + id:bdd9651f-565b-4f01-9b44-ecab0f8d03cc . + +id:4f87d9db-d488-4386-be6e-1d7a65449be4 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7c1d8e3101dbcdba . + +id:5736c82f-9794-4cec-b080-2a584974f965 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e6c4b36c-d9f7-4cdf-af54-9574a03c7cc4 ; + prov:pairKey "hashes"^^xsd:string . + +id:60645176-f281-4f11-a8ba-19998f73214c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:61c482a1-fcb0-4e6c-a464-5ee8e731bbce a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:331b5070-e37d-4cc2-a1d2-42fa8a860fcc ; + prov:pairKey "object_id"^^xsd:string . + +id:69f2e9bb-0e88-4b99-bae6-84e0c090bf40 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:6a97f8d9-a34a-450f-9091-70462ef9cab8 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:7035f1f8-c649-48dc-9cec-36026f8fd37b ; + prov:pairKey "__current_case__"^^xsd:string . + +id:72473707-f240-4058-9ccd-e8503f35a8c0 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:3d61a5b6-35cc-4b40-9709-8ddea0a6838c ; + prov:pairKey "__index__"^^xsd:string . + +id:749da440-59c3-4769-824c-a46ba41f6a96 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:3b075671-c68a-4cfa-a1ca-ba3402f7f8e0 ; + prov:pairKey "input2"^^xsd:string . + +id:75614749-0504-46e7-918c-d552b6ef6873 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +id:7646cc43-0998-44e3-ad50-a4066c301445 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:6277e935-5850-4603-ad47-9eadba7ed319 ; + prov:pairKey "check_content"^^xsd:string . + +id:789f87ee-4c9e-410a-8e0d-d56b88ff8894 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:08561888-4226-440a-8346-d02fa58d7124, + id:12aeb197-393c-474f-8c02-2a646dd3ff45, + id:2a5c2479-5e36-4f56-b5e1-c4bb157d8c1f, + id:6a97f8d9-a34a-450f-9091-70462ef9cab8 ; + prov:hadMember data:0, + data:set_seed, + , + id:7035f1f8-c649-48dc-9cec-36026f8fd37b . + +id:78f2923d-b049-46db-b855-68fe4b39fba7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:7c47812e-a743-471e-bc60-289ff2412086 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset1.txt ; + prov:pairKey "name"^^xsd:string . + +id:7e9d3f8d-26fa-4a75-a7be-8bf19a988a22 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:2699f676-0e8d-45f9-83e4-e18d42c8ea37 ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:7eaadbec-4494-4367-82b6-0cd14b4fffc4 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:7646cc43-0998-44e3-ad50-a4066c301445, + id:c2dd6553-a377-4b35-8f6e-2114447a8164, + id:fffb0f2d-0bc8-470b-ae81-9e6483e51141 ; + prov:hadMember , + id:6277e935-5850-4603-ad47-9eadba7ed319, + id:d193f76c-bf93-47b3-9f2e-adeedb1b9b83 . + +id:7eb26f31-0568-4a19-8bd6-250d198af74f a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:a0d80900-bfe5-430d-8b2a-d84f1e30819b ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:848b21af-2337-43b4-88d3-556edb65da6d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:858bcf6c-d3e9-4cbb-98db-e3e23a10b56e a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:775bc9b3c1750167 . + +id:8595276a-419f-4efd-9104-bb8af8e7c9ad a prov:Agent ; + prov:actedOnBehalfOf orcid:0000-0002-8940-4946 . + +id:89888457-0be2-482a-a5f4-78df6215c738 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:8a1d73d2-c260-4522-93da-9853539f0fb1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:181d6f96-e6ff-4cac-acb5-d357537f5d69 ; + prov:pairKey "in_place"^^xsd:string . + +id:8f861bcc-f5e6-48b8-a1c5-df3fecdd0380 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:92ea61f0-9411-4237-afe1-124e9a791e0c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:98ab820f-380b-4de0-921b-3e5eefa05895 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:9ae83fa5-9f2a-495c-b6ef-a67a2c1282af a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:8b9d60fe-9459-4a11-9316-a07b8564b9bf ; + prov:pairKey "__index__"^^xsd:string . + +id:9f8e537f-7734-4846-a1dc-10072021fede a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:72473707-f240-4058-9ccd-e8503f35a8c0, + id:749da440-59c3-4769-824c-a46ba41f6a96, + id:ab7ad9b2-5937-477c-a4de-81d4017e0caf ; + prov:hadMember , + id:3b075671-c68a-4cfa-a1ca-ba3402f7f8e0, + id:3d61a5b6-35cc-4b40-9709-8ddea0a6838c . + +id:9ff8d7db-bc2e-4c36-96a9-ba9b0acc5d66 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:fcc931f3-252e-4db0-81ae-44745d02e60b ; + prov:pairKey "values"^^xsd:string . + +id:a37e6a38-7f99-400b-91fb-a7f2eee116a9 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:69f2e9bb-0e88-4b99-bae6-84e0c090bf40, + id:9ae83fa5-9f2a-495c-b6ef-a67a2c1282af, + id:bed207ba-d46d-4b13-861d-726e592bbb18 ; + prov:hadMember , + , + id:8b9d60fe-9459-4a11-9316-a07b8564b9bf . + +id:a3f935f2-2c2d-4e7e-80a0-f7865180ae06 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:01747b41-76b6-4ee3-8baa-f2a38ef2588b, + id:4886ee12-8a4c-4ace-9612-a99c59d60862, + id:5736c82f-9794-4cec-b080-2a584974f965, + id:60645176-f281-4f11-a8ba-19998f73214c, + id:7c47812e-a743-471e-bc60-289ff2412086, + id:8a1d73d2-c260-4522-93da-9853539f0fb1, + id:afbc9621-dc4b-43ba-8ff2-09f77d9dd3e3, + id:b4379925-f8d0-44f5-ab8a-0530fa73fd0f, + id:d9709813-bb67-4546-89ab-827a698ac0fa, + id:df157f5e-cea3-48da-97fd-f819d1a472ae, + id:fbe70690-fffc-4c7b-bbc3-0acc8baa2dbc ; + prov:hadMember , + , + data:auto, + data:dataset1.txt, + data:path, + , + id:14e7c198-8f10-4656-94e4-e6afb569d09c, + id:181d6f96-e6ff-4cac-acb5-d357537f5d69, + id:a665694e-38a7-4443-bc4e-f45cb26d0f6a, + id:e6c4b36c-d9f7-4cdf-af54-9574a03c7cc4, + id:fa3e442b-6fc6-4104-8f98-831e3a228339 . + +id:a42768b7-eb03-4adf-9acf-d3f246ec1180 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a80d46cc-57ae-40eb-8e57-94c8a9c0d01f a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:8f861bcc-f5e6-48b8-a1c5-df3fecdd0380, + id:aa4b73d5-8e85-4263-bc4c-6512c3273d52, + id:ca6e1da9-b31d-47b2-9a07-4720646d02e0 ; + prov:hadMember , + , + id:1c95730f-eb41-432b-add7-8dd293286dbb . + +id:a865a7ee-e00a-4a5f-9e9d-e38d4e9c7ff2 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset2.txt ; + prov:pairKey "name"^^xsd:string . + +id:aa4b73d5-8e85-4263-bc4c-6512c3273d52 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:ab7ad9b2-5937-477c-a4de-81d4017e0caf a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:ae22b859-366d-4823-8dc3-8246dde1d038 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:afbc9621-dc4b-43ba-8ff2-09f77d9dd3e3 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:fa3e442b-6fc6-4104-8f98-831e3a228339 ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:b2c2277d-6021-4112-850d-e6919b16ffe2 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7ca3de8f49293d1a . + +id:b42d5b13-379e-4dba-8280-37e5e1ad9bfe a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:d26ae8a8-25ea-44f6-b525-60c07c6d5a26 ; + prov:pairKey "hashes"^^xsd:string . + +id:b4379925-f8d0-44f5-ab8a-0530fa73fd0f a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:b7b35e57-4bea-4854-92b9-9b15830459a1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:b8857908-272e-4afc-a3d9-8410e083d311 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e370a05b-53e5-4110-ab4b-ad5aee8255a1 ; + prov:pairKey "destination"^^xsd:string . + +id:bdde3981-0ad0-49f9-b228-60858920e96d a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:a37e6a38-7f99-400b-91fb-a7f2eee116a9 . + +id:bed207ba-d46d-4b13-861d-726e592bbb18 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:c2dd6553-a377-4b35-8f6e-2114447a8164 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:d193f76c-bf93-47b3-9f2e-adeedb1b9b83 ; + prov:pairKey "targets"^^xsd:string . + +id:c9e82030-9dc0-4ecb-b5e2-1080e851476b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:ca6e1da9-b31d-47b2-9a07-4720646d02e0 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:1c95730f-eb41-432b-add7-8dd293286dbb ; + prov:pairKey "__index__"^^xsd:string . + +id:cfa5924e-df83-482f-9986-1126f46a08fb a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:9f8e537f-7734-4846-a1dc-10072021fede . + +id:d2fd94f5-3b74-4275-b2e6-9a740901bd12 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +id:d321fdc7-b41e-4773-a9d8-fb8a310a77cd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:f09d70dc-44ec-43ac-afb4-a3994541ff53 ; + prov:pairKey "elements"^^xsd:string . + +id:d71b0844-dcb3-4f95-8ef4-a123c1fda9ab a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:47576d8c-0376-4b0a-b92a-62986ff6d530 ; + prov:pairKey "elements"^^xsd:string . + +id:d78b7d83-0649-4480-88c3-d5031257914a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:d9709813-bb67-4546-89ab-827a698ac0fa a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:d9b124d2-3709-42e8-a9d6-46741deaedcd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:df157f5e-cea3-48da-97fd-f819d1a472ae a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:e00df3b8-b936-45aa-931b-e55aa48d5845 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2e789aae2475b7da . + +id:e246c224-ec3f-4188-82b7-86fdf5391aa5 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:19c2fef7-4841-43bb-9e84-5578ec8c0fe1, + id:3cb906bd-a339-4dce-9f10-8830e77064dd, + id:b8857908-272e-4afc-a3d9-8410e083d311, + id:d321fdc7-b41e-4773-a9d8-fb8a310a77cd ; + prov:hadMember , + id:aba904a4-c936-440b-8a8e-f0c785e5d6f6, + id:e370a05b-53e5-4110-ab4b-ad5aee8255a1, + id:f09d70dc-44ec-43ac-afb4-a3994541ff53 . + +id:e38a5ee3-57ea-4bd2-98ed-ae29ba42f819 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:2e789aae2475b7da ; + prov:pairKey "id"^^xsd:string . + +id:e3e5c826-43a9-44c6-905c-a8a4a1105eff a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:a80d46cc-57ae-40eb-8e57-94c8a9c0d01f . + +id:eae74a98-c429-4feb-b5ec-f4337ecd310a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:5c7939ed-17c6-4258-97a2-cbddf4e53571 ; + prov:pairKey "values"^^xsd:string . + +id:f2a08bca-e609-45bb-a7e2-461ffd56a888 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:f718bf7a-9772-4df8-a79b-065ac0f48060 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:f81db514-cf8d-496e-8a20-2124f9ec7106 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:20e2d794-4254-4633-aae0-ec5e89a26cf7 ; + prov:pairKey "purge_source"^^xsd:string . + +id:fbe70690-fffc-4c7b-bbc3-0acc8baa2dbc a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:a665694e-38a7-4443-bc4e-f45cb26d0f6a ; + prov:pairKey "purge_source"^^xsd:string . + +id:fffb0f2d-0bc8-470b-ae81-9e6483e51141 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +data: a wfprov:Artifact, + prov:Entity ; + prov:value ""^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^xsd:string . + +data:0 a wfprov:Artifact, + prov:Entity ; + prov:value "0"^^xsd:string . + +data:42f21c0ad41011eb87defa163eba836f a wfprov:Artifact, + prov:Entity ; + prov:value "42f21c0ad41011eb87defa163eba836f"^^xsd:string . + +data:dataset1.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset1.txt"^^xsd:string . + +data:dataset2.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset2.txt"^^xsd:string . + +data:set_seed a wfprov:Artifact, + prov:Entity ; + prov:value "set_seed"^^xsd:string . + +data:txt a wfprov:Artifact, + prov:Entity ; + prov:value "txt"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:0d405ad5-5e6f-409f-9ed8-6d6e0f6305e4"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:16a9f31d-a9fd-410b-ab7e-4a3c2f6902e0"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:35336b14-07be-4324-a3e2-b1ae386ec383"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:3b075671-c68a-4cfa-a1ca-ba3402f7f8e0"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:3e80874d-b085-4be6-b7e6-6752a504df15"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:4211e9db-3e4c-4c72-b40b-5cd61e509919"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:435fe41f-0b33-476d-ac9e-0ae09aa868aa"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:458ba136-e386-4887-81d2-0dc58f05d613"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:4e9f2201-16ee-411e-b0b5-6b721a31961b"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:789f87ee-4c9e-410a-8e0d-d56b88ff8894"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:7eaadbec-4494-4367-82b6-0cd14b4fffc4"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:9f8e537f-7734-4846-a1dc-10072021fede"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:a37e6a38-7f99-400b-91fb-a7f2eee116a9"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:a3f935f2-2c2d-4e7e-80a0-f7865180ae06"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:a80d46cc-57ae-40eb-8e57-94c8a9c0d01f"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:bdd9651f-565b-4f01-9b44-ecab0f8d03cc"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:e246c224-ec3f-4188-82b7-86fdf5391aa5"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:e370a05b-53e5-4110-ab4b-ad5aee8255a1"^^xsd:string . + +id:14e7c198-8f10-4656-94e4-e6afb569d09c a prov:Entity ; + prov:value "155707"^^xsd:int . + +id:181d6f96-e6ff-4cac-acb5-d357537f5d69 a prov:Entity ; + prov:value false . + +id:1c95730f-eb41-432b-add7-8dd293286dbb a prov:Entity ; + prov:value "0"^^xsd:int . + +id:20e2d794-4254-4633-aae0-ec5e89a26cf7 a prov:Entity ; + prov:value false . + +id:2699f676-0e8d-45f9-83e4-e18d42c8ea37 a prov:Entity ; + prov:value false . + +id:331b5070-e37d-4cc2-a1d2-42fa8a860fcc a prov:Entity ; + prov:value "155708"^^xsd:int . + +id:3b075671-c68a-4cfa-a1ca-ba3402f7f8e0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1dde2384-f621-4430-ad69-7b882879ec12, + id:2d340838-6c11-4b9b-8efb-a3cdd1daf03e ; + prov:hadMember , + id:56995ae6-a9bf-446a-8ff2-a3f6b6e4c3d9 . + +id:3d61a5b6-35cc-4b40-9709-8ddea0a6838c a prov:Entity ; + prov:value "0"^^xsd:int . + +id:47576d8c-0376-4b0a-b92a-62986ff6d530 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:458ba136-e386-4887-81d2-0dc58f05d613 . + +id:56995ae6-a9bf-446a-8ff2-a3f6b6e4c3d9 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:435fe41f-0b33-476d-ac9e-0ae09aa868aa . + +id:5c7939ed-17c6-4258-97a2-cbddf4e53571 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:3e80874d-b085-4be6-b7e6-6752a504df15 . + +id:6277e935-5850-4603-ad47-9eadba7ed319 a prov:Entity ; + prov:value true . + +id:7035f1f8-c649-48dc-9cec-36026f8fd37b a prov:Entity ; + prov:value "1"^^xsd:int . + +id:8b9d60fe-9459-4a11-9316-a07b8564b9bf a prov:Entity ; + prov:value "0"^^xsd:int . + +id:a0d80900-bfe5-430d-8b2a-d84f1e30819b a prov:Entity ; + prov:value true . + +id:a665694e-38a7-4443-bc4e-f45cb26d0f6a a prov:Entity ; + prov:value false . + +id:aba904a4-c936-440b-8a8e-f0c785e5d6f6 a prov:Entity ; + prov:value false . + +id:bdd9651f-565b-4f01-9b44-ecab0f8d03cc a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:78f2923d-b049-46db-b855-68fe4b39fba7, + id:89888457-0be2-482a-a5f4-78df6215c738 ; + prov:hadMember data:hdas, + . + +id:c306ccbe-5c38-409f-8e8c-d07b90071064 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:4e9f2201-16ee-411e-b0b5-6b721a31961b . + +id:d193f76c-bf93-47b3-9f2e-adeedb1b9b83 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:e246c224-ec3f-4188-82b7-86fdf5391aa5 . + +id:d26ae8a8-25ea-44f6-b525-60c07c6d5a26 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:e370a05b-53e5-4110-ab4b-ad5aee8255a1 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:135c7d70-dce8-4495-b383-c205f7a09377, + id:b7b35e57-4bea-4854-92b9-9b15830459a1 ; + prov:hadMember data:hdas, + . + +id:e539820a-376d-4d6b-9b76-83fd6b45fc06 a prov:Entity ; + prov:value true . + +id:e6c4b36c-d9f7-4cdf-af54-9574a03c7cc4 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:f09d70dc-44ec-43ac-afb4-a3994541ff53 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:a3f935f2-2c2d-4e7e-80a0-f7865180ae06 . + +id:f8b6a64b-c2a7-4379-9332-e56cd20a5205 a prov:Entity ; + prov:value false . + +id:fa3e442b-6fc6-4104-8f98-831e3a228339 a prov:Entity ; + prov:value true . + +id:fcc931f3-252e-4db0-81ae-44745d02e60b a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:35336b14-07be-4324-a3e2-b1ae386ec383 . + +data:2e789aae2475b7da a wfprov:Artifact, + prov:Entity ; + prov:value "2e789aae2475b7da"^^xsd:string . + +data:7ca3de8f49293d1a a wfprov:Artifact, + prov:Entity ; + prov:value "7ca3de8f49293d1a"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"^^xsd:string . + +data:1 a wfprov:Artifact, + prov:Entity ; + prov:value "1"^^xsd:string . + +data:auto a wfprov:Artifact, + prov:Entity ; + prov:value "auto"^^xsd:string . + +data:fd7fec473f1e6c6b a wfprov:Artifact, + prov:Entity ; + prov:value "fd7fec473f1e6c6b"^^xsd:string . + +data:hdas a wfprov:Artifact, + prov:Entity ; + prov:value "hdas"^^xsd:string . + +data:path a wfprov:Artifact, + prov:Entity ; + prov:value "path"^^xsd:string . + +id:20e49739-c446-4fa8-b564-c002a6762af8 a wfprov:WorkflowRun, + prov:Activity ; + rdfs:label "Run of galaxy workflow"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan wf:main ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-03-07T12:43:03.028231"^^xsd:dateTime ; + prov:hadActivity id:e1515807-7299-444b-a8ff-366789285b60 ] ; + prov:startedAtTime "2022-03-07T12:43:03.028137"^^xsd:dateTime ; + prov:wasAssociatedWith id:e1515807-7299-444b-a8ff-366789285b60 . + + a wfprov:Artifact, + prov:Entity ; + prov:value "?"^^xsd:string . + +data:hda a wfprov:Artifact, + prov:Entity ; + prov:value "hda"^^xsd:string . + +id:e1515807-7299-444b-a8ff-366789285b60 a wfprov:WorkflowEngine, + prov:Agent, + prov:SoftwareAgent ; + rdfs:label "galaxy_version_placeholder"^^xsd:string ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-03-07T12:43:03.028086"^^xsd:dateTime ; + prov:hadActivity id:8595276a-419f-4efd-9104-bb8af8e7c9ad ] . + From 0e32c41c4691213d3f51d101443ed3787266a117 Mon Sep 17 00:00:00 2001 From: pauldg Date: Wed, 30 Mar 2022 15:13:21 +0200 Subject: [PATCH 08/27] updated provenance_profile tests --- rocrate/provenance_profile.py | 31 +- .../ga_export.cwlprov.json | 2883 ++++++++++++ .../ga_export.cwlprov.jsonld | 3869 +++++++++++++++++ .../ga_export.cwlprov.nt | 942 ++++ .../ga_export.cwlprov.provn | 332 ++ .../ga_export.cwlprov.ttl | 1081 +++++ .../ga_export.cwlprov.xml | 1457 +++++++ test/test_parse_ga_export.py | 11 +- 8 files changed, 10586 insertions(+), 20 deletions(-) create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.json create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.jsonld create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.nt create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index f69e9df9..99263b6d 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -88,7 +88,8 @@ def __init__( self, ga_export: Dict, full_name: str, - orcid: str, + orcid: str, + prov_name: str = None, # fsaccess: StdFsAccess, run_uuid: Optional[uuid.UUID] = None, ) -> None: @@ -98,6 +99,7 @@ def __init__( ga_export -- the galaxy metadata export (Dict) full_name -- author name orcid -- orcid (optional) + prov_name -- provenance file name run_uuid -- uuid for the workflow run """ # self.fsaccess = fsaccess @@ -123,6 +125,7 @@ def __init__( self.jobs.append(job_attrs.attributes) self.declare_process(job_attrs.attributes) + self.finalize_prov_profile(prov_name) # print(self.document.serialize(format="rdf", rdf_format="turtle")) def __str__(self) -> str: @@ -724,7 +727,7 @@ def activity_has_provenance(self, activity, prov_ids): uris = [i.uri for i in prov_ids] # self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) - def finalize_prov_profile(self, name): + def finalize_prov_profile(self, name=None): # type: (Optional[str]) -> List[Identifier] """Transfer the provenance related files to the RO-crate""" # NOTE: Relative posix path @@ -740,7 +743,9 @@ def finalize_prov_profile(self, name): # multiple places or iterations filename = f"{wf_name}.{self.workflow_run_uuid}.cwlprov" - basename = str(PurePosixPath(PROVENANCE) / filename) + # basename = str(PurePosixPath(crate_path) / filename) + basename = filename + print(basename) # TODO: Also support other profiles than CWLProv, e.g. ProvOne @@ -748,19 +753,17 @@ def finalize_prov_profile(self, name): prov_ids = [] # https://www.w3.org/TR/prov-xml/ - with self.research_object.write_bag_file(basename + ".xml") as provenance_file: + with open(basename + ".xml", "w") as provenance_file: self.document.serialize(provenance_file, format="xml", indent=4) prov_ids.append(self.provenance_ns[filename + ".xml"]) # https://www.w3.org/TR/prov-n/ - with self.research_object.write_bag_file( - basename + ".provn" - ) as provenance_file: + with open(basename + ".provn", "w") as provenance_file: self.document.serialize(provenance_file, format="provn", indent=2) prov_ids.append(self.provenance_ns[filename + ".provn"]) # https://www.w3.org/Submission/prov-json/ - with self.research_object.write_bag_file(basename + ".json") as provenance_file: + with open(basename + ".json", "w") as provenance_file: self.document.serialize(provenance_file, format="json", indent=2) prov_ids.append(self.provenance_ns[filename + ".json"]) @@ -768,24 +771,20 @@ def finalize_prov_profile(self, name): # which can be serialized to ttl/nt/jsonld (and more!) # https://www.w3.org/TR/turtle/ - with self.research_object.write_bag_file(basename + ".ttl") as provenance_file: + with open(basename + ".ttl", "w") as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="turtle") prov_ids.append(self.provenance_ns[filename + ".ttl"]) # https://www.w3.org/TR/n-triples/ - with self.research_object.write_bag_file(basename + ".nt") as provenance_file: - self.document.serialize( - provenance_file, format="rdf", rdf_format="ntriples" - ) + with open(basename + ".nt", "w") as provenance_file: + self.document.serialize(provenance_file, format="rdf", rdf_format="ntriples") prov_ids.append(self.provenance_ns[filename + ".nt"]) # https://www.w3.org/TR/json-ld/ # TODO: Use a nice JSON-LD context # see also https://eprints.soton.ac.uk/395985/ # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld :( - with self.research_object.write_bag_file( - basename + ".jsonld" - ) as provenance_file: + with open(basename + ".jsonld", "w") as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") prov_ids.append(self.provenance_ns[filename + ".jsonld"]) diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.json b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.json new file mode 100644 index 00000000..3492c7c1 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.json @@ -0,0 +1,2883 @@ +{ + "prefix": { + "wfprov": "http://purl.org/wf4ever/wfprov#", + "wfdesc": "http://purl.org/wf4ever/wfdesc#", + "cwlprov": "https://w3id.org/cwl/prov#", + "foaf": "http://xmlns.com/foaf/0.1/", + "schema": "http://schema.org/", + "orcid": "https://orcid.org/", + "id": "urn:uuid:", + "data": "urn:hash::sha1:", + "provenance": "arcp://uuid,d144da35-75c5-4bb2-bce4-b3a81dbf525d/metadata/provenance/", + "wf": "arcp://uuid,d144da35-75c5-4bb2-bce4-b3a81dbf525d/ga_export/", + "input": "arcp://uuid,d144da35-75c5-4bb2-bce4-b3a81dbf525d/ga_export/datasets#" + }, + "agent": { + "id:acc5b84a-046f-4fd2-9136-82d08877386a": {}, + "orcid:0000-0002-8940-4946": { + "prov:type": [ + { + "$": "schema:Person", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Person", + "type": "prov:QUALIFIED_NAME" + } + ], + "prov:label": "PDG", + "foaf:name": "PDG", + "schema:name": "PDG" + }, + "id:34d8946d-cc68-4ad9-8ecf-53026817187c": { + "prov:type": [ + { + "$": "prov:SoftwareAgent", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "wfprov:WorkflowEngine", + "type": "prov:QUALIFIED_NAME" + } + ], + "prov:label": "galaxy_version_placeholder" + } + }, + "actedOnBehalfOf": { + "_:id1": { + "prov:delegate": "id:acc5b84a-046f-4fd2-9136-82d08877386a", + "prov:responsible": "orcid:0000-0002-8940-4946" + } + }, + "wasStartedBy": { + "_:id2": { + "prov:activity": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:starter": "id:acc5b84a-046f-4fd2-9136-82d08877386a", + "prov:time": "2022-03-30T14:10:06.231396" + }, + "_:id4": { + "prov:activity": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:starter": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:time": "2022-03-30T14:10:06.231499" + }, + "_:id6": { + "prov:activity": "id:43861f75-9aa7-42b3-80e0-15cf9927d993", + "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:time": "2021-06-23T10:20:22.770291" + }, + "_:id41": { + "prov:activity": "id:0f0bc88f-e599-4a4e-8681-4edd21226161", + "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:time": "2021-06-23T10:20:00.981702" + }, + "_:id76": { + "prov:activity": "id:6b19db35-6d60-4351-be9b-7257b737a427", + "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:time": "2021-06-23T10:46:28.351123" + }, + "_:id106": { + "prov:activity": "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d", + "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:time": "2021-06-23T10:46:28.526901" + } + }, + "activity": { + "id:d76ec743-0418-4a56-88f2-b81a404a63bc": { + "prov:startTime": "2022-03-30T14:10:06.231425", + "prov:type": { + "$": "wfprov:WorkflowRun", + "type": "prov:QUALIFIED_NAME" + }, + "prov:label": "Run of galaxy workflow" + }, + "id:43861f75-9aa7-42b3-80e0-15cf9927d993": { + "prov:startTime": "2021-06-23T10:20:22.770291", + "prov:endTime": "2021-06-23T10:20:42.041319", + "prov:type": { + "$": "wfprov:ProcessRun", + "type": "prov:QUALIFIED_NAME" + }, + "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" + }, + "id:0f0bc88f-e599-4a4e-8681-4edd21226161": { + "prov:startTime": "2021-06-23T10:20:00.981702", + "prov:endTime": "2021-06-23T10:20:22.202678", + "prov:type": { + "$": "wfprov:ProcessRun", + "type": "prov:QUALIFIED_NAME" + }, + "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" + }, + "id:6b19db35-6d60-4351-be9b-7257b737a427": { + "prov:startTime": "2021-06-23T10:46:28.351123", + "prov:endTime": "2021-06-23T10:46:44.738703", + "prov:type": { + "$": "wfprov:ProcessRun", + "type": "prov:QUALIFIED_NAME" + }, + "prov:label": "Run of ga_export/jobs_attrs.txt#cat1" + }, + "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d": { + "prov:startTime": "2021-06-23T10:46:28.526901", + "prov:endTime": "2021-06-23T10:47:04.837750", + "prov:type": { + "$": "wfprov:ProcessRun", + "type": "prov:QUALIFIED_NAME" + }, + "prov:label": "Run of ga_export/jobs_attrs.txt#random_lines1" + } + }, + "wasAssociatedWith": { + "_:id3": { + "prov:activity": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:plan": "wf:main" + }, + "_:id5": { + "prov:activity": "id:43861f75-9aa7-42b3-80e0-15cf9927d993", + "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:plan": "wf:main/__DATA_FETCH__" + }, + "_:id40": { + "prov:activity": "id:0f0bc88f-e599-4a4e-8681-4edd21226161", + "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:plan": "wf:main/__DATA_FETCH__" + }, + "_:id75": { + "prov:activity": "id:6b19db35-6d60-4351-be9b-7257b737a427", + "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:plan": "wf:main/cat1" + }, + "_:id105": { + "prov:activity": "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d", + "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:plan": "wf:main/random_lines1" + } + }, + "entity": { + "data:2524d3d3b68ad39a": { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "2524d3d3b68ad39a" + }, + "id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047": { + "prov:type": [ + { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Collection", + "type": "prov:QUALIFIED_NAME" + } + ] + }, + "data:1": [ + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "1" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "1" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "1" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "1" + } + ], + "id:f5582681-806f-4e35-9028-631eab68c8db": { + "prov:type": [ + { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Collection", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Dictionary", + "type": "prov:QUALIFIED_NAME" + } + ], + "prov:hadDictionaryMember": [ + { + "$": "id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:4319f013-ecd8-4341-a5b9-8e9d8420bd31", + "type": "prov:QUALIFIED_NAME" + } + ] + }, + "id:456f97d2-4118-4fd3-a7e0-0bed64b7e343": { + "prov:value": { + "$": 0, + "type": "xsd:int" + } + }, + "id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "__index__", + "prov:pairEntity": { + "$": "id:456f97d2-4118-4fd3-a7e0-0bed64b7e343", + "type": "prov:QUALIFIED_NAME" + } + }, + "data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2": [ + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" + } + ], + "id:4319f013-ecd8-4341-a5b9-8e9d8420bd31": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "file_data", + "prov:pairEntity": { + "$": "data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2", + "type": "prov:QUALIFIED_NAME" + } + }, + "data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db": { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "urn:uuid:f5582681-806f-4e35-9028-631eab68c8db" + }, + "id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "@id", + "prov:pairEntity": { + "$": "data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db", + "type": "prov:QUALIFIED_NAME" + } + }, + "id:10a92b31-e38a-4eee-a163-d05f0c942e28": { + "prov:type": [ + { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Collection", + "type": "prov:QUALIFIED_NAME" + } + ] + }, + "data:": [ + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "" + } + ], + "id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5": { + "prov:type": [ + { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Collection", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Dictionary", + "type": "prov:QUALIFIED_NAME" + } + ], + "prov:hadDictionaryMember": [ + { + "$": "id:9be744cb-071c-4610-91d9-d2a8cca5fbf4", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:2f407424-3110-457d-b6f4-3d86f1c76cc8", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:f102ded2-603b-4c97-898e-b71bffb17a71", + "type": "prov:QUALIFIED_NAME" + } + ] + }, + "id:68b2355f-eec1-44a4-8751-11da17591063": { + "prov:type": [ + { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Collection", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Dictionary", + "type": "prov:QUALIFIED_NAME" + } + ], + "prov:hadDictionaryMember": [ + { + "$": "id:5b034fbf-1f17-485f-9c10-7b9b4872862c", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:c974472d-dbf4-4997-b690-62de731fa7a0", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:ab29cf85-149a-412a-92ff-e3a6b605ff16", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:bd679175-0778-4d62-856a-9da7f503a8b0", + "type": "prov:QUALIFIED_NAME" + } + ] + }, + "id:b98d6421-2cca-422c-b778-57480f86de92": { + "prov:type": [ + { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Collection", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Dictionary", + "type": "prov:QUALIFIED_NAME" + } + ], + "prov:hadDictionaryMember": [ + { + "$": "id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:24b14bfa-62b8-4d41-a724-90379c5708c1", + "type": "prov:QUALIFIED_NAME" + } + ] + }, + "data:hdas": [ + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "hdas" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "hdas" + } + ], + "id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "type", + "prov:pairEntity": { + "$": "data:hdas", + "type": "prov:QUALIFIED_NAME" + } + }, + "data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92": { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "urn:uuid:b98d6421-2cca-422c-b778-57480f86de92" + }, + "id:24b14bfa-62b8-4d41-a724-90379c5708c1": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "@id", + "prov:pairEntity": { + "$": "data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92", + "type": "prov:QUALIFIED_NAME" + } + }, + "id:5b034fbf-1f17-485f-9c10-7b9b4872862c": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "destination", + "prov:pairEntity": { + "$": "id:b98d6421-2cca-422c-b778-57480f86de92", + "type": "prov:QUALIFIED_NAME" + } + }, + "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c": { + "prov:type": [ + { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Collection", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "prov:Dictionary", + "type": "prov:QUALIFIED_NAME" + } + ], + "prov:hadDictionaryMember": [ + { + "$": "id:45379ceb-7d92-431f-a123-8ee411eedefa", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:60971e6c-b050-4d63-9ca2-b74f7fab78da", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:d96d9941-8860-4c3d-a573-666266e9e9fe", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:b09b2fa3-1624-428f-880d-b3890200a943", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:341b47e4-0ed6-416a-b290-ec06d3966f75", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:adff57da-d615-4087-8dd9-f32586a3d183", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:1090150b-6f8f-4ab5-8a27-802721f05c5a", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:2b1a8432-a59b-4f1b-87ee-912ca464e17c", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:e1aa5ec1-4083-4477-8266-9e68d6afdf66", + "type": "prov:QUALIFIED_NAME" + }, + { + "$": "id:56295d4d-8276-4557-b9f2-b4b3b653865f", + "type": "prov:QUALIFIED_NAME" + } + ] + }, + "data:auto": [ + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "auto" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "auto" + } + ], + "id:adff57da-d615-4087-8dd9-f32586a3d183": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "ext", + "prov:pairEntity": { + "$": "data:auto", + "type": "prov:QUALIFIED_NAME" + } + }, + "data:?": [ + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "?" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "?" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "?" + }, + { + "prov:type": { + "$": "wfprov:Artifact", + "type": "prov:QUALIFIED_NAME" + }, + "prov:value": "?" + } + ], + "id:b09b2fa3-1624-428f-880d-b3890200a943": { + "prov:type": { + "$": "prov:KeyEntityPair", + "type": "prov:QUALIFIED_NAME" + }, + "prov:pairKey": "dbkey", + "prov:pairEntity": { + "$": "data:?", + "type": "prov:QUALIFIED_NAME" + } + }, + "id:2d11fff4-3195-426d-991e-39f46c18caf7": { + "prov:value": true + }, + "id:341b47e4-0ed6-416a-b290-ec06d3966f75": { + "prov:type": { + 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+_:Nd79d38512c3843c79f5ee8e8ae821679 "2022-03-30T14:10:06.237016"^^ . +_:N3f7a223f432740c7b70c361a1c16c7e9 . + . + . + . +_:N15a00823f1534f33b4e2a4a08f457443 "2022-03-30T14:10:06.236603"^^ . + . + . + . + . + . + . +_:N32c8820be4bf48f1be3b8ac6d4b3354b "2022-03-30T14:10:06.237290"^^ . +_:N3f7a223f432740c7b70c361a1c16c7e9 . + "false"^^ . + "targets"^^ . + . + "src"^^ . + _:N4e5d7857c1bc4565a261f7a22a24c408 . + . + . + . + . + . + . + "__index__"^^ . + . + "ext"^^ . + . + . + . + . +_:Nfa683ea3c3704d4083d5203160881fa3 . + . + . + . + . + "@id"^^ . + . + "auto_decompress"^^ . +_:Nfa683ea3c3704d4083d5203160881fa3 . + . +_:N015f24b0074541a2bc828533b743f5d0 . + . + . +_:Nf2d4866c24b14f31813f592702bcbc69 . + "2021-06-23T10:46:28.351123"^^ . + "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^ . + . + . + . + . +_:N15a00823f1534f33b4e2a4a08f457443 . + . +_:N4a60e2fde86b4a9795dce7065619fb7b . + . + . + . + . + . + . + . + . + . + . +_:N133f7a923eb44208a2327771ac40d459 "2022-03-30T14:10:06.237196"^^ . + . + . + "path"^^ . + . + . + . + . + . + . + . + "dataset2.txt"^^ . + "urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a"^^ . + . + . + "2022-03-30T14:10:06.231425"^^ . + diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn new file mode 100644 index 00000000..ca0f0328 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn @@ -0,0 +1,332 @@ +document + prefix wfprov + prefix wfdesc + prefix cwlprov + prefix foaf + prefix schema + prefix orcid + prefix id + prefix data + prefix provenance + prefix wf + prefix input + + agent(id:acc5b84a-046f-4fd2-9136-82d08877386a) + agent(orcid:0000-0002-8940-4946, [prov:type='schema:Person', prov:type='prov:Person', prov:label="PDG", foaf:name="PDG", schema:name="PDG"]) + actedOnBehalfOf(id:acc5b84a-046f-4fd2-9136-82d08877386a, orcid:0000-0002-8940-4946, -) + agent(id:34d8946d-cc68-4ad9-8ecf-53026817187c, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="galaxy_version_placeholder"]) + wasStartedBy(id:34d8946d-cc68-4ad9-8ecf-53026817187c, -, id:acc5b84a-046f-4fd2-9136-82d08877386a, 2022-03-30T14:10:06.231396) + activity(id:d76ec743-0418-4a56-88f2-b81a404a63bc, 2022-03-30T14:10:06.231425, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of galaxy workflow"]) + wasAssociatedWith(id:d76ec743-0418-4a56-88f2-b81a404a63bc, id:34d8946d-cc68-4ad9-8ecf-53026817187c, wf:main) + wasStartedBy(id:d76ec743-0418-4a56-88f2-b81a404a63bc, -, id:34d8946d-cc68-4ad9-8ecf-53026817187c, 2022-03-30T14:10:06.231499) + activity(id:43861f75-9aa7-42b3-80e0-15cf9927d993, 2021-06-23T10:20:22.770291, 2021-06-23T10:20:42.041319, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) + wasAssociatedWith(id:43861f75-9aa7-42b3-80e0-15cf9927d993, id:34d8946d-cc68-4ad9-8ecf-53026817187c, wf:main/__DATA_FETCH__) + wasStartedBy(id:43861f75-9aa7-42b3-80e0-15cf9927d993, -, id:d76ec743-0418-4a56-88f2-b81a404a63bc, 2021-06-23T10:20:22.770291) + entity(data:2524d3d3b68ad39a, [prov:type='wfprov:Artifact', prov:value="2524d3d3b68ad39a"]) + entity(id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047, data:2524d3d3b68ad39a) + used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047, 2022-03-30T14:10:06.232136, [prov:role='wf:main/__DATA_FETCH__/output0']) + entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) + used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, data:1, 2022-03-30T14:10:06.232201, [prov:role='wf:main/__DATA_FETCH__/file_count']) + entity(id:f5582681-806f-4e35-9028-631eab68c8db, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603', prov:hadDictionaryMember='id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc', prov:hadDictionaryMember='id:4319f013-ecd8-4341-a5b9-8e9d8420bd31']) + entity(id:456f97d2-4118-4fd3-a7e0-0bed64b7e343, [prov:value=0]) + hadMember(id:f5582681-806f-4e35-9028-631eab68c8db, id:456f97d2-4118-4fd3-a7e0-0bed64b7e343) + entity(id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:456f97d2-4118-4fd3-a7e0-0bed64b7e343']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) + hadMember(id:f5582681-806f-4e35-9028-631eab68c8db, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:4319f013-ecd8-4341-a5b9-8e9d8420bd31, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db, [prov:type='wfprov:Artifact', prov:value="urn:uuid:f5582681-806f-4e35-9028-631eab68c8db"]) + hadMember(id:f5582681-806f-4e35-9028-631eab68c8db, data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db) + entity(id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db']) + entity(id:10a92b31-e38a-4eee-a163-d05f0c942e28, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:10a92b31-e38a-4eee-a163-d05f0c942e28, id:f5582681-806f-4e35-9028-631eab68c8db) + used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, id:10a92b31-e38a-4eee-a163-d05f0c942e28, 2022-03-30T14:10:06.232547, [prov:role='wf:main/__DATA_FETCH__/files']) + entity(data:, [prov:type='wfprov:Artifact', prov:value=""]) + used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, data:, 2022-03-30T14:10:06.232599, [prov:role='wf:main/__DATA_FETCH__/paramfile']) + entity(id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:9be744cb-071c-4610-91d9-d2a8cca5fbf4', prov:hadDictionaryMember='id:2f407424-3110-457d-b6f4-3d86f1c76cc8', prov:hadDictionaryMember='id:f102ded2-603b-4c97-898e-b71bffb17a71']) + entity(id:68b2355f-eec1-44a4-8751-11da17591063, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:5b034fbf-1f17-485f-9c10-7b9b4872862c', prov:hadDictionaryMember='id:c974472d-dbf4-4997-b690-62de731fa7a0', prov:hadDictionaryMember='id:ab29cf85-149a-412a-92ff-e3a6b605ff16', prov:hadDictionaryMember='id:bd679175-0778-4d62-856a-9da7f503a8b0']) + entity(id:b98d6421-2cca-422c-b778-57480f86de92, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0', prov:hadDictionaryMember='id:24b14bfa-62b8-4d41-a724-90379c5708c1']) + entity(data:hdas, [prov:type='wfprov:Artifact', prov:value="hdas"]) + hadMember(id:b98d6421-2cca-422c-b778-57480f86de92, data:hdas) + entity(id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0, [prov:type='prov:KeyEntityPair', prov:pairKey="type", prov:pairEntity='data:hdas']) + entity(data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92, [prov:type='wfprov:Artifact', prov:value="urn:uuid:b98d6421-2cca-422c-b778-57480f86de92"]) + hadMember(id:b98d6421-2cca-422c-b778-57480f86de92, data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92) + entity(id:24b14bfa-62b8-4d41-a724-90379c5708c1, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92']) + hadMember(id:68b2355f-eec1-44a4-8751-11da17591063, id:b98d6421-2cca-422c-b778-57480f86de92) + entity(id:5b034fbf-1f17-485f-9c10-7b9b4872862c, [prov:type='prov:KeyEntityPair', prov:pairKey="destination", prov:pairEntity='id:b98d6421-2cca-422c-b778-57480f86de92']) + entity(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:45379ceb-7d92-431f-a123-8ee411eedefa', prov:hadDictionaryMember='id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7', prov:hadDictionaryMember='id:60971e6c-b050-4d63-9ca2-b74f7fab78da', prov:hadDictionaryMember='id:d96d9941-8860-4c3d-a573-666266e9e9fe', prov:hadDictionaryMember='id:b09b2fa3-1624-428f-880d-b3890200a943', prov:hadDictionaryMember='id:341b47e4-0ed6-416a-b290-ec06d3966f75', prov:hadDictionaryMember='id:adff57da-d615-4087-8dd9-f32586a3d183', prov:hadDictionaryMember='id:1090150b-6f8f-4ab5-8a27-802721f05c5a', prov:hadDictionaryMember='id:2b1a8432-a59b-4f1b-87ee-912ca464e17c', prov:hadDictionaryMember='id:e1aa5ec1-4083-4477-8266-9e68d6afdf66', prov:hadDictionaryMember='id:56295d4d-8276-4557-b9f2-b4b3b653865f']) + entity(data:auto, [prov:type='wfprov:Artifact', prov:value="auto"]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, data:auto) + entity(id:adff57da-d615-4087-8dd9-f32586a3d183, [prov:type='prov:KeyEntityPair', prov:pairKey="ext", prov:pairEntity='data:auto']) + entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, data:?) + entity(id:b09b2fa3-1624-428f-880d-b3890200a943, [prov:type='prov:KeyEntityPair', prov:pairKey="dbkey", prov:pairEntity='data:?']) + entity(id:2d11fff4-3195-426d-991e-39f46c18caf7, [prov:value="1" %% xsd:boolean]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, id:2d11fff4-3195-426d-991e-39f46c18caf7) + entity(id:341b47e4-0ed6-416a-b290-ec06d3966f75, [prov:type='prov:KeyEntityPair', prov:pairKey="to_posix_lines", prov:pairEntity='id:2d11fff4-3195-426d-991e-39f46c18caf7']) + entity(data:path, [prov:type='wfprov:Artifact', prov:value="path"]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, data:path) + entity(id:1090150b-6f8f-4ab5-8a27-802721f05c5a, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:path']) + entity(data:dataset2.txt, [prov:type='wfprov:Artifact', prov:value="dataset2.txt"]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, data:dataset2.txt) + entity(id:45379ceb-7d92-431f-a123-8ee411eedefa, [prov:type='prov:KeyEntityPair', prov:pairKey="name", prov:pairEntity='data:dataset2.txt']) + entity(id:43d5b201-ede9-419e-8b39-1bac02df6546, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:EmptyCollection']) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, id:43d5b201-ede9-419e-8b39-1bac02df6546) + entity(id:60971e6c-b050-4d63-9ca2-b74f7fab78da, [prov:type='prov:KeyEntityPair', prov:pairKey="hashes", prov:pairEntity='id:43d5b201-ede9-419e-8b39-1bac02df6546']) + entity(id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c, [prov:value="0" %% xsd:boolean]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c) + entity(id:56295d4d-8276-4557-b9f2-b4b3b653865f, [prov:type='prov:KeyEntityPair', prov:pairKey="in_place", prov:pairEntity='id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c']) + entity(id:556f2e68-82d3-4ceb-aa48-e93d1a75be64, [prov:value="0" %% xsd:boolean]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, id:556f2e68-82d3-4ceb-aa48-e93d1a75be64) + entity(id:e1aa5ec1-4083-4477-8266-9e68d6afdf66, [prov:type='prov:KeyEntityPair', prov:pairKey="purge_source", prov:pairEntity='id:556f2e68-82d3-4ceb-aa48-e93d1a75be64']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:2b1a8432-a59b-4f1b-87ee-912ca464e17c, [prov:type='prov:KeyEntityPair', prov:pairKey="path", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(id:c8ef7d57-8650-4fb8-a748-a692bffac0b5, [prov:value=155708]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, id:c8ef7d57-8650-4fb8-a748-a692bffac0b5) + entity(id:d96d9941-8860-4c3d-a573-666266e9e9fe, [prov:type='prov:KeyEntityPair', prov:pairKey="object_id", prov:pairEntity='id:c8ef7d57-8650-4fb8-a748-a692bffac0b5']) + entity(data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, [prov:type='wfprov:Artifact', prov:value="urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c"]) + hadMember(id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c, data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c) + entity(id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c']) + entity(id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1, id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c) + hadMember(id:68b2355f-eec1-44a4-8751-11da17591063, id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1) + entity(id:bd679175-0778-4d62-856a-9da7f503a8b0, [prov:type='prov:KeyEntityPair', prov:pairKey="elements", prov:pairEntity='id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1']) + entity(id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5, [prov:value="0" %% xsd:boolean]) + hadMember(id:68b2355f-eec1-44a4-8751-11da17591063, id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5) + entity(id:ab29cf85-149a-412a-92ff-e3a6b605ff16, [prov:type='prov:KeyEntityPair', prov:pairKey="auto_decompress", prov:pairEntity='id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5']) + entity(data:urn:uuid:68b2355f-eec1-44a4-8751-11da17591063, [prov:type='wfprov:Artifact', prov:value="urn:uuid:68b2355f-eec1-44a4-8751-11da17591063"]) + hadMember(id:68b2355f-eec1-44a4-8751-11da17591063, data:urn:uuid:68b2355f-eec1-44a4-8751-11da17591063) + entity(id:c974472d-dbf4-4997-b690-62de731fa7a0, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:68b2355f-eec1-44a4-8751-11da17591063']) + entity(id:de1ab5b2-d45d-4735-8166-1a8af8fcd980, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:de1ab5b2-d45d-4735-8166-1a8af8fcd980, id:68b2355f-eec1-44a4-8751-11da17591063) + hadMember(id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5, id:de1ab5b2-d45d-4735-8166-1a8af8fcd980) + entity(id:f102ded2-603b-4c97-898e-b71bffb17a71, [prov:type='prov:KeyEntityPair', prov:pairKey="targets", prov:pairEntity='id:de1ab5b2-d45d-4735-8166-1a8af8fcd980']) + entity(id:2d0a8975-d3b6-43aa-b902-a42b9483374b, [prov:value="1" %% xsd:boolean]) + hadMember(id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5, id:2d0a8975-d3b6-43aa-b902-a42b9483374b) + entity(id:2f407424-3110-457d-b6f4-3d86f1c76cc8, [prov:type='prov:KeyEntityPair', prov:pairKey="check_content", prov:pairEntity='id:2d0a8975-d3b6-43aa-b902-a42b9483374b']) + entity(data:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5, [prov:type='wfprov:Artifact', prov:value="urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5"]) + hadMember(id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5, data:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5) + entity(id:9be744cb-071c-4610-91d9-d2a8cca5fbf4, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5']) + used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5, 2022-03-30T14:10:06.234091, [prov:role='wf:main/__DATA_FETCH__/request_json']) + entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) + used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, data:1, 2022-03-30T14:10:06.234137, [prov:role='wf:main/__DATA_FETCH__/request_version']) + activity(id:0f0bc88f-e599-4a4e-8681-4edd21226161, 2021-06-23T10:20:00.981702, 2021-06-23T10:20:22.202678, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) + wasAssociatedWith(id:0f0bc88f-e599-4a4e-8681-4edd21226161, id:34d8946d-cc68-4ad9-8ecf-53026817187c, wf:main/__DATA_FETCH__) + wasStartedBy(id:0f0bc88f-e599-4a4e-8681-4edd21226161, -, id:d76ec743-0418-4a56-88f2-b81a404a63bc, 2021-06-23T10:20:00.981702) + entity(data:7c1d8e3101dbcdba, [prov:type='wfprov:Artifact', prov:value="7c1d8e3101dbcdba"]) + entity(id:eaec06da-6307-4712-80ca-f89bebb4abc2, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:eaec06da-6307-4712-80ca-f89bebb4abc2, data:7c1d8e3101dbcdba) + used(id:0f0bc88f-e599-4a4e-8681-4edd21226161, id:eaec06da-6307-4712-80ca-f89bebb4abc2, 2022-03-30T14:10:06.234586, [prov:role='wf:main/__DATA_FETCH__/output0']) + entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) + used(id:0f0bc88f-e599-4a4e-8681-4edd21226161, data:1, 2022-03-30T14:10:06.234629, [prov:role='wf:main/__DATA_FETCH__/file_count']) + entity(id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:f582aab0-3308-432a-a5e7-8c2a0d069acf', prov:hadDictionaryMember='id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c', prov:hadDictionaryMember='id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd']) + entity(id:4e23da19-5664-4972-94b0-b2d3365672b1, [prov:value=0]) + hadMember(id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d, id:4e23da19-5664-4972-94b0-b2d3365672b1) + entity(id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:4e23da19-5664-4972-94b0-b2d3365672b1']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"]) + hadMember(id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a) + entity(id:f582aab0-3308-432a-a5e7-8c2a0d069acf, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a']) + entity(data:urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d, [prov:type='wfprov:Artifact', prov:value="urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d"]) + hadMember(id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d, data:urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d) + entity(id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d']) + entity(id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a, id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d) + used(id:0f0bc88f-e599-4a4e-8681-4edd21226161, id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a, 2022-03-30T14:10:06.234977, [prov:role='wf:main/__DATA_FETCH__/files']) + entity(data:, [prov:type='wfprov:Artifact', prov:value=""]) + used(id:0f0bc88f-e599-4a4e-8681-4edd21226161, data:, 2022-03-30T14:10:06.235023, [prov:role='wf:main/__DATA_FETCH__/paramfile']) + entity(id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:28c49a54-4fce-484f-bbf3-754c514865bd', prov:hadDictionaryMember='id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700', prov:hadDictionaryMember='id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789']) + entity(id:f6641719-90a2-47d4-96dd-a847725d5d37, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4', prov:hadDictionaryMember='id:decc5efa-759a-4165-9034-88a8de8ff547', prov:hadDictionaryMember='id:1210a0ac-c6d4-4639-8b29-7866ac72a541', prov:hadDictionaryMember='id:a4beeb97-7076-4d47-8015-e6779877af9e']) + entity(id:afa54a2b-dd93-4fa1-aa45-49b521d7d002, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:a3df1b9d-8a6a-4a15-b880-565871b262e2', prov:hadDictionaryMember='id:b1c0e073-72ee-42f6-a512-d8b0a120f260']) + entity(data:hdas, [prov:type='wfprov:Artifact', prov:value="hdas"]) + hadMember(id:afa54a2b-dd93-4fa1-aa45-49b521d7d002, data:hdas) + entity(id:b1c0e073-72ee-42f6-a512-d8b0a120f260, [prov:type='prov:KeyEntityPair', prov:pairKey="type", prov:pairEntity='data:hdas']) + entity(data:urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002, [prov:type='wfprov:Artifact', prov:value="urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002"]) + hadMember(id:afa54a2b-dd93-4fa1-aa45-49b521d7d002, data:urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002) + entity(id:a3df1b9d-8a6a-4a15-b880-565871b262e2, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002']) + hadMember(id:f6641719-90a2-47d4-96dd-a847725d5d37, id:afa54a2b-dd93-4fa1-aa45-49b521d7d002) + entity(id:a4beeb97-7076-4d47-8015-e6779877af9e, [prov:type='prov:KeyEntityPair', prov:pairKey="destination", prov:pairEntity='id:afa54a2b-dd93-4fa1-aa45-49b521d7d002']) + entity(id:f2a60dac-8878-4bad-98f1-782ebf300df9, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:738ba6b7-e61e-4d37-abb6-3cee1f782367', prov:hadDictionaryMember='id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af', prov:hadDictionaryMember='id:4f7a8626-cbee-41ea-835b-76ddc79fcbce', prov:hadDictionaryMember='id:e64e532c-b1a6-454d-ac58-bde6809a1841', prov:hadDictionaryMember='id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565', prov:hadDictionaryMember='id:f7e87688-b315-448f-82c3-a18665a84053', prov:hadDictionaryMember='id:343ac668-db1a-47ca-af95-093b7cc710e1', prov:hadDictionaryMember='id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26', prov:hadDictionaryMember='id:4389b350-32eb-48e4-8da0-aaf191209de3', prov:hadDictionaryMember='id:a89b8834-c5ec-45c4-8760-213c4cc36302', prov:hadDictionaryMember='id:a69fb546-67ad-460f-b6f5-01ce7c181db7']) + entity(data:auto, [prov:type='wfprov:Artifact', prov:value="auto"]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, data:auto) + entity(id:a89b8834-c5ec-45c4-8760-213c4cc36302, [prov:type='prov:KeyEntityPair', prov:pairKey="ext", prov:pairEntity='data:auto']) + entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, data:?) + entity(id:738ba6b7-e61e-4d37-abb6-3cee1f782367, [prov:type='prov:KeyEntityPair', prov:pairKey="dbkey", prov:pairEntity='data:?']) + entity(id:5f8fd80e-f00f-4078-9660-55806bdbd100, [prov:value="1" %% xsd:boolean]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, id:5f8fd80e-f00f-4078-9660-55806bdbd100) + entity(id:4389b350-32eb-48e4-8da0-aaf191209de3, [prov:type='prov:KeyEntityPair', prov:pairKey="to_posix_lines", prov:pairEntity='id:5f8fd80e-f00f-4078-9660-55806bdbd100']) + entity(data:path, [prov:type='wfprov:Artifact', prov:value="path"]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, data:path) + entity(id:a69fb546-67ad-460f-b6f5-01ce7c181db7, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:path']) + entity(data:dataset1.txt, [prov:type='wfprov:Artifact', prov:value="dataset1.txt"]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, data:dataset1.txt) + entity(id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af, [prov:type='prov:KeyEntityPair', prov:pairKey="name", prov:pairEntity='data:dataset1.txt']) + entity(id:b35ba485-3a40-4743-9a58-b207f5becd69, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:EmptyCollection']) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, id:b35ba485-3a40-4743-9a58-b207f5becd69) + entity(id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565, [prov:type='prov:KeyEntityPair', prov:pairKey="hashes", prov:pairEntity='id:b35ba485-3a40-4743-9a58-b207f5becd69']) + entity(id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601, [prov:value="0" %% xsd:boolean]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601) + entity(id:e64e532c-b1a6-454d-ac58-bde6809a1841, [prov:type='prov:KeyEntityPair', prov:pairKey="in_place", prov:pairEntity='id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601']) + entity(id:afbd3904-77af-4cab-92f0-f7a1d1e4f467, [prov:value="0" %% xsd:boolean]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, id:afbd3904-77af-4cab-92f0-f7a1d1e4f467) + entity(id:343ac668-db1a-47ca-af95-093b7cc710e1, [prov:type='prov:KeyEntityPair', prov:pairKey="purge_source", prov:pairEntity='id:afbd3904-77af-4cab-92f0-f7a1d1e4f467']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a) + entity(id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26, [prov:type='prov:KeyEntityPair', prov:pairKey="path", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a']) + entity(id:35a147fd-c38e-4a85-bd9a-6a509ccd1245, [prov:value=155707]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, id:35a147fd-c38e-4a85-bd9a-6a509ccd1245) + entity(id:4f7a8626-cbee-41ea-835b-76ddc79fcbce, [prov:type='prov:KeyEntityPair', prov:pairKey="object_id", prov:pairEntity='id:35a147fd-c38e-4a85-bd9a-6a509ccd1245']) + entity(data:urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9, [prov:type='wfprov:Artifact', prov:value="urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9"]) + hadMember(id:f2a60dac-8878-4bad-98f1-782ebf300df9, data:urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9) + entity(id:f7e87688-b315-448f-82c3-a18665a84053, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9']) + entity(id:411a358d-2596-4506-b64a-74b54ea779d4, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:411a358d-2596-4506-b64a-74b54ea779d4, id:f2a60dac-8878-4bad-98f1-782ebf300df9) + hadMember(id:f6641719-90a2-47d4-96dd-a847725d5d37, id:411a358d-2596-4506-b64a-74b54ea779d4) + entity(id:decc5efa-759a-4165-9034-88a8de8ff547, [prov:type='prov:KeyEntityPair', prov:pairKey="elements", prov:pairEntity='id:411a358d-2596-4506-b64a-74b54ea779d4']) + entity(id:77f3c59e-7ec9-4e8b-9401-857b6c311c83, [prov:value="0" %% xsd:boolean]) + hadMember(id:f6641719-90a2-47d4-96dd-a847725d5d37, id:77f3c59e-7ec9-4e8b-9401-857b6c311c83) + entity(id:1210a0ac-c6d4-4639-8b29-7866ac72a541, [prov:type='prov:KeyEntityPair', prov:pairKey="auto_decompress", prov:pairEntity='id:77f3c59e-7ec9-4e8b-9401-857b6c311c83']) + entity(data:urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37, [prov:type='wfprov:Artifact', prov:value="urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37"]) + hadMember(id:f6641719-90a2-47d4-96dd-a847725d5d37, data:urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37) + entity(id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37']) + entity(id:2f356100-3315-4ff7-87cf-54b1d4d3ea49, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:2f356100-3315-4ff7-87cf-54b1d4d3ea49, id:f6641719-90a2-47d4-96dd-a847725d5d37) + hadMember(id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990, id:2f356100-3315-4ff7-87cf-54b1d4d3ea49) + entity(id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700, [prov:type='prov:KeyEntityPair', prov:pairKey="targets", prov:pairEntity='id:2f356100-3315-4ff7-87cf-54b1d4d3ea49']) + entity(id:ff95d010-cdcb-45d8-8418-aa53e7681b10, [prov:value="1" %% xsd:boolean]) + hadMember(id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990, id:ff95d010-cdcb-45d8-8418-aa53e7681b10) + entity(id:28c49a54-4fce-484f-bbf3-754c514865bd, [prov:type='prov:KeyEntityPair', prov:pairKey="check_content", prov:pairEntity='id:ff95d010-cdcb-45d8-8418-aa53e7681b10']) + 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[prov:role='wf:main/random_lines1/chromInfo']) + entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) + used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, data:?, 2022-03-30T14:10:06.239316, [prov:role='wf:main/random_lines1/dbkey']) + entity(id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:428da699-3449-41e2-b395-a770b9b49467', prov:hadDictionaryMember='id:8041c95b-4fe2-4663-bcfe-6d4292c9d678']) + entity(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:36bf5f2c-3bf9-46aa-aac5-8b6249738317', prov:hadDictionaryMember='id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd', prov:hadDictionaryMember='id:bdc9be97-2541-4e9d-9b66-e93b350046f5']) + entity(data:fd7fec473f1e6c6b, [prov:type='wfprov:Artifact', prov:value="fd7fec473f1e6c6b"]) + hadMember(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, data:fd7fec473f1e6c6b) + entity(id:36bf5f2c-3bf9-46aa-aac5-8b6249738317, [prov:type='prov:KeyEntityPair', prov:pairKey="id", prov:pairEntity='data:fd7fec473f1e6c6b']) + entity(data:hda, [prov:type='wfprov:Artifact', prov:value="hda"]) + hadMember(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, data:hda) + entity(id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:hda']) + entity(data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89, [prov:type='wfprov:Artifact', prov:value="urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89"]) + hadMember(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89) + entity(id:bdc9be97-2541-4e9d-9b66-e93b350046f5, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89']) + entity(id:7da8d1bc-cc46-4312-9331-0e417f123152, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:7da8d1bc-cc46-4312-9331-0e417f123152, id:2ff086c3-1d26-439e-8b37-02eb82ba2a89) + hadMember(id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, id:7da8d1bc-cc46-4312-9331-0e417f123152) + entity(id:428da699-3449-41e2-b395-a770b9b49467, [prov:type='prov:KeyEntityPair', prov:pairKey="values", prov:pairEntity='id:7da8d1bc-cc46-4312-9331-0e417f123152']) + entity(data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, [prov:type='wfprov:Artifact', prov:value="urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a"]) + hadMember(id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a) + entity(id:8041c95b-4fe2-4663-bcfe-6d4292c9d678, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a']) + used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, 2022-03-30T14:10:06.239940, [prov:role='wf:main/random_lines1/input']) + entity(data:3, [prov:type='wfprov:Artifact', prov:value="3"]) + used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, data:3, 2022-03-30T14:10:06.239990, [prov:role='wf:main/random_lines1/num_lines']) + entity(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:8329dc4f-308b-4258-bc73-9e55abd502a5', prov:hadDictionaryMember='id:7cc407df-6449-4722-bd58-5d9fb44288c4', prov:hadDictionaryMember='id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c', prov:hadDictionaryMember='id:3d1d3c32-7457-4abf-bb66-12aac16561b1']) + entity(id:2be3e6ed-24b7-444d-a4ee-5770d93987d4, [prov:value=1]) + hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, id:2be3e6ed-24b7-444d-a4ee-5770d93987d4) + entity(id:7cc407df-6449-4722-bd58-5d9fb44288c4, [prov:type='prov:KeyEntityPair', prov:pairKey="__current_case__", prov:pairEntity='id:2be3e6ed-24b7-444d-a4ee-5770d93987d4']) + entity(data:0, [prov:type='wfprov:Artifact', prov:value="0"]) + hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, data:0) + entity(id:8329dc4f-308b-4258-bc73-9e55abd502a5, [prov:type='prov:KeyEntityPair', prov:pairKey="seed", prov:pairEntity='data:0']) + entity(data:set_seed, [prov:type='wfprov:Artifact', prov:value="set_seed"]) + hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, data:set_seed) + entity(id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c, [prov:type='prov:KeyEntityPair', prov:pairKey="seed_source_selector", prov:pairEntity='data:set_seed']) + entity(data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4, [prov:type='wfprov:Artifact', prov:value="urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4"]) + hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4) + entity(id:3d1d3c32-7457-4abf-bb66-12aac16561b1, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4']) + used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, 2022-03-30T14:10:06.240395, [prov:role='wf:main/random_lines1/seed_source']) +endDocument \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl new file mode 100644 index 00000000..403e63f3 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl @@ -0,0 +1,1081 @@ +@prefix data: . +@prefix foaf: . +@prefix id: . +@prefix orcid: . +@prefix prov: . +@prefix rdfs: . +@prefix schema: . +@prefix wf: . +@prefix wfprov: . +@prefix xsd: . + +id:0f0bc88f-e599-4a4e-8681-4edd21226161 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.235023"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.234977"^^xsd:dateTime ; + prov:entity id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.236603"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.234629"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.236555"^^xsd:dateTime ; + prov:entity id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.234586"^^xsd:dateTime ; + prov:entity id:eaec06da-6307-4712-80ca-f89bebb4abc2 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . + +id:43861f75-9aa7-42b3-80e0-15cf9927d993 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.234091"^^xsd:dateTime ; + prov:entity id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.232136"^^xsd:dateTime ; + prov:entity id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.232547"^^xsd:dateTime ; + prov:entity id:10a92b31-e38a-4eee-a163-d05f0c942e28 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.234137"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.232201"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.232599"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . + +id:6b19db35-6d60-4351-be9b-7257b737a427 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237336"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237196"^^xsd:dateTime ; + prov:entity id:1673a6bb-e7f1-4e69-9403-15c343f59b98 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237107"^^xsd:dateTime ; + prov:entity id:232855e1-8392-4f99-b38d-028c22b047d8 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.238506"^^xsd:dateTime ; + prov:entity id:142f1b95-3ba6-4998-b6a6-72d299494e68 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237846"^^xsd:dateTime ; + prov:entity id:6c67cd25-9da2-4eb8-9145-ab14b36c9771 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237424"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237383"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237290"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.237016"^^xsd:dateTime ; + prov:entity id:595e172f-01c4-4ca4-bd82-532ac4e0195d ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . + +id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.239316"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.239056"^^xsd:dateTime ; + prov:entity id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.240395"^^xsd:dateTime ; + prov:entity id:a6de5b1b-da32-4449-81b5-4efcdb27bad4 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.239121"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.239990"^^xsd:dateTime ; + prov:entity data:3 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.238912"^^xsd:dateTime ; + prov:entity id:425cb32b-54a2-410a-a915-c025f76640d3 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.239940"^^xsd:dateTime ; + prov:entity id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.239189"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-30T14:10:06.239255"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . + +orcid:0000-0002-8940-4946 a schema:Person, + prov:Agent, + prov:Person ; + rdfs:label "PDG"^^xsd:string ; + schema:name "PDG"^^xsd:string ; + foaf:name "PDG"^^xsd:string . + +data:2524d3d3b68ad39a a wfprov:Artifact, + prov:Entity ; + prov:value "2524d3d3b68ad39a"^^xsd:string . + +data:3 a wfprov:Artifact, + prov:Entity ; + prov:value "3"^^xsd:string . + +data:775bc9b3c1750167 a wfprov:Artifact, + prov:Entity ; + prov:value "775bc9b3c1750167"^^xsd:string . + +data:7c1d8e3101dbcdba a wfprov:Artifact, + prov:Entity ; + prov:value "7c1d8e3101dbcdba"^^xsd:string . + +id:1090150b-6f8f-4ab5-8a27-802721f05c5a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:10a92b31-e38a-4eee-a163-d05f0c942e28 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:f5582681-806f-4e35-9028-631eab68c8db . + +id:1210a0ac-c6d4-4639-8b29-7866ac72a541 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:77f3c59e-7ec9-4e8b-9401-857b6c311c83 ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:142f1b95-3ba6-4998-b6a6-72d299494e68 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 . + +id:1673a6bb-e7f1-4e69-9403-15c343f59b98 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +id:1d168b92-47a6-448c-baf8-f585f12a3d33 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:232855e1-8392-4f99-b38d-028c22b047d8 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2e789aae2475b7da . + +id:24b14bfa-62b8-4d41-a724-90379c5708c1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:28c49a54-4fce-484f-bbf3-754c514865bd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:ff95d010-cdcb-45d8-8418-aa53e7681b10 ; + prov:pairKey "check_content"^^xsd:string . + +id:2b1a8432-a59b-4f1b-87ee-912ca464e17c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:2f407424-3110-457d-b6f4-3d86f1c76cc8 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:2d0a8975-d3b6-43aa-b902-a42b9483374b ; + prov:pairKey "check_content"^^xsd:string . + +id:2f80b5e3-3925-49fd-9339-86ed10571ea9 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06, + id:b3a09002-26d2-44b7-80a1-f3a0accdcacc, + id:ea79a0ce-8267-474e-adc3-0d37ec935565 ; + prov:hadMember data:7ca3de8f49293d1a, + data:hda, + . + +id:2ff086c3-1d26-439e-8b37-02eb82ba2a89 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:36bf5f2c-3bf9-46aa-aac5-8b6249738317, + id:bdc9be97-2541-4e9d-9b66-e93b350046f5, + id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd ; + prov:hadMember data:fd7fec473f1e6c6b, + data:hda, + . + +id:341b47e4-0ed6-416a-b290-ec06d3966f75 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:2d11fff4-3195-426d-991e-39f46c18caf7 ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:343ac668-db1a-47ca-af95-093b7cc710e1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:afbd3904-77af-4cab-92f0-f7a1d1e4f467 ; + prov:pairKey "purge_source"^^xsd:string . + +id:36bf5f2c-3bf9-46aa-aac5-8b6249738317 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:fd7fec473f1e6c6b ; + prov:pairKey "id"^^xsd:string . + +id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d . + +id:3d1d3c32-7457-4abf-bb66-12aac16561b1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:set_seed ; + prov:pairKey "seed_source_selector"^^xsd:string . + +id:425cb32b-54a2-410a-a915-c025f76640d3 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +id:428da699-3449-41e2-b395-a770b9b49467 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:7da8d1bc-cc46-4312-9331-0e417f123152 ; + prov:pairKey "values"^^xsd:string . + +id:4319f013-ecd8-4341-a5b9-8e9d8420bd31 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:4389b350-32eb-48e4-8da0-aaf191209de3 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:5f8fd80e-f00f-4078-9660-55806bdbd100 ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:45379ceb-7d92-431f-a123-8ee411eedefa a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset2.txt ; + prov:pairKey "name"^^xsd:string . + +id:4b824c76-227e-430f-919c-853ff66133a4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:2e789aae2475b7da ; + prov:pairKey "id"^^xsd:string . + +id:4f7a8626-cbee-41ea-835b-76ddc79fcbce a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:35a147fd-c38e-4a85-bd9a-6a509ccd1245 ; + prov:pairKey "object_id"^^xsd:string . + +id:56295d4d-8276-4557-b9f2-b4b3b653865f a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c ; + prov:pairKey "in_place"^^xsd:string . + +id:595e172f-01c4-4ca4-bd82-532ac4e0195d a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7ca3de8f49293d1a . + +id:5b034fbf-1f17-485f-9c10-7b9b4872862c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:b98d6421-2cca-422c-b778-57480f86de92 ; + prov:pairKey "destination"^^xsd:string . + +id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:775bc9b3c1750167 . + +id:60971e6c-b050-4d63-9ca2-b74f7fab78da a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:43d5b201-ede9-419e-8b39-1bac02df6546 ; + prov:pairKey "hashes"^^xsd:string . + +id:641250eb-2adc-4c98-afcd-00428ee7bc8a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset1.txt ; + prov:pairKey "name"^^xsd:string . + +id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd, + id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c, + id:f582aab0-3308-432a-a5e7-8c2a0d069acf ; + prov:hadMember , + , + id:4e23da19-5664-4972-94b0-b2d3365672b1 . + +id:68b2355f-eec1-44a4-8751-11da17591063 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:5b034fbf-1f17-485f-9c10-7b9b4872862c, + id:ab29cf85-149a-412a-92ff-e3a6b605ff16, + id:bd679175-0778-4d62-856a-9da7f503a8b0, + id:c974472d-dbf4-4997-b690-62de731fa7a0 ; + prov:hadMember , + id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1, + id:b98d6421-2cca-422c-b778-57480f86de92, + id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 . + +id:6c67cd25-9da2-4eb8-9145-ab14b36c9771 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:ec4fdb41-ede8-4f37-a220-34eb67952e01, + id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc ; + prov:hadMember , + id:7ac72e2f-5815-47ff-9592-b89492e1804c . + +id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:b35ba485-3a40-4743-9a58-b207f5becd69 ; + prov:pairKey "hashes"^^xsd:string . + +id:738ba6b7-e61e-4d37-abb6-3cee1f782367 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:7cc407df-6449-4722-bd58-5d9fb44288c4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 ; + prov:pairKey "__current_case__"^^xsd:string . + +id:8041c95b-4fe2-4663-bcfe-6d4292c9d678 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:8329dc4f-308b-4258-bc73-9e55abd502a5 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:0 ; + prov:pairKey "seed"^^xsd:string . + +id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:7ca3de8f49293d1a ; + prov:pairKey "id"^^xsd:string . + +id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:4e23da19-5664-4972-94b0-b2d3365672b1 ; + prov:pairKey "__index__"^^xsd:string . + +id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1d168b92-47a6-448c-baf8-f585f12a3d33, + id:4b824c76-227e-430f-919c-853ff66133a4, + id:641250eb-2adc-4c98-afcd-00428ee7bc8a ; + prov:hadMember data:2e789aae2475b7da, + data:hda, + . + +id:9781f372-1be1-48e3-a9d3-2dda2b581134 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:1754bbe0-77b5-453b-8542-e83b9bc45798 ; + prov:pairKey "input2"^^xsd:string . + +id:9be744cb-071c-4610-91d9-d2a8cca5fbf4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1090150b-6f8f-4ab5-8a27-802721f05c5a, + id:2b1a8432-a59b-4f1b-87ee-912ca464e17c, + id:341b47e4-0ed6-416a-b290-ec06d3966f75, + id:45379ceb-7d92-431f-a123-8ee411eedefa, + id:56295d4d-8276-4557-b9f2-b4b3b653865f, + id:60971e6c-b050-4d63-9ca2-b74f7fab78da, + id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7, + id:adff57da-d615-4087-8dd9-f32586a3d183, + id:b09b2fa3-1624-428f-880d-b3890200a943, + id:d96d9941-8860-4c3d-a573-666266e9e9fe, + id:e1aa5ec1-4083-4477-8266-9e68d6afdf66 ; + prov:hadMember , + , + data:auto, + data:dataset2.txt, + data:path, + , + id:2d11fff4-3195-426d-991e-39f46c18caf7, + id:43d5b201-ede9-419e-8b39-1bac02df6546, + id:556f2e68-82d3-4ceb-aa48-e93d1a75be64, + id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c, + id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 . + +id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a11456da-294c-4173-96c9-9becdc7af2fc a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a3df1b9d-8a6a-4a15-b880-565871b262e2 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a4beeb97-7076-4d47-8015-e6779877af9e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 ; + prov:pairKey "destination"^^xsd:string . + +id:a69fb546-67ad-460f-b6f5-01ce7c181db7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:a6de5b1b-da32-4449-81b5-4efcdb27bad4 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:3d1d3c32-7457-4abf-bb66-12aac16561b1, + id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c, + id:7cc407df-6449-4722-bd58-5d9fb44288c4, + id:8329dc4f-308b-4258-bc73-9e55abd502a5 ; + prov:hadMember data:0, + data:set_seed, + , + id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 . + +id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 ; + prov:pairKey "__index__"^^xsd:string . + +id:a89b8834-c5ec-45c4-8760-213c4cc36302 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:ab29cf85-149a-412a-92ff-e3a6b605ff16 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:acc5b84a-046f-4fd2-9136-82d08877386a a prov:Agent ; + prov:actedOnBehalfOf orcid:0000-0002-8940-4946 . + +id:adff57da-d615-4087-8dd9-f32586a3d183 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:b095ce58-2b16-49a3-8873-73a85d09b84e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:20c6c642-7356-4161-a861-7cebbb063751 ; + prov:pairKey "__index__"^^xsd:string . + +id:b09b2fa3-1624-428f-880d-b3890200a943 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:b1c0e073-72ee-42f6-a512-d8b0a120f260 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:b3a09002-26d2-44b7-80a1-f3a0accdcacc a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2524d3d3b68ad39a . + +id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2, + id:9781f372-1be1-48e3-a9d3-2dda2b581134, + id:b095ce58-2b16-49a3-8873-73a85d09b84e ; + prov:hadMember , + id:1754bbe0-77b5-453b-8542-e83b9bc45798, + id:20c6c642-7356-4161-a861-7cebbb063751 . + +id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:2f407424-3110-457d-b6f4-3d86f1c76cc8, + id:9be744cb-071c-4610-91d9-d2a8cca5fbf4, + id:f102ded2-603b-4c97-898e-b71bffb17a71 ; + prov:hadMember , + id:2d0a8975-d3b6-43aa-b902-a42b9483374b, + id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 . + +id:bd679175-0778-4d62-856a-9da7f503a8b0 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1 ; + prov:pairKey "elements"^^xsd:string . + +id:bdc9be97-2541-4e9d-9b66-e93b350046f5 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:c974472d-dbf4-4997-b690-62de731fa7a0 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:2f356100-3315-4ff7-87cf-54b1d4d3ea49 ; + prov:pairKey "targets"^^xsd:string . + +id:d96d9941-8860-4c3d-a573-666266e9e9fe a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 ; + prov:pairKey "object_id"^^xsd:string . + +id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:decc5efa-759a-4165-9034-88a8de8ff547 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:411a358d-2596-4506-b64a-74b54ea779d4 ; + prov:pairKey "elements"^^xsd:string . + +id:e1aa5ec1-4083-4477-8266-9e68d6afdf66 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:556f2e68-82d3-4ceb-aa48-e93d1a75be64 ; + prov:pairKey "purge_source"^^xsd:string . + +id:e64e532c-b1a6-454d-ac58-bde6809a1841 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601 ; + prov:pairKey "in_place"^^xsd:string . + +id:ea79a0ce-8267-474e-adc3-0d37ec935565 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:eac8a16e-c68a-457a-871d-47f710712b41 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 ; + prov:pairKey "values"^^xsd:string . + +id:eaec06da-6307-4712-80ca-f89bebb4abc2 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7c1d8e3101dbcdba . + +id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:28c49a54-4fce-484f-bbf3-754c514865bd, + id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789, + id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700 ; + prov:hadMember , + id:2f356100-3315-4ff7-87cf-54b1d4d3ea49, + id:ff95d010-cdcb-45d8-8418-aa53e7681b10 . + +id:ec4fdb41-ede8-4f37-a220-34eb67952e01 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:f102ded2-603b-4c97-898e-b71bffb17a71 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 ; + prov:pairKey "targets"^^xsd:string . + +id:f2a60dac-8878-4bad-98f1-782ebf300df9 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:343ac668-db1a-47ca-af95-093b7cc710e1, + id:4389b350-32eb-48e4-8da0-aaf191209de3, + id:4f7a8626-cbee-41ea-835b-76ddc79fcbce, + id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af, + id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565, + id:738ba6b7-e61e-4d37-abb6-3cee1f782367, + id:a69fb546-67ad-460f-b6f5-01ce7c181db7, + id:a89b8834-c5ec-45c4-8760-213c4cc36302, + id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26, + id:e64e532c-b1a6-454d-ac58-bde6809a1841, + id:f7e87688-b315-448f-82c3-a18665a84053 ; + prov:hadMember , + , + data:auto, + data:dataset1.txt, + data:path, + , + id:35a147fd-c38e-4a85-bd9a-6a509ccd1245, + id:5f8fd80e-f00f-4078-9660-55806bdbd100, + id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601, + id:afbd3904-77af-4cab-92f0-f7a1d1e4f467, + id:b35ba485-3a40-4743-9a58-b207f5becd69 . + +id:f5582681-806f-4e35-9028-631eab68c8db a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:4319f013-ecd8-4341-a5b9-8e9d8420bd31, + id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603, + id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc ; + prov:hadMember , + , + id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 . + +id:f582aab0-3308-432a-a5e7-8c2a0d069acf a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:f6641719-90a2-47d4-96dd-a847725d5d37 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1210a0ac-c6d4-4639-8b29-7866ac72a541, + id:a4beeb97-7076-4d47-8015-e6779877af9e, + id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4, + id:decc5efa-759a-4165-9034-88a8de8ff547 ; + prov:hadMember , + id:411a358d-2596-4506-b64a-74b54ea779d4, + id:77f3c59e-7ec9-4e8b-9401-857b6c311c83, + id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 . + +id:f7e87688-b315-448f-82c3-a18665a84053 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:428da699-3449-41e2-b395-a770b9b49467, + id:8041c95b-4fe2-4663-bcfe-6d4292c9d678 ; + prov:hadMember , + id:7da8d1bc-cc46-4312-9331-0e417f123152 . + +id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:7ac72e2f-5815-47ff-9592-b89492e1804c ; + prov:pairKey "values"^^xsd:string . + +data: a wfprov:Artifact, + prov:Entity ; + prov:value ""^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^xsd:string . + +data:0 a wfprov:Artifact, + prov:Entity ; + prov:value "0"^^xsd:string . + +data:42f21c0ad41011eb87defa163eba836f a wfprov:Artifact, + prov:Entity ; + prov:value "42f21c0ad41011eb87defa163eba836f"^^xsd:string . + +data:dataset1.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset1.txt"^^xsd:string . + +data:dataset2.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset2.txt"^^xsd:string . + +data:set_seed a wfprov:Artifact, + prov:Entity ; + prov:value "set_seed"^^xsd:string . + +data:txt a wfprov:Artifact, + prov:Entity ; + prov:value "txt"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:68b2355f-eec1-44a4-8751-11da17591063"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:b98d6421-2cca-422c-b778-57480f86de92"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:f5582681-806f-4e35-9028-631eab68c8db"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a"^^xsd:string . + +id:1754bbe0-77b5-453b-8542-e83b9bc45798 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:a11456da-294c-4173-96c9-9becdc7af2fc, + id:eac8a16e-c68a-457a-871d-47f710712b41 ; + prov:hadMember , + id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 . + +id:20c6c642-7356-4161-a861-7cebbb063751 a prov:Entity ; + prov:value "0"^^xsd:int . + +id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 a prov:Entity ; + prov:value "1"^^xsd:int . + +id:2d0a8975-d3b6-43aa-b902-a42b9483374b a prov:Entity ; + prov:value true . + +id:2d11fff4-3195-426d-991e-39f46c18caf7 a prov:Entity ; + prov:value true . + +id:2f356100-3315-4ff7-87cf-54b1d4d3ea49 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:f6641719-90a2-47d4-96dd-a847725d5d37 . + +id:35a147fd-c38e-4a85-bd9a-6a509ccd1245 a prov:Entity ; + prov:value "155707"^^xsd:int . + +id:411a358d-2596-4506-b64a-74b54ea779d4 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:f2a60dac-8878-4bad-98f1-782ebf300df9 . + +id:43d5b201-ede9-419e-8b39-1bac02df6546 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 a prov:Entity ; + prov:value "0"^^xsd:int . + +id:4e23da19-5664-4972-94b0-b2d3365672b1 a prov:Entity ; + prov:value "0"^^xsd:int . + +id:556f2e68-82d3-4ceb-aa48-e93d1a75be64 a prov:Entity ; + prov:value false . + +id:5f8fd80e-f00f-4078-9660-55806bdbd100 a prov:Entity ; + prov:value true . + +id:77f3c59e-7ec9-4e8b-9401-857b6c311c83 a prov:Entity ; + prov:value false . + +id:7ac72e2f-5815-47ff-9592-b89492e1804c a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:2f80b5e3-3925-49fd-9339-86ed10571ea9 . + +id:7da8d1bc-cc46-4312-9331-0e417f123152 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:2ff086c3-1d26-439e-8b37-02eb82ba2a89 . + +id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c . + +id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601 a prov:Entity ; + prov:value false . + +id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:a3df1b9d-8a6a-4a15-b880-565871b262e2, + id:b1c0e073-72ee-42f6-a512-d8b0a120f260 ; + prov:hadMember data:hdas, + . + +id:afbd3904-77af-4cab-92f0-f7a1d1e4f467 a prov:Entity ; + prov:value false . + +id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c a prov:Entity ; + prov:value false . + +id:b35ba485-3a40-4743-9a58-b207f5becd69 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:b98d6421-2cca-422c-b778-57480f86de92 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:24b14bfa-62b8-4d41-a724-90379c5708c1, + id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0 ; + prov:hadMember data:hdas, + . + +id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 a prov:Entity ; + prov:value "155708"^^xsd:int . + +id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 a prov:Entity ; + prov:value false . + +id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 . + +id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:68b2355f-eec1-44a4-8751-11da17591063 . + +id:ff95d010-cdcb-45d8-8418-aa53e7681b10 a prov:Entity ; + prov:value true . + +data:2e789aae2475b7da a wfprov:Artifact, + prov:Entity ; + prov:value "2e789aae2475b7da"^^xsd:string . + +data:7ca3de8f49293d1a a wfprov:Artifact, + prov:Entity ; + prov:value "7ca3de8f49293d1a"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"^^xsd:string . + +data:1 a wfprov:Artifact, + prov:Entity ; + prov:value "1"^^xsd:string . + +data:auto a wfprov:Artifact, + prov:Entity ; + prov:value "auto"^^xsd:string . + +data:fd7fec473f1e6c6b a wfprov:Artifact, + prov:Entity ; + prov:value "fd7fec473f1e6c6b"^^xsd:string . + +data:hdas a wfprov:Artifact, + prov:Entity ; + prov:value "hdas"^^xsd:string . + +data:path a wfprov:Artifact, + prov:Entity ; + prov:value "path"^^xsd:string . + +id:d76ec743-0418-4a56-88f2-b81a404a63bc a wfprov:WorkflowRun, + prov:Activity ; + rdfs:label "Run of galaxy workflow"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan wf:main ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-03-30T14:10:06.231499"^^xsd:dateTime ; + prov:hadActivity id:34d8946d-cc68-4ad9-8ecf-53026817187c ] ; + prov:startedAtTime "2022-03-30T14:10:06.231425"^^xsd:dateTime ; + prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . + + a wfprov:Artifact, + prov:Entity ; + prov:value "?"^^xsd:string . + +data:hda a wfprov:Artifact, + prov:Entity ; + prov:value "hda"^^xsd:string . + +id:34d8946d-cc68-4ad9-8ecf-53026817187c a wfprov:WorkflowEngine, + prov:Agent, + prov:SoftwareAgent ; + rdfs:label "galaxy_version_placeholder"^^xsd:string ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-03-30T14:10:06.231396"^^xsd:dateTime ; + prov:hadActivity id:acc5b84a-046f-4fd2-9136-82d08877386a ] . + diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml new file mode 100644 index 00000000..93af1788 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml @@ -0,0 +1,1457 @@ + + + + + PDG + schema:Person + PDG + PDG + + + + + + + galaxy_version_placeholder + wfprov:WorkflowEngine + + + + + 2022-03-30T14:10:06.231396 + + + 2022-03-30T14:10:06.231425 + Run of galaxy workflow + wfprov:WorkflowRun + + + + + + + + + + 2022-03-30T14:10:06.231499 + + + 2021-06-23T10:20:22.770291 + 2021-06-23T10:20:42.041319 + Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:20:22.770291 + + + wfprov:Artifact + 2524d3d3b68ad39a + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.232136 + wf:main/__DATA_FETCH__/output0 + + + wfprov:Artifact + 1 + + + + + 2022-03-30T14:10:06.232201 + wf:main/__DATA_FETCH__/file_count + + + prov:Dictionary + wfprov:Artifact + id:4319f013-ecd8-4341-a5b9-8e9d8420bd31 + id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603 + id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc + + + 0 + + + + + + + prov:KeyEntityPair + id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 + __index__ + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + file_data + + + wfprov:Artifact + urn:uuid:f5582681-806f-4e35-9028-631eab68c8db + + + + + + + prov:KeyEntityPair + data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db + @id + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.232547 + wf:main/__DATA_FETCH__/files + + + wfprov:Artifact + + + + + + 2022-03-30T14:10:06.232599 + wf:main/__DATA_FETCH__/paramfile + + + prov:Dictionary + wfprov:Artifact + id:2f407424-3110-457d-b6f4-3d86f1c76cc8 + id:9be744cb-071c-4610-91d9-d2a8cca5fbf4 + id:f102ded2-603b-4c97-898e-b71bffb17a71 + + + prov:Dictionary + wfprov:Artifact + id:5b034fbf-1f17-485f-9c10-7b9b4872862c + id:ab29cf85-149a-412a-92ff-e3a6b605ff16 + id:bd679175-0778-4d62-856a-9da7f503a8b0 + id:c974472d-dbf4-4997-b690-62de731fa7a0 + + + prov:Dictionary + wfprov:Artifact + id:24b14bfa-62b8-4d41-a724-90379c5708c1 + id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0 + + + wfprov:Artifact + hdas + + + + + + + prov:KeyEntityPair + data:hdas + type + + + wfprov:Artifact + urn:uuid:b98d6421-2cca-422c-b778-57480f86de92 + + + + + + + prov:KeyEntityPair + data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92 + @id + + + + + + + prov:KeyEntityPair + id:b98d6421-2cca-422c-b778-57480f86de92 + destination + + + prov:Dictionary + wfprov:Artifact + id:1090150b-6f8f-4ab5-8a27-802721f05c5a + id:2b1a8432-a59b-4f1b-87ee-912ca464e17c + id:341b47e4-0ed6-416a-b290-ec06d3966f75 + id:45379ceb-7d92-431f-a123-8ee411eedefa + id:56295d4d-8276-4557-b9f2-b4b3b653865f + id:60971e6c-b050-4d63-9ca2-b74f7fab78da + id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7 + id:adff57da-d615-4087-8dd9-f32586a3d183 + id:b09b2fa3-1624-428f-880d-b3890200a943 + id:d96d9941-8860-4c3d-a573-666266e9e9fe + id:e1aa5ec1-4083-4477-8266-9e68d6afdf66 + + + wfprov:Artifact + auto + + + + + + + prov:KeyEntityPair + data:auto + ext + + + wfprov:Artifact + ? + + + + + + + prov:KeyEntityPair + data:? + dbkey + + + true + + + + + + + prov:KeyEntityPair + id:2d11fff4-3195-426d-991e-39f46c18caf7 + to_posix_lines + + + wfprov:Artifact + path + + + + + + + prov:KeyEntityPair + data:path + src + + + wfprov:Artifact + dataset2.txt + + + + + + + prov:KeyEntityPair + data:dataset2.txt + name + + + prov:EmptyCollection + wfprov:Artifact + + + + + + + prov:KeyEntityPair + id:43d5b201-ede9-419e-8b39-1bac02df6546 + hashes + + + false + + + + + + + prov:KeyEntityPair + id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c + in_place + + + false + + + + + + + prov:KeyEntityPair + id:556f2e68-82d3-4ceb-aa48-e93d1a75be64 + purge_source + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + path + + + 155708 + + + + + + + prov:KeyEntityPair + id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 + object_id + + + wfprov:Artifact + urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c + + + + + + + prov:KeyEntityPair + data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1 + elements + + + false + + + + + + + prov:KeyEntityPair + id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 + auto_decompress + + + wfprov:Artifact + urn:uuid:68b2355f-eec1-44a4-8751-11da17591063 + + + + + + + prov:KeyEntityPair + data:urn:uuid:68b2355f-eec1-44a4-8751-11da17591063 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 + targets + + + true + + + + + + + prov:KeyEntityPair + id:2d0a8975-d3b6-43aa-b902-a42b9483374b + check_content + + + wfprov:Artifact + urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 + + + + + + + prov:KeyEntityPair + data:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 + @id + + + + + 2022-03-30T14:10:06.234091 + wf:main/__DATA_FETCH__/request_json + + + wfprov:Artifact + 1 + + + + + 2022-03-30T14:10:06.234137 + wf:main/__DATA_FETCH__/request_version + + + 2021-06-23T10:20:00.981702 + 2021-06-23T10:20:22.202678 + Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:20:00.981702 + + + wfprov:Artifact + 7c1d8e3101dbcdba + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.234586 + wf:main/__DATA_FETCH__/output0 + + + wfprov:Artifact + 1 + + + + + 2022-03-30T14:10:06.234629 + wf:main/__DATA_FETCH__/file_count + + + prov:Dictionary + wfprov:Artifact + id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd + id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c + id:f582aab0-3308-432a-a5e7-8c2a0d069acf + + + 0 + + + + + + + prov:KeyEntityPair + id:4e23da19-5664-4972-94b0-b2d3365672b1 + __index__ + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + file_data + + + wfprov:Artifact + urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d + + + + + + + prov:KeyEntityPair + data:urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d + @id + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.234977 + wf:main/__DATA_FETCH__/files + + + wfprov:Artifact + + + + + + 2022-03-30T14:10:06.235023 + wf:main/__DATA_FETCH__/paramfile + + + prov:Dictionary + wfprov:Artifact + id:28c49a54-4fce-484f-bbf3-754c514865bd + id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789 + id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700 + + + prov:Dictionary + wfprov:Artifact + id:1210a0ac-c6d4-4639-8b29-7866ac72a541 + id:a4beeb97-7076-4d47-8015-e6779877af9e + id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4 + id:decc5efa-759a-4165-9034-88a8de8ff547 + + + prov:Dictionary + wfprov:Artifact + id:a3df1b9d-8a6a-4a15-b880-565871b262e2 + id:b1c0e073-72ee-42f6-a512-d8b0a120f260 + + + wfprov:Artifact + hdas + + + + + + + prov:KeyEntityPair + data:hdas + type + + + wfprov:Artifact + urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002 + + + + + + + prov:KeyEntityPair + data:urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002 + @id + + + + + + + prov:KeyEntityPair + id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 + destination + + + prov:Dictionary + wfprov:Artifact + id:343ac668-db1a-47ca-af95-093b7cc710e1 + id:4389b350-32eb-48e4-8da0-aaf191209de3 + id:4f7a8626-cbee-41ea-835b-76ddc79fcbce + id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af + id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565 + id:738ba6b7-e61e-4d37-abb6-3cee1f782367 + id:a69fb546-67ad-460f-b6f5-01ce7c181db7 + id:a89b8834-c5ec-45c4-8760-213c4cc36302 + id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26 + id:e64e532c-b1a6-454d-ac58-bde6809a1841 + id:f7e87688-b315-448f-82c3-a18665a84053 + + + wfprov:Artifact + auto + + + + + + + prov:KeyEntityPair + data:auto + ext + + + wfprov:Artifact + ? + + + + + + + prov:KeyEntityPair + data:? + dbkey + + + true + + + + + + + prov:KeyEntityPair + id:5f8fd80e-f00f-4078-9660-55806bdbd100 + to_posix_lines + + + wfprov:Artifact + path + + + + + + + prov:KeyEntityPair + data:path + src + + + wfprov:Artifact + dataset1.txt + + + + + + + prov:KeyEntityPair + data:dataset1.txt + name + + + prov:EmptyCollection + wfprov:Artifact + + + + + + + prov:KeyEntityPair + id:b35ba485-3a40-4743-9a58-b207f5becd69 + hashes + + + false + + + + + + + prov:KeyEntityPair + id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601 + in_place + + + false + + + + + + + prov:KeyEntityPair + id:afbd3904-77af-4cab-92f0-f7a1d1e4f467 + purge_source + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + path + + + 155707 + + + + + + + prov:KeyEntityPair + id:35a147fd-c38e-4a85-bd9a-6a509ccd1245 + object_id + + + wfprov:Artifact + urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9 + + + + + + + prov:KeyEntityPair + data:urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:411a358d-2596-4506-b64a-74b54ea779d4 + elements + + + false + + + + + + + prov:KeyEntityPair + id:77f3c59e-7ec9-4e8b-9401-857b6c311c83 + auto_decompress + + + wfprov:Artifact + urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37 + + + + + + + prov:KeyEntityPair + data:urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:2f356100-3315-4ff7-87cf-54b1d4d3ea49 + targets + + + true + + + + + + + prov:KeyEntityPair + id:ff95d010-cdcb-45d8-8418-aa53e7681b10 + check_content + + + wfprov:Artifact + urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 + + + + + + + prov:KeyEntityPair + data:urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 + @id + + + + + 2022-03-30T14:10:06.236555 + wf:main/__DATA_FETCH__/request_json + + + wfprov:Artifact + 1 + + + + + 2022-03-30T14:10:06.236603 + wf:main/__DATA_FETCH__/request_version + + + 2021-06-23T10:46:28.351123 + 2021-06-23T10:46:44.738703 + Run of ga_export/jobs_attrs.txt#cat1 + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:46:28.351123 + + + wfprov:Artifact + 7ca3de8f49293d1a + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.237016 + wf:main/cat1/input1 + + + wfprov:Artifact + 2e789aae2475b7da + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.237107 + wf:main/cat1/queries_0_input2 + + + wfprov:Artifact + fd7fec473f1e6c6b + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.237196 + wf:main/cat1/out_file1 + + + wfprov:Artifact + txt + + + + + 2022-03-30T14:10:06.237290 + wf:main/cat1/__input_ext + + + wfprov:Artifact + 42f21c0ad41011eb87defa163eba836f + + + + + 2022-03-30T14:10:06.237336 + wf:main/cat1/__workflow_invocation_uuid__ + + + wfprov:Artifact + /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len + + + + + 2022-03-30T14:10:06.237383 + wf:main/cat1/chromInfo + + + wfprov:Artifact + ? + + + + + 2022-03-30T14:10:06.237424 + wf:main/cat1/dbkey + + + prov:Dictionary + wfprov:Artifact + id:ec4fdb41-ede8-4f37-a220-34eb67952e01 + id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc + + + prov:Dictionary + wfprov:Artifact + id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06 + id:b3a09002-26d2-44b7-80a1-f3a0accdcacc + id:ea79a0ce-8267-474e-adc3-0d37ec935565 + + + wfprov:Artifact + 7ca3de8f49293d1a + + + + + + + prov:KeyEntityPair + data:7ca3de8f49293d1a + id + + + wfprov:Artifact + hda + + + + + + + prov:KeyEntityPair + data:hda + src + + + wfprov:Artifact + urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9 + + + + + + + prov:KeyEntityPair + data:urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:7ac72e2f-5815-47ff-9592-b89492e1804c + values + + + wfprov:Artifact + urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771 + + + + + + + prov:KeyEntityPair + data:urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771 + @id + + + + + 2022-03-30T14:10:06.237846 + wf:main/cat1/input1 + + + prov:Dictionary + wfprov:Artifact + id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2 + id:9781f372-1be1-48e3-a9d3-2dda2b581134 + id:b095ce58-2b16-49a3-8873-73a85d09b84e + + + 0 + + + + + + + prov:KeyEntityPair + id:20c6c642-7356-4161-a861-7cebbb063751 + __index__ + + + prov:Dictionary + wfprov:Artifact + id:a11456da-294c-4173-96c9-9becdc7af2fc + id:eac8a16e-c68a-457a-871d-47f710712b41 + + + prov:Dictionary + wfprov:Artifact + id:1d168b92-47a6-448c-baf8-f585f12a3d33 + id:4b824c76-227e-430f-919c-853ff66133a4 + id:641250eb-2adc-4c98-afcd-00428ee7bc8a + + + wfprov:Artifact + 2e789aae2475b7da + + + + + + + prov:KeyEntityPair + data:2e789aae2475b7da + id + + + wfprov:Artifact + hda + + + + + + + prov:KeyEntityPair + data:hda + src + + + wfprov:Artifact + urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 + + + + + + + prov:KeyEntityPair + data:urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 + values + + + wfprov:Artifact + urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798 + + + + + + + prov:KeyEntityPair + data:urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798 + @id + + + + + + + prov:KeyEntityPair + id:1754bbe0-77b5-453b-8542-e83b9bc45798 + input2 + + + wfprov:Artifact + urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 + + + + + + + prov:KeyEntityPair + data:urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 + @id + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.238506 + wf:main/cat1/queries + + + 2021-06-23T10:46:28.526901 + 2021-06-23T10:47:04.837750 + Run of ga_export/jobs_attrs.txt#random_lines1 + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:46:28.526901 + + + wfprov:Artifact + fd7fec473f1e6c6b + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.238912 + wf:main/random_lines1/input + + + wfprov:Artifact + 775bc9b3c1750167 + + + wfprov:Artifact + + + + + + + + + 2022-03-30T14:10:06.239056 + wf:main/random_lines1/out_file1 + + + wfprov:Artifact + txt + + + + + 2022-03-30T14:10:06.239121 + wf:main/random_lines1/__input_ext + + + wfprov:Artifact + 42f21c0ad41011eb87defa163eba836f + + + + + 2022-03-30T14:10:06.239189 + wf:main/random_lines1/__workflow_invocation_uuid__ + + + wfprov:Artifact + /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len + + + + + 2022-03-30T14:10:06.239255 + wf:main/random_lines1/chromInfo + + + wfprov:Artifact + ? + + + + + 2022-03-30T14:10:06.239316 + wf:main/random_lines1/dbkey + + + prov:Dictionary + wfprov:Artifact + id:428da699-3449-41e2-b395-a770b9b49467 + id:8041c95b-4fe2-4663-bcfe-6d4292c9d678 + + + prov:Dictionary + wfprov:Artifact + id:36bf5f2c-3bf9-46aa-aac5-8b6249738317 + id:bdc9be97-2541-4e9d-9b66-e93b350046f5 + id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd + + + wfprov:Artifact + fd7fec473f1e6c6b + + + + + + + prov:KeyEntityPair + data:fd7fec473f1e6c6b + id + + + wfprov:Artifact + hda + + + + + + + prov:KeyEntityPair + data:hda + src + + + wfprov:Artifact + urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89 + + + + + + + prov:KeyEntityPair + data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:7da8d1bc-cc46-4312-9331-0e417f123152 + values + + + wfprov:Artifact + urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a + + + + + + + prov:KeyEntityPair + data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a + @id + + + + + 2022-03-30T14:10:06.239940 + wf:main/random_lines1/input + + + wfprov:Artifact + 3 + + + + + 2022-03-30T14:10:06.239990 + wf:main/random_lines1/num_lines + + + prov:Dictionary + wfprov:Artifact + id:3d1d3c32-7457-4abf-bb66-12aac16561b1 + id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c + id:7cc407df-6449-4722-bd58-5d9fb44288c4 + id:8329dc4f-308b-4258-bc73-9e55abd502a5 + + + 1 + + + + + + + prov:KeyEntityPair + id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 + __current_case__ + + + wfprov:Artifact + 0 + + + + + + + prov:KeyEntityPair + data:0 + seed + + + wfprov:Artifact + set_seed + + + + + + + prov:KeyEntityPair + data:set_seed + seed_source_selector + + + wfprov:Artifact + urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4 + + + + + + + prov:KeyEntityPair + data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4 + @id + + + + + 2022-03-30T14:10:06.240395 + wf:main/random_lines1/seed_source + + diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index 12d9c2e2..7b181e20 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -25,19 +25,22 @@ def test_ga_history_loading(test_data_dir, tmpdir, helpers): jobs.append(job_attrs.attributes) assert isinstance(job_attrs, GalaxyJob) - print(jobs[0]) + # print(jobs[0]) assert len(jobs) == 4 def test_ga_history_parsing(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" export_path = test_data_dir / export_dir / "history_export" + # prov_name = "ga_export.cwlprov" + # crate_path = test_data_dir / export_dir / "history_export_crate" # metadata_export = load_ga_history_export(export_path) prov = ProvenanceProfile(export_path, "PDG", "https://orcid.org/0000-0002-8940-4946") + # print(len(metadata_export['jobs_attrs'])) - print(prov.document.serialize(format="rdf", rdf_format="turtle")) - with open("test_prov.ttl","w") as provenance_file: - prov.document.serialize(provenance_file,format="rdf", rdf_format="turtle") + # print(prov.document.serialize(format="rdf", rdf_format="turtle")) + # with open("test_prov.ttl","w") as provenance_file: + # prov.document.serialize(provenance_file,format="rdf", rdf_format="turtle") assert isinstance(prov, ProvenanceProfile) From a06d9adaa27f8f956fdb136a3405da569580903a Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 31 Mar 2022 15:54:25 +0200 Subject: [PATCH 09/27] updates to prov extraction --- rocrate/provenance_profile.py | 55 +- rocrate/rocrate_api.py | 17 +- .../provenance}/ga_export.cwlprov.json | 1126 +++--- .../provenance}/ga_export.cwlprov.jsonld | 3576 ++++++++--------- .../provenance/ga_export.cwlprov.nt | 942 +++++ .../provenance/ga_export.cwlprov.provn | 332 ++ .../provenance/ga_export.cwlprov.ttl | 1081 +++++ .../provenance/ga_export.cwlprov.xml | 1457 +++++++ .../ga_export.cwlprov.nt | 942 ----- .../ga_export.cwlprov.provn | 332 -- .../ga_export.cwlprov.ttl | 1081 ----- .../ga_export.cwlprov.xml | 1457 ------- test/test_parse_ga_export.py | 5 + 13 files changed, 6217 insertions(+), 6186 deletions(-) rename test/test-data/test_ga_history_export/{history_export_ro_crate => history_export/provenance}/ga_export.cwlprov.json (63%) rename test/test-data/test_ga_history_export/{history_export_ro_crate => history_export/provenance}/ga_export.cwlprov.jsonld (67%) create mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt create mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn create mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl create mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.nt delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 99263b6d..b2effddc 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -27,6 +27,7 @@ from typing_extensions import TYPE_CHECKING from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset from ast import literal_eval +import os # from .errors import WorkflowException # from .job import CommandLineJob, JobBase @@ -87,9 +88,10 @@ class ProvenanceProfile: def __init__( self, ga_export: Dict, - full_name: str, - orcid: str, - prov_name: str = None, + full_name: str = None, + orcid: str = None, + # prov_name: str = None, + # prov_path: Path = None, # fsaccess: StdFsAccess, run_uuid: Optional[uuid.UUID] = None, ) -> None: @@ -97,7 +99,7 @@ def __init__( Initialize the provenance profile. Keyword arguments: ga_export -- the galaxy metadata export (Dict) - full_name -- author name + full_name -- author name (optional) orcid -- orcid (optional) prov_name -- provenance file name run_uuid -- uuid for the workflow run @@ -115,6 +117,7 @@ def __init__( self.workflow_run_uuid = run_uuid or uuid.uuid4() self.workflow_run_uri = self.workflow_run_uuid.urn # type: str + # move to separate function metadata_export = load_ga_history_export(ga_export) self.generate_prov_doc() self.jobs = [] @@ -125,9 +128,6 @@ def __init__( self.jobs.append(job_attrs.attributes) self.declare_process(job_attrs.attributes) - self.finalize_prov_profile(prov_name) - # print(self.document.serialize(format="rdf", rdf_format="turtle")) - def __str__(self) -> str: """Represent this Provenvance profile as a string.""" return "ProvenanceProfile <{}>".format( @@ -727,8 +727,8 @@ def activity_has_provenance(self, activity, prov_ids): uris = [i.uri for i in prov_ids] # self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) - def finalize_prov_profile(self, name=None): - # type: (Optional[str]) -> List[Identifier] + def finalize_prov_profile(self, name=None, out_path=None): + # type: (Optional[str],Optional[str]) -> Tuple[Dict,List[Identifier]] """Transfer the provenance related files to the RO-crate""" # NOTE: Relative posix path if name is None: @@ -743,50 +743,63 @@ def finalize_prov_profile(self, name=None): # multiple places or iterations filename = f"{wf_name}.{self.workflow_run_uuid}.cwlprov" - # basename = str(PurePosixPath(crate_path) / filename) - basename = filename - print(basename) + if out_path is not None: + basename = str(PurePosixPath(out_path) / filename) + # else: + # basename = filename - # TODO: Also support other profiles than CWLProv, e.g. ProvOne + if not os.path.exists(out_path): + os.makedirs(out_path) + print(basename) + # serialized prov documents + serialized_prov_docs = {} # list of prov identifiers of provenance files prov_ids = [] # https://www.w3.org/TR/prov-xml/ + # serialized_prov_docs["xml"] = self.document.serialize(format="xml", indent=4) + prov_ids.append(self.provenance_ns[filename + ".xml"]) with open(basename + ".xml", "w") as provenance_file: self.document.serialize(provenance_file, format="xml", indent=4) - prov_ids.append(self.provenance_ns[filename + ".xml"]) # https://www.w3.org/TR/prov-n/ + # serialized_prov_docs["provn"] = self.document.serialize(format="provn", indent=2) + prov_ids.append(self.provenance_ns[filename + ".provn"]) with open(basename + ".provn", "w") as provenance_file: self.document.serialize(provenance_file, format="provn", indent=2) - prov_ids.append(self.provenance_ns[filename + ".provn"]) + # https://www.w3.org/Submission/prov-json/ + # serialized_prov_docs["json"] = self.document.serialize(format="json", indent=2) + prov_ids.append(self.provenance_ns[filename + ".json"]) with open(basename + ".json", "w") as provenance_file: self.document.serialize(provenance_file, format="json", indent=2) - prov_ids.append(self.provenance_ns[filename + ".json"]) # "rdf" aka https://www.w3.org/TR/prov-o/ # which can be serialized to ttl/nt/jsonld (and more!) # https://www.w3.org/TR/turtle/ + # serialized_prov_docs["turtle"] = self.document.serialize(format="rdf", rdf_format="turtle") + prov_ids.append(self.provenance_ns[filename + ".ttl"]) with open(basename + ".ttl", "w") as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="turtle") - prov_ids.append(self.provenance_ns[filename + ".ttl"]) # https://www.w3.org/TR/n-triples/ + # serialized_prov_docs["ntriples"] = self.document.serialize(format="rdf", rdf_format="ntriples") + prov_ids.append(self.provenance_ns[filename + ".nt"]) with open(basename + ".nt", "w") as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="ntriples") - prov_ids.append(self.provenance_ns[filename + ".nt"]) # https://www.w3.org/TR/json-ld/ # TODO: Use a nice JSON-LD context # see also https://eprints.soton.ac.uk/395985/ - # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld :( + # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld : + # serialized_prov_docs["jsonld"] = self.document.serialize(format="rdf", rdf_format="json-ld") + prov_ids.append(self.provenance_ns[filename + ".jsonld"]) with open(basename + ".jsonld", "w") as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") - prov_ids.append(self.provenance_ns[filename + ".jsonld"]) + #_logger.debug("[provenance] added provenance: %s", prov_ids) - return prov_ids + return (serialized_prov_docs, prov_ids) diff --git a/rocrate/rocrate_api.py b/rocrate/rocrate_api.py index c944a3ee..f6f912ce 100644 --- a/rocrate/rocrate_api.py +++ b/rocrate/rocrate_api.py @@ -18,8 +18,10 @@ # limitations under the License. from pathlib import Path +import os import rocrate.rocrate as roc +from rocrate.provenance_profile import ProvenanceProfile def make_workflow_rocrate(workflow_path, wf_type, include_files=[], @@ -77,8 +79,9 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], return wf_crate -def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata, author=None, include_files=[], - fetch_remote=False, cwl=None, diagram=None): +# WIP +def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, author=None, orcid=None, + include_files=[], fetch_remote=False, prov_name=None, prov_path=None, cwl=None, diagram=None): wfr_crate = roc.ROCrate() workflow_path = Path(workflow_path) @@ -86,6 +89,16 @@ def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata, author=None, workflow_path, workflow_path.name, fetch_remote=fetch_remote, main=True, lang=wf_type, gen_cwl=(cwl is None) ) + wfr_metadata_path = Path(wfr_metadata_path) + prov = ProvenanceProfile(wfr_metadata_path, author, orcid) + prov_path = "provenance" + prov.finalize_prov_profile(out_path=wfr_metadata_path / prov_path) + + # add serialized provenance documents + wfr_crate.add_directory(wfr_metadata_path / prov_path) + # for doc in serialized_prov_docs.values(): + # # print(doc) + # wfr_crate.add_file(doc) # if the source is a remote URL then add https://schema.org/codeRepository # property to it this can be checked by checking if the source is a URL diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.json b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json similarity index 63% rename from test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.json rename to test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json index 3492c7c1..8a2298c3 100644 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.json +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json @@ -8,12 +8,12 @@ "orcid": "https://orcid.org/", "id": "urn:uuid:", "data": "urn:hash::sha1:", - "provenance": "arcp://uuid,d144da35-75c5-4bb2-bce4-b3a81dbf525d/metadata/provenance/", - "wf": "arcp://uuid,d144da35-75c5-4bb2-bce4-b3a81dbf525d/ga_export/", - "input": "arcp://uuid,d144da35-75c5-4bb2-bce4-b3a81dbf525d/ga_export/datasets#" + "provenance": "arcp://uuid,bdf8ae0f-d0e0-4338-9513-e6fecbbeb255/metadata/provenance/", + "wf": "arcp://uuid,bdf8ae0f-d0e0-4338-9513-e6fecbbeb255/ga_export/", + "input": "arcp://uuid,bdf8ae0f-d0e0-4338-9513-e6fecbbeb255/ga_export/datasets#" }, "agent": { - "id:acc5b84a-046f-4fd2-9136-82d08877386a": {}, + "id:c98b0b95-d818-4ba1-b535-11c4e6909fa3": {}, "orcid:0000-0002-8940-4946": { "prov:type": [ { @@ -29,7 +29,7 @@ "foaf:name": "PDG", "schema:name": "PDG" }, - "id:34d8946d-cc68-4ad9-8ecf-53026817187c": { + "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd": { "prov:type": [ { "$": "prov:SoftwareAgent", @@ -45,52 +45,52 @@ }, "actedOnBehalfOf": { "_:id1": { - "prov:delegate": "id:acc5b84a-046f-4fd2-9136-82d08877386a", + "prov:delegate": "id:c98b0b95-d818-4ba1-b535-11c4e6909fa3", "prov:responsible": "orcid:0000-0002-8940-4946" } }, "wasStartedBy": { "_:id2": { - "prov:activity": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", - "prov:starter": "id:acc5b84a-046f-4fd2-9136-82d08877386a", - "prov:time": "2022-03-30T14:10:06.231396" + "prov:activity": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", + "prov:starter": "id:c98b0b95-d818-4ba1-b535-11c4e6909fa3", + "prov:time": "2022-03-31T15:39:11.759268" }, "_:id4": { - "prov:activity": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", - "prov:starter": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", - "prov:time": "2022-03-30T14:10:06.231499" + "prov:activity": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", + "prov:starter": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", + "prov:time": "2022-03-31T15:39:11.759353" }, "_:id6": { - "prov:activity": "id:43861f75-9aa7-42b3-80e0-15cf9927d993", - "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:activity": "id:a1a08c93-d0b2-4806-8abb-697cf651f9a4", + "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", "prov:time": "2021-06-23T10:20:22.770291" }, "_:id41": { - "prov:activity": "id:0f0bc88f-e599-4a4e-8681-4edd21226161", - "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:activity": "id:414221e9-e943-451a-bde9-ef492e1cf85c", + "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", "prov:time": "2021-06-23T10:20:00.981702" }, "_:id76": { - "prov:activity": "id:6b19db35-6d60-4351-be9b-7257b737a427", - "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:activity": "id:cade945a-1ff3-4273-a78e-7b5358804c89", + "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", "prov:time": "2021-06-23T10:46:28.351123" }, "_:id106": { - "prov:activity": "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d", - "prov:starter": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", + "prov:activity": "id:2341e04b-a08b-400e-97ef-3151f01a17fa", + "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", "prov:time": "2021-06-23T10:46:28.526901" } }, "activity": { - "id:d76ec743-0418-4a56-88f2-b81a404a63bc": { - "prov:startTime": "2022-03-30T14:10:06.231425", + "id:dd421f2f-c538-44d3-aeeb-484022c6541d": { + "prov:startTime": "2022-03-31T15:39:11.759294", "prov:type": { "$": "wfprov:WorkflowRun", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Run of galaxy workflow" }, - "id:43861f75-9aa7-42b3-80e0-15cf9927d993": { + "id:a1a08c93-d0b2-4806-8abb-697cf651f9a4": { "prov:startTime": "2021-06-23T10:20:22.770291", "prov:endTime": "2021-06-23T10:20:42.041319", "prov:type": { @@ -99,7 +99,7 @@ }, "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" }, - "id:0f0bc88f-e599-4a4e-8681-4edd21226161": { + "id:414221e9-e943-451a-bde9-ef492e1cf85c": { "prov:startTime": "2021-06-23T10:20:00.981702", "prov:endTime": "2021-06-23T10:20:22.202678", "prov:type": { @@ -108,7 +108,7 @@ }, "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" }, - "id:6b19db35-6d60-4351-be9b-7257b737a427": { + "id:cade945a-1ff3-4273-a78e-7b5358804c89": { "prov:startTime": "2021-06-23T10:46:28.351123", "prov:endTime": "2021-06-23T10:46:44.738703", "prov:type": { @@ -117,7 +117,7 @@ }, "prov:label": "Run of ga_export/jobs_attrs.txt#cat1" }, - "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d": { + "id:2341e04b-a08b-400e-97ef-3151f01a17fa": { "prov:startTime": "2021-06-23T10:46:28.526901", "prov:endTime": "2021-06-23T10:47:04.837750", "prov:type": { @@ -129,28 +129,28 @@ }, "wasAssociatedWith": { "_:id3": { - "prov:activity": "id:d76ec743-0418-4a56-88f2-b81a404a63bc", - "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:activity": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", + "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", "prov:plan": "wf:main" }, "_:id5": { - "prov:activity": "id:43861f75-9aa7-42b3-80e0-15cf9927d993", - "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:activity": "id:a1a08c93-d0b2-4806-8abb-697cf651f9a4", + "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", "prov:plan": "wf:main/__DATA_FETCH__" }, "_:id40": { - "prov:activity": "id:0f0bc88f-e599-4a4e-8681-4edd21226161", - "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:activity": "id:414221e9-e943-451a-bde9-ef492e1cf85c", + "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", "prov:plan": "wf:main/__DATA_FETCH__" }, "_:id75": { - "prov:activity": "id:6b19db35-6d60-4351-be9b-7257b737a427", - "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:activity": "id:cade945a-1ff3-4273-a78e-7b5358804c89", + "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", "prov:plan": "wf:main/cat1" }, "_:id105": { - "prov:activity": "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d", - "prov:agent": "id:34d8946d-cc68-4ad9-8ecf-53026817187c", + "prov:activity": "id:2341e04b-a08b-400e-97ef-3151f01a17fa", + "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", "prov:plan": "wf:main/random_lines1" } }, @@ -162,7 +162,7 @@ }, "prov:value": "2524d3d3b68ad39a" }, - "id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047": { + "id:d4c2d49d-ab80-43ab-b347-a7db85bf7262": { "prov:type": [ { "$": "wfprov:Artifact", @@ -204,50 +204,50 @@ "prov:value": "1" } ], - "id:f5582681-806f-4e35-9028-631eab68c8db": { + "id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603", + "$": "id:a1bb89e0-badf-490a-af30-375efe69c057", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc", + "$": "id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:4319f013-ecd8-4341-a5b9-8e9d8420bd31", + "$": "id:869277c3-8c88-4381-bbef-de17240b1c23", "type": "prov:QUALIFIED_NAME" } ] }, - "id:456f97d2-4118-4fd3-a7e0-0bed64b7e343": { + "id:0c54448a-8444-42cd-9dd1-b65dfb0656ba": { "prov:value": { "$": 0, "type": "xsd:int" } }, - "id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc": { + "id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__index__", "prov:pairEntity": { - "$": "id:456f97d2-4118-4fd3-a7e0-0bed64b7e343", + "$": "id:0c54448a-8444-42cd-9dd1-b65dfb0656ba", "type": "prov:QUALIFIED_NAME" } }, @@ -267,7 +267,7 @@ "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" } ], - "id:4319f013-ecd8-4341-a5b9-8e9d8420bd31": { + "id:869277c3-8c88-4381-bbef-de17240b1c23": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -278,25 +278,25 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db": { + "data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:f5582681-806f-4e35-9028-631eab68c8db" + "prov:value": "urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6" }, - "id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603": { + "id:a1bb89e0-badf-490a-af30-375efe69c057": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db", + "$": "data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6", "type": "prov:QUALIFIED_NAME" } }, - "id:10a92b31-e38a-4eee-a163-d05f0c942e28": { + "id:5c05f71f-74dc-4238-a591-9df8dfa779f8": { "prov:type": [ { "$": "wfprov:Artifact", @@ -324,92 +324,92 @@ "prov:value": "" } ], - "id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5": { + "id:594019f6-4154-49a8-be37-3d511a35f066": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:9be744cb-071c-4610-91d9-d2a8cca5fbf4", + "$": "id:e2f3637a-f559-46a0-a630-9f3e47800b70", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:2f407424-3110-457d-b6f4-3d86f1c76cc8", + "$": "id:1e8684e9-896e-4a38-bfe9-1995d0893fdd", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:f102ded2-603b-4c97-898e-b71bffb17a71", + "$": "id:7067149e-f997-4e01-810a-41ed1aaae3f1", "type": "prov:QUALIFIED_NAME" } ] }, - "id:68b2355f-eec1-44a4-8751-11da17591063": { + "id:641c238b-2832-4fab-b949-f5f4fc01deb1": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:5b034fbf-1f17-485f-9c10-7b9b4872862c", + "$": "id:ab8003d1-3e46-4af7-9325-fffe09639b01", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:c974472d-dbf4-4997-b690-62de731fa7a0", + "$": "id:3b176baa-a8f8-426c-ab0d-aa428d41923d", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:ab29cf85-149a-412a-92ff-e3a6b605ff16", + "$": "id:47d09ccc-4b59-4330-9361-9f1b65b860a8", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:bd679175-0778-4d62-856a-9da7f503a8b0", + "$": "id:9f4835d1-a5f0-499e-9315-42fed1edd2a1", "type": "prov:QUALIFIED_NAME" } ] }, - "id:b98d6421-2cca-422c-b778-57480f86de92": { + "id:d84bb265-2540-4cad-a026-511b7a21323e": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0", + "$": "id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:24b14bfa-62b8-4d41-a724-90379c5708c1", + "$": "id:f923bbf9-1c94-4771-9333-77547e7e828e", "type": "prov:QUALIFIED_NAME" } ] @@ -430,7 +430,7 @@ "prov:value": "hdas" } ], - "id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0": { + "id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -441,93 +441,93 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92": { + "data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:b98d6421-2cca-422c-b778-57480f86de92" + "prov:value": "urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e" }, - "id:24b14bfa-62b8-4d41-a724-90379c5708c1": { + "id:f923bbf9-1c94-4771-9333-77547e7e828e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92", + "$": "data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e", "type": "prov:QUALIFIED_NAME" } }, - "id:5b034fbf-1f17-485f-9c10-7b9b4872862c": { + "id:47d09ccc-4b59-4330-9361-9f1b65b860a8": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "destination", "prov:pairEntity": { - "$": "id:b98d6421-2cca-422c-b778-57480f86de92", + "$": "id:d84bb265-2540-4cad-a026-511b7a21323e", "type": "prov:QUALIFIED_NAME" } }, - "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c": { + "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:45379ceb-7d92-431f-a123-8ee411eedefa", + "$": "id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7", + "$": "id:79566035-3dfd-4779-837a-344529381251", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:60971e6c-b050-4d63-9ca2-b74f7fab78da", + "$": "id:97939793-b619-47e0-8ec3-d3baf5965151", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:d96d9941-8860-4c3d-a573-666266e9e9fe", + "$": "id:f67dbd55-b05c-4a56-aea3-4041399b62d1", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:b09b2fa3-1624-428f-880d-b3890200a943", + "$": "id:792b7ecd-597e-41ad-ac59-b0767919b4b7", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:341b47e4-0ed6-416a-b290-ec06d3966f75", + "$": "id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:adff57da-d615-4087-8dd9-f32586a3d183", + "$": "id:c0c38d7d-cd18-4050-b5e8-0faf10393207", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:1090150b-6f8f-4ab5-8a27-802721f05c5a", + "$": "id:66fde9d0-4440-4811-8b03-ae8c34cfebb6", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:2b1a8432-a59b-4f1b-87ee-912ca464e17c", + "$": "id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:e1aa5ec1-4083-4477-8266-9e68d6afdf66", + "$": "id:069bb313-b651-474e-9a28-fdc7af0fc87b", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:56295d4d-8276-4557-b9f2-b4b3b653865f", + "$": "id:f45f9536-1278-4069-8b91-7edd97d3ff80", "type": "prov:QUALIFIED_NAME" } ] @@ -548,7 +548,7 @@ "prov:value": "auto" } ], - "id:adff57da-d615-4087-8dd9-f32586a3d183": { + "id:79566035-3dfd-4779-837a-344529381251": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -589,7 +589,7 @@ "prov:value": "?" } ], - "id:b09b2fa3-1624-428f-880d-b3890200a943": { + "id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -600,17 +600,17 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:2d11fff4-3195-426d-991e-39f46c18caf7": { + "id:9e633b9f-343d-4b29-a78a-85afdd8eef53": { "prov:value": true }, - "id:341b47e4-0ed6-416a-b290-ec06d3966f75": { + "id:792b7ecd-597e-41ad-ac59-b0767919b4b7": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "to_posix_lines", "prov:pairEntity": { - "$": "id:2d11fff4-3195-426d-991e-39f46c18caf7", + "$": "id:9e633b9f-343d-4b29-a78a-85afdd8eef53", "type": "prov:QUALIFIED_NAME" } }, @@ -630,7 +630,7 @@ "prov:value": "path" } ], - "id:1090150b-6f8f-4ab5-8a27-802721f05c5a": { + "id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -648,7 +648,7 @@ }, "prov:value": "dataset2.txt" }, - "id:45379ceb-7d92-431f-a123-8ee411eedefa": { + "id:97939793-b619-47e0-8ec3-d3baf5965151": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -659,62 +659,62 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:43d5b201-ede9-419e-8b39-1bac02df6546": { + "id:780092f0-87bd-42bc-a3d8-50143d44998b": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:EmptyCollection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:EmptyCollection", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ] }, - "id:60971e6c-b050-4d63-9ca2-b74f7fab78da": { + "id:f45f9536-1278-4069-8b91-7edd97d3ff80": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "hashes", "prov:pairEntity": { - "$": "id:43d5b201-ede9-419e-8b39-1bac02df6546", + "$": "id:780092f0-87bd-42bc-a3d8-50143d44998b", "type": "prov:QUALIFIED_NAME" } }, - "id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c": { + "id:0f5709cc-12f6-430c-a605-fd3e8978f6c4": { "prov:value": false }, - "id:56295d4d-8276-4557-b9f2-b4b3b653865f": { + "id:c0c38d7d-cd18-4050-b5e8-0faf10393207": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "in_place", "prov:pairEntity": { - "$": "id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c", + "$": "id:0f5709cc-12f6-430c-a605-fd3e8978f6c4", "type": "prov:QUALIFIED_NAME" } }, - "id:556f2e68-82d3-4ceb-aa48-e93d1a75be64": { + "id:87e7e990-d873-4d20-a6ee-b15094940df1": { "prov:value": false }, - "id:e1aa5ec1-4083-4477-8266-9e68d6afdf66": { + "id:f67dbd55-b05c-4a56-aea3-4041399b62d1": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "purge_source", "prov:pairEntity": { - "$": "id:556f2e68-82d3-4ceb-aa48-e93d1a75be64", + "$": "id:87e7e990-d873-4d20-a6ee-b15094940df1", "type": "prov:QUALIFIED_NAME" } }, - "id:2b1a8432-a59b-4f1b-87ee-912ca464e17c": { + "id:069bb313-b651-474e-9a28-fdc7af0fc87b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -725,42 +725,42 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:c8ef7d57-8650-4fb8-a748-a692bffac0b5": { + "id:bd860612-ca87-49c5-9d5c-d086f706f789": { "prov:value": { "$": 155708, "type": "xsd:int" } }, - "id:d96d9941-8860-4c3d-a573-666266e9e9fe": { + "id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "object_id", "prov:pairEntity": { - "$": "id:c8ef7d57-8650-4fb8-a748-a692bffac0b5", + "$": "id:bd860612-ca87-49c5-9d5c-d086f706f789", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c": { + "data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c" + "prov:value": "urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9" }, - "id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7": { + "id:66fde9d0-4440-4811-8b03-ae8c34cfebb6": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", + "$": "data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", "type": "prov:QUALIFIED_NAME" } }, - "id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1": { + "id:e7516c89-e4ed-494b-bf16-74b40fa66bd1": { "prov:type": [ { "$": "wfprov:Artifact", @@ -772,50 +772,50 @@ } ] }, - "id:bd679175-0778-4d62-856a-9da7f503a8b0": { + "id:3b176baa-a8f8-426c-ab0d-aa428d41923d": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "elements", "prov:pairEntity": { - "$": "id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1", + "$": "id:e7516c89-e4ed-494b-bf16-74b40fa66bd1", "type": "prov:QUALIFIED_NAME" } }, - "id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5": { + "id:e8c438c4-7544-4049-8d34-f825ecd3b5e1": { "prov:value": false }, - "id:ab29cf85-149a-412a-92ff-e3a6b605ff16": { + "id:ab8003d1-3e46-4af7-9325-fffe09639b01": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "auto_decompress", "prov:pairEntity": { - "$": "id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5", + "$": "id:e8c438c4-7544-4049-8d34-f825ecd3b5e1", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:68b2355f-eec1-44a4-8751-11da17591063": { + "data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:68b2355f-eec1-44a4-8751-11da17591063" + "prov:value": "urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1" }, - "id:c974472d-dbf4-4997-b690-62de731fa7a0": { + "id:9f4835d1-a5f0-499e-9315-42fed1edd2a1": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:68b2355f-eec1-44a4-8751-11da17591063", + "$": "data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1", "type": "prov:QUALIFIED_NAME" } }, - "id:de1ab5b2-d45d-4735-8166-1a8af8fcd980": { + "id:34aa3429-439f-49df-b575-0c7aee2caa81": { "prov:type": [ { "$": "wfprov:Artifact", @@ -827,46 +827,46 @@ } ] }, - "id:f102ded2-603b-4c97-898e-b71bffb17a71": { + "id:7067149e-f997-4e01-810a-41ed1aaae3f1": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "targets", "prov:pairEntity": { - "$": "id:de1ab5b2-d45d-4735-8166-1a8af8fcd980", + "$": "id:34aa3429-439f-49df-b575-0c7aee2caa81", "type": "prov:QUALIFIED_NAME" } }, - "id:2d0a8975-d3b6-43aa-b902-a42b9483374b": { + "id:ffdb63df-93ba-4e67-8097-308bfd9ba39d": { "prov:value": true }, - "id:2f407424-3110-457d-b6f4-3d86f1c76cc8": { + "id:e2f3637a-f559-46a0-a630-9f3e47800b70": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "check_content", "prov:pairEntity": { - "$": "id:2d0a8975-d3b6-43aa-b902-a42b9483374b", + "$": "id:ffdb63df-93ba-4e67-8097-308bfd9ba39d", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5": { + "data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5" + "prov:value": "urn:uuid:594019f6-4154-49a8-be37-3d511a35f066" }, - "id:9be744cb-071c-4610-91d9-d2a8cca5fbf4": { + "id:1e8684e9-896e-4a38-bfe9-1995d0893fdd": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5", + "$": "data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066", "type": "prov:QUALIFIED_NAME" } }, @@ -877,7 +877,7 @@ }, "prov:value": "7c1d8e3101dbcdba" }, - "id:eaec06da-6307-4712-80ca-f89bebb4abc2": { + "id:ebf027ac-b671-468a-91c6-1bfd7e45eb36": { "prov:type": [ { "$": "wfprov:Artifact", @@ -889,50 +889,50 @@ } ] }, - "id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d": { + "id:5ab542a0-7a79-4f00-b120-b14b0542e568": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:f582aab0-3308-432a-a5e7-8c2a0d069acf", + "$": "id:ef96000b-e230-40a1-a36a-a45f4ca78a0e", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c", + "$": "id:d3a55e5b-c1fb-4523-b77d-993b00128b05", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd", + "$": "id:88aa880c-c240-4877-b1e7-a0c20e29ef3e", "type": "prov:QUALIFIED_NAME" } ] }, - "id:4e23da19-5664-4972-94b0-b2d3365672b1": { + "id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4": { "prov:value": { "$": 0, "type": "xsd:int" } }, - "id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd": { + "id:ef96000b-e230-40a1-a36a-a45f4ca78a0e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__index__", "prov:pairEntity": { - "$": "id:4e23da19-5664-4972-94b0-b2d3365672b1", + "$": "id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4", "type": "prov:QUALIFIED_NAME" } }, @@ -952,7 +952,7 @@ "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a" } ], - "id:f582aab0-3308-432a-a5e7-8c2a0d069acf": { + "id:d3a55e5b-c1fb-4523-b77d-993b00128b05": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -963,25 +963,25 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d": { + "data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d" + "prov:value": "urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568" }, - "id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c": { + "id:88aa880c-c240-4877-b1e7-a0c20e29ef3e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d", + "$": "data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568", "type": "prov:QUALIFIED_NAME" } }, - "id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a": { + "id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3": { "prov:type": [ { "$": "wfprov:Artifact", @@ -993,97 +993,97 @@ } ] }, - "id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990": { + "id:71e28368-850b-441f-a008-8b6173a866d7": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:28c49a54-4fce-484f-bbf3-754c514865bd", + "$": "id:68c6bdfd-f17d-41b8-bdba-eb3a46749940", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700", + "$": "id:a75e7105-d7f0-4a77-865c-2ff5b3162e47", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789", + "$": "id:6d29c983-528d-46cf-b420-1c9210619f0d", "type": "prov:QUALIFIED_NAME" } ] }, - "id:f6641719-90a2-47d4-96dd-a847725d5d37": { + "id:7fc57149-e802-47ce-bf01-348e6e787dd0": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4", + "$": "id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:decc5efa-759a-4165-9034-88a8de8ff547", + "$": "id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:1210a0ac-c6d4-4639-8b29-7866ac72a541", + "$": "id:34523c4b-aa54-4d13-8d25-76acadcc8df7", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:a4beeb97-7076-4d47-8015-e6779877af9e", + "$": "id:9e45fea1-39c5-4b99-be26-72b06a5e8786", "type": "prov:QUALIFIED_NAME" } ] }, - "id:afa54a2b-dd93-4fa1-aa45-49b521d7d002": { + "id:4fa4bb93-f67a-414c-8420-9272773cb5e2": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:a3df1b9d-8a6a-4a15-b880-565871b262e2", + "$": "id:93b6a52a-f266-4837-9e8e-ed928fbd2775", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:b1c0e073-72ee-42f6-a512-d8b0a120f260", + "$": "id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be", "type": "prov:QUALIFIED_NAME" } ] }, - "id:b1c0e073-72ee-42f6-a512-d8b0a120f260": { + "id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1094,98 +1094,98 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002": { + "data:urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002" + "prov:value": "urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2" }, - "id:a3df1b9d-8a6a-4a15-b880-565871b262e2": { + "id:93b6a52a-f266-4837-9e8e-ed928fbd2775": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002", + "$": "data:urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2", "type": "prov:QUALIFIED_NAME" } }, - "id:a4beeb97-7076-4d47-8015-e6779877af9e": { + "id:9e45fea1-39c5-4b99-be26-72b06a5e8786": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "destination", "prov:pairEntity": { - "$": "id:afa54a2b-dd93-4fa1-aa45-49b521d7d002", + "$": "id:4fa4bb93-f67a-414c-8420-9272773cb5e2", "type": "prov:QUALIFIED_NAME" } }, - "id:f2a60dac-8878-4bad-98f1-782ebf300df9": { + "id:6d494d29-2bc7-4da4-ba43-e816ee0b1266": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:738ba6b7-e61e-4d37-abb6-3cee1f782367", + "$": "id:d9811e1d-402f-4343-bc31-7dd5643dbdac", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af", + "$": "id:feb54146-911b-4d39-90cf-ef6d66b46fe4", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:4f7a8626-cbee-41ea-835b-76ddc79fcbce", + "$": "id:8ced01f6-47ea-4320-b65a-6af7a668fbe9", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:e64e532c-b1a6-454d-ac58-bde6809a1841", + "$": "id:98a55032-1c60-4303-8ca0-5cff21b96b9d", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565", + "$": "id:286ffa7a-a1f3-424c-90cf-f36d112b13f0", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:f7e87688-b315-448f-82c3-a18665a84053", + "$": "id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:343ac668-db1a-47ca-af95-093b7cc710e1", + "$": "id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26", + "$": "id:ab51fb43-4e4d-459e-ae56-672b92ac89ea", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:4389b350-32eb-48e4-8da0-aaf191209de3", + "$": "id:fbca4ec6-e519-477f-84ce-23e70dddcc8b", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:a89b8834-c5ec-45c4-8760-213c4cc36302", + "$": "id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:a69fb546-67ad-460f-b6f5-01ce7c181db7", + "$": "id:4745fa68-123c-4afb-9176-dcf61732f695", "type": "prov:QUALIFIED_NAME" } ] }, - "id:a89b8834-c5ec-45c4-8760-213c4cc36302": { + "id:d9811e1d-402f-4343-bc31-7dd5643dbdac": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1196,7 +1196,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:738ba6b7-e61e-4d37-abb6-3cee1f782367": { + "id:98a55032-1c60-4303-8ca0-5cff21b96b9d": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1207,21 +1207,21 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:5f8fd80e-f00f-4078-9660-55806bdbd100": { + "id:03d9f2a8-6e48-40b3-84e4-f13e161decf1": { "prov:value": true }, - "id:4389b350-32eb-48e4-8da0-aaf191209de3": { + "id:4745fa68-123c-4afb-9176-dcf61732f695": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "to_posix_lines", "prov:pairEntity": { - "$": "id:5f8fd80e-f00f-4078-9660-55806bdbd100", + "$": "id:03d9f2a8-6e48-40b3-84e4-f13e161decf1", "type": "prov:QUALIFIED_NAME" } }, - "id:a69fb546-67ad-460f-b6f5-01ce7c181db7": { + "id:8ced01f6-47ea-4320-b65a-6af7a668fbe9": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1239,7 +1239,7 @@ }, "prov:value": "dataset1.txt" }, - "id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af": { + "id:286ffa7a-a1f3-424c-90cf-f36d112b13f0": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1250,62 +1250,62 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:b35ba485-3a40-4743-9a58-b207f5becd69": { + "id:8bae3361-cfbe-4b69-bfa0-34901d319a21": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:EmptyCollection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:EmptyCollection", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ] }, - "id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565": { + "id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "hashes", "prov:pairEntity": { - "$": "id:b35ba485-3a40-4743-9a58-b207f5becd69", + "$": "id:8bae3361-cfbe-4b69-bfa0-34901d319a21", "type": "prov:QUALIFIED_NAME" } }, - "id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601": { + "id:368b85e6-a18c-4452-90ef-32ee5ccd0308": { "prov:value": false }, - "id:e64e532c-b1a6-454d-ac58-bde6809a1841": { + "id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "in_place", "prov:pairEntity": { - "$": "id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601", + "$": "id:368b85e6-a18c-4452-90ef-32ee5ccd0308", "type": "prov:QUALIFIED_NAME" } }, - "id:afbd3904-77af-4cab-92f0-f7a1d1e4f467": { + "id:f350a230-ff86-44a3-8560-e35c1ba07b59": { "prov:value": false }, - "id:343ac668-db1a-47ca-af95-093b7cc710e1": { + "id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "purge_source", "prov:pairEntity": { - "$": "id:afbd3904-77af-4cab-92f0-f7a1d1e4f467", + "$": "id:f350a230-ff86-44a3-8560-e35c1ba07b59", "type": "prov:QUALIFIED_NAME" } }, - "id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26": { + "id:ab51fb43-4e4d-459e-ae56-672b92ac89ea": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1316,42 +1316,42 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:35a147fd-c38e-4a85-bd9a-6a509ccd1245": { + "id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a": { "prov:value": { "$": 155707, "type": "xsd:int" } }, - "id:4f7a8626-cbee-41ea-835b-76ddc79fcbce": { + "id:fbca4ec6-e519-477f-84ce-23e70dddcc8b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "object_id", "prov:pairEntity": { - "$": "id:35a147fd-c38e-4a85-bd9a-6a509ccd1245", + "$": "id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9": { + "data:urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9" + "prov:value": "urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266" }, - "id:f7e87688-b315-448f-82c3-a18665a84053": { + "id:feb54146-911b-4d39-90cf-ef6d66b46fe4": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9", + "$": "data:urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266", "type": "prov:QUALIFIED_NAME" } }, - "id:411a358d-2596-4506-b64a-74b54ea779d4": { + "id:8dbadfd6-d421-4d18-95ae-36fc4defb317": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1363,50 +1363,50 @@ } ] }, - "id:decc5efa-759a-4165-9034-88a8de8ff547": { + "id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "elements", "prov:pairEntity": { - "$": "id:411a358d-2596-4506-b64a-74b54ea779d4", + "$": "id:8dbadfd6-d421-4d18-95ae-36fc4defb317", "type": "prov:QUALIFIED_NAME" } }, - "id:77f3c59e-7ec9-4e8b-9401-857b6c311c83": { + "id:65dace90-ed17-46f9-b809-d98a90563655": { "prov:value": false }, - "id:1210a0ac-c6d4-4639-8b29-7866ac72a541": { + "id:34523c4b-aa54-4d13-8d25-76acadcc8df7": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "auto_decompress", "prov:pairEntity": { - "$": "id:77f3c59e-7ec9-4e8b-9401-857b6c311c83", + "$": "id:65dace90-ed17-46f9-b809-d98a90563655", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37": { + "data:urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37" + "prov:value": "urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0" }, - "id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4": { + "id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37", + "$": "data:urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0", "type": "prov:QUALIFIED_NAME" } }, - "id:2f356100-3315-4ff7-87cf-54b1d4d3ea49": { + "id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1418,46 +1418,46 @@ } ] }, - "id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700": { + "id:a75e7105-d7f0-4a77-865c-2ff5b3162e47": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "targets", "prov:pairEntity": { - "$": "id:2f356100-3315-4ff7-87cf-54b1d4d3ea49", + "$": "id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1", "type": "prov:QUALIFIED_NAME" } }, - "id:ff95d010-cdcb-45d8-8418-aa53e7681b10": { + "id:fc84f9f8-5bb4-402d-ba90-697df02824ca": { "prov:value": true }, - "id:28c49a54-4fce-484f-bbf3-754c514865bd": { + "id:6d29c983-528d-46cf-b420-1c9210619f0d": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "check_content", "prov:pairEntity": { - "$": "id:ff95d010-cdcb-45d8-8418-aa53e7681b10", + "$": "id:fc84f9f8-5bb4-402d-ba90-697df02824ca", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990": { + "data:urn:uuid:71e28368-850b-441f-a008-8b6173a866d7": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990" + "prov:value": "urn:uuid:71e28368-850b-441f-a008-8b6173a866d7" }, - "id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789": { + "id:68c6bdfd-f17d-41b8-bdba-eb3a46749940": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990", + "$": "data:urn:uuid:71e28368-850b-441f-a008-8b6173a866d7", "type": "prov:QUALIFIED_NAME" } }, @@ -1477,7 +1477,7 @@ "prov:value": "7ca3de8f49293d1a" } ], - "id:595e172f-01c4-4ca4-bd82-532ac4e0195d": { + "id:837879db-a58f-45bc-980d-2da57fd19cd1": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1505,7 +1505,7 @@ "prov:value": "2e789aae2475b7da" } ], - "id:232855e1-8392-4f99-b38d-028c22b047d8": { + "id:730e5d81-2c3c-44d7-9916-9cc0b7bcdd81": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1540,7 +1540,7 @@ "prov:value": "fd7fec473f1e6c6b" } ], - "id:1673a6bb-e7f1-4e69-9403-15c343f59b98": { + "id:a1110187-8be9-4aff-b03e-3530ed7f6cbf": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1600,63 +1600,63 @@ "prov:value": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len" } ], - "id:6c67cd25-9da2-4eb8-9145-ab14b36c9771": { + "id:a9607900-c633-4837-a4a7-eaee6edcaf3b": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:ec4fdb41-ede8-4f37-a220-34eb67952e01", + "$": "id:57844284-ccc8-45f3-a7fa-6ce0246cf99b", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc", + "$": "id:e9967a89-6747-4067-95ed-5160b763f0b1", "type": "prov:QUALIFIED_NAME" } ] }, - "id:2f80b5e3-3925-49fd-9339-86ed10571ea9": { + "id:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:b3a09002-26d2-44b7-80a1-f3a0accdcacc", + "$": "id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:ea79a0ce-8267-474e-adc3-0d37ec935565", + "$": "id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06", + "$": "id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d", "type": "prov:QUALIFIED_NAME" } ] }, - "id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06": { + "id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1690,7 +1690,7 @@ "prov:value": "hda" } ], - "id:ea79a0ce-8267-474e-adc3-0d37ec935565": { + "id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1701,25 +1701,25 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9": { + "data:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9" + "prov:value": "urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0" }, - "id:b3a09002-26d2-44b7-80a1-f3a0accdcacc": { + "id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9", + "$": "data:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0", "type": "prov:QUALIFIED_NAME" } }, - "id:7ac72e2f-5815-47ff-9592-b89492e1804c": { + "id:7827651a-85f5-48a4-8f9d-1427fc02bda4": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1731,139 +1731,139 @@ } ] }, - "id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc": { + "id:57844284-ccc8-45f3-a7fa-6ce0246cf99b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "values", "prov:pairEntity": { - "$": "id:7ac72e2f-5815-47ff-9592-b89492e1804c", + "$": "id:7827651a-85f5-48a4-8f9d-1427fc02bda4", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771": { + "data:urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771" + "prov:value": "urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b" }, - "id:ec4fdb41-ede8-4f37-a220-34eb67952e01": { + "id:e9967a89-6747-4067-95ed-5160b763f0b1": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771", + "$": "data:urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b", "type": "prov:QUALIFIED_NAME" } }, - "id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0": { + "id:f39be690-c7d7-4911-be28-6afc1abe40b0": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:b095ce58-2b16-49a3-8873-73a85d09b84e", + "$": "id:951bb963-10a7-4234-8119-1b13921f9629", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2", + "$": "id:9578a96e-6635-4000-9c81-2951341b65c8", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:9781f372-1be1-48e3-a9d3-2dda2b581134", + "$": "id:4529ad17-6e7b-4493-bba5-475a60c4a11a", "type": "prov:QUALIFIED_NAME" } ] }, - "id:20c6c642-7356-4161-a861-7cebbb063751": { + "id:f40fd446-41cb-442e-bbb7-9a23d27296e5": { "prov:value": { "$": 0, "type": "xsd:int" } }, - "id:b095ce58-2b16-49a3-8873-73a85d09b84e": { + "id:951bb963-10a7-4234-8119-1b13921f9629": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__index__", "prov:pairEntity": { - "$": "id:20c6c642-7356-4161-a861-7cebbb063751", + "$": "id:f40fd446-41cb-442e-bbb7-9a23d27296e5", "type": "prov:QUALIFIED_NAME" } }, - "id:1754bbe0-77b5-453b-8542-e83b9bc45798": { + "id:e6248791-d7c3-49a7-9660-5cb622189a3c": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:a11456da-294c-4173-96c9-9becdc7af2fc", + "$": "id:8170c31b-5a5f-4150-8531-8b0adac0f282", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:eac8a16e-c68a-457a-871d-47f710712b41", + "$": "id:ff80c261-0171-44d9-86fa-546f8aea6cd8", "type": "prov:QUALIFIED_NAME" } ] }, - "id:93055cbf-80fe-4acc-a0a6-fdefdaefcce1": { + "id:062d0748-7b74-4d45-98f3-80bd22ed2672": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:1d168b92-47a6-448c-baf8-f585f12a3d33", + "$": "id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:641250eb-2adc-4c98-afcd-00428ee7bc8a", + "$": "id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:4b824c76-227e-430f-919c-853ff66133a4", + "$": "id:51656ecb-5b39-4ad7-9888-d7b93ca28266", "type": "prov:QUALIFIED_NAME" } ] }, - "id:4b824c76-227e-430f-919c-853ff66133a4": { + "id:51656ecb-5b39-4ad7-9888-d7b93ca28266": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1874,7 +1874,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:1d168b92-47a6-448c-baf8-f585f12a3d33": { + "id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1885,25 +1885,25 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1": { + "data:urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1" + "prov:value": "urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672" }, - "id:641250eb-2adc-4c98-afcd-00428ee7bc8a": { + "id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1", + "$": "data:urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672", "type": "prov:QUALIFIED_NAME" } }, - "id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6": { + "id:55af6a73-efbe-4e5c-8b47-6ff94872e6de": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1915,65 +1915,65 @@ } ] }, - "id:eac8a16e-c68a-457a-871d-47f710712b41": { + "id:ff80c261-0171-44d9-86fa-546f8aea6cd8": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "values", "prov:pairEntity": { - "$": "id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6", + "$": "id:55af6a73-efbe-4e5c-8b47-6ff94872e6de", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798": { + "data:urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798" + "prov:value": "urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c" }, - "id:a11456da-294c-4173-96c9-9becdc7af2fc": { + "id:8170c31b-5a5f-4150-8531-8b0adac0f282": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798", + "$": "data:urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c", "type": "prov:QUALIFIED_NAME" } }, - "id:9781f372-1be1-48e3-a9d3-2dda2b581134": { + "id:4529ad17-6e7b-4493-bba5-475a60c4a11a": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "input2", "prov:pairEntity": { - "$": "id:1754bbe0-77b5-453b-8542-e83b9bc45798", + "$": "id:e6248791-d7c3-49a7-9660-5cb622189a3c", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0": { + "data:urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0" + "prov:value": "urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0" }, - "id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2": { + "id:9578a96e-6635-4000-9c81-2951341b65c8": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0", + "$": "data:urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0", "type": "prov:QUALIFIED_NAME" } }, - "id:142f1b95-3ba6-4998-b6a6-72d299494e68": { + "id:682cbd95-9570-4f19-a8bb-a639bfb641e2": { "prov:type": [ { "$": "wfprov:Artifact", @@ -1985,7 +1985,7 @@ } ] }, - "id:425cb32b-54a2-410a-a915-c025f76640d3": { + "id:8a1a4095-2cbb-468e-80d6-25ebab181a3e": { "prov:type": [ { "$": "wfprov:Artifact", @@ -2004,7 +2004,7 @@ }, "prov:value": "775bc9b3c1750167" }, - "id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1": { + "id:6cf20326-6a50-4476-910c-c40be8829bc4": { "prov:type": [ { "$": "wfprov:Artifact", @@ -2016,63 +2016,63 @@ } ] }, - "id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a": { + "id:fd40a61e-108c-42c4-8b49-c20815d2d9e5": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:428da699-3449-41e2-b395-a770b9b49467", + "$": "id:81d81eab-2874-43f4-9d2e-ce5ad6236054", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:8041c95b-4fe2-4663-bcfe-6d4292c9d678", + "$": "id:279428d4-794f-42cd-9419-0c8c71385b78", "type": "prov:QUALIFIED_NAME" } ] }, - "id:2ff086c3-1d26-439e-8b37-02eb82ba2a89": { + "id:24d7454e-9885-40b1-8a85-cc272df4fa40": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:36bf5f2c-3bf9-46aa-aac5-8b6249738317", + "$": "id:96981ec2-dac6-4477-9ac3-431cdc24f7ac", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd", + "$": "id:c40c9210-5155-480f-ba36-5f86aaa39d77", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:bdc9be97-2541-4e9d-9b66-e93b350046f5", + "$": "id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94", "type": "prov:QUALIFIED_NAME" } ] }, - "id:36bf5f2c-3bf9-46aa-aac5-8b6249738317": { + "id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2083,7 +2083,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd": { + "id:c40c9210-5155-480f-ba36-5f86aaa39d77": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2094,25 +2094,25 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89": { + "data:urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89" + "prov:value": "urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40" }, - "id:bdc9be97-2541-4e9d-9b66-e93b350046f5": { + "id:96981ec2-dac6-4477-9ac3-431cdc24f7ac": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89", + "$": "data:urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40", "type": "prov:QUALIFIED_NAME" } }, - "id:7da8d1bc-cc46-4312-9331-0e417f123152": { + "id:23fbeb5c-eebc-41ef-a966-be8a191c7ede": { "prov:type": [ { "$": "wfprov:Artifact", @@ -2124,32 +2124,32 @@ } ] }, - "id:428da699-3449-41e2-b395-a770b9b49467": { + "id:279428d4-794f-42cd-9419-0c8c71385b78": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "values", "prov:pairEntity": { - "$": "id:7da8d1bc-cc46-4312-9331-0e417f123152", + "$": "id:23fbeb5c-eebc-41ef-a966-be8a191c7ede", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a": { + "data:urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a" + "prov:value": "urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5" }, - "id:8041c95b-4fe2-4663-bcfe-6d4292c9d678": { + "id:81d81eab-2874-43f4-9d2e-ce5ad6236054": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a", + "$": "data:urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5", "type": "prov:QUALIFIED_NAME" } }, @@ -2160,54 +2160,54 @@ }, "prov:value": "3" }, - "id:a6de5b1b-da32-4449-81b5-4efcdb27bad4": { + "id:7e6d530d-6c05-48b1-8d69-879b6e790c9d": { "prov:type": [ { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:Dictionary", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Dictionary", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:8329dc4f-308b-4258-bc73-9e55abd502a5", + "$": "id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:7cc407df-6449-4722-bd58-5d9fb44288c4", + "$": "id:903792cc-566c-4ffe-ade9-be65cf4f1fb4", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c", + "$": "id:5ba613ce-6eaa-412d-89bf-eb8f580823a3", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:3d1d3c32-7457-4abf-bb66-12aac16561b1", + "$": "id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e", "type": "prov:QUALIFIED_NAME" } ] }, - "id:2be3e6ed-24b7-444d-a4ee-5770d93987d4": { + "id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad": { "prov:value": { "$": 1, "type": "xsd:int" } }, - "id:7cc407df-6449-4722-bd58-5d9fb44288c4": { + "id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__current_case__", "prov:pairEntity": { - "$": "id:2be3e6ed-24b7-444d-a4ee-5770d93987d4", + "$": "id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad", "type": "prov:QUALIFIED_NAME" } }, @@ -2218,7 +2218,7 @@ }, "prov:value": "0" }, - "id:8329dc4f-308b-4258-bc73-9e55abd502a5": { + "id:5ba613ce-6eaa-412d-89bf-eb8f580823a3": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2236,7 +2236,7 @@ }, "prov:value": "set_seed" }, - "id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c": { + "id:903792cc-566c-4ffe-ade9-be65cf4f1fb4": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2247,633 +2247,633 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4": { + "data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4" + "prov:value": "urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d" }, - "id:3d1d3c32-7457-4abf-bb66-12aac16561b1": { + "id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4", + "$": "data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d", "type": "prov:QUALIFIED_NAME" } } }, "hadMember": { "_:id7": { - "prov:collection": "id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047", + "prov:collection": "id:d4c2d49d-ab80-43ab-b347-a7db85bf7262", "prov:entity": "data:2524d3d3b68ad39a" }, "_:id10": { - "prov:collection": "id:f5582681-806f-4e35-9028-631eab68c8db", - "prov:entity": "id:456f97d2-4118-4fd3-a7e0-0bed64b7e343" + "prov:collection": "id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6", + "prov:entity": "id:0c54448a-8444-42cd-9dd1-b65dfb0656ba" }, "_:id11": { - "prov:collection": "id:f5582681-806f-4e35-9028-631eab68c8db", + "prov:collection": "id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6", "prov:entity": "data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" }, "_:id12": { - "prov:collection": "id:f5582681-806f-4e35-9028-631eab68c8db", - "prov:entity": "data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db" + "prov:collection": "id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6", + "prov:entity": "data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6" }, "_:id13": { - "prov:collection": "id:10a92b31-e38a-4eee-a163-d05f0c942e28", - "prov:entity": "id:f5582681-806f-4e35-9028-631eab68c8db" + "prov:collection": "id:5c05f71f-74dc-4238-a591-9df8dfa779f8", + "prov:entity": "id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6" }, "_:id16": { - "prov:collection": "id:b98d6421-2cca-422c-b778-57480f86de92", + "prov:collection": "id:d84bb265-2540-4cad-a026-511b7a21323e", "prov:entity": "data:hdas" }, "_:id17": { - "prov:collection": "id:b98d6421-2cca-422c-b778-57480f86de92", - "prov:entity": "data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92" + "prov:collection": "id:d84bb265-2540-4cad-a026-511b7a21323e", + "prov:entity": "data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e" }, "_:id18": { - "prov:collection": "id:68b2355f-eec1-44a4-8751-11da17591063", - "prov:entity": "id:b98d6421-2cca-422c-b778-57480f86de92" + "prov:collection": "id:641c238b-2832-4fab-b949-f5f4fc01deb1", + "prov:entity": "id:d84bb265-2540-4cad-a026-511b7a21323e" }, "_:id19": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", "prov:entity": "data:auto" }, "_:id20": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", "prov:entity": "data:?" }, "_:id21": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", - "prov:entity": "id:2d11fff4-3195-426d-991e-39f46c18caf7" + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", + "prov:entity": "id:9e633b9f-343d-4b29-a78a-85afdd8eef53" }, "_:id22": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", "prov:entity": "data:path" }, "_:id23": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", "prov:entity": "data:dataset2.txt" }, "_:id24": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", - "prov:entity": "id:43d5b201-ede9-419e-8b39-1bac02df6546" + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", + "prov:entity": "id:780092f0-87bd-42bc-a3d8-50143d44998b" }, "_:id25": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", - "prov:entity": "id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c" + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", + "prov:entity": "id:0f5709cc-12f6-430c-a605-fd3e8978f6c4" }, "_:id26": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", - "prov:entity": "id:556f2e68-82d3-4ceb-aa48-e93d1a75be64" + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", + "prov:entity": "id:87e7e990-d873-4d20-a6ee-b15094940df1" }, "_:id27": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", "prov:entity": "data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" }, "_:id28": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", - "prov:entity": "id:c8ef7d57-8650-4fb8-a748-a692bffac0b5" + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", + "prov:entity": "id:bd860612-ca87-49c5-9d5c-d086f706f789" }, "_:id29": { - "prov:collection": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c", - "prov:entity": "data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c" + "prov:collection": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", + "prov:entity": "data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9" }, "_:id30": { - "prov:collection": "id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1", - "prov:entity": "id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c" + "prov:collection": "id:e7516c89-e4ed-494b-bf16-74b40fa66bd1", + "prov:entity": "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9" }, 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"type": "prov:QUALIFIED_NAME" } }, "_:id122": { - "prov:activity": "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d", + "prov:activity": "id:2341e04b-a08b-400e-97ef-3151f01a17fa", "prov:entity": "data:3", - "prov:time": "2022-03-30T14:10:06.239990", + "prov:time": "2022-03-31T15:39:11.769848", "prov:role": { "$": "wf:main/random_lines1/num_lines", "type": "prov:QUALIFIED_NAME" } }, "_:id127": { - "prov:activity": "id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d", - "prov:entity": "id:a6de5b1b-da32-4449-81b5-4efcdb27bad4", - "prov:time": "2022-03-30T14:10:06.240395", + "prov:activity": "id:2341e04b-a08b-400e-97ef-3151f01a17fa", + "prov:entity": "id:7e6d530d-6c05-48b1-8d69-879b6e790c9d", + "prov:time": "2022-03-31T15:39:11.770390", "prov:role": { "$": "wf:main/random_lines1/seed_source", "type": "prov:QUALIFIED_NAME" diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.jsonld b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld similarity index 67% rename from test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.jsonld rename to test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld index 108b3282..864f4681 100644 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.jsonld +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld @@ -1,1415 +1,1054 @@ [ { - "@id": "urn:uuid:8041c95b-4fe2-4663-bcfe-6d4292c9d678", + "@id": "urn:uuid:ace28a14-6cc4-4efc-adcb-4668dcc9cd60", "@type": [ "http://www.w3.org/ns/prov#Entity", "http://www.w3.org/ns/prov#KeyEntityPair" ], "http://www.w3.org/ns/prov#pairEntity": [ { - "@id": "urn:hash::sha1:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a" + "@id": "urn:hash::sha1:?" } ], "http://www.w3.org/ns/prov#pairKey": [ { - "@value": "@id" + "@value": "dbkey" } ] }, { 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"urn:uuid:dbb9844d-466e-46b5-bf9b-d2eec40c2b26", + "@id": "_:Nd053a2e7044a421a97aa1b76c33fd272", "@type": [ - "http://www.w3.org/ns/prov#Entity", - "http://www.w3.org/ns/prov#KeyEntityPair" + "http://www.w3.org/ns/prov#Usage" ], - "http://www.w3.org/ns/prov#pairEntity": [ + "http://www.w3.org/ns/prov#atTime": [ { - "@id": "urn:hash::sha1:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a" + "@type": "http://www.w3.org/2001/XMLSchema#dateTime", + "@value": "2022-03-31T15:39:11.770390" } ], - "http://www.w3.org/ns/prov#pairKey": [ + "http://www.w3.org/ns/prov#entity": [ { - "@value": "path" + "@id": "urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d" + } + ], + "http://www.w3.org/ns/prov#hadRole": [ + { + "@id": "arcp://uuid,bdf8ae0f-d0e0-4338-9513-e6fecbbeb255/ga_export/main/random_lines1/seed_source" } ] }, { - "@id": "urn:uuid:56295d4d-8276-4557-b9f2-b4b3b653865f", + "@id": "_:N3b678216b83245c7927b3fb16c6a6a98", "@type": [ - "http://www.w3.org/ns/prov#Entity", - 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"http://www.w3.org/ns/prov#hadActivity": [ { - "@value": "file_data" + "@id": "urn:uuid:dd421f2f-c538-44d3-aeeb-484022c6541d" } ] }, { - "@id": "urn:uuid:3d1d3c32-7457-4abf-bb66-12aac16561b1", + "@id": "urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0", "@type": [ - "http://www.w3.org/ns/prov#KeyEntityPair", + "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Collection", + "http://www.w3.org/ns/prov#Dictionary", "http://www.w3.org/ns/prov#Entity" ], - "http://www.w3.org/ns/prov#pairEntity": [ + "http://www.w3.org/ns/prov#hadDictionaryMember": [ + { + "@id": "urn:uuid:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99" + }, + { + "@id": "urn:uuid:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d" + }, { - "@id": "urn:hash::sha1:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4" + "@id": "urn:uuid:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813" } ], - "http://www.w3.org/ns/prov#pairKey": [ + "http://www.w3.org/ns/prov#hadMember": [ { - "@value": "@id" + "@id": "urn:hash::sha1:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0" + }, + { + "@id": "urn:hash::sha1:hda" + }, + { + "@id": "urn:hash::sha1:7ca3de8f49293d1a" } ] }, { - "@id": "urn:uuid:4319f013-ecd8-4341-a5b9-8e9d8420bd31", + "@id": "urn:uuid:d5ba27cc-fd05-4540-baac-a8e0c6a7de01", "@type": [ "http://www.w3.org/ns/prov#Entity", "http://www.w3.org/ns/prov#KeyEntityPair" ], "http://www.w3.org/ns/prov#pairEntity": [ { - "@id": "urn:hash::sha1:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" + "@id": "urn:hash::sha1:path" } ], "http://www.w3.org/ns/prov#pairKey": [ { - "@value": "file_data" + "@value": "src" } ] }, { - "@id": "urn:uuid:9781f372-1be1-48e3-a9d3-2dda2b581134", + "@id": "urn:uuid:fbca4ec6-e519-477f-84ce-23e70dddcc8b", "@type": [ "http://www.w3.org/ns/prov#KeyEntityPair", "http://www.w3.org/ns/prov#Entity" ], "http://www.w3.org/ns/prov#pairEntity": [ { - "@id": "urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798" + "@id": "urn:uuid:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a" } ], "http://www.w3.org/ns/prov#pairKey": [ { - "@value": "input2" + "@value": "object_id" } ] }, { - "@id": "urn:uuid:1210a0ac-c6d4-4639-8b29-7866ac72a541", + "@id": "urn:hash::sha1:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0", "@type": [ "http://www.w3.org/ns/prov#Entity", - "http://www.w3.org/ns/prov#KeyEntityPair" - ], - "http://www.w3.org/ns/prov#pairEntity": [ - { - "@id": "urn:uuid:77f3c59e-7ec9-4e8b-9401-857b6c311c83" - } - ], - "http://www.w3.org/ns/prov#pairKey": [ - { - "@value": "auto_decompress" - } - ] - }, - { - "@id": "urn:uuid:9be744cb-071c-4610-91d9-d2a8cca5fbf4", - "@type": [ - "http://www.w3.org/ns/prov#KeyEntityPair", - "http://www.w3.org/ns/prov#Entity" - ], - "http://www.w3.org/ns/prov#pairEntity": [ - { - "@id": "urn:hash::sha1:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5" - } + "http://purl.org/wf4ever/wfprov#Artifact" ], - "http://www.w3.org/ns/prov#pairKey": [ + "http://www.w3.org/ns/prov#value": [ { - "@value": "@id" + "@value": "urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0" } ] }, { - "@id": "urn:uuid:2b1a8432-a59b-4f1b-87ee-912ca464e17c", + "@id": "urn:hash::sha1:1", "@type": [ - "http://www.w3.org/ns/prov#KeyEntityPair", + "http://purl.org/wf4ever/wfprov#Artifact", "http://www.w3.org/ns/prov#Entity" ], - "http://www.w3.org/ns/prov#pairEntity": [ - { - "@id": "urn:hash::sha1:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" - } - ], - "http://www.w3.org/ns/prov#pairKey": [ + "http://www.w3.org/ns/prov#value": [ { - "@value": "path" + "@value": "1" } ] } diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt new file mode 100644 index 00000000..7f407de2 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt @@ -0,0 +1,942 @@ + "elements"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "1"^^ . + . + "src"^^ . + "155707"^^ . + . +_:Nce2d56e6ec1148ef96f00432a5d143a4 . + . + . + . + "dbkey"^^ . + "urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0"^^ . + . +_:Ndda3f852178b41df93d682778b30de68 . + _:Na92402de90f14681a1fc4c098d4f253e . +_:N2f06695db9b54b5fa0b321d256789020 "2022-03-31T15:39:11.765900"^^ . + . +_:N0ded116190a84793bcc622c066529856 . + _:N90b3a6506b334ccbb557f8536d3ac873 . + . + _:N24aba0e97dbc4fe69e1137800e93b683 . +_:Nb79bb954c4134c8d8dff856be6f5dcdd "2022-03-31T15:39:11.763447"^^ . +_:N932919aa9f4a4c31bf196d8bf8fce201 . + . + "values"^^ . + . +_:Nf64e03a753aa40b79e4b06699ae76944 . + . + . + . + . + . + . + . + . +_:Nb0027efc48c442aebdf8723a09a6b2a7 . + . + . + _:Nb974275df6e84c43b2d268ce35d17f5d . + . +_:N24aba0e97dbc4fe69e1137800e93b683 . + . + . + . + . + _:N08fca9271ba54c33b392e1a288848614 . + . + "false"^^ . + . + . + . + . + . +_:N932919aa9f4a4c31bf196d8bf8fce201 "2022-03-31T15:39:11.765313"^^ . + "check_content"^^ . + "@id"^^ . + . + . + . +_:N8761a0fd566b4688a9e4a6fd9839b527 . + "id"^^ . +_:N7892c1c304be478482995f67fcc40f35 . + . + "urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2"^^ . + . + . + . + _:N9eff600bf1924eaaa9585bd011a708f7 . + . + . + "Run of ga_export/jobs_attrs.txt#random_lines1"^^ . + . +_:N621571548bb741eeb7018c410acf4441 . +_:Ndc331aea228e4d2fa951660049228dd7 "2022-03-31T15:39:11.769116"^^ . +_:N6c8e9fe0d6cc4f0aa1b32337ce8e70ef . + . + . + "hashes"^^ . + . + . + . + "in_place"^^ . + . + . + . +_:N2bea0b227964438589d9d35a0828a9b5 . + "purge_source"^^ . + . + "2021-06-23T10:20:22.770291"^^ . +_:Nd75d0d9f2ab24726847d6a36acf5572f "2022-03-31T15:39:11.759917"^^ . + "txt"^^ . + . + . + . + "3"^^ . +_:N9eff600bf1924eaaa9585bd011a708f7 "2021-06-23T10:20:00.981702"^^ . + . + "hdas"^^ . + . + . + . + "name"^^ . + . + _:N704fdcfec018436383e492f6c5b2eee6 . + _:Nce6998e02860423487cf4b4b36285921 . +_:Ne954aaea715a4c7f83cddf209be99f58 . + . + . +_:Nb0027efc48c442aebdf8723a09a6b2a7 . + _:Nb79bb954c4134c8d8dff856be6f5dcdd . + . + . + . + . + . + 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+_:N2f06695db9b54b5fa0b321d256789020 . + "auto_decompress"^^ . + "@id"^^ . + . + . +_:N0ded116190a84793bcc622c066529856 . +_:N9eff600bf1924eaaa9585bd011a708f7 . +_:Nce6998e02860423487cf4b4b36285921 . +_:N90b3a6506b334ccbb557f8536d3ac873 . + . + . + . + . + . + . + . +_:Na92402de90f14681a1fc4c098d4f253e "2022-03-31T15:39:11.769848"^^ . + . + . + . + . + . + "src"^^ . + "destination"^^ . + "auto_decompress"^^ . + diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn new file mode 100644 index 00000000..7014e23c --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn @@ -0,0 +1,332 @@ +document + prefix wfprov + prefix wfdesc + prefix cwlprov + prefix foaf + prefix schema + prefix orcid + prefix id + prefix data + prefix provenance + prefix wf + prefix input + + agent(id:c98b0b95-d818-4ba1-b535-11c4e6909fa3) + agent(orcid:0000-0002-8940-4946, [prov:type='schema:Person', prov:type='prov:Person', prov:label="PDG", foaf:name="PDG", schema:name="PDG"]) + actedOnBehalfOf(id:c98b0b95-d818-4ba1-b535-11c4e6909fa3, orcid:0000-0002-8940-4946, -) + agent(id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="galaxy_version_placeholder"]) + wasStartedBy(id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, -, id:c98b0b95-d818-4ba1-b535-11c4e6909fa3, 2022-03-31T15:39:11.759268) + activity(id:dd421f2f-c538-44d3-aeeb-484022c6541d, 2022-03-31T15:39:11.759294, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of galaxy workflow"]) + wasAssociatedWith(id:dd421f2f-c538-44d3-aeeb-484022c6541d, id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, wf:main) + wasStartedBy(id:dd421f2f-c538-44d3-aeeb-484022c6541d, -, id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, 2022-03-31T15:39:11.759353) + activity(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, 2021-06-23T10:20:22.770291, 2021-06-23T10:20:42.041319, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) + wasAssociatedWith(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, wf:main/__DATA_FETCH__) + wasStartedBy(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, -, id:dd421f2f-c538-44d3-aeeb-484022c6541d, 2021-06-23T10:20:22.770291) + entity(data:2524d3d3b68ad39a, [prov:type='wfprov:Artifact', prov:value="2524d3d3b68ad39a"]) + entity(id:d4c2d49d-ab80-43ab-b347-a7db85bf7262, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:d4c2d49d-ab80-43ab-b347-a7db85bf7262, data:2524d3d3b68ad39a) + used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:d4c2d49d-ab80-43ab-b347-a7db85bf7262, 2022-03-31T15:39:11.759864, [prov:role='wf:main/__DATA_FETCH__/output0']) + entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) + used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, data:1, 2022-03-31T15:39:11.759917, [prov:role='wf:main/__DATA_FETCH__/file_count']) + entity(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:a1bb89e0-badf-490a-af30-375efe69c057', prov:hadDictionaryMember='id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98', prov:hadDictionaryMember='id:869277c3-8c88-4381-bbef-de17240b1c23']) + entity(id:0c54448a-8444-42cd-9dd1-b65dfb0656ba, [prov:value=0]) + hadMember(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, id:0c54448a-8444-42cd-9dd1-b65dfb0656ba) + entity(id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:0c54448a-8444-42cd-9dd1-b65dfb0656ba']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) + hadMember(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:869277c3-8c88-4381-bbef-de17240b1c23, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, [prov:type='wfprov:Artifact', prov:value="urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6"]) + hadMember(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6) + entity(id:a1bb89e0-badf-490a-af30-375efe69c057, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6']) + entity(id:5c05f71f-74dc-4238-a591-9df8dfa779f8, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:5c05f71f-74dc-4238-a591-9df8dfa779f8, id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6) + used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:5c05f71f-74dc-4238-a591-9df8dfa779f8, 2022-03-31T15:39:11.760237, [prov:role='wf:main/__DATA_FETCH__/files']) + entity(data:, [prov:type='wfprov:Artifact', prov:value=""]) + used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, data:, 2022-03-31T15:39:11.760286, [prov:role='wf:main/__DATA_FETCH__/paramfile']) + entity(id:594019f6-4154-49a8-be37-3d511a35f066, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:e2f3637a-f559-46a0-a630-9f3e47800b70', prov:hadDictionaryMember='id:1e8684e9-896e-4a38-bfe9-1995d0893fdd', prov:hadDictionaryMember='id:7067149e-f997-4e01-810a-41ed1aaae3f1']) + entity(id:641c238b-2832-4fab-b949-f5f4fc01deb1, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:ab8003d1-3e46-4af7-9325-fffe09639b01', prov:hadDictionaryMember='id:3b176baa-a8f8-426c-ab0d-aa428d41923d', prov:hadDictionaryMember='id:47d09ccc-4b59-4330-9361-9f1b65b860a8', prov:hadDictionaryMember='id:9f4835d1-a5f0-499e-9315-42fed1edd2a1']) + entity(id:d84bb265-2540-4cad-a026-511b7a21323e, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5', prov:hadDictionaryMember='id:f923bbf9-1c94-4771-9333-77547e7e828e']) + entity(data:hdas, [prov:type='wfprov:Artifact', prov:value="hdas"]) + hadMember(id:d84bb265-2540-4cad-a026-511b7a21323e, data:hdas) + entity(id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5, [prov:type='prov:KeyEntityPair', prov:pairKey="type", prov:pairEntity='data:hdas']) + entity(data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e, [prov:type='wfprov:Artifact', prov:value="urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e"]) + hadMember(id:d84bb265-2540-4cad-a026-511b7a21323e, data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e) + entity(id:f923bbf9-1c94-4771-9333-77547e7e828e, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e']) + hadMember(id:641c238b-2832-4fab-b949-f5f4fc01deb1, id:d84bb265-2540-4cad-a026-511b7a21323e) + entity(id:47d09ccc-4b59-4330-9361-9f1b65b860a8, [prov:type='prov:KeyEntityPair', prov:pairKey="destination", prov:pairEntity='id:d84bb265-2540-4cad-a026-511b7a21323e']) + entity(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60', prov:hadDictionaryMember='id:79566035-3dfd-4779-837a-344529381251', prov:hadDictionaryMember='id:97939793-b619-47e0-8ec3-d3baf5965151', prov:hadDictionaryMember='id:f67dbd55-b05c-4a56-aea3-4041399b62d1', prov:hadDictionaryMember='id:792b7ecd-597e-41ad-ac59-b0767919b4b7', prov:hadDictionaryMember='id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01', prov:hadDictionaryMember='id:c0c38d7d-cd18-4050-b5e8-0faf10393207', prov:hadDictionaryMember='id:66fde9d0-4440-4811-8b03-ae8c34cfebb6', prov:hadDictionaryMember='id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64', prov:hadDictionaryMember='id:069bb313-b651-474e-9a28-fdc7af0fc87b', prov:hadDictionaryMember='id:f45f9536-1278-4069-8b91-7edd97d3ff80']) + entity(data:auto, [prov:type='wfprov:Artifact', prov:value="auto"]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:auto) + entity(id:79566035-3dfd-4779-837a-344529381251, [prov:type='prov:KeyEntityPair', prov:pairKey="ext", prov:pairEntity='data:auto']) + entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:?) + entity(id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60, [prov:type='prov:KeyEntityPair', prov:pairKey="dbkey", prov:pairEntity='data:?']) + entity(id:9e633b9f-343d-4b29-a78a-85afdd8eef53, [prov:value="1" %% xsd:boolean]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:9e633b9f-343d-4b29-a78a-85afdd8eef53) + entity(id:792b7ecd-597e-41ad-ac59-b0767919b4b7, [prov:type='prov:KeyEntityPair', prov:pairKey="to_posix_lines", prov:pairEntity='id:9e633b9f-343d-4b29-a78a-85afdd8eef53']) + entity(data:path, [prov:type='wfprov:Artifact', prov:value="path"]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:path) + entity(id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:path']) + entity(data:dataset2.txt, [prov:type='wfprov:Artifact', prov:value="dataset2.txt"]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:dataset2.txt) + entity(id:97939793-b619-47e0-8ec3-d3baf5965151, [prov:type='prov:KeyEntityPair', prov:pairKey="name", prov:pairEntity='data:dataset2.txt']) + entity(id:780092f0-87bd-42bc-a3d8-50143d44998b, [prov:type='wfprov:Artifact', prov:type='prov:EmptyCollection', prov:type='prov:Collection']) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:780092f0-87bd-42bc-a3d8-50143d44998b) + entity(id:f45f9536-1278-4069-8b91-7edd97d3ff80, [prov:type='prov:KeyEntityPair', prov:pairKey="hashes", prov:pairEntity='id:780092f0-87bd-42bc-a3d8-50143d44998b']) + entity(id:0f5709cc-12f6-430c-a605-fd3e8978f6c4, [prov:value="0" %% xsd:boolean]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:0f5709cc-12f6-430c-a605-fd3e8978f6c4) + entity(id:c0c38d7d-cd18-4050-b5e8-0faf10393207, [prov:type='prov:KeyEntityPair', prov:pairKey="in_place", prov:pairEntity='id:0f5709cc-12f6-430c-a605-fd3e8978f6c4']) + entity(id:87e7e990-d873-4d20-a6ee-b15094940df1, [prov:value="0" %% xsd:boolean]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:87e7e990-d873-4d20-a6ee-b15094940df1) + entity(id:f67dbd55-b05c-4a56-aea3-4041399b62d1, [prov:type='prov:KeyEntityPair', prov:pairKey="purge_source", prov:pairEntity='id:87e7e990-d873-4d20-a6ee-b15094940df1']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:069bb313-b651-474e-9a28-fdc7af0fc87b, [prov:type='prov:KeyEntityPair', prov:pairKey="path", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(id:bd860612-ca87-49c5-9d5c-d086f706f789, [prov:value=155708]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:bd860612-ca87-49c5-9d5c-d086f706f789) + entity(id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64, [prov:type='prov:KeyEntityPair', prov:pairKey="object_id", prov:pairEntity='id:bd860612-ca87-49c5-9d5c-d086f706f789']) + entity(data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, [prov:type='wfprov:Artifact', prov:value="urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9"]) + hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9) + entity(id:66fde9d0-4440-4811-8b03-ae8c34cfebb6, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9']) + entity(id:e7516c89-e4ed-494b-bf16-74b40fa66bd1, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:e7516c89-e4ed-494b-bf16-74b40fa66bd1, id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9) + hadMember(id:641c238b-2832-4fab-b949-f5f4fc01deb1, id:e7516c89-e4ed-494b-bf16-74b40fa66bd1) + entity(id:3b176baa-a8f8-426c-ab0d-aa428d41923d, [prov:type='prov:KeyEntityPair', prov:pairKey="elements", prov:pairEntity='id:e7516c89-e4ed-494b-bf16-74b40fa66bd1']) + entity(id:e8c438c4-7544-4049-8d34-f825ecd3b5e1, [prov:value="0" %% xsd:boolean]) + hadMember(id:641c238b-2832-4fab-b949-f5f4fc01deb1, id:e8c438c4-7544-4049-8d34-f825ecd3b5e1) + entity(id:ab8003d1-3e46-4af7-9325-fffe09639b01, [prov:type='prov:KeyEntityPair', prov:pairKey="auto_decompress", prov:pairEntity='id:e8c438c4-7544-4049-8d34-f825ecd3b5e1']) + entity(data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1, [prov:type='wfprov:Artifact', prov:value="urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1"]) + hadMember(id:641c238b-2832-4fab-b949-f5f4fc01deb1, data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1) + entity(id:9f4835d1-a5f0-499e-9315-42fed1edd2a1, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1']) + entity(id:34aa3429-439f-49df-b575-0c7aee2caa81, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:34aa3429-439f-49df-b575-0c7aee2caa81, id:641c238b-2832-4fab-b949-f5f4fc01deb1) + hadMember(id:594019f6-4154-49a8-be37-3d511a35f066, id:34aa3429-439f-49df-b575-0c7aee2caa81) + entity(id:7067149e-f997-4e01-810a-41ed1aaae3f1, [prov:type='prov:KeyEntityPair', prov:pairKey="targets", prov:pairEntity='id:34aa3429-439f-49df-b575-0c7aee2caa81']) + entity(id:ffdb63df-93ba-4e67-8097-308bfd9ba39d, [prov:value="1" %% xsd:boolean]) + hadMember(id:594019f6-4154-49a8-be37-3d511a35f066, id:ffdb63df-93ba-4e67-8097-308bfd9ba39d) + entity(id:e2f3637a-f559-46a0-a630-9f3e47800b70, [prov:type='prov:KeyEntityPair', prov:pairKey="check_content", prov:pairEntity='id:ffdb63df-93ba-4e67-8097-308bfd9ba39d']) + entity(data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066, [prov:type='wfprov:Artifact', prov:value="urn:uuid:594019f6-4154-49a8-be37-3d511a35f066"]) + hadMember(id:594019f6-4154-49a8-be37-3d511a35f066, data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066) + entity(id:1e8684e9-896e-4a38-bfe9-1995d0893fdd, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066']) + used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:594019f6-4154-49a8-be37-3d511a35f066, 2022-03-31T15:39:11.762940, [prov:role='wf:main/__DATA_FETCH__/request_json']) + entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) + used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, data:1, 2022-03-31T15:39:11.762994, [prov:role='wf:main/__DATA_FETCH__/request_version']) + activity(id:414221e9-e943-451a-bde9-ef492e1cf85c, 2021-06-23T10:20:00.981702, 2021-06-23T10:20:22.202678, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) + wasAssociatedWith(id:414221e9-e943-451a-bde9-ef492e1cf85c, id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, wf:main/__DATA_FETCH__) + wasStartedBy(id:414221e9-e943-451a-bde9-ef492e1cf85c, -, id:dd421f2f-c538-44d3-aeeb-484022c6541d, 2021-06-23T10:20:00.981702) + entity(data:7c1d8e3101dbcdba, [prov:type='wfprov:Artifact', prov:value="7c1d8e3101dbcdba"]) + entity(id:ebf027ac-b671-468a-91c6-1bfd7e45eb36, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:ebf027ac-b671-468a-91c6-1bfd7e45eb36, data:7c1d8e3101dbcdba) + used(id:414221e9-e943-451a-bde9-ef492e1cf85c, id:ebf027ac-b671-468a-91c6-1bfd7e45eb36, 2022-03-31T15:39:11.763447, [prov:role='wf:main/__DATA_FETCH__/output0']) + entity(data:1, 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prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"]) + hadMember(id:5ab542a0-7a79-4f00-b120-b14b0542e568, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a) + entity(id:d3a55e5b-c1fb-4523-b77d-993b00128b05, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a']) + entity(data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568, [prov:type='wfprov:Artifact', prov:value="urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568"]) + hadMember(id:5ab542a0-7a79-4f00-b120-b14b0542e568, data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568) + entity(id:88aa880c-c240-4877-b1e7-a0c20e29ef3e, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568']) + entity(id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) + hadMember(id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3, 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[prov:role='wf:main/random_lines1/__workflow_invocation_uuid__']) + entity(data:/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"]) + used(id:2341e04b-a08b-400e-97ef-3151f01a17fa, data:/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len, 2022-03-31T15:39:11.769026, [prov:role='wf:main/random_lines1/chromInfo']) + entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) + used(id:2341e04b-a08b-400e-97ef-3151f01a17fa, data:?, 2022-03-31T15:39:11.769116, [prov:role='wf:main/random_lines1/dbkey']) + entity(id:fd40a61e-108c-42c4-8b49-c20815d2d9e5, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:81d81eab-2874-43f4-9d2e-ce5ad6236054', prov:hadDictionaryMember='id:279428d4-794f-42cd-9419-0c8c71385b78']) + entity(id:24d7454e-9885-40b1-8a85-cc272df4fa40, [prov:type='wfprov:Artifact', 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entity(id:81d81eab-2874-43f4-9d2e-ce5ad6236054, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5']) + used(id:2341e04b-a08b-400e-97ef-3151f01a17fa, id:fd40a61e-108c-42c4-8b49-c20815d2d9e5, 2022-03-31T15:39:11.769772, [prov:role='wf:main/random_lines1/input']) + entity(data:3, [prov:type='wfprov:Artifact', prov:value="3"]) + used(id:2341e04b-a08b-400e-97ef-3151f01a17fa, data:3, 2022-03-31T15:39:11.769848, [prov:role='wf:main/random_lines1/num_lines']) + entity(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9', prov:hadDictionaryMember='id:903792cc-566c-4ffe-ade9-be65cf4f1fb4', prov:hadDictionaryMember='id:5ba613ce-6eaa-412d-89bf-eb8f580823a3', prov:hadDictionaryMember='id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e']) + entity(id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad, [prov:value=1]) + hadMember(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad) + entity(id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9, [prov:type='prov:KeyEntityPair', prov:pairKey="__current_case__", prov:pairEntity='id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad']) + entity(data:0, [prov:type='wfprov:Artifact', prov:value="0"]) + hadMember(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, data:0) + entity(id:5ba613ce-6eaa-412d-89bf-eb8f580823a3, [prov:type='prov:KeyEntityPair', prov:pairKey="seed", prov:pairEntity='data:0']) + entity(data:set_seed, [prov:type='wfprov:Artifact', prov:value="set_seed"]) + hadMember(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, data:set_seed) + entity(id:903792cc-566c-4ffe-ade9-be65cf4f1fb4, [prov:type='prov:KeyEntityPair', prov:pairKey="seed_source_selector", prov:pairEntity='data:set_seed']) + entity(data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d, [prov:type='wfprov:Artifact', prov:value="urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d"]) + hadMember(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d) + entity(id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d']) + used(id:2341e04b-a08b-400e-97ef-3151f01a17fa, id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, 2022-03-31T15:39:11.770390, [prov:role='wf:main/random_lines1/seed_source']) +endDocument \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl new file mode 100644 index 00000000..41da725e --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl @@ -0,0 +1,1081 @@ +@prefix data: . +@prefix foaf: . +@prefix id: . +@prefix orcid: . +@prefix prov: . +@prefix rdfs: . +@prefix schema: . +@prefix wf: . +@prefix wfprov: . +@prefix xsd: . + +id:2341e04b-a08b-400e-97ef-3151f01a17fa a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.769026"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.770390"^^xsd:dateTime ; + prov:entity id:7e6d530d-6c05-48b1-8d69-879b6e790c9d ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.769116"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.769772"^^xsd:dateTime ; + prov:entity id:fd40a61e-108c-42c4-8b49-c20815d2d9e5 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.768651"^^xsd:dateTime ; + prov:entity id:8a1a4095-2cbb-468e-80d6-25ebab181a3e ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.768810"^^xsd:dateTime ; + prov:entity id:6cf20326-6a50-4476-910c-c40be8829bc4 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.769848"^^xsd:dateTime ; + prov:entity data:3 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.768884"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.768956"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + +id:414221e9-e943-451a-bde9-ef492e1cf85c a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.763491"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.765267"^^xsd:dateTime ; + prov:entity id:71e28368-850b-441f-a008-8b6173a866d7 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.763447"^^xsd:dateTime ; + prov:entity id:ebf027ac-b671-468a-91c6-1bfd7e45eb36 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.763813"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.763772"^^xsd:dateTime ; + prov:entity id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.765313"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + +id:a1a08c93-d0b2-4806-8abb-697cf651f9a4 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.760237"^^xsd:dateTime ; + prov:entity id:5c05f71f-74dc-4238-a591-9df8dfa779f8 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.760286"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.759864"^^xsd:dateTime ; + prov:entity id:d4c2d49d-ab80-43ab-b347-a7db85bf7262 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.762940"^^xsd:dateTime ; + prov:entity id:594019f6-4154-49a8-be37-3d511a35f066 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.759917"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.762994"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + +id:cade945a-1ff3-4273-a78e-7b5358804c89 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.766037"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.765900"^^xsd:dateTime ; + prov:entity id:a1110187-8be9-4aff-b03e-3530ed7f6cbf ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.765788"^^xsd:dateTime ; + prov:entity id:730e5d81-2c3c-44d7-9916-9cc0b7bcdd81 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.767885"^^xsd:dateTime ; + prov:entity id:682cbd95-9570-4f19-a8bb-a639bfb641e2 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.766105"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.765700"^^xsd:dateTime ; + prov:entity id:837879db-a58f-45bc-980d-2da57fd19cd1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.766169"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.765965"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-03-31T15:39:11.766787"^^xsd:dateTime ; + prov:entity id:a9607900-c633-4837-a4a7-eaee6edcaf3b ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + +orcid:0000-0002-8940-4946 a schema:Person, + prov:Agent, + prov:Person ; + rdfs:label "PDG"^^xsd:string ; + schema:name "PDG"^^xsd:string ; + foaf:name "PDG"^^xsd:string . + +data:2524d3d3b68ad39a a wfprov:Artifact, + prov:Entity ; + prov:value "2524d3d3b68ad39a"^^xsd:string . + +data:3 a wfprov:Artifact, + prov:Entity ; + prov:value "3"^^xsd:string . + +data:775bc9b3c1750167 a wfprov:Artifact, + prov:Entity ; + prov:value "775bc9b3c1750167"^^xsd:string . + +data:7c1d8e3101dbcdba a wfprov:Artifact, + prov:Entity ; + prov:value "7c1d8e3101dbcdba"^^xsd:string . + +id:062d0748-7b74-4d45-98f3-80bd22ed2672 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:51656ecb-5b39-4ad7-9888-d7b93ca28266, + id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747, + id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748 ; + prov:hadMember data:2e789aae2475b7da, + data:hda, + . + +id:069bb313-b651-474e-9a28-fdc7af0fc87b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:bd860612-ca87-49c5-9d5c-d086f706f789 ; + prov:pairKey "object_id"^^xsd:string . + +id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad ; + prov:pairKey "__current_case__"^^xsd:string . + +id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:fd7fec473f1e6c6b ; + prov:pairKey "id"^^xsd:string . + +id:1e8684e9-896e-4a38-bfe9-1995d0893fdd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:24d7454e-9885-40b1-8a85-cc272df4fa40 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94, + id:96981ec2-dac6-4477-9ac3-431cdc24f7ac, + id:c40c9210-5155-480f-ba36-5f86aaa39d77 ; + prov:hadMember data:fd7fec473f1e6c6b, + data:hda, + . + +id:279428d4-794f-42cd-9419-0c8c71385b78 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:23fbeb5c-eebc-41ef-a966-be8a191c7ede ; + prov:pairKey "values"^^xsd:string . + +id:286ffa7a-a1f3-424c-90cf-f36d112b13f0 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset1.txt ; + prov:pairKey "name"^^xsd:string . + +id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:34523c4b-aa54-4d13-8d25-76acadcc8df7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:65dace90-ed17-46f9-b809-d98a90563655 ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98, + id:869277c3-8c88-4381-bbef-de17240b1c23, + id:a1bb89e0-badf-490a-af30-375efe69c057 ; + prov:hadMember , + , + id:0c54448a-8444-42cd-9dd1-b65dfb0656ba . + +id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:7ca3de8f49293d1a ; + prov:pairKey "id"^^xsd:string . + +id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:368b85e6-a18c-4452-90ef-32ee5ccd0308 ; + prov:pairKey "in_place"^^xsd:string . + +id:3b176baa-a8f8-426c-ab0d-aa428d41923d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e7516c89-e4ed-494b-bf16-74b40fa66bd1 ; + prov:pairKey "elements"^^xsd:string . + +id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:8dbadfd6-d421-4d18-95ae-36fc4defb317 ; + prov:pairKey "elements"^^xsd:string . + +id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:069bb313-b651-474e-9a28-fdc7af0fc87b, + id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64, + id:66fde9d0-4440-4811-8b03-ae8c34cfebb6, + id:792b7ecd-597e-41ad-ac59-b0767919b4b7, + id:79566035-3dfd-4779-837a-344529381251, + id:97939793-b619-47e0-8ec3-d3baf5965151, + id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60, + id:c0c38d7d-cd18-4050-b5e8-0faf10393207, + id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01, + id:f45f9536-1278-4069-8b91-7edd97d3ff80, + id:f67dbd55-b05c-4a56-aea3-4041399b62d1 ; + prov:hadMember , + , + data:auto, + data:dataset2.txt, + data:path, + , + id:0f5709cc-12f6-430c-a605-fd3e8978f6c4, + id:780092f0-87bd-42bc-a3d8-50143d44998b, + id:87e7e990-d873-4d20-a6ee-b15094940df1, + id:9e633b9f-343d-4b29-a78a-85afdd8eef53, + id:bd860612-ca87-49c5-9d5c-d086f706f789 . + +id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:4529ad17-6e7b-4493-bba5-475a60c4a11a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e6248791-d7c3-49a7-9660-5cb622189a3c ; + prov:pairKey "input2"^^xsd:string . + +id:4745fa68-123c-4afb-9176-dcf61732f695 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:03d9f2a8-6e48-40b3-84e4-f13e161decf1 ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:47d09ccc-4b59-4330-9361-9f1b65b860a8 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:d84bb265-2540-4cad-a026-511b7a21323e ; + prov:pairKey "destination"^^xsd:string . + +id:51656ecb-5b39-4ad7-9888-d7b93ca28266 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:2e789aae2475b7da ; + prov:pairKey "id"^^xsd:string . + +id:57844284-ccc8-45f3-a7fa-6ce0246cf99b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:7827651a-85f5-48a4-8f9d-1427fc02bda4 ; + prov:pairKey "values"^^xsd:string . + +id:594019f6-4154-49a8-be37-3d511a35f066 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1e8684e9-896e-4a38-bfe9-1995d0893fdd, + id:7067149e-f997-4e01-810a-41ed1aaae3f1, + id:e2f3637a-f559-46a0-a630-9f3e47800b70 ; + prov:hadMember , + id:34aa3429-439f-49df-b575-0c7aee2caa81, + id:ffdb63df-93ba-4e67-8097-308bfd9ba39d . + +id:5ab542a0-7a79-4f00-b120-b14b0542e568 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:88aa880c-c240-4877-b1e7-a0c20e29ef3e, + id:d3a55e5b-c1fb-4523-b77d-993b00128b05, + id:ef96000b-e230-40a1-a36a-a45f4ca78a0e ; + prov:hadMember , + , + id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 . + +id:5ba613ce-6eaa-412d-89bf-eb8f580823a3 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:0 ; + prov:pairKey "seed"^^xsd:string . + +id:5c05f71f-74dc-4238-a591-9df8dfa779f8 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 . + +id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:8bae3361-cfbe-4b69-bfa0-34901d319a21 ; + prov:pairKey "hashes"^^xsd:string . + +id:641c238b-2832-4fab-b949-f5f4fc01deb1 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:3b176baa-a8f8-426c-ab0d-aa428d41923d, + id:47d09ccc-4b59-4330-9361-9f1b65b860a8, + id:9f4835d1-a5f0-499e-9315-42fed1edd2a1, + id:ab8003d1-3e46-4af7-9325-fffe09639b01 ; + prov:hadMember , + id:d84bb265-2540-4cad-a026-511b7a21323e, + id:e7516c89-e4ed-494b-bf16-74b40fa66bd1, + id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 . + +id:66fde9d0-4440-4811-8b03-ae8c34cfebb6 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:682cbd95-9570-4f19-a8bb-a639bfb641e2 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:f39be690-c7d7-4911-be28-6afc1abe40b0 . + +id:68c6bdfd-f17d-41b8-bdba-eb3a46749940 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:6cf20326-6a50-4476-910c-c40be8829bc4 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:775bc9b3c1750167 . + +id:6d29c983-528d-46cf-b420-1c9210619f0d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:fc84f9f8-5bb4-402d-ba90-697df02824ca ; + prov:pairKey "check_content"^^xsd:string . + +id:6d494d29-2bc7-4da4-ba43-e816ee0b1266 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:286ffa7a-a1f3-424c-90cf-f36d112b13f0, + id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1, + id:4745fa68-123c-4afb-9176-dcf61732f695, + id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6, + id:8ced01f6-47ea-4320-b65a-6af7a668fbe9, + id:98a55032-1c60-4303-8ca0-5cff21b96b9d, + id:ab51fb43-4e4d-459e-ae56-672b92ac89ea, + id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5, + id:d9811e1d-402f-4343-bc31-7dd5643dbdac, + id:fbca4ec6-e519-477f-84ce-23e70dddcc8b, + id:feb54146-911b-4d39-90cf-ef6d66b46fe4 ; + prov:hadMember , + , + data:auto, + data:dataset1.txt, + data:path, + , + id:03d9f2a8-6e48-40b3-84e4-f13e161decf1, + id:368b85e6-a18c-4452-90ef-32ee5ccd0308, + id:8bae3361-cfbe-4b69-bfa0-34901d319a21, + id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a, + id:f350a230-ff86-44a3-8560-e35c1ba07b59 . + +id:7067149e-f997-4e01-810a-41ed1aaae3f1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:34aa3429-439f-49df-b575-0c7aee2caa81 ; + prov:pairKey "targets"^^xsd:string . + +id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:0c54448a-8444-42cd-9dd1-b65dfb0656ba ; + prov:pairKey "__index__"^^xsd:string . + +id:71e28368-850b-441f-a008-8b6173a866d7 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:68c6bdfd-f17d-41b8-bdba-eb3a46749940, + id:6d29c983-528d-46cf-b420-1c9210619f0d, + id:a75e7105-d7f0-4a77-865c-2ff5b3162e47 ; + prov:hadMember , + id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1, + id:fc84f9f8-5bb4-402d-ba90-697df02824ca . + +id:730e5d81-2c3c-44d7-9916-9cc0b7bcdd81 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2e789aae2475b7da . + +id:792b7ecd-597e-41ad-ac59-b0767919b4b7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:9e633b9f-343d-4b29-a78a-85afdd8eef53 ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:79566035-3dfd-4779-837a-344529381251 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:7e6d530d-6c05-48b1-8d69-879b6e790c9d a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9, + id:5ba613ce-6eaa-412d-89bf-eb8f580823a3, + id:903792cc-566c-4ffe-ade9-be65cf4f1fb4, + id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e ; + prov:hadMember data:0, + data:set_seed, + , + id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad . + +id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:5ab542a0-7a79-4f00-b120-b14b0542e568 . + +id:7fc57149-e802-47ce-bf01-348e6e787dd0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:34523c4b-aa54-4d13-8d25-76acadcc8df7, + id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4, + id:9e45fea1-39c5-4b99-be26-72b06a5e8786, + id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e ; + prov:hadMember , + id:4fa4bb93-f67a-414c-8420-9272773cb5e2, + id:65dace90-ed17-46f9-b809-d98a90563655, + id:8dbadfd6-d421-4d18-95ae-36fc4defb317 . + +id:8170c31b-5a5f-4150-8531-8b0adac0f282 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:81d81eab-2874-43f4-9d2e-ce5ad6236054 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:837879db-a58f-45bc-980d-2da57fd19cd1 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7ca3de8f49293d1a . + +id:869277c3-8c88-4381-bbef-de17240b1c23 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:88aa880c-c240-4877-b1e7-a0c20e29ef3e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:8a1a4095-2cbb-468e-80d6-25ebab181a3e a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +id:8ced01f6-47ea-4320-b65a-6af7a668fbe9 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:903792cc-566c-4ffe-ade9-be65cf4f1fb4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:set_seed ; + prov:pairKey "seed_source_selector"^^xsd:string . + +id:93b6a52a-f266-4837-9e8e-ed928fbd2775 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:951bb963-10a7-4234-8119-1b13921f9629 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:f40fd446-41cb-442e-bbb7-9a23d27296e5 ; + prov:pairKey "__index__"^^xsd:string . + +id:9578a96e-6635-4000-9c81-2951341b65c8 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:96981ec2-dac6-4477-9ac3-431cdc24f7ac a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:97939793-b619-47e0-8ec3-d3baf5965151 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset2.txt ; + prov:pairKey "name"^^xsd:string . + +id:98a55032-1c60-4303-8ca0-5cff21b96b9d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:9e45fea1-39c5-4b99-be26-72b06a5e8786 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:4fa4bb93-f67a-414c-8420-9272773cb5e2 ; + prov:pairKey "destination"^^xsd:string . + +id:9f4835d1-a5f0-499e-9315-42fed1edd2a1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a1110187-8be9-4aff-b03e-3530ed7f6cbf a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +id:a1bb89e0-badf-490a-af30-375efe69c057 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:a75e7105-d7f0-4a77-865c-2ff5b3162e47 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1 ; + prov:pairKey "targets"^^xsd:string . + +id:a9607900-c633-4837-a4a7-eaee6edcaf3b a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:57844284-ccc8-45f3-a7fa-6ce0246cf99b, + id:e9967a89-6747-4067-95ed-5160b763f0b1 ; + prov:hadMember , + id:7827651a-85f5-48a4-8f9d-1427fc02bda4 . + +id:ab51fb43-4e4d-459e-ae56-672b92ac89ea a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:ab8003d1-3e46-4af7-9325-fffe09639b01 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:f350a230-ff86-44a3-8560-e35c1ba07b59 ; + prov:pairKey "purge_source"^^xsd:string . + +id:c0c38d7d-cd18-4050-b5e8-0faf10393207 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:0f5709cc-12f6-430c-a605-fd3e8978f6c4 ; + prov:pairKey "in_place"^^xsd:string . + +id:c40c9210-5155-480f-ba36-5f86aaa39d77 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:c98b0b95-d818-4ba1-b535-11c4e6909fa3 a prov:Agent ; + prov:actedOnBehalfOf orcid:0000-0002-8940-4946 . + +id:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99, + id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813, + id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d ; + prov:hadMember data:7ca3de8f49293d1a, + data:hda, + . + +id:d3a55e5b-c1fb-4523-b77d-993b00128b05 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:d4c2d49d-ab80-43ab-b347-a7db85bf7262 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2524d3d3b68ad39a . + +id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:d9811e1d-402f-4343-bc31-7dd5643dbdac a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:e2f3637a-f559-46a0-a630-9f3e47800b70 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:ffdb63df-93ba-4e67-8097-308bfd9ba39d ; + prov:pairKey "check_content"^^xsd:string . + +id:e9967a89-6747-4067-95ed-5160b763f0b1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:ebf027ac-b671-468a-91c6-1bfd7e45eb36 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7c1d8e3101dbcdba . + +id:ef96000b-e230-40a1-a36a-a45f4ca78a0e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 ; + prov:pairKey "__index__"^^xsd:string . + +id:f39be690-c7d7-4911-be28-6afc1abe40b0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:4529ad17-6e7b-4493-bba5-475a60c4a11a, + id:951bb963-10a7-4234-8119-1b13921f9629, + id:9578a96e-6635-4000-9c81-2951341b65c8 ; + prov:hadMember , + id:e6248791-d7c3-49a7-9660-5cb622189a3c, + id:f40fd446-41cb-442e-bbb7-9a23d27296e5 . + +id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:f45f9536-1278-4069-8b91-7edd97d3ff80 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:780092f0-87bd-42bc-a3d8-50143d44998b ; + prov:pairKey "hashes"^^xsd:string . + +id:f67dbd55-b05c-4a56-aea3-4041399b62d1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:87e7e990-d873-4d20-a6ee-b15094940df1 ; + prov:pairKey "purge_source"^^xsd:string . + +id:f923bbf9-1c94-4771-9333-77547e7e828e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:fbca4ec6-e519-477f-84ce-23e70dddcc8b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a ; + prov:pairKey "object_id"^^xsd:string . + +id:fd40a61e-108c-42c4-8b49-c20815d2d9e5 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:279428d4-794f-42cd-9419-0c8c71385b78, + id:81d81eab-2874-43f4-9d2e-ce5ad6236054 ; + prov:hadMember , + id:23fbeb5c-eebc-41ef-a966-be8a191c7ede . + +id:feb54146-911b-4d39-90cf-ef6d66b46fe4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:ff80c261-0171-44d9-86fa-546f8aea6cd8 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:55af6a73-efbe-4e5c-8b47-6ff94872e6de ; + prov:pairKey "values"^^xsd:string . + +data: a wfprov:Artifact, + prov:Entity ; + prov:value ""^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^xsd:string . + +data:0 a wfprov:Artifact, + prov:Entity ; + prov:value "0"^^xsd:string . + +data:42f21c0ad41011eb87defa163eba836f a wfprov:Artifact, + prov:Entity ; + prov:value "42f21c0ad41011eb87defa163eba836f"^^xsd:string . + +data:dataset1.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset1.txt"^^xsd:string . + +data:dataset2.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset2.txt"^^xsd:string . + +data:set_seed a wfprov:Artifact, + prov:Entity ; + prov:value "set_seed"^^xsd:string . + +data:txt a wfprov:Artifact, + prov:Entity ; + prov:value "txt"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:594019f6-4154-49a8-be37-3d511a35f066"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:71e28368-850b-441f-a008-8b6173a866d7"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5"^^xsd:string . + +id:03d9f2a8-6e48-40b3-84e4-f13e161decf1 a prov:Entity ; + prov:value true . + +id:0c54448a-8444-42cd-9dd1-b65dfb0656ba a prov:Entity ; + prov:value "0"^^xsd:int . + +id:0f5709cc-12f6-430c-a605-fd3e8978f6c4 a prov:Entity ; + prov:value false . + +id:23fbeb5c-eebc-41ef-a966-be8a191c7ede a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:24d7454e-9885-40b1-8a85-cc272df4fa40 . + +id:34aa3429-439f-49df-b575-0c7aee2caa81 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:641c238b-2832-4fab-b949-f5f4fc01deb1 . + +id:368b85e6-a18c-4452-90ef-32ee5ccd0308 a prov:Entity ; + prov:value false . + +id:4fa4bb93-f67a-414c-8420-9272773cb5e2 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be, + id:93b6a52a-f266-4837-9e8e-ed928fbd2775 ; + prov:hadMember data:hdas, + . + +id:55af6a73-efbe-4e5c-8b47-6ff94872e6de a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:062d0748-7b74-4d45-98f3-80bd22ed2672 . + +id:65dace90-ed17-46f9-b809-d98a90563655 a prov:Entity ; + prov:value false . + +id:780092f0-87bd-42bc-a3d8-50143d44998b a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:7827651a-85f5-48a4-8f9d-1427fc02bda4 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 . + +id:87e7e990-d873-4d20-a6ee-b15094940df1 a prov:Entity ; + prov:value false . + +id:8bae3361-cfbe-4b69-bfa0-34901d319a21 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 a prov:Entity ; + prov:value "0"^^xsd:int . + +id:8dbadfd6-d421-4d18-95ae-36fc4defb317 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:6d494d29-2bc7-4da4-ba43-e816ee0b1266 . + +id:9e633b9f-343d-4b29-a78a-85afdd8eef53 a prov:Entity ; + prov:value true . + +id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:7fc57149-e802-47ce-bf01-348e6e787dd0 . + +id:bd860612-ca87-49c5-9d5c-d086f706f789 a prov:Entity ; + prov:value "155708"^^xsd:int . + +id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad a prov:Entity ; + prov:value "1"^^xsd:int . + +id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a a prov:Entity ; + prov:value "155707"^^xsd:int . + +id:d84bb265-2540-4cad-a026-511b7a21323e a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5, + id:f923bbf9-1c94-4771-9333-77547e7e828e ; + prov:hadMember data:hdas, + . + +id:e6248791-d7c3-49a7-9660-5cb622189a3c a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:8170c31b-5a5f-4150-8531-8b0adac0f282, + id:ff80c261-0171-44d9-86fa-546f8aea6cd8 ; + prov:hadMember , + id:55af6a73-efbe-4e5c-8b47-6ff94872e6de . + +id:e7516c89-e4ed-494b-bf16-74b40fa66bd1 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 . + +id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 a prov:Entity ; + prov:value false . + +id:f350a230-ff86-44a3-8560-e35c1ba07b59 a prov:Entity ; + prov:value false . + +id:f40fd446-41cb-442e-bbb7-9a23d27296e5 a prov:Entity ; + prov:value "0"^^xsd:int . + +id:fc84f9f8-5bb4-402d-ba90-697df02824ca a prov:Entity ; + prov:value true . + +id:ffdb63df-93ba-4e67-8097-308bfd9ba39d a prov:Entity ; + prov:value true . + +data:2e789aae2475b7da a wfprov:Artifact, + prov:Entity ; + prov:value "2e789aae2475b7da"^^xsd:string . + +data:7ca3de8f49293d1a a wfprov:Artifact, + prov:Entity ; + prov:value "7ca3de8f49293d1a"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"^^xsd:string . + +data:1 a wfprov:Artifact, + prov:Entity ; + prov:value "1"^^xsd:string . + +data:auto a wfprov:Artifact, + prov:Entity ; + prov:value "auto"^^xsd:string . + +data:fd7fec473f1e6c6b a wfprov:Artifact, + prov:Entity ; + prov:value "fd7fec473f1e6c6b"^^xsd:string . + +data:hdas a wfprov:Artifact, + prov:Entity ; + prov:value "hdas"^^xsd:string . + +data:path a wfprov:Artifact, + prov:Entity ; + prov:value "path"^^xsd:string . + +id:dd421f2f-c538-44d3-aeeb-484022c6541d a wfprov:WorkflowRun, + prov:Activity ; + rdfs:label "Run of galaxy workflow"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan wf:main ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-03-31T15:39:11.759353"^^xsd:dateTime ; + prov:hadActivity id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd ] ; + prov:startedAtTime "2022-03-31T15:39:11.759294"^^xsd:dateTime ; + prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + + a wfprov:Artifact, + prov:Entity ; + prov:value "?"^^xsd:string . + +data:hda a wfprov:Artifact, + prov:Entity ; + prov:value "hda"^^xsd:string . + +id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd a wfprov:WorkflowEngine, + prov:Agent, + prov:SoftwareAgent ; + rdfs:label "galaxy_version_placeholder"^^xsd:string ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-03-31T15:39:11.759268"^^xsd:dateTime ; + prov:hadActivity id:c98b0b95-d818-4ba1-b535-11c4e6909fa3 ] . + diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml new file mode 100644 index 00000000..6517529d --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml @@ -0,0 +1,1457 @@ + + + + + PDG + schema:Person + PDG + PDG + + + + + + + galaxy_version_placeholder + wfprov:WorkflowEngine + + + + + 2022-03-31T15:39:11.759268 + + + 2022-03-31T15:39:11.759294 + Run of galaxy workflow + wfprov:WorkflowRun + + + + + + + + + + 2022-03-31T15:39:11.759353 + + + 2021-06-23T10:20:22.770291 + 2021-06-23T10:20:42.041319 + Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:20:22.770291 + + + wfprov:Artifact + 2524d3d3b68ad39a + + + wfprov:Artifact + + + + + + + + + 2022-03-31T15:39:11.759864 + wf:main/__DATA_FETCH__/output0 + + + wfprov:Artifact + 1 + + + + + 2022-03-31T15:39:11.759917 + wf:main/__DATA_FETCH__/file_count + + + prov:Dictionary + wfprov:Artifact + id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98 + id:869277c3-8c88-4381-bbef-de17240b1c23 + id:a1bb89e0-badf-490a-af30-375efe69c057 + + + 0 + + + + + + + prov:KeyEntityPair + id:0c54448a-8444-42cd-9dd1-b65dfb0656ba + __index__ + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + file_data + + + wfprov:Artifact + urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 + + + + + + + prov:KeyEntityPair + data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 + @id + + + wfprov:Artifact + + + + + + + + + 2022-03-31T15:39:11.760237 + wf:main/__DATA_FETCH__/files + + + wfprov:Artifact + + + + + + 2022-03-31T15:39:11.760286 + wf:main/__DATA_FETCH__/paramfile + + + prov:Dictionary + wfprov:Artifact + id:1e8684e9-896e-4a38-bfe9-1995d0893fdd + id:7067149e-f997-4e01-810a-41ed1aaae3f1 + id:e2f3637a-f559-46a0-a630-9f3e47800b70 + + + prov:Dictionary + wfprov:Artifact + id:3b176baa-a8f8-426c-ab0d-aa428d41923d + id:47d09ccc-4b59-4330-9361-9f1b65b860a8 + id:9f4835d1-a5f0-499e-9315-42fed1edd2a1 + id:ab8003d1-3e46-4af7-9325-fffe09639b01 + + + prov:Dictionary + wfprov:Artifact + id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5 + id:f923bbf9-1c94-4771-9333-77547e7e828e + + + wfprov:Artifact + hdas + + + + + + + prov:KeyEntityPair + data:hdas + type + + + wfprov:Artifact + urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e + + + + + + + prov:KeyEntityPair + data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e + @id + + + + + + + prov:KeyEntityPair + id:d84bb265-2540-4cad-a026-511b7a21323e + destination + + + prov:Dictionary + wfprov:Artifact + id:069bb313-b651-474e-9a28-fdc7af0fc87b + id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64 + id:66fde9d0-4440-4811-8b03-ae8c34cfebb6 + id:792b7ecd-597e-41ad-ac59-b0767919b4b7 + id:79566035-3dfd-4779-837a-344529381251 + id:97939793-b619-47e0-8ec3-d3baf5965151 + id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60 + id:c0c38d7d-cd18-4050-b5e8-0faf10393207 + id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01 + id:f45f9536-1278-4069-8b91-7edd97d3ff80 + id:f67dbd55-b05c-4a56-aea3-4041399b62d1 + + + wfprov:Artifact + auto + + + + + + + prov:KeyEntityPair + data:auto + ext + + + wfprov:Artifact + ? + + + + + + + prov:KeyEntityPair + data:? + dbkey + + + true + + + + + + + prov:KeyEntityPair + id:9e633b9f-343d-4b29-a78a-85afdd8eef53 + to_posix_lines + + + wfprov:Artifact + path + + + + + + + prov:KeyEntityPair + data:path + src + + + wfprov:Artifact + dataset2.txt + + + + + + + prov:KeyEntityPair + data:dataset2.txt + name + + + prov:Collection + wfprov:Artifact + + + + + + + prov:KeyEntityPair + id:780092f0-87bd-42bc-a3d8-50143d44998b + hashes + + + false + + + + + + + prov:KeyEntityPair + id:0f5709cc-12f6-430c-a605-fd3e8978f6c4 + in_place + + + false + + + + + + + prov:KeyEntityPair + id:87e7e990-d873-4d20-a6ee-b15094940df1 + purge_source + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + path + + + 155708 + + + + + + + prov:KeyEntityPair + id:bd860612-ca87-49c5-9d5c-d086f706f789 + object_id + + + wfprov:Artifact + urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 + + + + + + + prov:KeyEntityPair + data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:e7516c89-e4ed-494b-bf16-74b40fa66bd1 + elements + + + false + + + + + + + prov:KeyEntityPair + id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 + auto_decompress + + + wfprov:Artifact + urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1 + + + + + + + prov:KeyEntityPair + data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:34aa3429-439f-49df-b575-0c7aee2caa81 + targets + + + true + + + + + + + prov:KeyEntityPair + id:ffdb63df-93ba-4e67-8097-308bfd9ba39d + check_content + + + wfprov:Artifact + urn:uuid:594019f6-4154-49a8-be37-3d511a35f066 + + + + + + + prov:KeyEntityPair + data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066 + @id + + + + + 2022-03-31T15:39:11.762940 + wf:main/__DATA_FETCH__/request_json + + + wfprov:Artifact + 1 + + + + + 2022-03-31T15:39:11.762994 + wf:main/__DATA_FETCH__/request_version + + + 2021-06-23T10:20:00.981702 + 2021-06-23T10:20:22.202678 + Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:20:00.981702 + + + wfprov:Artifact + 7c1d8e3101dbcdba + + + wfprov:Artifact + + + + + + + + + 2022-03-31T15:39:11.763447 + wf:main/__DATA_FETCH__/output0 + + + wfprov:Artifact + 1 + + + + + 2022-03-31T15:39:11.763491 + wf:main/__DATA_FETCH__/file_count + + + prov:Dictionary + wfprov:Artifact + id:88aa880c-c240-4877-b1e7-a0c20e29ef3e + id:d3a55e5b-c1fb-4523-b77d-993b00128b05 + id:ef96000b-e230-40a1-a36a-a45f4ca78a0e + + + 0 + + + + + + + prov:KeyEntityPair + id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 + __index__ + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + file_data + + + wfprov:Artifact + urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568 + + + + + + + prov:KeyEntityPair + data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568 + @id + + + wfprov:Artifact + + + + + + + + + 2022-03-31T15:39:11.763772 + wf:main/__DATA_FETCH__/files + + + wfprov:Artifact + + + + + + 2022-03-31T15:39:11.763813 + wf:main/__DATA_FETCH__/paramfile + + + prov:Dictionary + wfprov:Artifact + id:68c6bdfd-f17d-41b8-bdba-eb3a46749940 + id:6d29c983-528d-46cf-b420-1c9210619f0d + id:a75e7105-d7f0-4a77-865c-2ff5b3162e47 + + + prov:Dictionary + wfprov:Artifact + id:34523c4b-aa54-4d13-8d25-76acadcc8df7 + id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4 + id:9e45fea1-39c5-4b99-be26-72b06a5e8786 + id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e + + + prov:Dictionary + wfprov:Artifact + id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be + id:93b6a52a-f266-4837-9e8e-ed928fbd2775 + + + wfprov:Artifact + hdas + + + + + + + prov:KeyEntityPair + data:hdas + type + + + wfprov:Artifact + urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2 + + + + + + + prov:KeyEntityPair + data:urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2 + @id + + + + + + + prov:KeyEntityPair + id:4fa4bb93-f67a-414c-8420-9272773cb5e2 + destination + + + prov:Dictionary + wfprov:Artifact + id:286ffa7a-a1f3-424c-90cf-f36d112b13f0 + id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1 + id:4745fa68-123c-4afb-9176-dcf61732f695 + id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6 + id:8ced01f6-47ea-4320-b65a-6af7a668fbe9 + id:98a55032-1c60-4303-8ca0-5cff21b96b9d + id:ab51fb43-4e4d-459e-ae56-672b92ac89ea + id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5 + id:d9811e1d-402f-4343-bc31-7dd5643dbdac + id:fbca4ec6-e519-477f-84ce-23e70dddcc8b + id:feb54146-911b-4d39-90cf-ef6d66b46fe4 + + + wfprov:Artifact + auto + + + + + + + prov:KeyEntityPair + data:auto + ext + + + wfprov:Artifact + ? + + + + + + + prov:KeyEntityPair + data:? + dbkey + + + true + + + + + + + prov:KeyEntityPair + id:03d9f2a8-6e48-40b3-84e4-f13e161decf1 + to_posix_lines + + + wfprov:Artifact + path + + + + + + + prov:KeyEntityPair + data:path + src + + + wfprov:Artifact + dataset1.txt + + + + + + + prov:KeyEntityPair + data:dataset1.txt + name + + + prov:Collection + wfprov:Artifact + + + + + + + prov:KeyEntityPair + id:8bae3361-cfbe-4b69-bfa0-34901d319a21 + hashes + + + false + + + + + + + prov:KeyEntityPair + id:368b85e6-a18c-4452-90ef-32ee5ccd0308 + in_place + + + false + + + + + + + prov:KeyEntityPair + id:f350a230-ff86-44a3-8560-e35c1ba07b59 + purge_source + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + path + + + 155707 + + + + + + + prov:KeyEntityPair + id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a + object_id + + + wfprov:Artifact + urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266 + + + + + + + prov:KeyEntityPair + data:urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:8dbadfd6-d421-4d18-95ae-36fc4defb317 + elements + + + false + + + + + + + prov:KeyEntityPair + id:65dace90-ed17-46f9-b809-d98a90563655 + auto_decompress + + + wfprov:Artifact + urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0 + + + + + + + prov:KeyEntityPair + data:urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1 + targets + + + true + + + + + + + prov:KeyEntityPair + id:fc84f9f8-5bb4-402d-ba90-697df02824ca + check_content + + + wfprov:Artifact + urn:uuid:71e28368-850b-441f-a008-8b6173a866d7 + + + + + + + prov:KeyEntityPair + data:urn:uuid:71e28368-850b-441f-a008-8b6173a866d7 + @id + + + + + 2022-03-31T15:39:11.765267 + wf:main/__DATA_FETCH__/request_json + + + wfprov:Artifact + 1 + + + + + 2022-03-31T15:39:11.765313 + wf:main/__DATA_FETCH__/request_version + + + 2021-06-23T10:46:28.351123 + 2021-06-23T10:46:44.738703 + Run of ga_export/jobs_attrs.txt#cat1 + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:46:28.351123 + + + wfprov:Artifact + 7ca3de8f49293d1a + + + 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id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99 + id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813 + id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d + + + wfprov:Artifact + 7ca3de8f49293d1a + + + + + + + prov:KeyEntityPair + data:7ca3de8f49293d1a + id + + + wfprov:Artifact + hda + + + + + + + prov:KeyEntityPair + data:hda + src + + + wfprov:Artifact + urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 + + + + + + + prov:KeyEntityPair + data:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:7827651a-85f5-48a4-8f9d-1427fc02bda4 + values + + + wfprov:Artifact + urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b + + + + + + + prov:KeyEntityPair + data:urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b + @id + + + + + 2022-03-31T15:39:11.766787 + wf:main/cat1/input1 + + + prov:Dictionary + wfprov:Artifact + id:4529ad17-6e7b-4493-bba5-475a60c4a11a + id:951bb963-10a7-4234-8119-1b13921f9629 + id:9578a96e-6635-4000-9c81-2951341b65c8 + + + 0 + + + + + + + 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"2022-03-30T14:10:06.231425"^^ . - diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn deleted file mode 100644 index ca0f0328..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.provn +++ /dev/null @@ -1,332 +0,0 @@ -document - prefix wfprov - prefix wfdesc - prefix cwlprov - prefix foaf - prefix schema - prefix orcid - prefix id - prefix data - prefix provenance - prefix wf - prefix input - - agent(id:acc5b84a-046f-4fd2-9136-82d08877386a) - agent(orcid:0000-0002-8940-4946, [prov:type='schema:Person', prov:type='prov:Person', prov:label="PDG", foaf:name="PDG", schema:name="PDG"]) - actedOnBehalfOf(id:acc5b84a-046f-4fd2-9136-82d08877386a, orcid:0000-0002-8940-4946, -) - agent(id:34d8946d-cc68-4ad9-8ecf-53026817187c, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="galaxy_version_placeholder"]) - wasStartedBy(id:34d8946d-cc68-4ad9-8ecf-53026817187c, -, id:acc5b84a-046f-4fd2-9136-82d08877386a, 2022-03-30T14:10:06.231396) - activity(id:d76ec743-0418-4a56-88f2-b81a404a63bc, 2022-03-30T14:10:06.231425, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of galaxy workflow"]) - wasAssociatedWith(id:d76ec743-0418-4a56-88f2-b81a404a63bc, id:34d8946d-cc68-4ad9-8ecf-53026817187c, wf:main) - wasStartedBy(id:d76ec743-0418-4a56-88f2-b81a404a63bc, -, id:34d8946d-cc68-4ad9-8ecf-53026817187c, 2022-03-30T14:10:06.231499) - activity(id:43861f75-9aa7-42b3-80e0-15cf9927d993, 2021-06-23T10:20:22.770291, 2021-06-23T10:20:42.041319, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) - wasAssociatedWith(id:43861f75-9aa7-42b3-80e0-15cf9927d993, id:34d8946d-cc68-4ad9-8ecf-53026817187c, wf:main/__DATA_FETCH__) - wasStartedBy(id:43861f75-9aa7-42b3-80e0-15cf9927d993, -, id:d76ec743-0418-4a56-88f2-b81a404a63bc, 2021-06-23T10:20:22.770291) - entity(data:2524d3d3b68ad39a, [prov:type='wfprov:Artifact', prov:value="2524d3d3b68ad39a"]) - entity(id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047, data:2524d3d3b68ad39a) - used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047, 2022-03-30T14:10:06.232136, [prov:role='wf:main/__DATA_FETCH__/output0']) - entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) - used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, data:1, 2022-03-30T14:10:06.232201, [prov:role='wf:main/__DATA_FETCH__/file_count']) - entity(id:f5582681-806f-4e35-9028-631eab68c8db, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603', prov:hadDictionaryMember='id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc', prov:hadDictionaryMember='id:4319f013-ecd8-4341-a5b9-8e9d8420bd31']) - entity(id:456f97d2-4118-4fd3-a7e0-0bed64b7e343, [prov:value=0]) - hadMember(id:f5582681-806f-4e35-9028-631eab68c8db, id:456f97d2-4118-4fd3-a7e0-0bed64b7e343) - entity(id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:456f97d2-4118-4fd3-a7e0-0bed64b7e343']) - entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) - hadMember(id:f5582681-806f-4e35-9028-631eab68c8db, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) - entity(id:4319f013-ecd8-4341-a5b9-8e9d8420bd31, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) - entity(data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db, [prov:type='wfprov:Artifact', prov:value="urn:uuid:f5582681-806f-4e35-9028-631eab68c8db"]) - hadMember(id:f5582681-806f-4e35-9028-631eab68c8db, data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db) - entity(id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db']) - entity(id:10a92b31-e38a-4eee-a163-d05f0c942e28, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:10a92b31-e38a-4eee-a163-d05f0c942e28, id:f5582681-806f-4e35-9028-631eab68c8db) - used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, id:10a92b31-e38a-4eee-a163-d05f0c942e28, 2022-03-30T14:10:06.232547, [prov:role='wf:main/__DATA_FETCH__/files']) - entity(data:, [prov:type='wfprov:Artifact', prov:value=""]) - used(id:43861f75-9aa7-42b3-80e0-15cf9927d993, data:, 2022-03-30T14:10:06.232599, [prov:role='wf:main/__DATA_FETCH__/paramfile']) - entity(id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5, [prov:type='wfprov:Artifact', 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[prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:hda']) - entity(data:urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1, [prov:type='wfprov:Artifact', prov:value="urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1"]) - hadMember(id:93055cbf-80fe-4acc-a0a6-fdefdaefcce1, data:urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1) - entity(id:641250eb-2adc-4c98-afcd-00428ee7bc8a, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1']) - entity(id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6, id:93055cbf-80fe-4acc-a0a6-fdefdaefcce1) - hadMember(id:1754bbe0-77b5-453b-8542-e83b9bc45798, id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6) - entity(id:eac8a16e-c68a-457a-871d-47f710712b41, [prov:type='prov:KeyEntityPair', prov:pairKey="values", prov:pairEntity='id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6']) - entity(data:urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798, [prov:type='wfprov:Artifact', prov:value="urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798"]) - hadMember(id:1754bbe0-77b5-453b-8542-e83b9bc45798, data:urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798) - entity(id:a11456da-294c-4173-96c9-9becdc7af2fc, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798']) - hadMember(id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0, id:1754bbe0-77b5-453b-8542-e83b9bc45798) - entity(id:9781f372-1be1-48e3-a9d3-2dda2b581134, [prov:type='prov:KeyEntityPair', prov:pairKey="input2", prov:pairEntity='id:1754bbe0-77b5-453b-8542-e83b9bc45798']) - entity(data:urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0, [prov:type='wfprov:Artifact', prov:value="urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0"]) - hadMember(id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0, data:urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0) - entity(id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0']) - entity(id:142f1b95-3ba6-4998-b6a6-72d299494e68, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:142f1b95-3ba6-4998-b6a6-72d299494e68, id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0) - used(id:6b19db35-6d60-4351-be9b-7257b737a427, id:142f1b95-3ba6-4998-b6a6-72d299494e68, 2022-03-30T14:10:06.238506, [prov:role='wf:main/cat1/queries']) - activity(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, 2021-06-23T10:46:28.526901, 2021-06-23T10:47:04.837750, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#random_lines1"]) - wasAssociatedWith(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, id:34d8946d-cc68-4ad9-8ecf-53026817187c, wf:main/random_lines1) - wasStartedBy(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, -, id:d76ec743-0418-4a56-88f2-b81a404a63bc, 2021-06-23T10:46:28.526901) - entity(data:fd7fec473f1e6c6b, [prov:type='wfprov:Artifact', prov:value="fd7fec473f1e6c6b"]) - entity(id:425cb32b-54a2-410a-a915-c025f76640d3, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:425cb32b-54a2-410a-a915-c025f76640d3, data:fd7fec473f1e6c6b) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, id:425cb32b-54a2-410a-a915-c025f76640d3, 2022-03-30T14:10:06.238912, [prov:role='wf:main/random_lines1/input']) - entity(data:775bc9b3c1750167, [prov:type='wfprov:Artifact', prov:value="775bc9b3c1750167"]) - entity(id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1, data:775bc9b3c1750167) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1, 2022-03-30T14:10:06.239056, [prov:role='wf:main/random_lines1/out_file1']) - entity(data:txt, [prov:type='wfprov:Artifact', prov:value="txt"]) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, data:txt, 2022-03-30T14:10:06.239121, [prov:role='wf:main/random_lines1/__input_ext']) - entity(data:42f21c0ad41011eb87defa163eba836f, [prov:type='wfprov:Artifact', prov:value="42f21c0ad41011eb87defa163eba836f"]) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, data:42f21c0ad41011eb87defa163eba836f, 2022-03-30T14:10:06.239189, [prov:role='wf:main/random_lines1/__workflow_invocation_uuid__']) - entity(data:/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"]) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, data:/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len, 2022-03-30T14:10:06.239255, [prov:role='wf:main/random_lines1/chromInfo']) - entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, data:?, 2022-03-30T14:10:06.239316, [prov:role='wf:main/random_lines1/dbkey']) - entity(id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:428da699-3449-41e2-b395-a770b9b49467', prov:hadDictionaryMember='id:8041c95b-4fe2-4663-bcfe-6d4292c9d678']) - entity(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:36bf5f2c-3bf9-46aa-aac5-8b6249738317', prov:hadDictionaryMember='id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd', prov:hadDictionaryMember='id:bdc9be97-2541-4e9d-9b66-e93b350046f5']) - entity(data:fd7fec473f1e6c6b, [prov:type='wfprov:Artifact', prov:value="fd7fec473f1e6c6b"]) - hadMember(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, data:fd7fec473f1e6c6b) - entity(id:36bf5f2c-3bf9-46aa-aac5-8b6249738317, [prov:type='prov:KeyEntityPair', prov:pairKey="id", prov:pairEntity='data:fd7fec473f1e6c6b']) - entity(data:hda, [prov:type='wfprov:Artifact', prov:value="hda"]) - hadMember(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, data:hda) - entity(id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:hda']) - entity(data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89, [prov:type='wfprov:Artifact', prov:value="urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89"]) - hadMember(id:2ff086c3-1d26-439e-8b37-02eb82ba2a89, data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89) - entity(id:bdc9be97-2541-4e9d-9b66-e93b350046f5, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89']) - entity(id:7da8d1bc-cc46-4312-9331-0e417f123152, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:7da8d1bc-cc46-4312-9331-0e417f123152, id:2ff086c3-1d26-439e-8b37-02eb82ba2a89) - hadMember(id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, id:7da8d1bc-cc46-4312-9331-0e417f123152) - entity(id:428da699-3449-41e2-b395-a770b9b49467, [prov:type='prov:KeyEntityPair', prov:pairKey="values", prov:pairEntity='id:7da8d1bc-cc46-4312-9331-0e417f123152']) - entity(data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, [prov:type='wfprov:Artifact', prov:value="urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a"]) - hadMember(id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a) - entity(id:8041c95b-4fe2-4663-bcfe-6d4292c9d678, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a']) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a, 2022-03-30T14:10:06.239940, [prov:role='wf:main/random_lines1/input']) - entity(data:3, [prov:type='wfprov:Artifact', prov:value="3"]) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, data:3, 2022-03-30T14:10:06.239990, [prov:role='wf:main/random_lines1/num_lines']) - entity(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, [prov:type='wfprov:Artifact', prov:type='prov:Collection', prov:type='prov:Dictionary', prov:hadDictionaryMember='id:8329dc4f-308b-4258-bc73-9e55abd502a5', prov:hadDictionaryMember='id:7cc407df-6449-4722-bd58-5d9fb44288c4', prov:hadDictionaryMember='id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c', prov:hadDictionaryMember='id:3d1d3c32-7457-4abf-bb66-12aac16561b1']) - entity(id:2be3e6ed-24b7-444d-a4ee-5770d93987d4, [prov:value=1]) - hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, id:2be3e6ed-24b7-444d-a4ee-5770d93987d4) - entity(id:7cc407df-6449-4722-bd58-5d9fb44288c4, [prov:type='prov:KeyEntityPair', prov:pairKey="__current_case__", prov:pairEntity='id:2be3e6ed-24b7-444d-a4ee-5770d93987d4']) - entity(data:0, [prov:type='wfprov:Artifact', prov:value="0"]) - hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, data:0) - entity(id:8329dc4f-308b-4258-bc73-9e55abd502a5, [prov:type='prov:KeyEntityPair', prov:pairKey="seed", prov:pairEntity='data:0']) - entity(data:set_seed, [prov:type='wfprov:Artifact', prov:value="set_seed"]) - hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, data:set_seed) - entity(id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c, [prov:type='prov:KeyEntityPair', prov:pairKey="seed_source_selector", prov:pairEntity='data:set_seed']) - entity(data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4, [prov:type='wfprov:Artifact', prov:value="urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4"]) - hadMember(id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4) - entity(id:3d1d3c32-7457-4abf-bb66-12aac16561b1, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4']) - used(id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d, id:a6de5b1b-da32-4449-81b5-4efcdb27bad4, 2022-03-30T14:10:06.240395, [prov:role='wf:main/random_lines1/seed_source']) -endDocument \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl deleted file mode 100644 index 403e63f3..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.ttl +++ /dev/null @@ -1,1081 +0,0 @@ -@prefix data: . -@prefix foaf: . -@prefix id: . -@prefix orcid: . -@prefix prov: . -@prefix rdfs: . -@prefix schema: . -@prefix wf: . -@prefix wfprov: . -@prefix xsd: . - -id:0f0bc88f-e599-4a4e-8681-4edd21226161 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.235023"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.234977"^^xsd:dateTime ; - prov:entity id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.236603"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.234629"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.236555"^^xsd:dateTime ; - prov:entity id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.234586"^^xsd:dateTime ; - prov:entity id:eaec06da-6307-4712-80ca-f89bebb4abc2 ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . - -id:43861f75-9aa7-42b3-80e0-15cf9927d993 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.234091"^^xsd:dateTime ; - prov:entity id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.232136"^^xsd:dateTime ; - prov:entity id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.232547"^^xsd:dateTime ; - prov:entity id:10a92b31-e38a-4eee-a163-d05f0c942e28 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.234137"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.232201"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.232599"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . - -id:6b19db35-6d60-4351-be9b-7257b737a427 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237336"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237196"^^xsd:dateTime ; - prov:entity id:1673a6bb-e7f1-4e69-9403-15c343f59b98 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237107"^^xsd:dateTime ; - prov:entity id:232855e1-8392-4f99-b38d-028c22b047d8 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.238506"^^xsd:dateTime ; - prov:entity id:142f1b95-3ba6-4998-b6a6-72d299494e68 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237846"^^xsd:dateTime ; - prov:entity id:6c67cd25-9da2-4eb8-9145-ab14b36c9771 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237424"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237383"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237290"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.237016"^^xsd:dateTime ; - prov:entity id:595e172f-01c4-4ca4-bd82-532ac4e0195d ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . - -id:7742f4de-4ec4-4bb6-90bd-3772f6ef3e8d a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:hadActivity id:d76ec743-0418-4a56-88f2-b81a404a63bc ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.239316"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.239056"^^xsd:dateTime ; - prov:entity id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.240395"^^xsd:dateTime ; - prov:entity id:a6de5b1b-da32-4449-81b5-4efcdb27bad4 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.239121"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.239990"^^xsd:dateTime ; - prov:entity data:3 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.238912"^^xsd:dateTime ; - prov:entity id:425cb32b-54a2-410a-a915-c025f76640d3 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.239940"^^xsd:dateTime ; - prov:entity id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.239189"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-30T14:10:06.239255"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . - -orcid:0000-0002-8940-4946 a schema:Person, - prov:Agent, - prov:Person ; - rdfs:label "PDG"^^xsd:string ; - schema:name "PDG"^^xsd:string ; - foaf:name "PDG"^^xsd:string . - -data:2524d3d3b68ad39a a wfprov:Artifact, - prov:Entity ; - prov:value "2524d3d3b68ad39a"^^xsd:string . - -data:3 a wfprov:Artifact, - prov:Entity ; - prov:value "3"^^xsd:string . - -data:775bc9b3c1750167 a wfprov:Artifact, - prov:Entity ; - prov:value "775bc9b3c1750167"^^xsd:string . - -data:7c1d8e3101dbcdba a wfprov:Artifact, - prov:Entity ; - prov:value "7c1d8e3101dbcdba"^^xsd:string . - -id:1090150b-6f8f-4ab5-8a27-802721f05c5a a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:path ; - prov:pairKey "src"^^xsd:string . - -id:10a92b31-e38a-4eee-a163-d05f0c942e28 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:f5582681-806f-4e35-9028-631eab68c8db . - -id:1210a0ac-c6d4-4639-8b29-7866ac72a541 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:77f3c59e-7ec9-4e8b-9401-857b6c311c83 ; - prov:pairKey "auto_decompress"^^xsd:string . - -id:142f1b95-3ba6-4998-b6a6-72d299494e68 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 . - -id:1673a6bb-e7f1-4e69-9403-15c343f59b98 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:fd7fec473f1e6c6b . - -id:1d168b92-47a6-448c-baf8-f585f12a3d33 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . - -id:232855e1-8392-4f99-b38d-028c22b047d8 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:2e789aae2475b7da . - -id:24b14bfa-62b8-4d41-a724-90379c5708c1 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:28c49a54-4fce-484f-bbf3-754c514865bd a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:ff95d010-cdcb-45d8-8418-aa53e7681b10 ; - prov:pairKey "check_content"^^xsd:string . - -id:2b1a8432-a59b-4f1b-87ee-912ca464e17c a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "path"^^xsd:string . - -id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:2f407424-3110-457d-b6f4-3d86f1c76cc8 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:2d0a8975-d3b6-43aa-b902-a42b9483374b ; - prov:pairKey "check_content"^^xsd:string . - -id:2f80b5e3-3925-49fd-9339-86ed10571ea9 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06, - id:b3a09002-26d2-44b7-80a1-f3a0accdcacc, - id:ea79a0ce-8267-474e-adc3-0d37ec935565 ; - prov:hadMember data:7ca3de8f49293d1a, - data:hda, - . - -id:2ff086c3-1d26-439e-8b37-02eb82ba2a89 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:36bf5f2c-3bf9-46aa-aac5-8b6249738317, - id:bdc9be97-2541-4e9d-9b66-e93b350046f5, - id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd ; - prov:hadMember data:fd7fec473f1e6c6b, - data:hda, - . - -id:341b47e4-0ed6-416a-b290-ec06d3966f75 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:2d11fff4-3195-426d-991e-39f46c18caf7 ; - prov:pairKey "to_posix_lines"^^xsd:string . - -id:343ac668-db1a-47ca-af95-093b7cc710e1 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:afbd3904-77af-4cab-92f0-f7a1d1e4f467 ; - prov:pairKey "purge_source"^^xsd:string . - -id:36bf5f2c-3bf9-46aa-aac5-8b6249738317 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:fd7fec473f1e6c6b ; - prov:pairKey "id"^^xsd:string . - -id:3c9ad8bf-1c4b-427d-a33f-5ec75e75996a a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d . - -id:3d1d3c32-7457-4abf-bb66-12aac16561b1 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:set_seed ; - prov:pairKey "seed_source_selector"^^xsd:string . - -id:425cb32b-54a2-410a-a915-c025f76640d3 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:fd7fec473f1e6c6b . - -id:428da699-3449-41e2-b395-a770b9b49467 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:7da8d1bc-cc46-4312-9331-0e417f123152 ; - prov:pairKey "values"^^xsd:string . - -id:4319f013-ecd8-4341-a5b9-8e9d8420bd31 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "file_data"^^xsd:string . - -id:4389b350-32eb-48e4-8da0-aaf191209de3 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:5f8fd80e-f00f-4078-9660-55806bdbd100 ; - prov:pairKey "to_posix_lines"^^xsd:string . - -id:45379ceb-7d92-431f-a123-8ee411eedefa a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:dataset2.txt ; - prov:pairKey "name"^^xsd:string . - -id:4b824c76-227e-430f-919c-853ff66133a4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:2e789aae2475b7da ; - prov:pairKey "id"^^xsd:string . - -id:4f7a8626-cbee-41ea-835b-76ddc79fcbce a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:35a147fd-c38e-4a85-bd9a-6a509ccd1245 ; - prov:pairKey "object_id"^^xsd:string . - -id:56295d4d-8276-4557-b9f2-b4b3b653865f a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c ; - prov:pairKey "in_place"^^xsd:string . - -id:595e172f-01c4-4ca4-bd82-532ac4e0195d a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:7ca3de8f49293d1a . - -id:5b034fbf-1f17-485f-9c10-7b9b4872862c a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:b98d6421-2cca-422c-b778-57480f86de92 ; - prov:pairKey "destination"^^xsd:string . - -id:5d99245c-7548-4bc1-9e3f-5ab9c637fbf1 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:775bc9b3c1750167 . - -id:60971e6c-b050-4d63-9ca2-b74f7fab78da a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:43d5b201-ede9-419e-8b39-1bac02df6546 ; - prov:pairKey "hashes"^^xsd:string . - -id:641250eb-2adc-4c98-afcd-00428ee7bc8a a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:dataset1.txt ; - prov:pairKey "name"^^xsd:string . - -id:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd, - id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c, - id:f582aab0-3308-432a-a5e7-8c2a0d069acf ; - prov:hadMember , - , - id:4e23da19-5664-4972-94b0-b2d3365672b1 . - -id:68b2355f-eec1-44a4-8751-11da17591063 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:5b034fbf-1f17-485f-9c10-7b9b4872862c, - id:ab29cf85-149a-412a-92ff-e3a6b605ff16, - id:bd679175-0778-4d62-856a-9da7f503a8b0, - id:c974472d-dbf4-4997-b690-62de731fa7a0 ; - prov:hadMember , - id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1, - id:b98d6421-2cca-422c-b778-57480f86de92, - id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 . - -id:6c67cd25-9da2-4eb8-9145-ab14b36c9771 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:ec4fdb41-ede8-4f37-a220-34eb67952e01, - id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc ; - prov:hadMember , - id:7ac72e2f-5815-47ff-9592-b89492e1804c . - -id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:b35ba485-3a40-4743-9a58-b207f5becd69 ; - prov:pairKey "hashes"^^xsd:string . - -id:738ba6b7-e61e-4d37-abb6-3cee1f782367 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "dbkey"^^xsd:string . - -id:7cc407df-6449-4722-bd58-5d9fb44288c4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 ; - prov:pairKey "__current_case__"^^xsd:string . - -id:8041c95b-4fe2-4663-bcfe-6d4292c9d678 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:8329dc4f-308b-4258-bc73-9e55abd502a5 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:0 ; - prov:pairKey "seed"^^xsd:string . - -id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:7ca3de8f49293d1a ; - prov:pairKey "id"^^xsd:string . - -id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hdas ; - prov:pairKey "type"^^xsd:string . - -id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:4e23da19-5664-4972-94b0-b2d3365672b1 ; - prov:pairKey "__index__"^^xsd:string . - -id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:1d168b92-47a6-448c-baf8-f585f12a3d33, - id:4b824c76-227e-430f-919c-853ff66133a4, - id:641250eb-2adc-4c98-afcd-00428ee7bc8a ; - prov:hadMember data:2e789aae2475b7da, - data:hda, - . - -id:9781f372-1be1-48e3-a9d3-2dda2b581134 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:1754bbe0-77b5-453b-8542-e83b9bc45798 ; - prov:pairKey "input2"^^xsd:string . - -id:9be744cb-071c-4610-91d9-d2a8cca5fbf4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:1090150b-6f8f-4ab5-8a27-802721f05c5a, - id:2b1a8432-a59b-4f1b-87ee-912ca464e17c, - id:341b47e4-0ed6-416a-b290-ec06d3966f75, - id:45379ceb-7d92-431f-a123-8ee411eedefa, - id:56295d4d-8276-4557-b9f2-b4b3b653865f, - id:60971e6c-b050-4d63-9ca2-b74f7fab78da, - id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7, - id:adff57da-d615-4087-8dd9-f32586a3d183, - id:b09b2fa3-1624-428f-880d-b3890200a943, - id:d96d9941-8860-4c3d-a573-666266e9e9fe, - id:e1aa5ec1-4083-4477-8266-9e68d6afdf66 ; - prov:hadMember , - , - data:auto, - data:dataset2.txt, - data:path, - , - id:2d11fff4-3195-426d-991e-39f46c18caf7, - id:43d5b201-ede9-419e-8b39-1bac02df6546, - id:556f2e68-82d3-4ceb-aa48-e93d1a75be64, - id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c, - id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 . - -id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:a11456da-294c-4173-96c9-9becdc7af2fc a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:a3df1b9d-8a6a-4a15-b880-565871b262e2 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:a4beeb97-7076-4d47-8015-e6779877af9e a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 ; - prov:pairKey "destination"^^xsd:string . - -id:a69fb546-67ad-460f-b6f5-01ce7c181db7 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:path ; - prov:pairKey "src"^^xsd:string . - -id:a6de5b1b-da32-4449-81b5-4efcdb27bad4 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:3d1d3c32-7457-4abf-bb66-12aac16561b1, - id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c, - id:7cc407df-6449-4722-bd58-5d9fb44288c4, - id:8329dc4f-308b-4258-bc73-9e55abd502a5 ; - prov:hadMember data:0, - data:set_seed, - , - id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 . - -id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 ; - prov:pairKey "__index__"^^xsd:string . - -id:a89b8834-c5ec-45c4-8760-213c4cc36302 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:auto ; - prov:pairKey "ext"^^xsd:string . - -id:ab29cf85-149a-412a-92ff-e3a6b605ff16 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 ; - prov:pairKey "auto_decompress"^^xsd:string . - -id:acc5b84a-046f-4fd2-9136-82d08877386a a prov:Agent ; - prov:actedOnBehalfOf orcid:0000-0002-8940-4946 . - -id:adff57da-d615-4087-8dd9-f32586a3d183 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:auto ; - prov:pairKey "ext"^^xsd:string . - -id:b095ce58-2b16-49a3-8873-73a85d09b84e a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:20c6c642-7356-4161-a861-7cebbb063751 ; - prov:pairKey "__index__"^^xsd:string . - -id:b09b2fa3-1624-428f-880d-b3890200a943 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "dbkey"^^xsd:string . - -id:b1c0e073-72ee-42f6-a512-d8b0a120f260 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hdas ; - prov:pairKey "type"^^xsd:string . - -id:b3a09002-26d2-44b7-80a1-f3a0accdcacc a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:b7a9f1b5-8383-4b35-9c30-6e93bac0d047 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:2524d3d3b68ad39a . - -id:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2, - id:9781f372-1be1-48e3-a9d3-2dda2b581134, - id:b095ce58-2b16-49a3-8873-73a85d09b84e ; - prov:hadMember , - id:1754bbe0-77b5-453b-8542-e83b9bc45798, - id:20c6c642-7356-4161-a861-7cebbb063751 . - -id:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:2f407424-3110-457d-b6f4-3d86f1c76cc8, - id:9be744cb-071c-4610-91d9-d2a8cca5fbf4, - id:f102ded2-603b-4c97-898e-b71bffb17a71 ; - prov:hadMember , - id:2d0a8975-d3b6-43aa-b902-a42b9483374b, - id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 . - -id:bd679175-0778-4d62-856a-9da7f503a8b0 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1 ; - prov:pairKey "elements"^^xsd:string . - -id:bdc9be97-2541-4e9d-9b66-e93b350046f5 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:c974472d-dbf4-4997-b690-62de731fa7a0 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . - -id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:2f356100-3315-4ff7-87cf-54b1d4d3ea49 ; - prov:pairKey "targets"^^xsd:string . - -id:d96d9941-8860-4c3d-a573-666266e9e9fe a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 ; - prov:pairKey "object_id"^^xsd:string . - -id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "path"^^xsd:string . - -id:decc5efa-759a-4165-9034-88a8de8ff547 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:411a358d-2596-4506-b64a-74b54ea779d4 ; - prov:pairKey "elements"^^xsd:string . - -id:e1aa5ec1-4083-4477-8266-9e68d6afdf66 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:556f2e68-82d3-4ceb-aa48-e93d1a75be64 ; - prov:pairKey "purge_source"^^xsd:string . - -id:e64e532c-b1a6-454d-ac58-bde6809a1841 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601 ; - prov:pairKey "in_place"^^xsd:string . - -id:ea79a0ce-8267-474e-adc3-0d37ec935565 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . - -id:eac8a16e-c68a-457a-871d-47f710712b41 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 ; - prov:pairKey "values"^^xsd:string . - -id:eaec06da-6307-4712-80ca-f89bebb4abc2 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:7c1d8e3101dbcdba . - -id:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:28c49a54-4fce-484f-bbf3-754c514865bd, - id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789, - id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700 ; - prov:hadMember , - id:2f356100-3315-4ff7-87cf-54b1d4d3ea49, - id:ff95d010-cdcb-45d8-8418-aa53e7681b10 . - -id:ec4fdb41-ede8-4f37-a220-34eb67952e01 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:f102ded2-603b-4c97-898e-b71bffb17a71 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 ; - prov:pairKey "targets"^^xsd:string . - -id:f2a60dac-8878-4bad-98f1-782ebf300df9 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:343ac668-db1a-47ca-af95-093b7cc710e1, - id:4389b350-32eb-48e4-8da0-aaf191209de3, - id:4f7a8626-cbee-41ea-835b-76ddc79fcbce, - id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af, - id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565, - id:738ba6b7-e61e-4d37-abb6-3cee1f782367, - id:a69fb546-67ad-460f-b6f5-01ce7c181db7, - id:a89b8834-c5ec-45c4-8760-213c4cc36302, - id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26, - id:e64e532c-b1a6-454d-ac58-bde6809a1841, - id:f7e87688-b315-448f-82c3-a18665a84053 ; - prov:hadMember , - , - data:auto, - data:dataset1.txt, - data:path, - , - id:35a147fd-c38e-4a85-bd9a-6a509ccd1245, - id:5f8fd80e-f00f-4078-9660-55806bdbd100, - id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601, - id:afbd3904-77af-4cab-92f0-f7a1d1e4f467, - id:b35ba485-3a40-4743-9a58-b207f5becd69 . - -id:f5582681-806f-4e35-9028-631eab68c8db a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:4319f013-ecd8-4341-a5b9-8e9d8420bd31, - id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603, - id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc ; - prov:hadMember , - , - id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 . - -id:f582aab0-3308-432a-a5e7-8c2a0d069acf a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "file_data"^^xsd:string . - -id:f6641719-90a2-47d4-96dd-a847725d5d37 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:1210a0ac-c6d4-4639-8b29-7866ac72a541, - id:a4beeb97-7076-4d47-8015-e6779877af9e, - id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4, - id:decc5efa-759a-4165-9034-88a8de8ff547 ; - prov:hadMember , - id:411a358d-2596-4506-b64a-74b54ea779d4, - id:77f3c59e-7ec9-4e8b-9401-857b6c311c83, - id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 . - -id:f7e87688-b315-448f-82c3-a18665a84053 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:ffa6ade9-73aa-44bd-814b-2df33ba1e60a a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:428da699-3449-41e2-b395-a770b9b49467, - id:8041c95b-4fe2-4663-bcfe-6d4292c9d678 ; - prov:hadMember , - id:7da8d1bc-cc46-4312-9331-0e417f123152 . - -id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:7ac72e2f-5815-47ff-9592-b89492e1804c ; - prov:pairKey "values"^^xsd:string . - -data: a wfprov:Artifact, - prov:Entity ; - prov:value ""^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^xsd:string . - -data:0 a wfprov:Artifact, - prov:Entity ; - prov:value "0"^^xsd:string . - -data:42f21c0ad41011eb87defa163eba836f a wfprov:Artifact, - prov:Entity ; - prov:value "42f21c0ad41011eb87defa163eba836f"^^xsd:string . - -data:dataset1.txt a wfprov:Artifact, - prov:Entity ; - prov:value "dataset1.txt"^^xsd:string . - -data:dataset2.txt a wfprov:Artifact, - prov:Entity ; - prov:value "dataset2.txt"^^xsd:string . - -data:set_seed a wfprov:Artifact, - prov:Entity ; - prov:value "set_seed"^^xsd:string . - -data:txt a wfprov:Artifact, - prov:Entity ; - prov:value "txt"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:68b2355f-eec1-44a4-8751-11da17591063"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:b98d6421-2cca-422c-b778-57480f86de92"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:f5582681-806f-4e35-9028-631eab68c8db"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a"^^xsd:string . - -id:1754bbe0-77b5-453b-8542-e83b9bc45798 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:a11456da-294c-4173-96c9-9becdc7af2fc, - id:eac8a16e-c68a-457a-871d-47f710712b41 ; - prov:hadMember , - id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 . - -id:20c6c642-7356-4161-a861-7cebbb063751 a prov:Entity ; - prov:value "0"^^xsd:int . - -id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 a prov:Entity ; - prov:value "1"^^xsd:int . - -id:2d0a8975-d3b6-43aa-b902-a42b9483374b a prov:Entity ; - prov:value true . - -id:2d11fff4-3195-426d-991e-39f46c18caf7 a prov:Entity ; - prov:value true . - -id:2f356100-3315-4ff7-87cf-54b1d4d3ea49 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:f6641719-90a2-47d4-96dd-a847725d5d37 . - -id:35a147fd-c38e-4a85-bd9a-6a509ccd1245 a prov:Entity ; - prov:value "155707"^^xsd:int . - -id:411a358d-2596-4506-b64a-74b54ea779d4 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:f2a60dac-8878-4bad-98f1-782ebf300df9 . - -id:43d5b201-ede9-419e-8b39-1bac02df6546 a wfprov:Artifact, - prov:Collection, - prov:EmptyCollection, - prov:Entity . - -id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 a prov:Entity ; - prov:value "0"^^xsd:int . - -id:4e23da19-5664-4972-94b0-b2d3365672b1 a prov:Entity ; - prov:value "0"^^xsd:int . - -id:556f2e68-82d3-4ceb-aa48-e93d1a75be64 a prov:Entity ; - prov:value false . - -id:5f8fd80e-f00f-4078-9660-55806bdbd100 a prov:Entity ; - prov:value true . - -id:77f3c59e-7ec9-4e8b-9401-857b6c311c83 a prov:Entity ; - prov:value false . - -id:7ac72e2f-5815-47ff-9592-b89492e1804c a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:2f80b5e3-3925-49fd-9339-86ed10571ea9 . - -id:7da8d1bc-cc46-4312-9331-0e417f123152 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:2ff086c3-1d26-439e-8b37-02eb82ba2a89 . - -id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:9c7c25fa-abcb-41ab-a545-fbf9e96e818c . - -id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601 a prov:Entity ; - prov:value false . - -id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:a3df1b9d-8a6a-4a15-b880-565871b262e2, - id:b1c0e073-72ee-42f6-a512-d8b0a120f260 ; - prov:hadMember data:hdas, - . - -id:afbd3904-77af-4cab-92f0-f7a1d1e4f467 a prov:Entity ; - prov:value false . - -id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c a prov:Entity ; - prov:value false . - -id:b35ba485-3a40-4743-9a58-b207f5becd69 a wfprov:Artifact, - prov:Collection, - prov:EmptyCollection, - prov:Entity . - -id:b98d6421-2cca-422c-b778-57480f86de92 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:24b14bfa-62b8-4d41-a724-90379c5708c1, - id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0 ; - prov:hadMember data:hdas, - . - -id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 a prov:Entity ; - prov:value "155708"^^xsd:int . - -id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 a prov:Entity ; - prov:value false . - -id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 . - -id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:68b2355f-eec1-44a4-8751-11da17591063 . - -id:ff95d010-cdcb-45d8-8418-aa53e7681b10 a prov:Entity ; - prov:value true . - -data:2e789aae2475b7da a wfprov:Artifact, - prov:Entity ; - prov:value "2e789aae2475b7da"^^xsd:string . - -data:7ca3de8f49293d1a a wfprov:Artifact, - prov:Entity ; - prov:value "7ca3de8f49293d1a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"^^xsd:string . - -data:1 a wfprov:Artifact, - prov:Entity ; - prov:value "1"^^xsd:string . - -data:auto a wfprov:Artifact, - prov:Entity ; - prov:value "auto"^^xsd:string . - -data:fd7fec473f1e6c6b a wfprov:Artifact, - prov:Entity ; - prov:value "fd7fec473f1e6c6b"^^xsd:string . - -data:hdas a wfprov:Artifact, - prov:Entity ; - prov:value "hdas"^^xsd:string . - -data:path a wfprov:Artifact, - prov:Entity ; - prov:value "path"^^xsd:string . - -id:d76ec743-0418-4a56-88f2-b81a404a63bc a wfprov:WorkflowRun, - prov:Activity ; - rdfs:label "Run of galaxy workflow"^^xsd:string ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan wf:main ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-03-30T14:10:06.231499"^^xsd:dateTime ; - prov:hadActivity id:34d8946d-cc68-4ad9-8ecf-53026817187c ] ; - prov:startedAtTime "2022-03-30T14:10:06.231425"^^xsd:dateTime ; - prov:wasAssociatedWith id:34d8946d-cc68-4ad9-8ecf-53026817187c . - - a wfprov:Artifact, - prov:Entity ; - prov:value "?"^^xsd:string . - -data:hda a wfprov:Artifact, - prov:Entity ; - prov:value "hda"^^xsd:string . - -id:34d8946d-cc68-4ad9-8ecf-53026817187c a wfprov:WorkflowEngine, - prov:Agent, - prov:SoftwareAgent ; - rdfs:label "galaxy_version_placeholder"^^xsd:string ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-03-30T14:10:06.231396"^^xsd:dateTime ; - prov:hadActivity id:acc5b84a-046f-4fd2-9136-82d08877386a ] . - diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml b/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml deleted file mode 100644 index 93af1788..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/ga_export.cwlprov.xml +++ /dev/null @@ -1,1457 +0,0 @@ - - - - - PDG - schema:Person - PDG - PDG - - - - - - - galaxy_version_placeholder - wfprov:WorkflowEngine - - - - - 2022-03-30T14:10:06.231396 - - - 2022-03-30T14:10:06.231425 - Run of galaxy workflow - wfprov:WorkflowRun - - - - - - - - - - 2022-03-30T14:10:06.231499 - - - 2021-06-23T10:20:22.770291 - 2021-06-23T10:20:42.041319 - Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:20:22.770291 - - - wfprov:Artifact - 2524d3d3b68ad39a - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.232136 - wf:main/__DATA_FETCH__/output0 - - - wfprov:Artifact - 1 - - - - - 2022-03-30T14:10:06.232201 - wf:main/__DATA_FETCH__/file_count - - - prov:Dictionary - wfprov:Artifact - id:4319f013-ecd8-4341-a5b9-8e9d8420bd31 - id:8f4d7aba-da8e-43ea-bcf9-e2344e2bf603 - id:a7c2e57c-74d4-4834-a6ee-c687c438f0fc - - - 0 - - - - - - - prov:KeyEntityPair - id:456f97d2-4118-4fd3-a7e0-0bed64b7e343 - __index__ - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - file_data - - - wfprov:Artifact - urn:uuid:f5582681-806f-4e35-9028-631eab68c8db - - - - - - - prov:KeyEntityPair - data:urn:uuid:f5582681-806f-4e35-9028-631eab68c8db - @id - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.232547 - wf:main/__DATA_FETCH__/files - - - wfprov:Artifact - - - - - - 2022-03-30T14:10:06.232599 - wf:main/__DATA_FETCH__/paramfile - - - prov:Dictionary - wfprov:Artifact - id:2f407424-3110-457d-b6f4-3d86f1c76cc8 - id:9be744cb-071c-4610-91d9-d2a8cca5fbf4 - id:f102ded2-603b-4c97-898e-b71bffb17a71 - - - prov:Dictionary - wfprov:Artifact - id:5b034fbf-1f17-485f-9c10-7b9b4872862c - id:ab29cf85-149a-412a-92ff-e3a6b605ff16 - id:bd679175-0778-4d62-856a-9da7f503a8b0 - id:c974472d-dbf4-4997-b690-62de731fa7a0 - - - prov:Dictionary - wfprov:Artifact - id:24b14bfa-62b8-4d41-a724-90379c5708c1 - id:89a1250d-4cc3-4e58-a04c-bbf2e8d2feb0 - - - wfprov:Artifact - hdas - - - - - - - prov:KeyEntityPair - data:hdas - type - - - wfprov:Artifact - urn:uuid:b98d6421-2cca-422c-b778-57480f86de92 - - - - - - - prov:KeyEntityPair - data:urn:uuid:b98d6421-2cca-422c-b778-57480f86de92 - @id - - - - - - - prov:KeyEntityPair - id:b98d6421-2cca-422c-b778-57480f86de92 - destination - - - prov:Dictionary - wfprov:Artifact - id:1090150b-6f8f-4ab5-8a27-802721f05c5a - id:2b1a8432-a59b-4f1b-87ee-912ca464e17c - id:341b47e4-0ed6-416a-b290-ec06d3966f75 - id:45379ceb-7d92-431f-a123-8ee411eedefa - id:56295d4d-8276-4557-b9f2-b4b3b653865f - id:60971e6c-b050-4d63-9ca2-b74f7fab78da - id:6cf52bdb-35de-4cf3-b7b8-5e4869e115f7 - id:adff57da-d615-4087-8dd9-f32586a3d183 - id:b09b2fa3-1624-428f-880d-b3890200a943 - id:d96d9941-8860-4c3d-a573-666266e9e9fe - id:e1aa5ec1-4083-4477-8266-9e68d6afdf66 - - - wfprov:Artifact - auto - - - - - - - prov:KeyEntityPair - data:auto - ext - - - wfprov:Artifact - ? - - - - - - - prov:KeyEntityPair - data:? - dbkey - - - true - - - - - - - prov:KeyEntityPair - id:2d11fff4-3195-426d-991e-39f46c18caf7 - to_posix_lines - - - wfprov:Artifact - path - - - - - - - prov:KeyEntityPair - data:path - src - - - wfprov:Artifact - dataset2.txt - - - - - - - prov:KeyEntityPair - data:dataset2.txt - name - - - prov:EmptyCollection - wfprov:Artifact - - - - - - - prov:KeyEntityPair - id:43d5b201-ede9-419e-8b39-1bac02df6546 - hashes - - - false - - - - - - - prov:KeyEntityPair - id:b1f850c4-bfdd-453e-85ca-2cc389d0ed6c - in_place - - - false - - - - - - - prov:KeyEntityPair - id:556f2e68-82d3-4ceb-aa48-e93d1a75be64 - purge_source - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - path - - - 155708 - - - - - - - prov:KeyEntityPair - id:c8ef7d57-8650-4fb8-a748-a692bffac0b5 - object_id - - - wfprov:Artifact - urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c - - - - - - - prov:KeyEntityPair - data:urn:uuid:9c7c25fa-abcb-41ab-a545-fbf9e96e818c - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:8e1e71e1-82da-4573-a279-8b1afbf4f2a1 - elements - - - false - - - - - - - prov:KeyEntityPair - id:da3e3c09-db05-4e9f-8baf-785f70ec4bc5 - auto_decompress - - - wfprov:Artifact - urn:uuid:68b2355f-eec1-44a4-8751-11da17591063 - - - - - - - prov:KeyEntityPair - data:urn:uuid:68b2355f-eec1-44a4-8751-11da17591063 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:de1ab5b2-d45d-4735-8166-1a8af8fcd980 - targets - - - true - - - - - - - prov:KeyEntityPair - id:2d0a8975-d3b6-43aa-b902-a42b9483374b - check_content - - - wfprov:Artifact - urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 - - - - - - - prov:KeyEntityPair - data:urn:uuid:bb85c1d2-66ee-41d8-a0b0-7706fca358f5 - @id - - - - - 2022-03-30T14:10:06.234091 - wf:main/__DATA_FETCH__/request_json - - - wfprov:Artifact - 1 - - - - - 2022-03-30T14:10:06.234137 - wf:main/__DATA_FETCH__/request_version - - - 2021-06-23T10:20:00.981702 - 2021-06-23T10:20:22.202678 - Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:20:00.981702 - - - wfprov:Artifact - 7c1d8e3101dbcdba - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.234586 - wf:main/__DATA_FETCH__/output0 - - - wfprov:Artifact - 1 - - - - - 2022-03-30T14:10:06.234629 - wf:main/__DATA_FETCH__/file_count - - - prov:Dictionary - wfprov:Artifact - id:8b9a8177-e5bf-47ed-b5be-cde546d2bbcd - id:9d9b20b8-30cb-4a53-b3a8-b9cd63212e2c - id:f582aab0-3308-432a-a5e7-8c2a0d069acf - - - 0 - - - - - - - prov:KeyEntityPair - id:4e23da19-5664-4972-94b0-b2d3365672b1 - __index__ - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - file_data - - - wfprov:Artifact - urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d - - - - - - - prov:KeyEntityPair - data:urn:uuid:66ff88db-e2f9-4ae3-a9c8-dcd4f143143d - @id - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.234977 - wf:main/__DATA_FETCH__/files - - - wfprov:Artifact - - - - - - 2022-03-30T14:10:06.235023 - wf:main/__DATA_FETCH__/paramfile - - - prov:Dictionary - wfprov:Artifact - id:28c49a54-4fce-484f-bbf3-754c514865bd - id:c7bc39a8-f0b8-48fc-b5cf-fce2cbaa3789 - id:d2d5601f-a90d-4447-b5fb-ad53c1d8c700 - - - prov:Dictionary - wfprov:Artifact - id:1210a0ac-c6d4-4639-8b29-7866ac72a541 - id:a4beeb97-7076-4d47-8015-e6779877af9e - id:c10b49f9-d0fd-4c28-aaca-3c5300ccd4b4 - id:decc5efa-759a-4165-9034-88a8de8ff547 - - - prov:Dictionary - wfprov:Artifact - id:a3df1b9d-8a6a-4a15-b880-565871b262e2 - id:b1c0e073-72ee-42f6-a512-d8b0a120f260 - - - wfprov:Artifact - hdas - - - - - - - prov:KeyEntityPair - data:hdas - type - - - wfprov:Artifact - urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002 - - - - - - - prov:KeyEntityPair - data:urn:uuid:afa54a2b-dd93-4fa1-aa45-49b521d7d002 - @id - - - - - - - prov:KeyEntityPair - id:afa54a2b-dd93-4fa1-aa45-49b521d7d002 - destination - - - prov:Dictionary - wfprov:Artifact - id:343ac668-db1a-47ca-af95-093b7cc710e1 - id:4389b350-32eb-48e4-8da0-aaf191209de3 - id:4f7a8626-cbee-41ea-835b-76ddc79fcbce - id:6491ec37-904a-4bce-b8f2-8e4b5bd4c6af - id:6eb2a0a0-43fe-402a-87ab-27e9d44b7565 - id:738ba6b7-e61e-4d37-abb6-3cee1f782367 - id:a69fb546-67ad-460f-b6f5-01ce7c181db7 - id:a89b8834-c5ec-45c4-8760-213c4cc36302 - id:dbb9844d-466e-46b5-bf9b-d2eec40c2b26 - id:e64e532c-b1a6-454d-ac58-bde6809a1841 - id:f7e87688-b315-448f-82c3-a18665a84053 - - - wfprov:Artifact - auto - - - - - - - prov:KeyEntityPair - data:auto - ext - - - wfprov:Artifact - ? - - - - - - - prov:KeyEntityPair - data:? - dbkey - - - true - - - - - - - prov:KeyEntityPair - id:5f8fd80e-f00f-4078-9660-55806bdbd100 - to_posix_lines - - - wfprov:Artifact - path - - - - - - - prov:KeyEntityPair - data:path - src - - - wfprov:Artifact - dataset1.txt - - - - - - - prov:KeyEntityPair - data:dataset1.txt - name - - - prov:EmptyCollection - wfprov:Artifact - - - - - - - prov:KeyEntityPair - id:b35ba485-3a40-4743-9a58-b207f5becd69 - hashes - - - false - - - - - - - prov:KeyEntityPair - id:aceaab0e-1ae8-415b-a0c1-7aa1af7c1601 - in_place - - - false - - - - - - - prov:KeyEntityPair - id:afbd3904-77af-4cab-92f0-f7a1d1e4f467 - purge_source - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - path - - - 155707 - - - - - - - prov:KeyEntityPair - id:35a147fd-c38e-4a85-bd9a-6a509ccd1245 - object_id - - - wfprov:Artifact - urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9 - - - - - - - prov:KeyEntityPair - data:urn:uuid:f2a60dac-8878-4bad-98f1-782ebf300df9 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:411a358d-2596-4506-b64a-74b54ea779d4 - elements - - - false - - - - - - - prov:KeyEntityPair - id:77f3c59e-7ec9-4e8b-9401-857b6c311c83 - auto_decompress - - - wfprov:Artifact - urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37 - - - - - - - prov:KeyEntityPair - data:urn:uuid:f6641719-90a2-47d4-96dd-a847725d5d37 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:2f356100-3315-4ff7-87cf-54b1d4d3ea49 - targets - - - true - - - - - - - prov:KeyEntityPair - id:ff95d010-cdcb-45d8-8418-aa53e7681b10 - check_content - - - wfprov:Artifact - urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 - - - - - - - prov:KeyEntityPair - data:urn:uuid:eb8e9bbb-be72-4bc7-9ffc-2071d5675990 - @id - - - - - 2022-03-30T14:10:06.236555 - wf:main/__DATA_FETCH__/request_json - - - wfprov:Artifact - 1 - - - - - 2022-03-30T14:10:06.236603 - wf:main/__DATA_FETCH__/request_version - - - 2021-06-23T10:46:28.351123 - 2021-06-23T10:46:44.738703 - Run of ga_export/jobs_attrs.txt#cat1 - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:46:28.351123 - - - wfprov:Artifact - 7ca3de8f49293d1a - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.237016 - wf:main/cat1/input1 - - - wfprov:Artifact - 2e789aae2475b7da - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.237107 - wf:main/cat1/queries_0_input2 - - - wfprov:Artifact - fd7fec473f1e6c6b - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.237196 - wf:main/cat1/out_file1 - - - wfprov:Artifact - txt - - - - - 2022-03-30T14:10:06.237290 - wf:main/cat1/__input_ext - - - wfprov:Artifact - 42f21c0ad41011eb87defa163eba836f - - - - - 2022-03-30T14:10:06.237336 - wf:main/cat1/__workflow_invocation_uuid__ - - - wfprov:Artifact - /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - - - - - 2022-03-30T14:10:06.237383 - wf:main/cat1/chromInfo - - - wfprov:Artifact - ? - - - - - 2022-03-30T14:10:06.237424 - wf:main/cat1/dbkey - - - prov:Dictionary - wfprov:Artifact - id:ec4fdb41-ede8-4f37-a220-34eb67952e01 - id:ffcfbb80-81e9-4bc1-93ef-7e580c2cc9cc - - - prov:Dictionary - wfprov:Artifact - id:85aa28a8-5a91-4d18-9c0a-06bc0161ba06 - id:b3a09002-26d2-44b7-80a1-f3a0accdcacc - id:ea79a0ce-8267-474e-adc3-0d37ec935565 - - - wfprov:Artifact - 7ca3de8f49293d1a - - - - - - - prov:KeyEntityPair - data:7ca3de8f49293d1a - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9 - - - - - - - prov:KeyEntityPair - data:urn:uuid:2f80b5e3-3925-49fd-9339-86ed10571ea9 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:7ac72e2f-5815-47ff-9592-b89492e1804c - values - - - wfprov:Artifact - urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771 - - - - - - - prov:KeyEntityPair - data:urn:uuid:6c67cd25-9da2-4eb8-9145-ab14b36c9771 - @id - - - - - 2022-03-30T14:10:06.237846 - wf:main/cat1/input1 - - - prov:Dictionary - wfprov:Artifact - id:2d33047e-1c4c-401c-bcbf-c8aeac7326d2 - id:9781f372-1be1-48e3-a9d3-2dda2b581134 - id:b095ce58-2b16-49a3-8873-73a85d09b84e - - - 0 - - - - - - - prov:KeyEntityPair - id:20c6c642-7356-4161-a861-7cebbb063751 - __index__ - - - prov:Dictionary - wfprov:Artifact - id:a11456da-294c-4173-96c9-9becdc7af2fc - id:eac8a16e-c68a-457a-871d-47f710712b41 - - - prov:Dictionary - wfprov:Artifact - id:1d168b92-47a6-448c-baf8-f585f12a3d33 - id:4b824c76-227e-430f-919c-853ff66133a4 - id:641250eb-2adc-4c98-afcd-00428ee7bc8a - - - wfprov:Artifact - 2e789aae2475b7da - - - - - - - prov:KeyEntityPair - data:2e789aae2475b7da - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 - - - - - - - prov:KeyEntityPair - data:urn:uuid:93055cbf-80fe-4acc-a0a6-fdefdaefcce1 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:dc7ab89b-bab3-4633-89cc-8d6b4efb13e6 - values - - - wfprov:Artifact - urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798 - - - - - - - prov:KeyEntityPair - data:urn:uuid:1754bbe0-77b5-453b-8542-e83b9bc45798 - @id - - - - - - - prov:KeyEntityPair - id:1754bbe0-77b5-453b-8542-e83b9bc45798 - input2 - - - wfprov:Artifact - urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 - - - - - - - prov:KeyEntityPair - data:urn:uuid:bb63eff4-47db-4b53-9e0a-c2d92c215fb0 - @id - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.238506 - wf:main/cat1/queries - - - 2021-06-23T10:46:28.526901 - 2021-06-23T10:47:04.837750 - Run of ga_export/jobs_attrs.txt#random_lines1 - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:46:28.526901 - - - wfprov:Artifact - fd7fec473f1e6c6b - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.238912 - wf:main/random_lines1/input - - - wfprov:Artifact - 775bc9b3c1750167 - - - wfprov:Artifact - - - - - - - - - 2022-03-30T14:10:06.239056 - wf:main/random_lines1/out_file1 - - - wfprov:Artifact - txt - - - - - 2022-03-30T14:10:06.239121 - wf:main/random_lines1/__input_ext - - - wfprov:Artifact - 42f21c0ad41011eb87defa163eba836f - - - - - 2022-03-30T14:10:06.239189 - wf:main/random_lines1/__workflow_invocation_uuid__ - - - wfprov:Artifact - /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - - - - - 2022-03-30T14:10:06.239255 - wf:main/random_lines1/chromInfo - - - wfprov:Artifact - ? - - - - - 2022-03-30T14:10:06.239316 - wf:main/random_lines1/dbkey - - - prov:Dictionary - wfprov:Artifact - id:428da699-3449-41e2-b395-a770b9b49467 - id:8041c95b-4fe2-4663-bcfe-6d4292c9d678 - - - prov:Dictionary - wfprov:Artifact - id:36bf5f2c-3bf9-46aa-aac5-8b6249738317 - id:bdc9be97-2541-4e9d-9b66-e93b350046f5 - id:d207fad4-503a-4e39-9b0b-9e1d87bb6cdd - - - wfprov:Artifact - fd7fec473f1e6c6b - - - - - - - prov:KeyEntityPair - data:fd7fec473f1e6c6b - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89 - - - - - - - prov:KeyEntityPair - data:urn:uuid:2ff086c3-1d26-439e-8b37-02eb82ba2a89 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:7da8d1bc-cc46-4312-9331-0e417f123152 - values - - - wfprov:Artifact - urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a - - - - - - - prov:KeyEntityPair - data:urn:uuid:ffa6ade9-73aa-44bd-814b-2df33ba1e60a - @id - - - - - 2022-03-30T14:10:06.239940 - wf:main/random_lines1/input - - - wfprov:Artifact - 3 - - - - - 2022-03-30T14:10:06.239990 - wf:main/random_lines1/num_lines - - - prov:Dictionary - wfprov:Artifact - id:3d1d3c32-7457-4abf-bb66-12aac16561b1 - id:3ef1d34d-d7a6-4fe5-948f-2703f37a4e5c - id:7cc407df-6449-4722-bd58-5d9fb44288c4 - id:8329dc4f-308b-4258-bc73-9e55abd502a5 - - - 1 - - - - - - - prov:KeyEntityPair - id:2be3e6ed-24b7-444d-a4ee-5770d93987d4 - __current_case__ - - - wfprov:Artifact - 0 - - - - - - - prov:KeyEntityPair - data:0 - seed - - - wfprov:Artifact - set_seed - - - - - - - prov:KeyEntityPair - data:set_seed - seed_source_selector - - - wfprov:Artifact - urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4 - - - - - - - prov:KeyEntityPair - data:urn:uuid:a6de5b1b-da32-4449-81b5-4efcdb27bad4 - @id - - - - - 2022-03-30T14:10:06.240395 - wf:main/random_lines1/seed_source - - diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index 7b181e20..a4cabb17 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -31,6 +31,7 @@ def test_ga_history_loading(test_data_dir, tmpdir, helpers): def test_ga_history_parsing(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" export_path = test_data_dir / export_dir / "history_export" + prov_path = "/home/padge/Elixir/workflow-export/ro-crate-py/test/test-data/test_ga_history_export/history_export/provenance" # prov_name = "ga_export.cwlprov" # crate_path = test_data_dir / export_dir / "history_export_crate" @@ -43,6 +44,10 @@ def test_ga_history_parsing(test_data_dir, tmpdir, helpers): # prov.document.serialize(provenance_file,format="rdf", rdf_format="turtle") assert isinstance(prov, ProvenanceProfile) + prov.finalize_prov_profile(out_path=prov_path) + # print(serialized_prov_docs.keys()) + + def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): wf_id = 'test_galaxy_wf.ga' From d1b3f485560c2936cf66d3dd9ec3e2e53721a139 Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 31 Mar 2022 16:06:09 +0200 Subject: [PATCH 10/27] added section about galaxy workflow-run export to README --- README.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/README.md b/README.md index fdb2730c..df33cfa5 100644 --- a/README.md +++ b/README.md @@ -220,6 +220,27 @@ rocrate add test-instance \#test1 http://example.com -r jobs -i \#test1_1 rocrate add test-definition \#test1 test/test1/sort-and-change-case-test.yml -e planemo -v '>=0.70' ``` +Exporting a galaxy workflo-run export to an ro-crate. + +```python +from rocrate import rocrate_api + +wf_path = base_path + "example-history-export3.ga" +dataset_path = base_path + "example-history-export3/datasets/" +wfr_metadata_path = base_path + "example-history-export3" +files_list = os.listdir(dataset_path) +files_list = [dataset_path + f for f in files_list] + +# Create base package +wf_crate = rocrate_api.make_workflow_run_rocrate(workflow_path=wf_path, + wfr_metadata_path=wfr_metadata_path, author=None, orcid=None, + wf_type="Galaxy",include_files=files_list, prov_name="test_prov") + +# write crate to disk +out_path = base_path + "example-history-export3-crate-new" +wf_crate.write(out_path) +``` + ## License From d8efff7634283d85edfe1ad086895a79e07d3f2f Mon Sep 17 00:00:00 2001 From: pauldg Date: Mon, 4 Apr 2022 17:12:48 +0200 Subject: [PATCH 11/27] added generated ro-crate to test data --- .../provenance/ga_export.cwlprov.json | 1206 +++--- .../provenance/ga_export.cwlprov.jsonld | 3366 +++++++-------- .../provenance/ga_export.cwlprov.nt | 1852 ++++---- .../provenance/ga_export.cwlprov.provn | 554 +-- .../provenance/ga_export.cwlprov.ttl | 1268 +++--- .../provenance/ga_export.cwlprov.xml | 1050 ++--- ...tenate_datasets_on_data_2_and_data_1_3.txt | 4 + .../dataset1.txt_2.txt | 2 + .../dataset2.txt_1.txt | 2 + .../provenance/ga_export.cwlprov.json | 2862 ++++++++++++ .../provenance/ga_export.cwlprov.jsonld | 3841 +++++++++++++++++ .../provenance/ga_export.cwlprov.nt | 935 ++++ .../provenance/ga_export.cwlprov.provn | 330 ++ .../provenance/ga_export.cwlprov.ttl | 1070 +++++ .../provenance/ga_export.cwlprov.xml | 1447 +++++++ .../ro-crate-metadata.json | 123 + .../tutorial_output.txt_4.txt | 3 + .../history_export_ro_crate/wf_definition.cwl | 50 + .../history_export_ro_crate/wf_definition.ga | 131 + test/test_parse_ga_export.py | 53 +- 20 files changed, 15472 insertions(+), 4677 deletions(-) create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.jsonld create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.nt create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl create mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json index 8a2298c3..9708344f 100644 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json @@ -8,20 +8,20 @@ "orcid": "https://orcid.org/", "id": "urn:uuid:", "data": "urn:hash::sha1:", - "provenance": "arcp://uuid,bdf8ae0f-d0e0-4338-9513-e6fecbbeb255/metadata/provenance/", - "wf": "arcp://uuid,bdf8ae0f-d0e0-4338-9513-e6fecbbeb255/ga_export/", - "input": "arcp://uuid,bdf8ae0f-d0e0-4338-9513-e6fecbbeb255/ga_export/datasets#" + "provenance": "arcp://uuid,ebd18716-e481-43ab-8721-a7a8e342efb3/metadata/provenance/", + "wf": "arcp://uuid,ebd18716-e481-43ab-8721-a7a8e342efb3/ga_export/", + "input": "arcp://uuid,ebd18716-e481-43ab-8721-a7a8e342efb3/ga_export/datasets#" }, "agent": { - "id:c98b0b95-d818-4ba1-b535-11c4e6909fa3": {}, + "id:027f7717-78d8-4f9a-a887-87813339b23e": {}, "orcid:0000-0002-8940-4946": { "prov:type": [ { - "$": "schema:Person", + "$": "prov:Person", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Person", + "$": "schema:Person", "type": "prov:QUALIFIED_NAME" } ], @@ -29,14 +29,14 @@ "foaf:name": "PDG", "schema:name": "PDG" }, - "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd": { + "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec": { "prov:type": [ { - "$": "prov:SoftwareAgent", + "$": "wfprov:WorkflowEngine", "type": "prov:QUALIFIED_NAME" }, { - "$": "wfprov:WorkflowEngine", + "$": "prov:SoftwareAgent", "type": "prov:QUALIFIED_NAME" } ], @@ -45,52 +45,52 @@ }, "actedOnBehalfOf": { "_:id1": { - "prov:delegate": "id:c98b0b95-d818-4ba1-b535-11c4e6909fa3", + "prov:delegate": "id:027f7717-78d8-4f9a-a887-87813339b23e", "prov:responsible": "orcid:0000-0002-8940-4946" } }, "wasStartedBy": { "_:id2": { - "prov:activity": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", - "prov:starter": "id:c98b0b95-d818-4ba1-b535-11c4e6909fa3", - "prov:time": "2022-03-31T15:39:11.759268" + "prov:activity": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", + "prov:starter": "id:027f7717-78d8-4f9a-a887-87813339b23e", + "prov:time": "2022-04-04T16:59:09.402992" }, "_:id4": { - "prov:activity": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", - "prov:starter": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", - "prov:time": "2022-03-31T15:39:11.759353" + "prov:activity": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", + "prov:starter": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", + "prov:time": "2022-04-04T16:59:09.403118" }, "_:id6": { - "prov:activity": "id:a1a08c93-d0b2-4806-8abb-697cf651f9a4", - "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", + "prov:activity": "id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c", + "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", "prov:time": "2021-06-23T10:20:22.770291" }, "_:id41": { - "prov:activity": "id:414221e9-e943-451a-bde9-ef492e1cf85c", - "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", + "prov:activity": "id:b7a0ab16-c370-48aa-924b-74d57ab7d542", + "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", "prov:time": "2021-06-23T10:20:00.981702" }, "_:id76": { - "prov:activity": "id:cade945a-1ff3-4273-a78e-7b5358804c89", - "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", + "prov:activity": "id:290068a6-8ef9-4718-800b-cb22efbdfd62", + "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", "prov:time": "2021-06-23T10:46:28.351123" }, "_:id106": { - "prov:activity": "id:2341e04b-a08b-400e-97ef-3151f01a17fa", - "prov:starter": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", + "prov:activity": "id:1747ea92-6d32-4175-9aef-2893fc71c7a5", + "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", "prov:time": "2021-06-23T10:46:28.526901" } }, "activity": { - "id:dd421f2f-c538-44d3-aeeb-484022c6541d": { - "prov:startTime": "2022-03-31T15:39:11.759294", + "id:b9177644-871b-492a-ae5f-3ee833ba0ae5": { + "prov:startTime": "2022-04-04T16:59:09.403029", "prov:type": { "$": "wfprov:WorkflowRun", "type": "prov:QUALIFIED_NAME" }, "prov:label": "Run of galaxy workflow" }, - "id:a1a08c93-d0b2-4806-8abb-697cf651f9a4": { + "id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c": { "prov:startTime": "2021-06-23T10:20:22.770291", "prov:endTime": "2021-06-23T10:20:42.041319", "prov:type": { @@ -99,7 +99,7 @@ }, "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" }, - "id:414221e9-e943-451a-bde9-ef492e1cf85c": { + "id:b7a0ab16-c370-48aa-924b-74d57ab7d542": { "prov:startTime": "2021-06-23T10:20:00.981702", "prov:endTime": "2021-06-23T10:20:22.202678", "prov:type": { @@ -108,7 +108,7 @@ }, "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" }, - "id:cade945a-1ff3-4273-a78e-7b5358804c89": { + "id:290068a6-8ef9-4718-800b-cb22efbdfd62": { "prov:startTime": "2021-06-23T10:46:28.351123", "prov:endTime": "2021-06-23T10:46:44.738703", "prov:type": { @@ -117,7 +117,7 @@ }, "prov:label": "Run of ga_export/jobs_attrs.txt#cat1" }, - "id:2341e04b-a08b-400e-97ef-3151f01a17fa": { + "id:1747ea92-6d32-4175-9aef-2893fc71c7a5": { "prov:startTime": "2021-06-23T10:46:28.526901", "prov:endTime": "2021-06-23T10:47:04.837750", "prov:type": { @@ -129,28 +129,28 @@ }, "wasAssociatedWith": { "_:id3": { - "prov:activity": "id:dd421f2f-c538-44d3-aeeb-484022c6541d", - "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", + "prov:activity": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", + "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", "prov:plan": "wf:main" }, "_:id5": { - "prov:activity": "id:a1a08c93-d0b2-4806-8abb-697cf651f9a4", - "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", + "prov:activity": "id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c", + "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", "prov:plan": "wf:main/__DATA_FETCH__" }, "_:id40": { - "prov:activity": "id:414221e9-e943-451a-bde9-ef492e1cf85c", - "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", + "prov:activity": "id:b7a0ab16-c370-48aa-924b-74d57ab7d542", + "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", "prov:plan": "wf:main/__DATA_FETCH__" }, "_:id75": { - "prov:activity": "id:cade945a-1ff3-4273-a78e-7b5358804c89", - "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", + "prov:activity": "id:290068a6-8ef9-4718-800b-cb22efbdfd62", + "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", "prov:plan": "wf:main/cat1" }, "_:id105": { - "prov:activity": "id:2341e04b-a08b-400e-97ef-3151f01a17fa", - "prov:agent": "id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd", + "prov:activity": "id:1747ea92-6d32-4175-9aef-2893fc71c7a5", + "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", "prov:plan": "wf:main/random_lines1" } }, @@ -162,14 +162,14 @@ }, "prov:value": "2524d3d3b68ad39a" }, - "id:d4c2d49d-ab80-43ab-b347-a7db85bf7262": { + "id:e13acf9b-83e9-40f0-adc1-a7195e612fa3": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] @@ -204,10 +204,10 @@ "prov:value": "1" } ], - "id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6": { + "id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -215,39 +215,39 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:a1bb89e0-badf-490a-af30-375efe69c057", + "$": "id:e311b33d-139a-4e92-a5c1-3a04530b9128", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98", + "$": "id:f268cc7a-3474-404e-892f-8af376e98ae3", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:869277c3-8c88-4381-bbef-de17240b1c23", + "$": "id:a92435e7-0621-4629-80fa-d73aa1989363", "type": "prov:QUALIFIED_NAME" } ] }, - "id:0c54448a-8444-42cd-9dd1-b65dfb0656ba": { + "id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc": { "prov:value": { "$": 0, "type": "xsd:int" } }, - "id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98": { + "id:a92435e7-0621-4629-80fa-d73aa1989363": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__index__", "prov:pairEntity": { - "$": "id:0c54448a-8444-42cd-9dd1-b65dfb0656ba", + "$": "id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc", "type": "prov:QUALIFIED_NAME" } }, @@ -267,7 +267,7 @@ "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" } ], - "id:869277c3-8c88-4381-bbef-de17240b1c23": { + "id:f268cc7a-3474-404e-892f-8af376e98ae3": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -278,32 +278,32 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6": { + "data:urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6" + "prov:value": "urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a" }, - "id:a1bb89e0-badf-490a-af30-375efe69c057": { + "id:e311b33d-139a-4e92-a5c1-3a04530b9128": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6", + "$": "data:urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a", "type": "prov:QUALIFIED_NAME" } }, - "id:5c05f71f-74dc-4238-a591-9df8dfa779f8": { + "id:bef03503-1c1f-4f05-9a58-56449dcc9ac3": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] @@ -324,10 +324,10 @@ "prov:value": "" } ], - "id:594019f6-4154-49a8-be37-3d511a35f066": { + "id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -335,29 +335,29 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:e2f3637a-f559-46a0-a630-9f3e47800b70", + "$": "id:9af37a24-65f9-41cd-8191-228ec8108418", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:1e8684e9-896e-4a38-bfe9-1995d0893fdd", + "$": "id:441a9ce2-fada-464f-84fb-6dfd01a6379e", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:7067149e-f997-4e01-810a-41ed1aaae3f1", + "$": "id:15212ae6-d7ff-4660-870e-34f3caa32ceb", "type": "prov:QUALIFIED_NAME" } ] }, - "id:641c238b-2832-4fab-b949-f5f4fc01deb1": { + "id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -365,33 +365,33 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:ab8003d1-3e46-4af7-9325-fffe09639b01", + "$": "id:38113d6d-950c-4c1a-826d-636d3c6fa3ea", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:3b176baa-a8f8-426c-ab0d-aa428d41923d", + "$": "id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:47d09ccc-4b59-4330-9361-9f1b65b860a8", + "$": "id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:9f4835d1-a5f0-499e-9315-42fed1edd2a1", + "$": "id:0196242d-cfb9-45f3-965c-8fa2a037f104", "type": "prov:QUALIFIED_NAME" } ] }, - "id:d84bb265-2540-4cad-a026-511b7a21323e": { + "id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -399,17 +399,17 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5", + "$": "id:b17c488e-30c3-42cb-b2f0-092b0efe2427", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:f923bbf9-1c94-4771-9333-77547e7e828e", + "$": "id:e1829e51-7947-4db2-99a0-1ea7703ee764", "type": "prov:QUALIFIED_NAME" } ] @@ -430,7 +430,7 @@ "prov:value": "hdas" } ], - "id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5": { + "id:b17c488e-30c3-42cb-b2f0-092b0efe2427": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -441,39 +441,39 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e": { + "data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e" + "prov:value": "urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f" }, - "id:f923bbf9-1c94-4771-9333-77547e7e828e": { + "id:e1829e51-7947-4db2-99a0-1ea7703ee764": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e", + "$": "data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f", "type": "prov:QUALIFIED_NAME" } }, - "id:47d09ccc-4b59-4330-9361-9f1b65b860a8": { + "id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "destination", "prov:pairEntity": { - "$": "id:d84bb265-2540-4cad-a026-511b7a21323e", + "$": "id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f", "type": "prov:QUALIFIED_NAME" } }, - "id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9": { + "id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -481,53 +481,53 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60", + "$": "id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:79566035-3dfd-4779-837a-344529381251", + "$": "id:b0586419-dbb7-4757-9cfd-ae55abef3674", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:97939793-b619-47e0-8ec3-d3baf5965151", + "$": "id:3b543d5d-26b4-48f1-8c80-0c288c8df33f", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:f67dbd55-b05c-4a56-aea3-4041399b62d1", + "$": "id:5f9613d6-b39e-40e1-95d2-d26fb37550fe", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:792b7ecd-597e-41ad-ac59-b0767919b4b7", + "$": "id:8a2cf341-8042-40bd-8509-b56f1f4161c7", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01", + "$": "id:4b32d7ec-e96f-41ff-8feb-1e43324962da", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:c0c38d7d-cd18-4050-b5e8-0faf10393207", + "$": "id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:66fde9d0-4440-4811-8b03-ae8c34cfebb6", + "$": "id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64", + "$": "id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:069bb313-b651-474e-9a28-fdc7af0fc87b", + "$": "id:f5199f67-c23f-46de-a504-11e5465e2e8c", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:f45f9536-1278-4069-8b91-7edd97d3ff80", + "$": "id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01", "type": "prov:QUALIFIED_NAME" } ] @@ -548,7 +548,7 @@ "prov:value": "auto" } ], - "id:79566035-3dfd-4779-837a-344529381251": { + "id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -589,7 +589,7 @@ "prov:value": "?" } ], - "id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60": { + "id:5f9613d6-b39e-40e1-95d2-d26fb37550fe": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -600,17 +600,17 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:9e633b9f-343d-4b29-a78a-85afdd8eef53": { + "id:f23be627-a96d-47ce-b857-30e370a747a9": { "prov:value": true }, - "id:792b7ecd-597e-41ad-ac59-b0767919b4b7": { + "id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "to_posix_lines", "prov:pairEntity": { - "$": "id:9e633b9f-343d-4b29-a78a-85afdd8eef53", + "$": "id:f23be627-a96d-47ce-b857-30e370a747a9", "type": "prov:QUALIFIED_NAME" } }, @@ -630,7 +630,7 @@ "prov:value": "path" } ], - "id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01": { + "id:4b32d7ec-e96f-41ff-8feb-1e43324962da": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -648,7 +648,7 @@ }, "prov:value": "dataset2.txt" }, - "id:97939793-b619-47e0-8ec3-d3baf5965151": { + "id:b0586419-dbb7-4757-9cfd-ae55abef3674": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -659,62 +659,62 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:780092f0-87bd-42bc-a3d8-50143d44998b": { + "id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:EmptyCollection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:EmptyCollection", "type": "prov:QUALIFIED_NAME" } ] }, - "id:f45f9536-1278-4069-8b91-7edd97d3ff80": { + "id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "hashes", "prov:pairEntity": { - "$": "id:780092f0-87bd-42bc-a3d8-50143d44998b", + "$": "id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1", "type": "prov:QUALIFIED_NAME" } }, - "id:0f5709cc-12f6-430c-a605-fd3e8978f6c4": { + "id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7": { "prov:value": false }, - "id:c0c38d7d-cd18-4050-b5e8-0faf10393207": { + "id:8a2cf341-8042-40bd-8509-b56f1f4161c7": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "in_place", "prov:pairEntity": { - "$": "id:0f5709cc-12f6-430c-a605-fd3e8978f6c4", + "$": "id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7", "type": "prov:QUALIFIED_NAME" } }, - "id:87e7e990-d873-4d20-a6ee-b15094940df1": { + "id:76b51c9a-5a58-43ce-b9a9-7f4459602a11": { "prov:value": false }, - "id:f67dbd55-b05c-4a56-aea3-4041399b62d1": { + "id:3b543d5d-26b4-48f1-8c80-0c288c8df33f": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "purge_source", "prov:pairEntity": { - "$": "id:87e7e990-d873-4d20-a6ee-b15094940df1", + "$": "id:76b51c9a-5a58-43ce-b9a9-7f4459602a11", "type": "prov:QUALIFIED_NAME" } }, - "id:069bb313-b651-474e-9a28-fdc7af0fc87b": { + "id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -725,148 +725,148 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:bd860612-ca87-49c5-9d5c-d086f706f789": { + "id:4ed44fba-accb-410c-baef-53d2cb882954": { "prov:value": { "$": 155708, "type": "xsd:int" } }, - "id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64": { + "id:f5199f67-c23f-46de-a504-11e5465e2e8c": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "object_id", "prov:pairEntity": { - "$": "id:bd860612-ca87-49c5-9d5c-d086f706f789", + "$": "id:4ed44fba-accb-410c-baef-53d2cb882954", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9": { + "data:urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9" + "prov:value": "urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551" }, - "id:66fde9d0-4440-4811-8b03-ae8c34cfebb6": { + "id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9", + "$": "data:urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551", "type": "prov:QUALIFIED_NAME" } }, - "id:e7516c89-e4ed-494b-bf16-74b40fa66bd1": { + "id:56b63fc0-3bb2-448b-8115-c1cb4384d8db": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:3b176baa-a8f8-426c-ab0d-aa428d41923d": { + "id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "elements", "prov:pairEntity": { - "$": "id:e7516c89-e4ed-494b-bf16-74b40fa66bd1", + "$": "id:56b63fc0-3bb2-448b-8115-c1cb4384d8db", "type": "prov:QUALIFIED_NAME" } }, - "id:e8c438c4-7544-4049-8d34-f825ecd3b5e1": { + "id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d": { "prov:value": false }, - "id:ab8003d1-3e46-4af7-9325-fffe09639b01": { + "id:0196242d-cfb9-45f3-965c-8fa2a037f104": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "auto_decompress", "prov:pairEntity": { - "$": "id:e8c438c4-7544-4049-8d34-f825ecd3b5e1", + "$": "id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1": { + "data:urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1" + "prov:value": "urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2" }, - "id:9f4835d1-a5f0-499e-9315-42fed1edd2a1": { + "id:38113d6d-950c-4c1a-826d-636d3c6fa3ea": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1", + "$": "data:urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2", "type": "prov:QUALIFIED_NAME" } }, - "id:34aa3429-439f-49df-b575-0c7aee2caa81": { + "id:508b7a80-e3e7-442e-b9e9-4874e2916aad": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:7067149e-f997-4e01-810a-41ed1aaae3f1": { + "id:15212ae6-d7ff-4660-870e-34f3caa32ceb": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "targets", "prov:pairEntity": { - "$": "id:34aa3429-439f-49df-b575-0c7aee2caa81", + "$": "id:508b7a80-e3e7-442e-b9e9-4874e2916aad", "type": "prov:QUALIFIED_NAME" } }, - "id:ffdb63df-93ba-4e67-8097-308bfd9ba39d": { + "id:f715a46b-9eff-48c3-b88f-1f3a009ea573": { "prov:value": true }, - "id:e2f3637a-f559-46a0-a630-9f3e47800b70": { + "id:9af37a24-65f9-41cd-8191-228ec8108418": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "check_content", "prov:pairEntity": { - "$": "id:ffdb63df-93ba-4e67-8097-308bfd9ba39d", + "$": "id:f715a46b-9eff-48c3-b88f-1f3a009ea573", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066": { + "data:urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:594019f6-4154-49a8-be37-3d511a35f066" + "prov:value": "urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c" }, - "id:1e8684e9-896e-4a38-bfe9-1995d0893fdd": { + "id:441a9ce2-fada-464f-84fb-6dfd01a6379e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066", + "$": "data:urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c", "type": "prov:QUALIFIED_NAME" } }, @@ -877,22 +877,22 @@ }, "prov:value": "7c1d8e3101dbcdba" }, - "id:ebf027ac-b671-468a-91c6-1bfd7e45eb36": { + "id:fb247085-dfc8-42bc-bee7-a7475ce9289a": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:5ab542a0-7a79-4f00-b120-b14b0542e568": { + "id:02bb9d1c-f248-47fb-ac2c-9985301385a7": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -900,39 +900,39 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:ef96000b-e230-40a1-a36a-a45f4ca78a0e", + "$": "id:e0524eed-ea77-413b-b0db-5f72e16c365e", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:d3a55e5b-c1fb-4523-b77d-993b00128b05", + "$": "id:7c60b838-dd41-4166-aa41-6e652e5ef63b", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:88aa880c-c240-4877-b1e7-a0c20e29ef3e", + "$": "id:f8f974ae-cd55-4986-8a9e-1d987b76fd34", "type": "prov:QUALIFIED_NAME" } ] }, - "id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4": { + "id:5d7467bd-1ab8-46ea-8a56-0998f42b079c": { "prov:value": { "$": 0, "type": "xsd:int" } }, - "id:ef96000b-e230-40a1-a36a-a45f4ca78a0e": { + "id:e0524eed-ea77-413b-b0db-5f72e16c365e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__index__", "prov:pairEntity": { - "$": "id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4", + "$": "id:5d7467bd-1ab8-46ea-8a56-0998f42b079c", "type": "prov:QUALIFIED_NAME" } }, @@ -952,7 +952,7 @@ "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a" } ], - "id:d3a55e5b-c1fb-4523-b77d-993b00128b05": { + "id:7c60b838-dd41-4166-aa41-6e652e5ef63b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -963,40 +963,40 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568": { + "data:urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568" + "prov:value": "urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7" }, - "id:88aa880c-c240-4877-b1e7-a0c20e29ef3e": { + "id:f8f974ae-cd55-4986-8a9e-1d987b76fd34": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568", + "$": "data:urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7", "type": "prov:QUALIFIED_NAME" } }, - "id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3": { + "id:c00decaf-ac43-4246-8705-8c1bb0defce1": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:71e28368-850b-441f-a008-8b6173a866d7": { + "id:ce5712eb-9c70-401d-811e-a01bfdbf3b3f": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1004,29 +1004,29 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:68c6bdfd-f17d-41b8-bdba-eb3a46749940", + "$": "id:3f52ff7d-9aa8-45c7-8af1-1f7f474c6ad7", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:a75e7105-d7f0-4a77-865c-2ff5b3162e47", + "$": "id:9baabbde-52d6-4728-8ef7-738960d2a86f", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:6d29c983-528d-46cf-b420-1c9210619f0d", + "$": "id:689d969e-0df7-40c8-b733-b4e39fd49d34", "type": "prov:QUALIFIED_NAME" } ] }, - "id:7fc57149-e802-47ce-bf01-348e6e787dd0": { + "id:6102b40f-814e-41b4-8e21-caee1eab126b": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1034,33 +1034,33 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4", + "$": "id:0c415611-9c31-47d4-82f9-a6330b980a8e", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e", + "$": "id:788acdf9-5e3a-4774-aa66-3068819b5cae", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:34523c4b-aa54-4d13-8d25-76acadcc8df7", + "$": "id:2d384308-e0b1-4f82-811c-4bba81b92067", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:9e45fea1-39c5-4b99-be26-72b06a5e8786", + "$": "id:cc8b2ec1-0c34-4d44-bce6-9dfb3efd9298", "type": "prov:QUALIFIED_NAME" } ] }, - "id:4fa4bb93-f67a-414c-8420-9272773cb5e2": { + "id:9ae42623-faf1-431a-acd3-bce4a4c24a24": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1068,22 +1068,22 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:93b6a52a-f266-4837-9e8e-ed928fbd2775", + "$": "id:70fb9ca7-9038-4874-bbda-0f12fad1627a", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be", + "$": "id:3ad229e9-064d-4398-8617-d802f10ac40b", "type": "prov:QUALIFIED_NAME" } ] }, - "id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be": { + "id:3ad229e9-064d-4398-8617-d802f10ac40b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1094,39 +1094,39 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2": { + "data:urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2" + "prov:value": "urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24" }, - "id:93b6a52a-f266-4837-9e8e-ed928fbd2775": { + "id:70fb9ca7-9038-4874-bbda-0f12fad1627a": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2", + "$": "data:urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24", "type": "prov:QUALIFIED_NAME" } }, - "id:9e45fea1-39c5-4b99-be26-72b06a5e8786": { + "id:cc8b2ec1-0c34-4d44-bce6-9dfb3efd9298": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "destination", "prov:pairEntity": { - "$": "id:4fa4bb93-f67a-414c-8420-9272773cb5e2", + "$": "id:9ae42623-faf1-431a-acd3-bce4a4c24a24", "type": "prov:QUALIFIED_NAME" } }, - "id:6d494d29-2bc7-4da4-ba43-e816ee0b1266": { + "id:0ff29d35-01d6-471f-84e8-a1fc63c05daa": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1134,58 +1134,58 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:d9811e1d-402f-4343-bc31-7dd5643dbdac", + "$": "id:08ffc626-141c-4214-8d71-746a1218f209", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:feb54146-911b-4d39-90cf-ef6d66b46fe4", + "$": "id:919c8f14-f4f3-4151-b936-d7502f64caa4", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:8ced01f6-47ea-4320-b65a-6af7a668fbe9", + "$": "id:46ce5c94-417b-4bcf-a9af-fb60912d385a", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:98a55032-1c60-4303-8ca0-5cff21b96b9d", + "$": "id:7dc6f8f5-cce3-4da9-b386-0a18314af498", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:286ffa7a-a1f3-424c-90cf-f36d112b13f0", + "$": "id:bab1f03d-7ca6-4bb7-a57d-563c0e70808b", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6", + "$": "id:bb0b8464-83db-421e-9566-a31da915d209", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5", + "$": "id:d281fed1-869b-4451-8fda-95b26856a918", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:ab51fb43-4e4d-459e-ae56-672b92ac89ea", + "$": "id:06db435a-b77f-424b-8301-acb7e18cc2ce", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:fbca4ec6-e519-477f-84ce-23e70dddcc8b", + "$": "id:23fe35b3-2a01-4edf-952a-5769462abc6c", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1", + "$": "id:a05e1e9a-74e5-4efc-ad75-96c15f4a83ce", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:4745fa68-123c-4afb-9176-dcf61732f695", + "$": "id:c256e77e-7189-430a-8c59-03fa703dce07", "type": "prov:QUALIFIED_NAME" } ] }, - "id:d9811e1d-402f-4343-bc31-7dd5643dbdac": { + "id:d281fed1-869b-4451-8fda-95b26856a918": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1196,7 +1196,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:98a55032-1c60-4303-8ca0-5cff21b96b9d": { + "id:06db435a-b77f-424b-8301-acb7e18cc2ce": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1207,21 +1207,21 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:03d9f2a8-6e48-40b3-84e4-f13e161decf1": { + "id:493493b1-836f-404c-9084-95086d7ba06a": { "prov:value": true }, - "id:4745fa68-123c-4afb-9176-dcf61732f695": { + "id:23fe35b3-2a01-4edf-952a-5769462abc6c": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "to_posix_lines", "prov:pairEntity": { - "$": "id:03d9f2a8-6e48-40b3-84e4-f13e161decf1", + "$": "id:493493b1-836f-404c-9084-95086d7ba06a", "type": "prov:QUALIFIED_NAME" } }, - "id:8ced01f6-47ea-4320-b65a-6af7a668fbe9": { + "id:c256e77e-7189-430a-8c59-03fa703dce07": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1239,7 +1239,7 @@ }, "prov:value": "dataset1.txt" }, - "id:286ffa7a-a1f3-424c-90cf-f36d112b13f0": { + "id:a05e1e9a-74e5-4efc-ad75-96c15f4a83ce": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1250,62 +1250,62 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:8bae3361-cfbe-4b69-bfa0-34901d319a21": { + "id:addafc7d-4439-49fb-9870-b6b0ed7415c3": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:EmptyCollection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "prov:EmptyCollection", "type": "prov:QUALIFIED_NAME" } ] }, - "id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6": { + "id:bab1f03d-7ca6-4bb7-a57d-563c0e70808b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "hashes", "prov:pairEntity": { - "$": "id:8bae3361-cfbe-4b69-bfa0-34901d319a21", + "$": "id:addafc7d-4439-49fb-9870-b6b0ed7415c3", "type": "prov:QUALIFIED_NAME" } }, - "id:368b85e6-a18c-4452-90ef-32ee5ccd0308": { + "id:721f1551-f868-4e7d-8cb4-6f196df24a97": { "prov:value": false }, - "id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1": { + "id:46ce5c94-417b-4bcf-a9af-fb60912d385a": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "in_place", "prov:pairEntity": { - "$": "id:368b85e6-a18c-4452-90ef-32ee5ccd0308", + "$": "id:721f1551-f868-4e7d-8cb4-6f196df24a97", "type": "prov:QUALIFIED_NAME" } }, - "id:f350a230-ff86-44a3-8560-e35c1ba07b59": { + "id:87697625-c033-4483-b5fa-d00140b03808": { "prov:value": false }, - "id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5": { + "id:7dc6f8f5-cce3-4da9-b386-0a18314af498": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "purge_source", "prov:pairEntity": { - "$": "id:f350a230-ff86-44a3-8560-e35c1ba07b59", + "$": "id:87697625-c033-4483-b5fa-d00140b03808", "type": "prov:QUALIFIED_NAME" } }, - "id:ab51fb43-4e4d-459e-ae56-672b92ac89ea": { + "id:08ffc626-141c-4214-8d71-746a1218f209": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1316,148 +1316,148 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a": { + "id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80": { "prov:value": { "$": 155707, "type": "xsd:int" } }, - "id:fbca4ec6-e519-477f-84ce-23e70dddcc8b": { + "id:919c8f14-f4f3-4151-b936-d7502f64caa4": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "object_id", "prov:pairEntity": { - "$": "id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a", + "$": "id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266": { + "data:urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266" + "prov:value": "urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa" }, - "id:feb54146-911b-4d39-90cf-ef6d66b46fe4": { + "id:bb0b8464-83db-421e-9566-a31da915d209": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266", + "$": "data:urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa", "type": "prov:QUALIFIED_NAME" } }, - "id:8dbadfd6-d421-4d18-95ae-36fc4defb317": { + "id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4": { + "id:0c415611-9c31-47d4-82f9-a6330b980a8e": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "elements", "prov:pairEntity": { - "$": "id:8dbadfd6-d421-4d18-95ae-36fc4defb317", + "$": "id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea", "type": "prov:QUALIFIED_NAME" } }, - "id:65dace90-ed17-46f9-b809-d98a90563655": { + "id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f": { "prov:value": false }, - "id:34523c4b-aa54-4d13-8d25-76acadcc8df7": { + "id:2d384308-e0b1-4f82-811c-4bba81b92067": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "auto_decompress", "prov:pairEntity": { - "$": "id:65dace90-ed17-46f9-b809-d98a90563655", + "$": "id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0": { + "data:urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0" + "prov:value": "urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b" }, - "id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e": { + "id:788acdf9-5e3a-4774-aa66-3068819b5cae": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0", + "$": "data:urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b", "type": "prov:QUALIFIED_NAME" } }, - "id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1": { + "id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:a75e7105-d7f0-4a77-865c-2ff5b3162e47": { + "id:689d969e-0df7-40c8-b733-b4e39fd49d34": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "targets", "prov:pairEntity": { - "$": "id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1", + "$": "id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab", "type": "prov:QUALIFIED_NAME" } }, - "id:fc84f9f8-5bb4-402d-ba90-697df02824ca": { + "id:016238d2-8ca1-4335-b232-acae7f43ed72": { "prov:value": true }, - "id:6d29c983-528d-46cf-b420-1c9210619f0d": { + "id:9baabbde-52d6-4728-8ef7-738960d2a86f": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "check_content", "prov:pairEntity": { - "$": "id:fc84f9f8-5bb4-402d-ba90-697df02824ca", + "$": "id:016238d2-8ca1-4335-b232-acae7f43ed72", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:71e28368-850b-441f-a008-8b6173a866d7": { + "data:urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:71e28368-850b-441f-a008-8b6173a866d7" + "prov:value": "urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f" }, - "id:68c6bdfd-f17d-41b8-bdba-eb3a46749940": { + "id:3f52ff7d-9aa8-45c7-8af1-1f7f474c6ad7": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:71e28368-850b-441f-a008-8b6173a866d7", + "$": "data:urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f", "type": "prov:QUALIFIED_NAME" } }, @@ -1477,14 +1477,14 @@ "prov:value": "7ca3de8f49293d1a" } ], - "id:837879db-a58f-45bc-980d-2da57fd19cd1": { + "id:d731fa25-6b69-4910-80ab-897579cd74ba": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] @@ -1505,14 +1505,14 @@ "prov:value": "2e789aae2475b7da" } ], - "id:730e5d81-2c3c-44d7-9916-9cc0b7bcdd81": { + "id:6c4049ff-bf0b-4c3e-829d-16e5ece01b8e": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] @@ -1540,14 +1540,14 @@ "prov:value": "fd7fec473f1e6c6b" } ], - "id:a1110187-8be9-4aff-b03e-3530ed7f6cbf": { + "id:90923c5c-2bd8-4aa7-a029-817e8b57037a": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] @@ -1600,10 +1600,10 @@ "prov:value": "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len" } ], - "id:a9607900-c633-4837-a4a7-eaee6edcaf3b": { + "id:b040da72-a0ee-4309-ad1e-353be140b04a": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1611,25 +1611,25 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:57844284-ccc8-45f3-a7fa-6ce0246cf99b", + "$": "id:4ee5e287-4b5d-4d40-be38-1bf1c3236934", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:e9967a89-6747-4067-95ed-5160b763f0b1", + "$": "id:551327a9-e8db-4d46-8ec4-cde270df080b", "type": "prov:QUALIFIED_NAME" } ] }, - "id:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0": { + "id:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1637,26 +1637,26 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813", + "$": "id:9fb40382-f182-481e-90e6-0e24006c71c5", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99", + "$": "id:c0fce355-42ca-41f4-88b0-ccc3b4fec7d2", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d", + "$": "id:49e48096-0a9e-4ebd-8d9b-2b3647acb1b5", "type": "prov:QUALIFIED_NAME" } ] }, - "id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813": { + "id:9fb40382-f182-481e-90e6-0e24006c71c5": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1690,7 +1690,7 @@ "prov:value": "hda" } ], - "id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d": { + "id:49e48096-0a9e-4ebd-8d9b-2b3647acb1b5": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1701,69 +1701,69 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0": { + "data:urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0" + "prov:value": "urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0" }, - "id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99": { + "id:c0fce355-42ca-41f4-88b0-ccc3b4fec7d2": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0", + "$": "data:urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0", "type": "prov:QUALIFIED_NAME" } }, - "id:7827651a-85f5-48a4-8f9d-1427fc02bda4": { + "id:f8915280-6e26-4eef-b378-cf27df3f8f1d": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:57844284-ccc8-45f3-a7fa-6ce0246cf99b": { + "id:551327a9-e8db-4d46-8ec4-cde270df080b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "values", "prov:pairEntity": { - "$": "id:7827651a-85f5-48a4-8f9d-1427fc02bda4", + "$": "id:f8915280-6e26-4eef-b378-cf27df3f8f1d", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b": { + "data:urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b" + "prov:value": "urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a" }, - "id:e9967a89-6747-4067-95ed-5160b763f0b1": { + "id:4ee5e287-4b5d-4d40-be38-1bf1c3236934": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b", + "$": "data:urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a", "type": "prov:QUALIFIED_NAME" } }, - "id:f39be690-c7d7-4911-be28-6afc1abe40b0": { + "id:7519c8b1-64da-4255-9960-acb3dda9ab98": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1771,46 +1771,46 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:951bb963-10a7-4234-8119-1b13921f9629", + "$": "id:dc09c4fe-c4a9-4cc5-9770-0a4f19369ac0", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:9578a96e-6635-4000-9c81-2951341b65c8", + "$": "id:b397cf2b-901a-454c-bfc2-e966b6838269", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:4529ad17-6e7b-4493-bba5-475a60c4a11a", + "$": "id:92b2afc9-fc96-4764-adbe-73d014ba2357", "type": "prov:QUALIFIED_NAME" } ] }, - "id:f40fd446-41cb-442e-bbb7-9a23d27296e5": { + "id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a": { "prov:value": { "$": 0, "type": "xsd:int" } }, - "id:951bb963-10a7-4234-8119-1b13921f9629": { + "id:dc09c4fe-c4a9-4cc5-9770-0a4f19369ac0": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__index__", "prov:pairEntity": { - "$": "id:f40fd446-41cb-442e-bbb7-9a23d27296e5", + "$": "id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a", "type": "prov:QUALIFIED_NAME" } }, - "id:e6248791-d7c3-49a7-9660-5cb622189a3c": { + "id:ac40b633-8521-462b-aea0-bea86dcaef7c": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1818,25 +1818,25 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:8170c31b-5a5f-4150-8531-8b0adac0f282", + "$": "id:d22a3287-f5fa-4465-8383-a6b1a3b0f242", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:ff80c261-0171-44d9-86fa-546f8aea6cd8", + "$": "id:70e6aab8-ec0d-4ff2-a2d6-03a4ce5062fd", "type": "prov:QUALIFIED_NAME" } ] }, - "id:062d0748-7b74-4d45-98f3-80bd22ed2672": { + "id:c9198eaf-36fb-42c4-bf4b-d740591fe470": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -1844,26 +1844,26 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747", + "$": "id:10f720aa-40e7-4c83-9ad1-02ffc26a7944", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748", + "$": "id:34e6b60d-4d4a-496d-bb9c-a4d34040155c", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:51656ecb-5b39-4ad7-9888-d7b93ca28266", + "$": "id:ebaa0943-a400-4daf-a2e7-f781b714a666", "type": "prov:QUALIFIED_NAME" } ] }, - "id:51656ecb-5b39-4ad7-9888-d7b93ca28266": { + "id:ebaa0943-a400-4daf-a2e7-f781b714a666": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1874,7 +1874,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748": { + "id:34e6b60d-4d4a-496d-bb9c-a4d34040155c": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -1885,114 +1885,114 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672": { + "data:urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672" + "prov:value": "urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470" }, - "id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747": { + "id:10f720aa-40e7-4c83-9ad1-02ffc26a7944": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672", + "$": "data:urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470", "type": "prov:QUALIFIED_NAME" } }, - "id:55af6a73-efbe-4e5c-8b47-6ff94872e6de": { + "id:351d875a-c130-42f7-ba2f-735780ea4ca8": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:ff80c261-0171-44d9-86fa-546f8aea6cd8": { + "id:70e6aab8-ec0d-4ff2-a2d6-03a4ce5062fd": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "values", "prov:pairEntity": { - "$": "id:55af6a73-efbe-4e5c-8b47-6ff94872e6de", + "$": "id:351d875a-c130-42f7-ba2f-735780ea4ca8", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c": { + "data:urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c" + "prov:value": "urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c" }, - "id:8170c31b-5a5f-4150-8531-8b0adac0f282": { + "id:d22a3287-f5fa-4465-8383-a6b1a3b0f242": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c", + "$": "data:urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c", "type": "prov:QUALIFIED_NAME" } }, - "id:4529ad17-6e7b-4493-bba5-475a60c4a11a": { + "id:b397cf2b-901a-454c-bfc2-e966b6838269": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "input2", "prov:pairEntity": { - "$": "id:e6248791-d7c3-49a7-9660-5cb622189a3c", + "$": "id:ac40b633-8521-462b-aea0-bea86dcaef7c", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0": { + "data:urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0" + "prov:value": "urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98" }, - "id:9578a96e-6635-4000-9c81-2951341b65c8": { + "id:92b2afc9-fc96-4764-adbe-73d014ba2357": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0", + "$": "data:urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98", "type": "prov:QUALIFIED_NAME" } }, - "id:682cbd95-9570-4f19-a8bb-a639bfb641e2": { + "id:67c5d8ae-be1d-41a2-85c9-d0543a97dd3e": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:8a1a4095-2cbb-468e-80d6-25ebab181a3e": { + "id:c857b436-a405-4bf1-9b58-1f2d255d91b5": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] @@ -2004,22 +2004,22 @@ }, "prov:value": "775bc9b3c1750167" }, - "id:6cf20326-6a50-4476-910c-c40be8829bc4": { + "id:a8ba8607-96e1-4d6f-a17e-3e4d3a1168c8": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:fd40a61e-108c-42c4-8b49-c20815d2d9e5": { + "id:db786d1e-928b-4b0f-b118-bd235731ea9a": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -2027,25 +2027,25 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:81d81eab-2874-43f4-9d2e-ce5ad6236054", + "$": "id:298c9e09-232d-4854-bf61-8116b1323f5b", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:279428d4-794f-42cd-9419-0c8c71385b78", + "$": "id:838aa24d-f8b4-4ddd-a76c-82460c5b6391", "type": "prov:QUALIFIED_NAME" } ] }, - "id:24d7454e-9885-40b1-8a85-cc272df4fa40": { + "id:abbdd009-c520-4098-baf6-6400cf916ffa": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -2053,26 +2053,26 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:96981ec2-dac6-4477-9ac3-431cdc24f7ac", + "$": "id:947491c9-a106-4578-b804-16c3100e0111", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:c40c9210-5155-480f-ba36-5f86aaa39d77", + "$": "id:ad223424-b8ff-4704-a618-0a033ceaf3ea", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94", + "$": "id:994bb2e3-42f8-4fd1-9d6f-aff742a0b9b0", "type": "prov:QUALIFIED_NAME" } ] }, - "id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94": { + "id:994bb2e3-42f8-4fd1-9d6f-aff742a0b9b0": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2083,7 +2083,7 @@ "type": "prov:QUALIFIED_NAME" } }, - "id:c40c9210-5155-480f-ba36-5f86aaa39d77": { + "id:947491c9-a106-4578-b804-16c3100e0111": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2094,62 +2094,62 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40": { + "data:urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40" + "prov:value": "urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa" }, - "id:96981ec2-dac6-4477-9ac3-431cdc24f7ac": { + "id:ad223424-b8ff-4704-a618-0a033ceaf3ea": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40", + "$": "data:urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa", "type": "prov:QUALIFIED_NAME" } }, - "id:23fbeb5c-eebc-41ef-a966-be8a191c7ede": { + "id:663c25a0-9302-4b8f-aa89-765f3284aeca": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ] }, - "id:279428d4-794f-42cd-9419-0c8c71385b78": { + "id:298c9e09-232d-4854-bf61-8116b1323f5b": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "values", "prov:pairEntity": { - "$": "id:23fbeb5c-eebc-41ef-a966-be8a191c7ede", + "$": "id:663c25a0-9302-4b8f-aa89-765f3284aeca", "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5": { + "data:urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5" + "prov:value": "urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a" }, - "id:81d81eab-2874-43f4-9d2e-ce5ad6236054": { + "id:838aa24d-f8b4-4ddd-a76c-82460c5b6391": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5", + "$": "data:urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a", "type": "prov:QUALIFIED_NAME" } }, @@ -2160,10 +2160,10 @@ }, "prov:value": "3" }, - "id:7e6d530d-6c05-48b1-8d69-879b6e790c9d": { + "id:cb9975e1-3882-4cc3-9995-9352d37f1948": { "prov:type": [ { - "$": "wfprov:Artifact", + "$": "prov:Collection", "type": "prov:QUALIFIED_NAME" }, { @@ -2171,43 +2171,43 @@ "type": "prov:QUALIFIED_NAME" }, { - "$": "prov:Collection", + "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" } ], "prov:hadDictionaryMember": [ { - "$": "id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9", + "$": "id:1b548405-6990-454a-98a6-128dccf12014", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:903792cc-566c-4ffe-ade9-be65cf4f1fb4", + "$": "id:3f28e37f-bba8-4b0d-b4d8-ad4749630604", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:5ba613ce-6eaa-412d-89bf-eb8f580823a3", + "$": "id:7884960e-a973-4e8f-bb01-58005de82366", "type": "prov:QUALIFIED_NAME" }, { - "$": "id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e", + "$": "id:c753b9e4-3908-491a-a7a8-a0d4e1543e34", "type": "prov:QUALIFIED_NAME" } ] }, - "id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad": { + "id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd": { "prov:value": { "$": 1, "type": "xsd:int" } }, - "id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9": { + "id:1b548405-6990-454a-98a6-128dccf12014": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "__current_case__", "prov:pairEntity": { - "$": "id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad", + "$": "id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd", "type": "prov:QUALIFIED_NAME" } }, @@ -2218,7 +2218,7 @@ }, "prov:value": "0" }, - "id:5ba613ce-6eaa-412d-89bf-eb8f580823a3": { + "id:3f28e37f-bba8-4b0d-b4d8-ad4749630604": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2236,7 +2236,7 @@ }, "prov:value": "set_seed" }, - "id:903792cc-566c-4ffe-ade9-be65cf4f1fb4": { + "id:7884960e-a973-4e8f-bb01-58005de82366": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" @@ -2247,633 +2247,633 @@ "type": "prov:QUALIFIED_NAME" } }, - "data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d": { + "data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948": { "prov:type": { "$": "wfprov:Artifact", "type": "prov:QUALIFIED_NAME" }, - "prov:value": "urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d" + "prov:value": "urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948" }, - "id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e": { + "id:c753b9e4-3908-491a-a7a8-a0d4e1543e34": { "prov:type": { "$": "prov:KeyEntityPair", "type": "prov:QUALIFIED_NAME" }, "prov:pairKey": "@id", "prov:pairEntity": { - "$": "data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d", + "$": "data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948", "type": "prov:QUALIFIED_NAME" } } }, "hadMember": { "_:id7": { - "prov:collection": "id:d4c2d49d-ab80-43ab-b347-a7db85bf7262", + "prov:collection": "id:e13acf9b-83e9-40f0-adc1-a7195e612fa3", "prov:entity": 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"id:7e6d530d-6c05-48b1-8d69-879b6e790c9d", - "prov:time": "2022-03-31T15:39:11.770390", + "prov:activity": "id:1747ea92-6d32-4175-9aef-2893fc71c7a5", + "prov:entity": "id:cb9975e1-3882-4cc3-9995-9352d37f1948", + "prov:time": "2022-04-04T16:59:09.414862", "prov:role": { "$": "wf:main/random_lines1/seed_source", "type": "prov:QUALIFIED_NAME" diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld index 864f4681..6db3c8f6 100644 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld @@ -1,81 +1,102 @@ [ { - "@id": "urn:uuid:ace28a14-6cc4-4efc-adcb-4668dcc9cd60", + "@id": "urn:uuid:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72", "@type": [ - "http://www.w3.org/ns/prov#Entity", - "http://www.w3.org/ns/prov#KeyEntityPair" + "http://www.w3.org/ns/prov#KeyEntityPair", + "http://www.w3.org/ns/prov#Entity" ], "http://www.w3.org/ns/prov#pairEntity": [ { - "@id": "urn:hash::sha1:?" + "@id": "urn:uuid:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1" } ], "http://www.w3.org/ns/prov#pairKey": [ { - "@value": "dbkey" + "@value": "hashes" } ] }, { - "@id": "urn:uuid:79566035-3dfd-4779-837a-344529381251", + "@id": "urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa", "@type": [ + "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Collection", "http://www.w3.org/ns/prov#Entity", - "http://www.w3.org/ns/prov#KeyEntityPair" + "http://www.w3.org/ns/prov#Dictionary" ], - "http://www.w3.org/ns/prov#pairEntity": [ + "http://www.w3.org/ns/prov#hadDictionaryMember": [ { - "@id": "urn:hash::sha1:auto" + "@id": "urn:uuid:947491c9-a106-4578-b804-16c3100e0111" + }, + { + "@id": "urn:uuid:ad223424-b8ff-4704-a618-0a033ceaf3ea" + }, + { + "@id": "urn:uuid:994bb2e3-42f8-4fd1-9d6f-aff742a0b9b0" } ], - 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"@id": "urn:hash::sha1:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0", + "@id": "urn:uuid:fb247085-dfc8-42bc-bee7-a7475ce9289a", "@type": [ - "http://www.w3.org/ns/prov#Entity", - "http://purl.org/wf4ever/wfprov#Artifact" + "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Collection", + "http://www.w3.org/ns/prov#Entity" + ], + "http://www.w3.org/ns/prov#hadMember": [ + { + "@id": "urn:hash::sha1:7c1d8e3101dbcdba" + } + ] + }, + { + "@id": "urn:hash::sha1:urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c", + "@type": [ + "http://purl.org/wf4ever/wfprov#Artifact", + "http://www.w3.org/ns/prov#Entity" ], "http://www.w3.org/ns/prov#value": [ { - "@value": "urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0" + "@value": "urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c" } ] }, { - "@id": "urn:hash::sha1:1", + "@id": "urn:uuid:f23be627-a96d-47ce-b857-30e370a747a9", + "@type": [ + "http://www.w3.org/ns/prov#Entity" + ], + "http://www.w3.org/ns/prov#value": [ + { + "@value": true + } + ] + }, + { + "@id": "urn:hash::sha1:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f", "@type": [ "http://purl.org/wf4ever/wfprov#Artifact", "http://www.w3.org/ns/prov#Entity" ], "http://www.w3.org/ns/prov#value": [ { - "@value": "1" + "@value": "urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f" } ] } diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt index 7f407de2..6c66a0e4 100644 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt @@ -1,942 +1,942 @@ - "elements"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "1"^^ . - . - "src"^^ . - "155707"^^ . - . -_:Nce2d56e6ec1148ef96f00432a5d143a4 . - . - . - . - "dbkey"^^ . - "urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0"^^ . - . -_:Ndda3f852178b41df93d682778b30de68 . - 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"2021-06-23T10:20:22.770291"^^ . + . +_:N36b0b58717ec4d8bb56a28398f1be777 . +_:Naba823961c754ac4840af8c91ee45c7c . + . + . + . +_:Nb988423e8de84734b663e3587f7d6c41 . + . + . + . + _:Nee78ee74888442ec9f8002ff16ceb431 . + "purge_source"^^ . + . + _:N5c83056e021a4fcea3729b5122412bbc . + . + . + . + "false"^^ . + _:N6ce934634fe946129922717f89d39329 . + . + . + . + . + . +_:Ncaf0f28ce28a472fa7776f223d406baa "2022-04-04T16:59:09.411369"^^ . + _:Nc54b38689fc84bbb9274306eedffd6e0 . + "1"^^ . + "targets"^^ . + . +_:Ndf5094575d6540878c5f493a32f05423 . + . + . + . + . + . + . + . + _:Nd2ee12d18c074df590350b7abc4480c1 . +_:Nf154a67ced074d9e859f3503fd9596d1 . + . + . + . + . + "@id"^^ . + . + . + . + "@id"^^ . + "155707"^^ . + . + . +_:Nf4ead2639f754549b6bf8147ab40c606 . . - . - . - . - . - . - . - . - "0"^^ . - . - "targets"^^ . - . - "values"^^ . - . -_:N90b3a6506b334ccbb557f8536d3ac873 . - "urn:uuid:594019f6-4154-49a8-be37-3d511a35f066"^^ . - . - . - . -_:N8761a0fd566b4688a9e4a6fd9839b527 . - 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-_:Nb0027efc48c442aebdf8723a09a6b2a7 . - . - . - . - . - . - . -_:Na92402de90f14681a1fc4c098d4f253e . - . - . - . + . + "type"^^ . + . + . + . + . + . + . + . + . +_:Nc54b38689fc84bbb9274306eedffd6e0 "2022-04-04T16:59:09.413588"^^ . +_:N2daf12059393442f9ef4a4694ac1eab4 . +_:N79f8c261421e46bda291b67e346e0971 . + . + . +_:Nb09343b74ce849a4bfae64e8a076ddc3 . + . + . + "3"^^ . + "@id"^^ . + "file_data"^^ . + . + . +_:Nad7f19bf98ed4c588ecae7bf291089bc . + . + "Run of ga_export/jobs_attrs.txt#cat1"^^ . + "urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a"^^ . + . + . + . + _:Ne265eace236b449b8327451f7d3d8a21 . + . + . + . +_:N95e001197ce14a69ae2164ef3d39d11a "2021-06-23T10:46:28.351123"^^ . + . + . . - _:Nb0027efc48c442aebdf8723a09a6b2a7 . - . - . -_:N94b827c9be884c53970acf072c517a92 . - . - "__current_case__"^^ . - . - . - . - . - "@id"^^ . - . - . - "true"^^ . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - ""^^ . - . - _:Nd75d0d9f2ab24726847d6a36acf5572f . -_:N12972f97490d48bd81c2cb57f479188b "2022-03-31T15:39:11.760237"^^ . - "path"^^ . -_:N516c7073f23d45258ca502a3f0f48988 "2022-03-31T15:39:11.759268"^^ . - _:Ne954aaea715a4c7f83cddf209be99f58 . - . - . - . -_:N6c8e9fe0d6cc4f0aa1b32337ce8e70ef . - . - "1"^^ . - . - "id"^^ . - . - . - . - . - . -_:Nc1c76e018a0249bca02bbeaa55854219 . - . - "@id"^^ . - . - "false"^^ . - . -_:Nce6998e02860423487cf4b4b36285921 . -_:N7892c1c304be478482995f67fcc40f35 "2022-03-31T15:39:11.766169"^^ . - . - "2021-06-23T10:46:28.526901"^^ . - . - . - . - "ext"^^ . - . - . - . - "to_posix_lines"^^ . - "auto"^^ . - "true"^^ . -_:Nccf21e5229144314b75dae9dbaa6d631 "2021-06-23T10:46:28.526901"^^ . - . - . - "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^ . -_:Nccf21e5229144314b75dae9dbaa6d631 . - . - . - . - . -_:N704fdcfec018436383e492f6c5b2eee6 . - . - . -_:Nce2d56e6ec1148ef96f00432a5d143a4 . - . - . - . - . - . - . - . -_:N9eff600bf1924eaaa9585bd011a708f7 . - . - . - . - _:N8cbcc228c7a946a49898943e3cf98982 . - . - . -_:N034e5519cec84270bb120ef96ac31e6d "2022-03-31T15:39:11.759353"^^ . - . - _:N3ee1c73bfa0e44098abf588bff3096b6 . - . - . - _:Nf64e03a753aa40b79e4b06699ae76944 . -_:N516c7073f23d45258ca502a3f0f48988 . - . - . - . - . - . - . - . - . + . + . + "@id"^^ . + . +_:N9338235fa2904486b9788d4cefe87279 . + . + . + . +_:Nae56c22f23664bfea2b347c12ab20f06 . + . + . + . + "Run of galaxy workflow"^^ . +_:N2daf12059393442f9ef4a4694ac1eab4 . + . + . + . + . + . + . +_:N05a67543be8c471e8ec771d8b3751676 . . - . - . -_:N3ee1c73bfa0e44098abf588bff3096b6 . - . - "urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b"^^ . - _:Nfd4c410bcb104724b92d5a1d814dd200 . - "false"^^ . -_:Ned651b93b9bb421b95431182463202ae . - . - . -_:N08fca9271ba54c33b392e1a288848614 . - . - _:N47e01cff8f5d47e282b0893879e5d359 . - . - . - . - . -_:N704fdcfec018436383e492f6c5b2eee6 "2022-03-31T15:39:11.768810"^^ . - . - . - . - "urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c"^^ . - . - . - . - "?"^^ . - . - . - . - . - . - . - "in_place"^^ . - . - . -_:N12972f97490d48bd81c2cb57f479188b . -_:N12972f97490d48bd81c2cb57f479188b . - . -_:N2f06695db9b54b5fa0b321d256789020 . - . - . - . -_:N12972f97490d48bd81c2cb57f479188b . - . - . - . - . - . - . -_:N2f06695db9b54b5fa0b321d256789020 . - "auto_decompress"^^ . - "@id"^^ . - . - . -_:N0ded116190a84793bcc622c066529856 . -_:N9eff600bf1924eaaa9585bd011a708f7 . -_:Nce6998e02860423487cf4b4b36285921 . -_:N90b3a6506b334ccbb557f8536d3ac873 . - . - . - . - . - . - . - . -_:Na92402de90f14681a1fc4c098d4f253e "2022-03-31T15:39:11.769848"^^ . - . - . - . - . - . - "src"^^ . - "destination"^^ . - "auto_decompress"^^ . + . + . + . + . + . + . + "__index__"^^ . + . + . +_:N2daf12059393442f9ef4a4694ac1eab4 . + . +_:Nad7f19bf98ed4c588ecae7bf291089bc "2022-04-04T16:59:09.407566"^^ . + . + . + . + "dbkey"^^ . +_:Nd5944ac86de24f8e987c43d06f5735bb . +_:N92fb5db2bb0b4ef3a50d59cd2f0eca9c . + "7c1d8e3101dbcdba"^^ . + "__current_case__"^^ . +_:Naba823961c754ac4840af8c91ee45c7c "2022-04-04T16:59:09.412881"^^ . + . + . + . + . diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn index 7014e23c..5aae4048 100644 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn @@ -7,326 +7,326 @@ document prefix orcid prefix id prefix data - prefix provenance - prefix wf - prefix input + prefix provenance + prefix wf + prefix input - agent(id:c98b0b95-d818-4ba1-b535-11c4e6909fa3) - agent(orcid:0000-0002-8940-4946, [prov:type='schema:Person', prov:type='prov:Person', prov:label="PDG", foaf:name="PDG", schema:name="PDG"]) - actedOnBehalfOf(id:c98b0b95-d818-4ba1-b535-11c4e6909fa3, orcid:0000-0002-8940-4946, -) - agent(id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, [prov:type='prov:SoftwareAgent', prov:type='wfprov:WorkflowEngine', prov:label="galaxy_version_placeholder"]) - wasStartedBy(id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, -, id:c98b0b95-d818-4ba1-b535-11c4e6909fa3, 2022-03-31T15:39:11.759268) - activity(id:dd421f2f-c538-44d3-aeeb-484022c6541d, 2022-03-31T15:39:11.759294, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of galaxy workflow"]) - wasAssociatedWith(id:dd421f2f-c538-44d3-aeeb-484022c6541d, id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, wf:main) - wasStartedBy(id:dd421f2f-c538-44d3-aeeb-484022c6541d, -, id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, 2022-03-31T15:39:11.759353) - activity(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, 2021-06-23T10:20:22.770291, 2021-06-23T10:20:42.041319, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) - wasAssociatedWith(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd, wf:main/__DATA_FETCH__) - wasStartedBy(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, -, id:dd421f2f-c538-44d3-aeeb-484022c6541d, 2021-06-23T10:20:22.770291) + agent(id:027f7717-78d8-4f9a-a887-87813339b23e) + agent(orcid:0000-0002-8940-4946, [prov:type='prov:Person', prov:type='schema:Person', prov:label="PDG", foaf:name="PDG", schema:name="PDG"]) + actedOnBehalfOf(id:027f7717-78d8-4f9a-a887-87813339b23e, orcid:0000-0002-8940-4946, -) + agent(id:ade93562-cbf5-453b-a445-cc9a5f95f0ec, [prov:type='wfprov:WorkflowEngine', prov:type='prov:SoftwareAgent', prov:label="galaxy_version_placeholder"]) + wasStartedBy(id:ade93562-cbf5-453b-a445-cc9a5f95f0ec, -, id:027f7717-78d8-4f9a-a887-87813339b23e, 2022-04-04T16:59:09.402992) + activity(id:b9177644-871b-492a-ae5f-3ee833ba0ae5, 2022-04-04T16:59:09.403029, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of galaxy workflow"]) + wasAssociatedWith(id:b9177644-871b-492a-ae5f-3ee833ba0ae5, id:ade93562-cbf5-453b-a445-cc9a5f95f0ec, wf:main) + wasStartedBy(id:b9177644-871b-492a-ae5f-3ee833ba0ae5, -, id:ade93562-cbf5-453b-a445-cc9a5f95f0ec, 2022-04-04T16:59:09.403118) + activity(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, 2021-06-23T10:20:22.770291, 2021-06-23T10:20:42.041319, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) + wasAssociatedWith(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, id:ade93562-cbf5-453b-a445-cc9a5f95f0ec, wf:main/__DATA_FETCH__) + wasStartedBy(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, -, id:b9177644-871b-492a-ae5f-3ee833ba0ae5, 2021-06-23T10:20:22.770291) entity(data:2524d3d3b68ad39a, [prov:type='wfprov:Artifact', prov:value="2524d3d3b68ad39a"]) - entity(id:d4c2d49d-ab80-43ab-b347-a7db85bf7262, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:d4c2d49d-ab80-43ab-b347-a7db85bf7262, data:2524d3d3b68ad39a) - used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:d4c2d49d-ab80-43ab-b347-a7db85bf7262, 2022-03-31T15:39:11.759864, [prov:role='wf:main/__DATA_FETCH__/output0']) + entity(id:e13acf9b-83e9-40f0-adc1-a7195e612fa3, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:e13acf9b-83e9-40f0-adc1-a7195e612fa3, data:2524d3d3b68ad39a) + used(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, id:e13acf9b-83e9-40f0-adc1-a7195e612fa3, 2022-04-04T16:59:09.403801, [prov:role='wf:main/__DATA_FETCH__/output0']) entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) - used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, data:1, 2022-03-31T15:39:11.759917, [prov:role='wf:main/__DATA_FETCH__/file_count']) - entity(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:a1bb89e0-badf-490a-af30-375efe69c057', prov:hadDictionaryMember='id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98', prov:hadDictionaryMember='id:869277c3-8c88-4381-bbef-de17240b1c23']) - entity(id:0c54448a-8444-42cd-9dd1-b65dfb0656ba, [prov:value=0]) - hadMember(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, id:0c54448a-8444-42cd-9dd1-b65dfb0656ba) - entity(id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:0c54448a-8444-42cd-9dd1-b65dfb0656ba']) + used(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, data:1, 2022-04-04T16:59:09.403870, [prov:role='wf:main/__DATA_FETCH__/file_count']) + entity(id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:e311b33d-139a-4e92-a5c1-3a04530b9128', prov:hadDictionaryMember='id:f268cc7a-3474-404e-892f-8af376e98ae3', prov:hadDictionaryMember='id:a92435e7-0621-4629-80fa-d73aa1989363']) + entity(id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc, [prov:value=0]) + hadMember(id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a, id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc) + entity(id:a92435e7-0621-4629-80fa-d73aa1989363, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc']) entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) - hadMember(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) - entity(id:869277c3-8c88-4381-bbef-de17240b1c23, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) - entity(data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, [prov:type='wfprov:Artifact', prov:value="urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6"]) - hadMember(id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6, data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6) - entity(id:a1bb89e0-badf-490a-af30-375efe69c057, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6']) - entity(id:5c05f71f-74dc-4238-a591-9df8dfa779f8, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:5c05f71f-74dc-4238-a591-9df8dfa779f8, id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6) - used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:5c05f71f-74dc-4238-a591-9df8dfa779f8, 2022-03-31T15:39:11.760237, [prov:role='wf:main/__DATA_FETCH__/files']) + hadMember(id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:f268cc7a-3474-404e-892f-8af376e98ae3, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(data:urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a, [prov:type='wfprov:Artifact', prov:value="urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a"]) + hadMember(id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a, data:urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a) + entity(id:e311b33d-139a-4e92-a5c1-3a04530b9128, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a']) + entity(id:bef03503-1c1f-4f05-9a58-56449dcc9ac3, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:bef03503-1c1f-4f05-9a58-56449dcc9ac3, id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a) + used(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, id:bef03503-1c1f-4f05-9a58-56449dcc9ac3, 2022-04-04T16:59:09.404286, [prov:role='wf:main/__DATA_FETCH__/files']) entity(data:, [prov:type='wfprov:Artifact', prov:value=""]) - used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, data:, 2022-03-31T15:39:11.760286, [prov:role='wf:main/__DATA_FETCH__/paramfile']) - entity(id:594019f6-4154-49a8-be37-3d511a35f066, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:e2f3637a-f559-46a0-a630-9f3e47800b70', prov:hadDictionaryMember='id:1e8684e9-896e-4a38-bfe9-1995d0893fdd', prov:hadDictionaryMember='id:7067149e-f997-4e01-810a-41ed1aaae3f1']) - entity(id:641c238b-2832-4fab-b949-f5f4fc01deb1, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:ab8003d1-3e46-4af7-9325-fffe09639b01', prov:hadDictionaryMember='id:3b176baa-a8f8-426c-ab0d-aa428d41923d', prov:hadDictionaryMember='id:47d09ccc-4b59-4330-9361-9f1b65b860a8', prov:hadDictionaryMember='id:9f4835d1-a5f0-499e-9315-42fed1edd2a1']) - entity(id:d84bb265-2540-4cad-a026-511b7a21323e, [prov:type='wfprov:Artifact', prov:type='prov:Dictionary', prov:type='prov:Collection', prov:hadDictionaryMember='id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5', prov:hadDictionaryMember='id:f923bbf9-1c94-4771-9333-77547e7e828e']) + used(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, data:, 2022-04-04T16:59:09.404363, [prov:role='wf:main/__DATA_FETCH__/paramfile']) + entity(id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:9af37a24-65f9-41cd-8191-228ec8108418', prov:hadDictionaryMember='id:441a9ce2-fada-464f-84fb-6dfd01a6379e', prov:hadDictionaryMember='id:15212ae6-d7ff-4660-870e-34f3caa32ceb']) + entity(id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:38113d6d-950c-4c1a-826d-636d3c6fa3ea', prov:hadDictionaryMember='id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a', prov:hadDictionaryMember='id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce', prov:hadDictionaryMember='id:0196242d-cfb9-45f3-965c-8fa2a037f104']) + entity(id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:b17c488e-30c3-42cb-b2f0-092b0efe2427', 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data:hdas) + entity(id:b17c488e-30c3-42cb-b2f0-092b0efe2427, [prov:type='prov:KeyEntityPair', prov:pairKey="type", prov:pairEntity='data:hdas']) + entity(data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f, [prov:type='wfprov:Artifact', prov:value="urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f"]) + hadMember(id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f, data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f) + entity(id:e1829e51-7947-4db2-99a0-1ea7703ee764, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f']) + hadMember(id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2, id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f) + entity(id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a, [prov:type='prov:KeyEntityPair', prov:pairKey="destination", prov:pairEntity='id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f']) + entity(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72', prov:hadDictionaryMember='id:b0586419-dbb7-4757-9cfd-ae55abef3674', prov:hadDictionaryMember='id:3b543d5d-26b4-48f1-8c80-0c288c8df33f', prov:hadDictionaryMember='id:5f9613d6-b39e-40e1-95d2-d26fb37550fe', prov:hadDictionaryMember='id:8a2cf341-8042-40bd-8509-b56f1f4161c7', prov:hadDictionaryMember='id:4b32d7ec-e96f-41ff-8feb-1e43324962da', prov:hadDictionaryMember='id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a', prov:hadDictionaryMember='id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca', prov:hadDictionaryMember='id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783', prov:hadDictionaryMember='id:f5199f67-c23f-46de-a504-11e5465e2e8c', prov:hadDictionaryMember='id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01']) entity(data:auto, [prov:type='wfprov:Artifact', prov:value="auto"]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:auto) - entity(id:79566035-3dfd-4779-837a-344529381251, [prov:type='prov:KeyEntityPair', prov:pairKey="ext", prov:pairEntity='data:auto']) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, data:auto) + entity(id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca, [prov:type='prov:KeyEntityPair', prov:pairKey="ext", prov:pairEntity='data:auto']) entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:?) - entity(id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60, [prov:type='prov:KeyEntityPair', prov:pairKey="dbkey", prov:pairEntity='data:?']) - entity(id:9e633b9f-343d-4b29-a78a-85afdd8eef53, [prov:value="1" %% xsd:boolean]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:9e633b9f-343d-4b29-a78a-85afdd8eef53) - entity(id:792b7ecd-597e-41ad-ac59-b0767919b4b7, [prov:type='prov:KeyEntityPair', prov:pairKey="to_posix_lines", prov:pairEntity='id:9e633b9f-343d-4b29-a78a-85afdd8eef53']) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, data:?) + entity(id:5f9613d6-b39e-40e1-95d2-d26fb37550fe, [prov:type='prov:KeyEntityPair', prov:pairKey="dbkey", prov:pairEntity='data:?']) + entity(id:f23be627-a96d-47ce-b857-30e370a747a9, [prov:value="1" %% xsd:boolean]) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, id:f23be627-a96d-47ce-b857-30e370a747a9) + entity(id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783, [prov:type='prov:KeyEntityPair', prov:pairKey="to_posix_lines", prov:pairEntity='id:f23be627-a96d-47ce-b857-30e370a747a9']) entity(data:path, [prov:type='wfprov:Artifact', prov:value="path"]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:path) - entity(id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:path']) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, data:path) + entity(id:4b32d7ec-e96f-41ff-8feb-1e43324962da, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:path']) entity(data:dataset2.txt, [prov:type='wfprov:Artifact', prov:value="dataset2.txt"]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:dataset2.txt) - entity(id:97939793-b619-47e0-8ec3-d3baf5965151, [prov:type='prov:KeyEntityPair', prov:pairKey="name", prov:pairEntity='data:dataset2.txt']) - entity(id:780092f0-87bd-42bc-a3d8-50143d44998b, [prov:type='wfprov:Artifact', prov:type='prov:EmptyCollection', prov:type='prov:Collection']) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:780092f0-87bd-42bc-a3d8-50143d44998b) - entity(id:f45f9536-1278-4069-8b91-7edd97d3ff80, [prov:type='prov:KeyEntityPair', prov:pairKey="hashes", prov:pairEntity='id:780092f0-87bd-42bc-a3d8-50143d44998b']) - entity(id:0f5709cc-12f6-430c-a605-fd3e8978f6c4, [prov:value="0" %% xsd:boolean]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:0f5709cc-12f6-430c-a605-fd3e8978f6c4) - entity(id:c0c38d7d-cd18-4050-b5e8-0faf10393207, [prov:type='prov:KeyEntityPair', prov:pairKey="in_place", prov:pairEntity='id:0f5709cc-12f6-430c-a605-fd3e8978f6c4']) - entity(id:87e7e990-d873-4d20-a6ee-b15094940df1, [prov:value="0" %% xsd:boolean]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:87e7e990-d873-4d20-a6ee-b15094940df1) - entity(id:f67dbd55-b05c-4a56-aea3-4041399b62d1, [prov:type='prov:KeyEntityPair', prov:pairKey="purge_source", prov:pairEntity='id:87e7e990-d873-4d20-a6ee-b15094940df1']) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, data:dataset2.txt) + entity(id:b0586419-dbb7-4757-9cfd-ae55abef3674, [prov:type='prov:KeyEntityPair', prov:pairKey="name", prov:pairEntity='data:dataset2.txt']) + entity(id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1, [prov:type='prov:Collection', prov:type='wfprov:Artifact', prov:type='prov:EmptyCollection']) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1) + entity(id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72, [prov:type='prov:KeyEntityPair', prov:pairKey="hashes", prov:pairEntity='id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1']) + entity(id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7, [prov:value="0" %% xsd:boolean]) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7) + entity(id:8a2cf341-8042-40bd-8509-b56f1f4161c7, [prov:type='prov:KeyEntityPair', prov:pairKey="in_place", prov:pairEntity='id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7']) + entity(id:76b51c9a-5a58-43ce-b9a9-7f4459602a11, [prov:value="0" %% xsd:boolean]) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, id:76b51c9a-5a58-43ce-b9a9-7f4459602a11) + entity(id:3b543d5d-26b4-48f1-8c80-0c288c8df33f, [prov:type='prov:KeyEntityPair', prov:pairKey="purge_source", prov:pairEntity='id:76b51c9a-5a58-43ce-b9a9-7f4459602a11']) entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) - entity(id:069bb313-b651-474e-9a28-fdc7af0fc87b, [prov:type='prov:KeyEntityPair', prov:pairKey="path", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) - entity(id:bd860612-ca87-49c5-9d5c-d086f706f789, [prov:value=155708]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, id:bd860612-ca87-49c5-9d5c-d086f706f789) - entity(id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64, [prov:type='prov:KeyEntityPair', prov:pairKey="object_id", prov:pairEntity='id:bd860612-ca87-49c5-9d5c-d086f706f789']) - entity(data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, [prov:type='wfprov:Artifact', prov:value="urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9"]) - hadMember(id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9, data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9) - entity(id:66fde9d0-4440-4811-8b03-ae8c34cfebb6, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9']) - entity(id:e7516c89-e4ed-494b-bf16-74b40fa66bd1, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:e7516c89-e4ed-494b-bf16-74b40fa66bd1, id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9) - hadMember(id:641c238b-2832-4fab-b949-f5f4fc01deb1, id:e7516c89-e4ed-494b-bf16-74b40fa66bd1) - entity(id:3b176baa-a8f8-426c-ab0d-aa428d41923d, [prov:type='prov:KeyEntityPair', prov:pairKey="elements", prov:pairEntity='id:e7516c89-e4ed-494b-bf16-74b40fa66bd1']) - entity(id:e8c438c4-7544-4049-8d34-f825ecd3b5e1, [prov:value="0" %% xsd:boolean]) - hadMember(id:641c238b-2832-4fab-b949-f5f4fc01deb1, id:e8c438c4-7544-4049-8d34-f825ecd3b5e1) - entity(id:ab8003d1-3e46-4af7-9325-fffe09639b01, [prov:type='prov:KeyEntityPair', prov:pairKey="auto_decompress", prov:pairEntity='id:e8c438c4-7544-4049-8d34-f825ecd3b5e1']) - entity(data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1, [prov:type='wfprov:Artifact', prov:value="urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1"]) - hadMember(id:641c238b-2832-4fab-b949-f5f4fc01deb1, data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1) - entity(id:9f4835d1-a5f0-499e-9315-42fed1edd2a1, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1']) - entity(id:34aa3429-439f-49df-b575-0c7aee2caa81, [prov:type='wfprov:Artifact', prov:type='prov:Collection']) - hadMember(id:34aa3429-439f-49df-b575-0c7aee2caa81, id:641c238b-2832-4fab-b949-f5f4fc01deb1) - hadMember(id:594019f6-4154-49a8-be37-3d511a35f066, id:34aa3429-439f-49df-b575-0c7aee2caa81) - entity(id:7067149e-f997-4e01-810a-41ed1aaae3f1, [prov:type='prov:KeyEntityPair', prov:pairKey="targets", prov:pairEntity='id:34aa3429-439f-49df-b575-0c7aee2caa81']) - entity(id:ffdb63df-93ba-4e67-8097-308bfd9ba39d, [prov:value="1" %% xsd:boolean]) - hadMember(id:594019f6-4154-49a8-be37-3d511a35f066, id:ffdb63df-93ba-4e67-8097-308bfd9ba39d) - entity(id:e2f3637a-f559-46a0-a630-9f3e47800b70, [prov:type='prov:KeyEntityPair', prov:pairKey="check_content", prov:pairEntity='id:ffdb63df-93ba-4e67-8097-308bfd9ba39d']) - entity(data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066, [prov:type='wfprov:Artifact', prov:value="urn:uuid:594019f6-4154-49a8-be37-3d511a35f066"]) - hadMember(id:594019f6-4154-49a8-be37-3d511a35f066, data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066) - entity(id:1e8684e9-896e-4a38-bfe9-1995d0893fdd, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066']) - used(id:a1a08c93-d0b2-4806-8abb-697cf651f9a4, id:594019f6-4154-49a8-be37-3d511a35f066, 2022-03-31T15:39:11.762940, [prov:role='wf:main/__DATA_FETCH__/request_json']) + hadMember(id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01, [prov:type='prov:KeyEntityPair', prov:pairKey="path", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(id:4ed44fba-accb-410c-baef-53d2cb882954, [prov:value=155708]) + 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entity(id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce, [prov:type='prov:KeyEntityPair', prov:pairKey="elements", prov:pairEntity='id:56b63fc0-3bb2-448b-8115-c1cb4384d8db']) + entity(id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d, [prov:value="0" %% xsd:boolean]) + hadMember(id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2, id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d) + entity(id:0196242d-cfb9-45f3-965c-8fa2a037f104, [prov:type='prov:KeyEntityPair', prov:pairKey="auto_decompress", prov:pairEntity='id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d']) + entity(data:urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2, [prov:type='wfprov:Artifact', prov:value="urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2"]) + hadMember(id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2, data:urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2) + entity(id:38113d6d-950c-4c1a-826d-636d3c6fa3ea, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2']) + entity(id:508b7a80-e3e7-442e-b9e9-4874e2916aad, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:508b7a80-e3e7-442e-b9e9-4874e2916aad, id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2) + hadMember(id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c, id:508b7a80-e3e7-442e-b9e9-4874e2916aad) + entity(id:15212ae6-d7ff-4660-870e-34f3caa32ceb, [prov:type='prov:KeyEntityPair', prov:pairKey="targets", prov:pairEntity='id:508b7a80-e3e7-442e-b9e9-4874e2916aad']) + entity(id:f715a46b-9eff-48c3-b88f-1f3a009ea573, [prov:value="1" %% xsd:boolean]) + hadMember(id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c, id:f715a46b-9eff-48c3-b88f-1f3a009ea573) + entity(id:9af37a24-65f9-41cd-8191-228ec8108418, [prov:type='prov:KeyEntityPair', prov:pairKey="check_content", prov:pairEntity='id:f715a46b-9eff-48c3-b88f-1f3a009ea573']) + entity(data:urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c, [prov:type='wfprov:Artifact', prov:value="urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c"]) + hadMember(id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c, 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prov:pairEntity='id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd']) entity(data:0, [prov:type='wfprov:Artifact', prov:value="0"]) - hadMember(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, data:0) - entity(id:5ba613ce-6eaa-412d-89bf-eb8f580823a3, [prov:type='prov:KeyEntityPair', prov:pairKey="seed", prov:pairEntity='data:0']) + hadMember(id:cb9975e1-3882-4cc3-9995-9352d37f1948, data:0) + entity(id:3f28e37f-bba8-4b0d-b4d8-ad4749630604, [prov:type='prov:KeyEntityPair', prov:pairKey="seed", prov:pairEntity='data:0']) entity(data:set_seed, [prov:type='wfprov:Artifact', prov:value="set_seed"]) - hadMember(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, data:set_seed) - entity(id:903792cc-566c-4ffe-ade9-be65cf4f1fb4, [prov:type='prov:KeyEntityPair', prov:pairKey="seed_source_selector", prov:pairEntity='data:set_seed']) - entity(data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d, [prov:type='wfprov:Artifact', prov:value="urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d"]) - hadMember(id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d) - entity(id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d']) - used(id:2341e04b-a08b-400e-97ef-3151f01a17fa, id:7e6d530d-6c05-48b1-8d69-879b6e790c9d, 2022-03-31T15:39:11.770390, [prov:role='wf:main/random_lines1/seed_source']) + hadMember(id:cb9975e1-3882-4cc3-9995-9352d37f1948, data:set_seed) + entity(id:7884960e-a973-4e8f-bb01-58005de82366, [prov:type='prov:KeyEntityPair', prov:pairKey="seed_source_selector", prov:pairEntity='data:set_seed']) + entity(data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948, [prov:type='wfprov:Artifact', prov:value="urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948"]) + hadMember(id:cb9975e1-3882-4cc3-9995-9352d37f1948, data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948) + entity(id:c753b9e4-3908-491a-a7a8-a0d4e1543e34, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948']) + used(id:1747ea92-6d32-4175-9aef-2893fc71c7a5, id:cb9975e1-3882-4cc3-9995-9352d37f1948, 2022-04-04T16:59:09.414862, [prov:role='wf:main/random_lines1/seed_source']) endDocument \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl index 41da725e..c7b80cee 100644 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl @@ -5,177 +5,177 @@ @prefix prov: . @prefix rdfs: . @prefix schema: . -@prefix wf: . +@prefix wf: . @prefix wfprov: . @prefix xsd: . -id:2341e04b-a08b-400e-97ef-3151f01a17fa a wfprov:ProcessRun, +id:1747ea92-6d32-4175-9aef-2893fc71c7a5 a wfprov:ProcessRun, prov:Activity ; rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; + prov:hadPlan ] ; prov:qualifiedStart [ a prov:Start ; prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.769026"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.414376"^^xsd:dateTime ; + prov:entity id:db786d1e-928b-4b0f-b118-bd235731ea9a ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.770390"^^xsd:dateTime ; - prov:entity id:7e6d530d-6c05-48b1-8d69-879b6e790c9d ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.413468"^^xsd:dateTime ; + prov:entity id:c857b436-a405-4bf1-9b58-1f2d255d91b5 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.769116"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.413652"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.769772"^^xsd:dateTime ; - prov:entity id:fd40a61e-108c-42c4-8b49-c20815d2d9e5 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.414444"^^xsd:dateTime ; + prov:entity data:3 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.768651"^^xsd:dateTime ; - prov:entity id:8a1a4095-2cbb-468e-80d6-25ebab181a3e ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.413710"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.768810"^^xsd:dateTime ; - prov:entity id:6cf20326-6a50-4476-910c-c40be8829bc4 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.413826"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.769848"^^xsd:dateTime ; - prov:entity data:3 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.413588"^^xsd:dateTime ; + prov:entity id:a8ba8607-96e1-4d6f-a17e-3e4d3a1168c8 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.768884"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.413770"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.768956"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ] ; + prov:atTime "2022-04-04T16:59:09.414862"^^xsd:dateTime ; + prov:entity id:cb9975e1-3882-4cc3-9995-9352d37f1948 ; + prov:hadRole ] ; prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . -id:414221e9-e943-451a-bde9-ef492e1cf85c a wfprov:ProcessRun, +id:290068a6-8ef9-4718-800b-cb22efbdfd62 a wfprov:ProcessRun, prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; + rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; + prov:hadPlan ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.763491"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.411252"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.765267"^^xsd:dateTime ; - prov:entity id:71e28368-850b-441f-a008-8b6173a866d7 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.411312"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.763447"^^xsd:dateTime ; - prov:entity id:ebf027ac-b671-468a-91c6-1bfd7e45eb36 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.411016"^^xsd:dateTime ; + prov:entity id:6c4049ff-bf0b-4c3e-829d-16e5ece01b8e ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.763813"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.411369"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.763772"^^xsd:dateTime ; - prov:entity id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.412881"^^xsd:dateTime ; + prov:entity id:67c5d8ae-be1d-41a2-85c9-d0543a97dd3e ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.765313"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + prov:atTime "2022-04-04T16:59:09.411131"^^xsd:dateTime ; + prov:entity id:90923c5c-2bd8-4aa7-a029-817e8b57037a ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.411190"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.410900"^^xsd:dateTime ; + prov:entity id:d731fa25-6b69-4910-80ab-897579cd74ba ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.411964"^^xsd:dateTime ; + prov:entity id:b040da72-a0ee-4309-ad1e-353be140b04a ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . -id:a1a08c93-d0b2-4806-8abb-697cf651f9a4 a wfprov:ProcessRun, +id:b7a0ab16-c370-48aa-924b-74d57ab7d542 a wfprov:ProcessRun, prov:Activity ; rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; + prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; + prov:hadPlan ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.760237"^^xsd:dateTime ; - prov:entity id:5c05f71f-74dc-4238-a591-9df8dfa779f8 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.410250"^^xsd:dateTime ; + prov:entity id:ce5712eb-9c70-401d-811e-a01bfdbf3b3f ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.760286"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.410320"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.759864"^^xsd:dateTime ; - prov:entity id:d4c2d49d-ab80-43ab-b347-a7db85bf7262 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.407631"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.762940"^^xsd:dateTime ; - prov:entity id:594019f6-4154-49a8-be37-3d511a35f066 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.408037"^^xsd:dateTime ; + prov:entity id:c00decaf-ac43-4246-8705-8c1bb0defce1 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.759917"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.407566"^^xsd:dateTime ; + prov:entity id:fb247085-dfc8-42bc-bee7-a7475ce9289a ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.762994"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + prov:atTime "2022-04-04T16:59:09.408097"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . -id:cade945a-1ff3-4273-a78e-7b5358804c89 a wfprov:ProcessRun, +id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c a wfprov:ProcessRun, prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; + prov:hadPlan ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:hadActivity id:dd421f2f-c538-44d3-aeeb-484022c6541d ] ; + prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.766037"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.765900"^^xsd:dateTime ; - prov:entity id:a1110187-8be9-4aff-b03e-3530ed7f6cbf ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.765788"^^xsd:dateTime ; - prov:entity id:730e5d81-2c3c-44d7-9916-9cc0b7bcdd81 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.767885"^^xsd:dateTime ; - prov:entity id:682cbd95-9570-4f19-a8bb-a639bfb641e2 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.406936"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.766105"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.403801"^^xsd:dateTime ; + prov:entity id:e13acf9b-83e9-40f0-adc1-a7195e612fa3 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.765700"^^xsd:dateTime ; - prov:entity id:837879db-a58f-45bc-980d-2da57fd19cd1 ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.406855"^^xsd:dateTime ; + prov:entity id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.766169"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.404363"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.765965"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], + prov:atTime "2022-04-04T16:59:09.404286"^^xsd:dateTime ; + prov:entity id:bef03503-1c1f-4f05-9a58-56449dcc9ac3 ; + prov:hadRole ], [ a prov:Usage ; - prov:atTime "2022-03-31T15:39:11.766787"^^xsd:dateTime ; - prov:entity id:a9607900-c633-4837-a4a7-eaee6edcaf3b ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + prov:atTime "2022-04-04T16:59:09.403870"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . orcid:0000-0002-8940-4946 a schema:Person, prov:Agent, @@ -200,597 +200,597 @@ data:7c1d8e3101dbcdba a wfprov:Artifact, prov:Entity ; prov:value "7c1d8e3101dbcdba"^^xsd:string . -id:062d0748-7b74-4d45-98f3-80bd22ed2672 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:51656ecb-5b39-4ad7-9888-d7b93ca28266, - id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747, - id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748 ; - prov:hadMember data:2e789aae2475b7da, - data:hda, - . - -id:069bb313-b651-474e-9a28-fdc7af0fc87b a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "path"^^xsd:string . - -id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64 a prov:Entity, +id:0196242d-cfb9-45f3-965c-8fa2a037f104 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:bd860612-ca87-49c5-9d5c-d086f706f789 ; - prov:pairKey "object_id"^^xsd:string . - -id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad ; - prov:pairKey "__current_case__"^^xsd:string . - -id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:fd7fec473f1e6c6b ; - prov:pairKey "id"^^xsd:string . + prov:pairEntity id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d ; + prov:pairKey "auto_decompress"^^xsd:string . -id:1e8684e9-896e-4a38-bfe9-1995d0893fdd a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . +id:027f7717-78d8-4f9a-a887-87813339b23e a prov:Agent ; + prov:actedOnBehalfOf orcid:0000-0002-8940-4946 . -id:24d7454e-9885-40b1-8a85-cc272df4fa40 a wfprov:Artifact, +id:02bb9d1c-f248-47fb-ac2c-9985301385a7 a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94, - id:96981ec2-dac6-4477-9ac3-431cdc24f7ac, - id:c40c9210-5155-480f-ba36-5f86aaa39d77 ; - prov:hadMember data:fd7fec473f1e6c6b, - data:hda, - . + prov:hadDictionaryMember id:7c60b838-dd41-4166-aa41-6e652e5ef63b, + id:e0524eed-ea77-413b-b0db-5f72e16c365e, + id:f8f974ae-cd55-4986-8a9e-1d987b76fd34 ; + prov:hadMember , + , + id:5d7467bd-1ab8-46ea-8a56-0998f42b079c . -id:279428d4-794f-42cd-9419-0c8c71385b78 a prov:Entity, +id:06db435a-b77f-424b-8301-acb7e18cc2ce a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:23fbeb5c-eebc-41ef-a966-be8a191c7ede ; - prov:pairKey "values"^^xsd:string . + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . -id:286ffa7a-a1f3-424c-90cf-f36d112b13f0 a prov:Entity, +id:08ffc626-141c-4214-8d71-746a1218f209 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:dataset1.txt ; - prov:pairKey "name"^^xsd:string . + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . -id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99 a prov:Entity, +id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity ; prov:pairKey "@id"^^xsd:string . -id:34523c4b-aa54-4d13-8d25-76acadcc8df7 a prov:Entity, +id:0c415611-9c31-47d4-82f9-a6330b980a8e a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:65dace90-ed17-46f9-b809-d98a90563655 ; - prov:pairKey "auto_decompress"^^xsd:string . + prov:pairEntity id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea ; + prov:pairKey "elements"^^xsd:string . -id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 a wfprov:Artifact, +id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98, - id:869277c3-8c88-4381-bbef-de17240b1c23, - id:a1bb89e0-badf-490a-af30-375efe69c057 ; + prov:hadDictionaryMember id:a92435e7-0621-4629-80fa-d73aa1989363, + id:e311b33d-139a-4e92-a5c1-3a04530b9128, + id:f268cc7a-3474-404e-892f-8af376e98ae3 ; prov:hadMember , - , - id:0c54448a-8444-42cd-9dd1-b65dfb0656ba . - -id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:7ca3de8f49293d1a ; - prov:pairKey "id"^^xsd:string . - -id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:368b85e6-a18c-4452-90ef-32ee5ccd0308 ; - prov:pairKey "in_place"^^xsd:string . - -id:3b176baa-a8f8-426c-ab0d-aa428d41923d a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:e7516c89-e4ed-494b-bf16-74b40fa66bd1 ; - prov:pairKey "elements"^^xsd:string . - -id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:8dbadfd6-d421-4d18-95ae-36fc4defb317 ; - prov:pairKey "elements"^^xsd:string . + , + id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc . -id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 a wfprov:Artifact, +id:0ff29d35-01d6-471f-84e8-a1fc63c05daa a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:069bb313-b651-474e-9a28-fdc7af0fc87b, - id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64, - id:66fde9d0-4440-4811-8b03-ae8c34cfebb6, - id:792b7ecd-597e-41ad-ac59-b0767919b4b7, - id:79566035-3dfd-4779-837a-344529381251, - id:97939793-b619-47e0-8ec3-d3baf5965151, - id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60, - id:c0c38d7d-cd18-4050-b5e8-0faf10393207, - id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01, - id:f45f9536-1278-4069-8b91-7edd97d3ff80, - id:f67dbd55-b05c-4a56-aea3-4041399b62d1 ; - prov:hadMember , + prov:hadDictionaryMember id:06db435a-b77f-424b-8301-acb7e18cc2ce, + id:08ffc626-141c-4214-8d71-746a1218f209, + id:23fe35b3-2a01-4edf-952a-5769462abc6c, + id:46ce5c94-417b-4bcf-a9af-fb60912d385a, + id:7dc6f8f5-cce3-4da9-b386-0a18314af498, + id:919c8f14-f4f3-4151-b936-d7502f64caa4, + id:a05e1e9a-74e5-4efc-ad75-96c15f4a83ce, + id:bab1f03d-7ca6-4bb7-a57d-563c0e70808b, + id:bb0b8464-83db-421e-9566-a31da915d209, + id:c256e77e-7189-430a-8c59-03fa703dce07, + id:d281fed1-869b-4451-8fda-95b26856a918 ; + prov:hadMember , , data:auto, - data:dataset2.txt, + data:dataset1.txt, data:path, - , - id:0f5709cc-12f6-430c-a605-fd3e8978f6c4, - id:780092f0-87bd-42bc-a3d8-50143d44998b, - id:87e7e990-d873-4d20-a6ee-b15094940df1, - id:9e633b9f-343d-4b29-a78a-85afdd8eef53, - id:bd860612-ca87-49c5-9d5c-d086f706f789 . + , + id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80, + id:493493b1-836f-404c-9084-95086d7ba06a, + id:721f1551-f868-4e7d-8cb4-6f196df24a97, + id:87697625-c033-4483-b5fa-d00140b03808, + id:addafc7d-4439-49fb-9870-b6b0ed7415c3 . -id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be a prov:Entity, +id:10f720aa-40e7-4c83-9ad1-02ffc26a7944 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:hdas ; - prov:pairKey "type"^^xsd:string . + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:4529ad17-6e7b-4493-bba5-475a60c4a11a a prov:Entity, +id:15212ae6-d7ff-4660-870e-34f3caa32ceb a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:e6248791-d7c3-49a7-9660-5cb622189a3c ; - prov:pairKey "input2"^^xsd:string . + prov:pairEntity id:508b7a80-e3e7-442e-b9e9-4874e2916aad ; + prov:pairKey "targets"^^xsd:string . + +id:1b548405-6990-454a-98a6-128dccf12014 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd ; + prov:pairKey "__current_case__"^^xsd:string . -id:4745fa68-123c-4afb-9176-dcf61732f695 a prov:Entity, +id:23fe35b3-2a01-4edf-952a-5769462abc6c a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:03d9f2a8-6e48-40b3-84e4-f13e161decf1 ; + prov:pairEntity id:493493b1-836f-404c-9084-95086d7ba06a ; prov:pairKey "to_posix_lines"^^xsd:string . -id:47d09ccc-4b59-4330-9361-9f1b65b860a8 a prov:Entity, +id:298c9e09-232d-4854-bf61-8116b1323f5b a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:d84bb265-2540-4cad-a026-511b7a21323e ; - prov:pairKey "destination"^^xsd:string . + prov:pairEntity id:663c25a0-9302-4b8f-aa89-765f3284aeca ; + prov:pairKey "values"^^xsd:string . -id:51656ecb-5b39-4ad7-9888-d7b93ca28266 a prov:Entity, +id:2d384308-e0b1-4f82-811c-4bba81b92067 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:2e789aae2475b7da ; - prov:pairKey "id"^^xsd:string . + prov:pairEntity id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f ; + prov:pairKey "auto_decompress"^^xsd:string . -id:57844284-ccc8-45f3-a7fa-6ce0246cf99b a prov:Entity, +id:34e6b60d-4d4a-496d-bb9c-a4d34040155c a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:7827651a-85f5-48a4-8f9d-1427fc02bda4 ; - prov:pairKey "values"^^xsd:string . + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . -id:594019f6-4154-49a8-be37-3d511a35f066 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:1e8684e9-896e-4a38-bfe9-1995d0893fdd, - id:7067149e-f997-4e01-810a-41ed1aaae3f1, - id:e2f3637a-f559-46a0-a630-9f3e47800b70 ; - prov:hadMember , - id:34aa3429-439f-49df-b575-0c7aee2caa81, - id:ffdb63df-93ba-4e67-8097-308bfd9ba39d . +id:38113d6d-950c-4c1a-826d-636d3c6fa3ea a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:5ab542a0-7a79-4f00-b120-b14b0542e568 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:88aa880c-c240-4877-b1e7-a0c20e29ef3e, - id:d3a55e5b-c1fb-4523-b77d-993b00128b05, - id:ef96000b-e230-40a1-a36a-a45f4ca78a0e ; - prov:hadMember , - , - id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 . +id:3ad229e9-064d-4398-8617-d802f10ac40b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:3b543d5d-26b4-48f1-8c80-0c288c8df33f a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:76b51c9a-5a58-43ce-b9a9-7f4459602a11 ; + prov:pairKey "purge_source"^^xsd:string . -id:5ba613ce-6eaa-412d-89bf-eb8f580823a3 a prov:Entity, +id:3f28e37f-bba8-4b0d-b4d8-ad4749630604 a prov:Entity, prov:KeyEntityPair ; prov:pairEntity data:0 ; prov:pairKey "seed"^^xsd:string . -id:5c05f71f-74dc-4238-a591-9df8dfa779f8 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 . - -id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6 a prov:Entity, +id:3f52ff7d-9aa8-45c7-8af1-1f7f474c6ad7 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:8bae3361-cfbe-4b69-bfa0-34901d319a21 ; - prov:pairKey "hashes"^^xsd:string . - -id:641c238b-2832-4fab-b949-f5f4fc01deb1 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:3b176baa-a8f8-426c-ab0d-aa428d41923d, - id:47d09ccc-4b59-4330-9361-9f1b65b860a8, - id:9f4835d1-a5f0-499e-9315-42fed1edd2a1, - id:ab8003d1-3e46-4af7-9325-fffe09639b01 ; - prov:hadMember , - id:d84bb265-2540-4cad-a026-511b7a21323e, - id:e7516c89-e4ed-494b-bf16-74b40fa66bd1, - id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 . + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:66fde9d0-4440-4811-8b03-ae8c34cfebb6 a prov:Entity, +id:441a9ce2-fada-464f-84fb-6dfd01a6379e a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity ; prov:pairKey "@id"^^xsd:string . -id:682cbd95-9570-4f19-a8bb-a639bfb641e2 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:f39be690-c7d7-4911-be28-6afc1abe40b0 . +id:46ce5c94-417b-4bcf-a9af-fb60912d385a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:721f1551-f868-4e7d-8cb4-6f196df24a97 ; + prov:pairKey "in_place"^^xsd:string . -id:68c6bdfd-f17d-41b8-bdba-eb3a46749940 a prov:Entity, +id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:pairEntity id:f23be627-a96d-47ce-b857-30e370a747a9 ; + prov:pairKey "to_posix_lines"^^xsd:string . -id:6cf20326-6a50-4476-910c-c40be8829bc4 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:775bc9b3c1750167 . +id:49e48096-0a9e-4ebd-8d9b-2b3647acb1b5 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . -id:6d29c983-528d-46cf-b420-1c9210619f0d a prov:Entity, +id:4b32d7ec-e96f-41ff-8feb-1e43324962da a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:fc84f9f8-5bb4-402d-ba90-697df02824ca ; - prov:pairKey "check_content"^^xsd:string . + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . -id:6d494d29-2bc7-4da4-ba43-e816ee0b1266 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:286ffa7a-a1f3-424c-90cf-f36d112b13f0, - id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1, - id:4745fa68-123c-4afb-9176-dcf61732f695, - id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6, - id:8ced01f6-47ea-4320-b65a-6af7a668fbe9, - id:98a55032-1c60-4303-8ca0-5cff21b96b9d, - id:ab51fb43-4e4d-459e-ae56-672b92ac89ea, - id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5, - id:d9811e1d-402f-4343-bc31-7dd5643dbdac, - id:fbca4ec6-e519-477f-84ce-23e70dddcc8b, - id:feb54146-911b-4d39-90cf-ef6d66b46fe4 ; - prov:hadMember , - , - data:auto, - data:dataset1.txt, - data:path, - , - id:03d9f2a8-6e48-40b3-84e4-f13e161decf1, - id:368b85e6-a18c-4452-90ef-32ee5ccd0308, - id:8bae3361-cfbe-4b69-bfa0-34901d319a21, - id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a, - id:f350a230-ff86-44a3-8560-e35c1ba07b59 . +id:4ee5e287-4b5d-4d40-be38-1bf1c3236934 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:7067149e-f997-4e01-810a-41ed1aaae3f1 a prov:Entity, +id:551327a9-e8db-4d46-8ec4-cde270df080b a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:34aa3429-439f-49df-b575-0c7aee2caa81 ; - prov:pairKey "targets"^^xsd:string . + prov:pairEntity id:f8915280-6e26-4eef-b378-cf27df3f8f1d ; + prov:pairKey "values"^^xsd:string . -id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98 a prov:Entity, +id:5f9613d6-b39e-40e1-95d2-d26fb37550fe a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:0c54448a-8444-42cd-9dd1-b65dfb0656ba ; - prov:pairKey "__index__"^^xsd:string . + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . -id:71e28368-850b-441f-a008-8b6173a866d7 a wfprov:Artifact, +id:6102b40f-814e-41b4-8e21-caee1eab126b a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:68c6bdfd-f17d-41b8-bdba-eb3a46749940, - id:6d29c983-528d-46cf-b420-1c9210619f0d, - id:a75e7105-d7f0-4a77-865c-2ff5b3162e47 ; - prov:hadMember , - id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1, - id:fc84f9f8-5bb4-402d-ba90-697df02824ca . + prov:hadDictionaryMember id:0c415611-9c31-47d4-82f9-a6330b980a8e, + id:2d384308-e0b1-4f82-811c-4bba81b92067, + id:788acdf9-5e3a-4774-aa66-3068819b5cae, + id:cc8b2ec1-0c34-4d44-bce6-9dfb3efd9298 ; + prov:hadMember , + id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f, + id:9ae42623-faf1-431a-acd3-bce4a4c24a24, + id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea . -id:730e5d81-2c3c-44d7-9916-9cc0b7bcdd81 a wfprov:Artifact, +id:67c5d8ae-be1d-41a2-85c9-d0543a97dd3e a wfprov:Artifact, prov:Collection, prov:Entity ; - prov:hadMember data:2e789aae2475b7da . + prov:hadMember id:7519c8b1-64da-4255-9960-acb3dda9ab98 . -id:792b7ecd-597e-41ad-ac59-b0767919b4b7 a prov:Entity, +id:689d969e-0df7-40c8-b733-b4e39fd49d34 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:9e633b9f-343d-4b29-a78a-85afdd8eef53 ; - prov:pairKey "to_posix_lines"^^xsd:string . - -id:79566035-3dfd-4779-837a-344529381251 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:auto ; - prov:pairKey "ext"^^xsd:string . + prov:pairEntity id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab ; + prov:pairKey "targets"^^xsd:string . -id:7e6d530d-6c05-48b1-8d69-879b6e790c9d a wfprov:Artifact, +id:6c4049ff-bf0b-4c3e-829d-16e5ece01b8e a wfprov:Artifact, prov:Collection, - prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9, - id:5ba613ce-6eaa-412d-89bf-eb8f580823a3, - id:903792cc-566c-4ffe-ade9-be65cf4f1fb4, - id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e ; - prov:hadMember data:0, - data:set_seed, - , - id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad . + prov:hadMember data:2e789aae2475b7da . -id:7f5d6ad7-2a1a-4c3a-84b4-33c006dd88d3 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:5ab542a0-7a79-4f00-b120-b14b0542e568 . +id:70e6aab8-ec0d-4ff2-a2d6-03a4ce5062fd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:351d875a-c130-42f7-ba2f-735780ea4ca8 ; + prov:pairKey "values"^^xsd:string . -id:7fc57149-e802-47ce-bf01-348e6e787dd0 a wfprov:Artifact, +id:70fb9ca7-9038-4874-bbda-0f12fad1627a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:7519c8b1-64da-4255-9960-acb3dda9ab98 a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:34523c4b-aa54-4d13-8d25-76acadcc8df7, - id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4, - id:9e45fea1-39c5-4b99-be26-72b06a5e8786, - id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e ; - prov:hadMember , - id:4fa4bb93-f67a-414c-8420-9272773cb5e2, - id:65dace90-ed17-46f9-b809-d98a90563655, - id:8dbadfd6-d421-4d18-95ae-36fc4defb317 . + prov:hadDictionaryMember id:92b2afc9-fc96-4764-adbe-73d014ba2357, + id:b397cf2b-901a-454c-bfc2-e966b6838269, + id:dc09c4fe-c4a9-4cc5-9770-0a4f19369ac0 ; + prov:hadMember , + id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a, + id:ac40b633-8521-462b-aea0-bea86dcaef7c . -id:8170c31b-5a5f-4150-8531-8b0adac0f282 a prov:Entity, +id:7884960e-a973-4e8f-bb01-58005de82366 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:pairEntity data:set_seed ; + prov:pairKey "seed_source_selector"^^xsd:string . -id:81d81eab-2874-43f4-9d2e-ce5ad6236054 a prov:Entity, +id:788acdf9-5e3a-4774-aa66-3068819b5cae a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity ; prov:pairKey "@id"^^xsd:string . -id:837879db-a58f-45bc-980d-2da57fd19cd1 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:7ca3de8f49293d1a . - -id:869277c3-8c88-4381-bbef-de17240b1c23 a prov:Entity, +id:7c60b838-dd41-4166-aa41-6e652e5ef63b a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity ; prov:pairKey "file_data"^^xsd:string . -id:88aa880c-c240-4877-b1e7-a0c20e29ef3e a prov:Entity, +id:7dc6f8f5-cce3-4da9-b386-0a18314af498 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity id:87697625-c033-4483-b5fa-d00140b03808 ; + prov:pairKey "purge_source"^^xsd:string . + +id:838aa24d-f8b4-4ddd-a76c-82460c5b6391 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; prov:pairKey "@id"^^xsd:string . -id:8a1a4095-2cbb-468e-80d6-25ebab181a3e a wfprov:Artifact, +id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2 a wfprov:Artifact, prov:Collection, + prov:Dictionary, prov:Entity ; - prov:hadMember data:fd7fec473f1e6c6b . + prov:hadDictionaryMember id:0196242d-cfb9-45f3-965c-8fa2a037f104, + id:38113d6d-950c-4c1a-826d-636d3c6fa3ea, + id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a, + id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce ; + prov:hadMember , + id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f, + id:56b63fc0-3bb2-448b-8115-c1cb4384d8db, + id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d . -id:8ced01f6-47ea-4320-b65a-6af7a668fbe9 a prov:Entity, +id:8a2cf341-8042-40bd-8509-b56f1f4161c7 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:path ; - prov:pairKey "src"^^xsd:string . + prov:pairEntity id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7 ; + prov:pairKey "in_place"^^xsd:string . + +id:90923c5c-2bd8-4aa7-a029-817e8b57037a a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . -id:903792cc-566c-4ffe-ade9-be65cf4f1fb4 a prov:Entity, +id:919c8f14-f4f3-4151-b936-d7502f64caa4 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:set_seed ; - prov:pairKey "seed_source_selector"^^xsd:string . + prov:pairEntity id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80 ; + prov:pairKey "object_id"^^xsd:string . -id:93b6a52a-f266-4837-9e8e-ed928fbd2775 a prov:Entity, +id:92b2afc9-fc96-4764-adbe-73d014ba2357 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity ; prov:pairKey "@id"^^xsd:string . -id:951bb963-10a7-4234-8119-1b13921f9629 a prov:Entity, +id:947491c9-a106-4578-b804-16c3100e0111 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:f40fd446-41cb-442e-bbb7-9a23d27296e5 ; - prov:pairKey "__index__"^^xsd:string . + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . -id:9578a96e-6635-4000-9c81-2951341b65c8 a prov:Entity, +id:994bb2e3-42f8-4fd1-9d6f-aff742a0b9b0 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:pairEntity data:fd7fec473f1e6c6b ; + prov:pairKey "id"^^xsd:string . -id:96981ec2-dac6-4477-9ac3-431cdc24f7ac a prov:Entity, +id:9af37a24-65f9-41cd-8191-228ec8108418 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:pairEntity id:f715a46b-9eff-48c3-b88f-1f3a009ea573 ; + prov:pairKey "check_content"^^xsd:string . -id:97939793-b619-47e0-8ec3-d3baf5965151 a prov:Entity, +id:9baabbde-52d6-4728-8ef7-738960d2a86f a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:dataset2.txt ; - prov:pairKey "name"^^xsd:string . + prov:pairEntity id:016238d2-8ca1-4335-b232-acae7f43ed72 ; + prov:pairKey "check_content"^^xsd:string . -id:98a55032-1c60-4303-8ca0-5cff21b96b9d a prov:Entity, +id:9fb40382-f182-481e-90e6-0e24006c71c5 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "dbkey"^^xsd:string . + prov:pairEntity data:7ca3de8f49293d1a ; + prov:pairKey "id"^^xsd:string . -id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5 a prov:Entity, +id:a05e1e9a-74e5-4efc-ad75-96c15f4a83ce a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:hdas ; - prov:pairKey "type"^^xsd:string . + prov:pairEntity data:dataset1.txt ; + prov:pairKey "name"^^xsd:string . -id:9e45fea1-39c5-4b99-be26-72b06a5e8786 a prov:Entity, +id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:4fa4bb93-f67a-414c-8420-9272773cb5e2 ; + prov:pairEntity id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f ; prov:pairKey "destination"^^xsd:string . -id:9f4835d1-a5f0-499e-9315-42fed1edd2a1 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . +id:a8ba8607-96e1-4d6f-a17e-3e4d3a1168c8 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:775bc9b3c1750167 . -id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e a prov:Entity, +id:a92435e7-0621-4629-80fa-d73aa1989363 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:pairEntity id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc ; + prov:pairKey "__index__"^^xsd:string . -id:a1110187-8be9-4aff-b03e-3530ed7f6cbf a wfprov:Artifact, +id:abbdd009-c520-4098-baf6-6400cf916ffa a wfprov:Artifact, prov:Collection, + prov:Dictionary, prov:Entity ; - prov:hadMember data:fd7fec473f1e6c6b . - -id:a1bb89e0-badf-490a-af30-375efe69c057 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:hadDictionaryMember id:947491c9-a106-4578-b804-16c3100e0111, + id:994bb2e3-42f8-4fd1-9d6f-aff742a0b9b0, + id:ad223424-b8ff-4704-a618-0a033ceaf3ea ; + prov:hadMember data:fd7fec473f1e6c6b, + data:hda, + . -id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747 a prov:Entity, +id:ad223424-b8ff-4704-a618-0a033ceaf3ea a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity ; prov:pairKey "@id"^^xsd:string . -id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . +id:b040da72-a0ee-4309-ad1e-353be140b04a a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:4ee5e287-4b5d-4d40-be38-1bf1c3236934, + id:551327a9-e8db-4d46-8ec4-cde270df080b ; + prov:hadMember , + id:f8915280-6e26-4eef-b378-cf27df3f8f1d . -id:a75e7105-d7f0-4a77-865c-2ff5b3162e47 a prov:Entity, +id:b0586419-dbb7-4757-9cfd-ae55abef3674 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1 ; - prov:pairKey "targets"^^xsd:string . + prov:pairEntity data:dataset2.txt ; + prov:pairKey "name"^^xsd:string . -id:a9607900-c633-4837-a4a7-eaee6edcaf3b a wfprov:Artifact, +id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:57844284-ccc8-45f3-a7fa-6ce0246cf99b, - id:e9967a89-6747-4067-95ed-5160b763f0b1 ; - prov:hadMember , - id:7827651a-85f5-48a4-8f9d-1427fc02bda4 . + prov:hadDictionaryMember id:15212ae6-d7ff-4660-870e-34f3caa32ceb, + id:441a9ce2-fada-464f-84fb-6dfd01a6379e, + id:9af37a24-65f9-41cd-8191-228ec8108418 ; + prov:hadMember , + id:508b7a80-e3e7-442e-b9e9-4874e2916aad, + id:f715a46b-9eff-48c3-b88f-1f3a009ea573 . -id:ab51fb43-4e4d-459e-ae56-672b92ac89ea a prov:Entity, +id:b17c488e-30c3-42cb-b2f0-092b0efe2427 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "path"^^xsd:string . + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . -id:ab8003d1-3e46-4af7-9325-fffe09639b01 a prov:Entity, +id:b397cf2b-901a-454c-bfc2-e966b6838269 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 ; - prov:pairKey "auto_decompress"^^xsd:string . + prov:pairEntity id:ac40b633-8521-462b-aea0-bea86dcaef7c ; + prov:pairKey "input2"^^xsd:string . -id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60 a prov:Entity, +id:bab1f03d-7ca6-4bb7-a57d-563c0e70808b a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "dbkey"^^xsd:string . + prov:pairEntity id:addafc7d-4439-49fb-9870-b6b0ed7415c3 ; + prov:pairKey "hashes"^^xsd:string . -id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5 a prov:Entity, +id:bb0b8464-83db-421e-9566-a31da915d209 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:f350a230-ff86-44a3-8560-e35c1ba07b59 ; - prov:pairKey "purge_source"^^xsd:string . + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:c0c38d7d-cd18-4050-b5e8-0faf10393207 a prov:Entity, +id:bef03503-1c1f-4f05-9a58-56449dcc9ac3 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a . + +id:c00decaf-ac43-4246-8705-8c1bb0defce1 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:02bb9d1c-f248-47fb-ac2c-9985301385a7 . + +id:c0fce355-42ca-41f4-88b0-ccc3b4fec7d2 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:0f5709cc-12f6-430c-a605-fd3e8978f6c4 ; - prov:pairKey "in_place"^^xsd:string . + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:c40c9210-5155-480f-ba36-5f86aaa39d77 a prov:Entity, +id:c256e77e-7189-430a-8c59-03fa703dce07 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:hda ; + prov:pairEntity data:path ; prov:pairKey "src"^^xsd:string . -id:c98b0b95-d818-4ba1-b535-11c4e6909fa3 a prov:Agent ; - prov:actedOnBehalfOf orcid:0000-0002-8940-4946 . +id:c753b9e4-3908-491a-a7a8-a0d4e1543e34 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:c857b436-a405-4bf1-9b58-1f2d255d91b5 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . -id:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 a wfprov:Artifact, +id:c9198eaf-36fb-42c4-bf4b-d740591fe470 a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99, - id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813, - id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d ; - prov:hadMember data:7ca3de8f49293d1a, + prov:hadDictionaryMember id:10f720aa-40e7-4c83-9ad1-02ffc26a7944, + id:34e6b60d-4d4a-496d-bb9c-a4d34040155c, + id:ebaa0943-a400-4daf-a2e7-f781b714a666 ; + prov:hadMember data:2e789aae2475b7da, data:hda, - . + . -id:d3a55e5b-c1fb-4523-b77d-993b00128b05 a prov:Entity, +id:cb9975e1-3882-4cc3-9995-9352d37f1948 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:1b548405-6990-454a-98a6-128dccf12014, + id:3f28e37f-bba8-4b0d-b4d8-ad4749630604, + id:7884960e-a973-4e8f-bb01-58005de82366, + id:c753b9e4-3908-491a-a7a8-a0d4e1543e34 ; + prov:hadMember data:0, + data:set_seed, + , + id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd . + +id:cc8b2ec1-0c34-4d44-bce6-9dfb3efd9298 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "file_data"^^xsd:string . + prov:pairEntity id:9ae42623-faf1-431a-acd3-bce4a4c24a24 ; + prov:pairKey "destination"^^xsd:string . -id:d4c2d49d-ab80-43ab-b347-a7db85bf7262 a wfprov:Artifact, +id:ce5712eb-9c70-401d-811e-a01bfdbf3b3f a wfprov:Artifact, prov:Collection, + prov:Dictionary, prov:Entity ; - prov:hadMember data:2524d3d3b68ad39a . + prov:hadDictionaryMember id:3f52ff7d-9aa8-45c7-8af1-1f7f474c6ad7, + id:689d969e-0df7-40c8-b733-b4e39fd49d34, + id:9baabbde-52d6-4728-8ef7-738960d2a86f ; + prov:hadMember , + id:016238d2-8ca1-4335-b232-acae7f43ed72, + id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab . -id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01 a prov:Entity, +id:d22a3287-f5fa-4465-8383-a6b1a3b0f242 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:path ; - prov:pairKey "src"^^xsd:string . + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:d9811e1d-402f-4343-bc31-7dd5643dbdac a prov:Entity, +id:d281fed1-869b-4451-8fda-95b26856a918 a prov:Entity, prov:KeyEntityPair ; prov:pairEntity data:auto ; prov:pairKey "ext"^^xsd:string . -id:e2f3637a-f559-46a0-a630-9f3e47800b70 a prov:Entity, +id:d731fa25-6b69-4910-80ab-897579cd74ba a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7ca3de8f49293d1a . + +id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:ffdb63df-93ba-4e67-8097-308bfd9ba39d ; - prov:pairKey "check_content"^^xsd:string . + prov:pairEntity id:56b63fc0-3bb2-448b-8115-c1cb4384d8db ; + prov:pairKey "elements"^^xsd:string . -id:e9967a89-6747-4067-95ed-5160b763f0b1 a prov:Entity, +id:db786d1e-928b-4b0f-b118-bd235731ea9a a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:298c9e09-232d-4854-bf61-8116b1323f5b, + id:838aa24d-f8b4-4ddd-a76c-82460c5b6391 ; + prov:hadMember , + id:663c25a0-9302-4b8f-aa89-765f3284aeca . + +id:dc09c4fe-c4a9-4cc5-9770-0a4f19369ac0 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:pairEntity id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a ; + prov:pairKey "__index__"^^xsd:string . -id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e a prov:Entity, +id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . -id:ebf027ac-b671-468a-91c6-1bfd7e45eb36 a wfprov:Artifact, +id:e0524eed-ea77-413b-b0db-5f72e16c365e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:5d7467bd-1ab8-46ea-8a56-0998f42b079c ; + prov:pairKey "__index__"^^xsd:string . + +id:e13acf9b-83e9-40f0-adc1-a7195e612fa3 a wfprov:Artifact, prov:Collection, prov:Entity ; - prov:hadMember data:7c1d8e3101dbcdba . + prov:hadMember data:2524d3d3b68ad39a . -id:ef96000b-e230-40a1-a36a-a45f4ca78a0e a prov:Entity, +id:e1829e51-7947-4db2-99a0-1ea7703ee764 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 ; - prov:pairKey "__index__"^^xsd:string . + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . -id:f39be690-c7d7-4911-be28-6afc1abe40b0 a wfprov:Artifact, +id:e311b33d-139a-4e92-a5c1-3a04530b9128 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:4529ad17-6e7b-4493-bba5-475a60c4a11a, - id:951bb963-10a7-4234-8119-1b13921f9629, - id:9578a96e-6635-4000-9c81-2951341b65c8 ; - prov:hadMember , - id:e6248791-d7c3-49a7-9660-5cb622189a3c, - id:f40fd446-41cb-442e-bbb7-9a23d27296e5 . + prov:hadDictionaryMember id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a, + id:3b543d5d-26b4-48f1-8c80-0c288c8df33f, + id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783, + id:4b32d7ec-e96f-41ff-8feb-1e43324962da, + id:5f9613d6-b39e-40e1-95d2-d26fb37550fe, + id:8a2cf341-8042-40bd-8509-b56f1f4161c7, + id:b0586419-dbb7-4757-9cfd-ae55abef3674, + id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01, + id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72, + id:f5199f67-c23f-46de-a504-11e5465e2e8c, + id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca ; + prov:hadMember , + , + data:auto, + data:dataset2.txt, + data:path, + , + id:4ed44fba-accb-410c-baef-53d2cb882954, + id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7, + id:76b51c9a-5a58-43ce-b9a9-7f4459602a11, + id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1, + id:f23be627-a96d-47ce-b857-30e370a747a9 . -id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d a prov:Entity, +id:ebaa0943-a400-4daf-a2e7-f781b714a666 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . + prov:pairEntity data:2e789aae2475b7da ; + prov:pairKey "id"^^xsd:string . -id:f45f9536-1278-4069-8b91-7edd97d3ff80 a prov:Entity, +id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:780092f0-87bd-42bc-a3d8-50143d44998b ; + prov:pairEntity id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1 ; prov:pairKey "hashes"^^xsd:string . -id:f67dbd55-b05c-4a56-aea3-4041399b62d1 a prov:Entity, +id:f268cc7a-3474-404e-892f-8af376e98ae3 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:87e7e990-d873-4d20-a6ee-b15094940df1 ; - prov:pairKey "purge_source"^^xsd:string . + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:f5199f67-c23f-46de-a504-11e5465e2e8c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:4ed44fba-accb-410c-baef-53d2cb882954 ; + prov:pairKey "object_id"^^xsd:string . -id:f923bbf9-1c94-4771-9333-77547e7e828e a prov:Entity, +id:f8f974ae-cd55-4986-8a9e-1d987b76fd34 a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity ; + prov:pairEntity ; prov:pairKey "@id"^^xsd:string . -id:fbca4ec6-e519-477f-84ce-23e70dddcc8b a prov:Entity, +id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca a prov:Entity, prov:KeyEntityPair ; - prov:pairEntity id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a ; - prov:pairKey "object_id"^^xsd:string . + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . -id:fd40a61e-108c-42c4-8b49-c20815d2d9e5 a wfprov:Artifact, +id:fb247085-dfc8-42bc-bee7-a7475ce9289a a wfprov:Artifact, prov:Collection, - prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:279428d4-794f-42cd-9419-0c8c71385b78, - id:81d81eab-2874-43f4-9d2e-ce5ad6236054 ; - prov:hadMember , - id:23fbeb5c-eebc-41ef-a966-be8a191c7ede . - -id:feb54146-911b-4d39-90cf-ef6d66b46fe4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . + prov:hadMember data:7c1d8e3101dbcdba . -id:ff80c261-0171-44d9-86fa-546f8aea6cd8 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:55af6a73-efbe-4e5c-8b47-6ff94872e6de ; - prov:pairKey "values"^^xsd:string . +id:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:49e48096-0a9e-4ebd-8d9b-2b3647acb1b5, + id:9fb40382-f182-481e-90e6-0e24006c71c5, + id:c0fce355-42ca-41f4-88b0-ccc3b4fec7d2 ; + prov:hadMember data:7ca3de8f49293d1a, + data:hda, + . data: a wfprov:Artifact, prov:Entity ; @@ -824,198 +824,198 @@ data:txt a wfprov:Artifact, prov:Entity ; prov:value "txt"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672"^^xsd:string . + prov:value "urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40"^^xsd:string . + prov:value "urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6"^^xsd:string . + prov:value "urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9"^^xsd:string . + prov:value "urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2"^^xsd:string . + prov:value "urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:594019f6-4154-49a8-be37-3d511a35f066"^^xsd:string . + prov:value "urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568"^^xsd:string . + prov:value "urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1"^^xsd:string . + prov:value "urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266"^^xsd:string . + prov:value "urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:71e28368-850b-441f-a008-8b6173a866d7"^^xsd:string . + prov:value "urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d"^^xsd:string . + prov:value "urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0"^^xsd:string . + prov:value "urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b"^^xsd:string . + prov:value "urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0"^^xsd:string . + prov:value "urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e"^^xsd:string . + prov:value "urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c"^^xsd:string . + prov:value "urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0"^^xsd:string . + prov:value "urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551"^^xsd:string . - a wfprov:Artifact, + a wfprov:Artifact, prov:Entity ; - prov:value "urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5"^^xsd:string . + prov:value "urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0"^^xsd:string . -id:03d9f2a8-6e48-40b3-84e4-f13e161decf1 a prov:Entity ; +id:016238d2-8ca1-4335-b232-acae7f43ed72 a prov:Entity ; prov:value true . -id:0c54448a-8444-42cd-9dd1-b65dfb0656ba a prov:Entity ; - prov:value "0"^^xsd:int . - -id:0f5709cc-12f6-430c-a605-fd3e8978f6c4 a prov:Entity ; +id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f a prov:Entity ; prov:value false . -id:23fbeb5c-eebc-41ef-a966-be8a191c7ede a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:24d7454e-9885-40b1-8a85-cc272df4fa40 . +id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80 a prov:Entity ; + prov:value "155707"^^xsd:int . -id:34aa3429-439f-49df-b575-0c7aee2caa81 a wfprov:Artifact, +id:351d875a-c130-42f7-ba2f-735780ea4ca8 a wfprov:Artifact, prov:Collection, prov:Entity ; - prov:hadMember id:641c238b-2832-4fab-b949-f5f4fc01deb1 . + prov:hadMember id:c9198eaf-36fb-42c4-bf4b-d740591fe470 . -id:368b85e6-a18c-4452-90ef-32ee5ccd0308 a prov:Entity ; - prov:value false . - -id:4fa4bb93-f67a-414c-8420-9272773cb5e2 a wfprov:Artifact, +id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be, - id:93b6a52a-f266-4837-9e8e-ed928fbd2775 ; + prov:hadDictionaryMember id:b17c488e-30c3-42cb-b2f0-092b0efe2427, + id:e1829e51-7947-4db2-99a0-1ea7703ee764 ; prov:hadMember data:hdas, - . - -id:55af6a73-efbe-4e5c-8b47-6ff94872e6de a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:062d0748-7b74-4d45-98f3-80bd22ed2672 . + . -id:65dace90-ed17-46f9-b809-d98a90563655 a prov:Entity ; - prov:value false . +id:493493b1-836f-404c-9084-95086d7ba06a a prov:Entity ; + prov:value true . -id:780092f0-87bd-42bc-a3d8-50143d44998b a wfprov:Artifact, - prov:Collection, - prov:EmptyCollection, - prov:Entity . +id:4ed44fba-accb-410c-baef-53d2cb882954 a prov:Entity ; + prov:value "155708"^^xsd:int . -id:7827651a-85f5-48a4-8f9d-1427fc02bda4 a wfprov:Artifact, +id:508b7a80-e3e7-442e-b9e9-4874e2916aad a wfprov:Artifact, prov:Collection, prov:Entity ; - prov:hadMember id:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 . + prov:hadMember id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2 . -id:87e7e990-d873-4d20-a6ee-b15094940df1 a prov:Entity ; - prov:value false . - -id:8bae3361-cfbe-4b69-bfa0-34901d319a21 a wfprov:Artifact, +id:56b63fc0-3bb2-448b-8115-c1cb4384d8db a wfprov:Artifact, prov:Collection, - prov:EmptyCollection, - prov:Entity . + prov:Entity ; + prov:hadMember id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 . -id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 a prov:Entity ; +id:5d7467bd-1ab8-46ea-8a56-0998f42b079c a prov:Entity ; prov:value "0"^^xsd:int . -id:8dbadfd6-d421-4d18-95ae-36fc4defb317 a wfprov:Artifact, +id:663c25a0-9302-4b8f-aa89-765f3284aeca a wfprov:Artifact, prov:Collection, prov:Entity ; - prov:hadMember id:6d494d29-2bc7-4da4-ba43-e816ee0b1266 . + prov:hadMember id:abbdd009-c520-4098-baf6-6400cf916ffa . -id:9e633b9f-343d-4b29-a78a-85afdd8eef53 a prov:Entity ; - prov:value true . +id:721f1551-f868-4e7d-8cb4-6f196df24a97 a prov:Entity ; + prov:value false . -id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:7fc57149-e802-47ce-bf01-348e6e787dd0 . +id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7 a prov:Entity ; + prov:value false . -id:bd860612-ca87-49c5-9d5c-d086f706f789 a prov:Entity ; - prov:value "155708"^^xsd:int . +id:76b51c9a-5a58-43ce-b9a9-7f4459602a11 a prov:Entity ; + prov:value false . -id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad a prov:Entity ; - prov:value "1"^^xsd:int . +id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a a prov:Entity ; + prov:value "0"^^xsd:int . -id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a a prov:Entity ; - prov:value "155707"^^xsd:int . +id:87697625-c033-4483-b5fa-d00140b03808 a prov:Entity ; + prov:value false . -id:d84bb265-2540-4cad-a026-511b7a21323e a wfprov:Artifact, +id:9ae42623-faf1-431a-acd3-bce4a4c24a24 a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5, - id:f923bbf9-1c94-4771-9333-77547e7e828e ; + prov:hadDictionaryMember id:3ad229e9-064d-4398-8617-d802f10ac40b, + id:70fb9ca7-9038-4874-bbda-0f12fad1627a ; prov:hadMember data:hdas, - . + . -id:e6248791-d7c3-49a7-9660-5cb622189a3c a wfprov:Artifact, +id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:0ff29d35-01d6-471f-84e8-a1fc63c05daa . + +id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc a prov:Entity ; + prov:value "0"^^xsd:int . + +id:ac40b633-8521-462b-aea0-bea86dcaef7c a wfprov:Artifact, prov:Collection, prov:Dictionary, prov:Entity ; - prov:hadDictionaryMember id:8170c31b-5a5f-4150-8531-8b0adac0f282, - id:ff80c261-0171-44d9-86fa-546f8aea6cd8 ; - prov:hadMember , - id:55af6a73-efbe-4e5c-8b47-6ff94872e6de . + prov:hadDictionaryMember id:70e6aab8-ec0d-4ff2-a2d6-03a4ce5062fd, + id:d22a3287-f5fa-4465-8383-a6b1a3b0f242 ; + prov:hadMember , + id:351d875a-c130-42f7-ba2f-735780ea4ca8 . -id:e7516c89-e4ed-494b-bf16-74b40fa66bd1 a wfprov:Artifact, +id:addafc7d-4439-49fb-9870-b6b0ed7415c3 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab a wfprov:Artifact, prov:Collection, prov:Entity ; - prov:hadMember id:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 . + prov:hadMember id:6102b40f-814e-41b4-8e21-caee1eab126b . -id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 a prov:Entity ; +id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d a prov:Entity ; prov:value false . -id:f350a230-ff86-44a3-8560-e35c1ba07b59 a prov:Entity ; - prov:value false . +id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . -id:f40fd446-41cb-442e-bbb7-9a23d27296e5 a prov:Entity ; - prov:value "0"^^xsd:int . +id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd a prov:Entity ; + prov:value "1"^^xsd:int . -id:fc84f9f8-5bb4-402d-ba90-697df02824ca a prov:Entity ; +id:f23be627-a96d-47ce-b857-30e370a747a9 a prov:Entity ; prov:value true . -id:ffdb63df-93ba-4e67-8097-308bfd9ba39d a prov:Entity ; +id:f715a46b-9eff-48c3-b88f-1f3a009ea573 a prov:Entity ; prov:value true . +id:f8915280-6e26-4eef-b378-cf27df3f8f1d a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0 . + data:2e789aae2475b7da a wfprov:Artifact, prov:Entity ; prov:value "2e789aae2475b7da"^^xsd:string . @@ -1052,16 +1052,16 @@ data:path a wfprov:Artifact, prov:Entity ; prov:value "path"^^xsd:string . -id:dd421f2f-c538-44d3-aeeb-484022c6541d a wfprov:WorkflowRun, +id:b9177644-871b-492a-ae5f-3ee833ba0ae5 a wfprov:WorkflowRun, prov:Activity ; rdfs:label "Run of galaxy workflow"^^xsd:string ; prov:qualifiedAssociation [ a prov:Association ; prov:hadPlan wf:main ] ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-03-31T15:39:11.759353"^^xsd:dateTime ; - prov:hadActivity id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd ] ; - prov:startedAtTime "2022-03-31T15:39:11.759294"^^xsd:dateTime ; - prov:wasAssociatedWith id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd . + prov:atTime "2022-04-04T16:59:09.403118"^^xsd:dateTime ; + prov:hadActivity id:ade93562-cbf5-453b-a445-cc9a5f95f0ec ] ; + prov:startedAtTime "2022-04-04T16:59:09.403029"^^xsd:dateTime ; + prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . a wfprov:Artifact, prov:Entity ; @@ -1071,11 +1071,11 @@ data:hda a wfprov:Artifact, prov:Entity ; prov:value "hda"^^xsd:string . -id:24f1df69-3788-45a1-80b3-cdf8fb8bb5bd a wfprov:WorkflowEngine, +id:ade93562-cbf5-453b-a445-cc9a5f95f0ec a wfprov:WorkflowEngine, prov:Agent, prov:SoftwareAgent ; rdfs:label "galaxy_version_placeholder"^^xsd:string ; prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-03-31T15:39:11.759268"^^xsd:dateTime ; - prov:hadActivity id:c98b0b95-d818-4ba1-b535-11c4e6909fa3 ] . + prov:atTime "2022-04-04T16:59:09.402992"^^xsd:dateTime ; + prov:hadActivity id:027f7717-78d8-4f9a-a887-87813339b23e ] . diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml index 6517529d..68097876 100644 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml +++ b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml @@ -1,6 +1,6 @@ - - + + PDG schema:Person @@ -8,64 +8,64 @@ PDG - + - + galaxy_version_placeholder wfprov:WorkflowEngine - - - 2022-03-31T15:39:11.759268 + + + 2022-04-04T16:59:09.402992 - - 2022-03-31T15:39:11.759294 + + 2022-04-04T16:59:09.403029 Run of galaxy workflow wfprov:WorkflowRun - - + + - - - 2022-03-31T15:39:11.759353 + + + 2022-04-04T16:59:09.403118 - + 2021-06-23T10:20:22.770291 2021-06-23T10:20:42.041319 Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ wfprov:ProcessRun - - + + - - + + 2021-06-23T10:20:22.770291 wfprov:Artifact 2524d3d3b68ad39a - + wfprov:Artifact - + - - - 2022-03-31T15:39:11.759864 + + + 2022-04-04T16:59:09.403801 wf:main/__DATA_FETCH__/output0 @@ -73,28 +73,28 @@ 1 - + - 2022-03-31T15:39:11.759917 + 2022-04-04T16:59:09.403870 wf:main/__DATA_FETCH__/file_count - + prov:Dictionary wfprov:Artifact - id:70e3cde6-97bb-451e-a958-1d6ecfb0dd98 - id:869277c3-8c88-4381-bbef-de17240b1c23 - id:a1bb89e0-badf-490a-af30-375efe69c057 + id:a92435e7-0621-4629-80fa-d73aa1989363 + id:e311b33d-139a-4e92-a5c1-3a04530b9128 + id:f268cc7a-3474-404e-892f-8af376e98ae3 - + 0 - - + + - + prov:KeyEntityPair - id:0c54448a-8444-42cd-9dd1-b65dfb0656ba + id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc __index__ @@ -102,38 +102,38 @@ /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - + - + prov:KeyEntityPair data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 file_data - + wfprov:Artifact - urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 + urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a - - + + - + prov:KeyEntityPair - data:urn:uuid:346a6375-2d0d-47f0-a5d8-bf5cfe3ef9f6 + data:urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a @id - + wfprov:Artifact - - + + - - - 2022-03-31T15:39:11.760237 + + + 2022-04-04T16:59:09.404286 wf:main/__DATA_FETCH__/files @@ -141,91 +141,91 @@ - + - 2022-03-31T15:39:11.760286 + 2022-04-04T16:59:09.404363 wf:main/__DATA_FETCH__/paramfile - + prov:Dictionary wfprov:Artifact - id:1e8684e9-896e-4a38-bfe9-1995d0893fdd - id:7067149e-f997-4e01-810a-41ed1aaae3f1 - id:e2f3637a-f559-46a0-a630-9f3e47800b70 + id:15212ae6-d7ff-4660-870e-34f3caa32ceb + id:441a9ce2-fada-464f-84fb-6dfd01a6379e + id:9af37a24-65f9-41cd-8191-228ec8108418 - + prov:Dictionary wfprov:Artifact - id:3b176baa-a8f8-426c-ab0d-aa428d41923d - id:47d09ccc-4b59-4330-9361-9f1b65b860a8 - id:9f4835d1-a5f0-499e-9315-42fed1edd2a1 - id:ab8003d1-3e46-4af7-9325-fffe09639b01 + id:0196242d-cfb9-45f3-965c-8fa2a037f104 + id:38113d6d-950c-4c1a-826d-636d3c6fa3ea + id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a + id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce - + prov:Dictionary wfprov:Artifact - id:9c7916f8-76a0-4bd5-8774-6e61fce1bea5 - id:f923bbf9-1c94-4771-9333-77547e7e828e + id:b17c488e-30c3-42cb-b2f0-092b0efe2427 + id:e1829e51-7947-4db2-99a0-1ea7703ee764 wfprov:Artifact hdas - + - + prov:KeyEntityPair data:hdas type - + wfprov:Artifact - urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e + urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f - - + + - + prov:KeyEntityPair - data:urn:uuid:d84bb265-2540-4cad-a026-511b7a21323e + data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f @id - - + + - + prov:KeyEntityPair - id:d84bb265-2540-4cad-a026-511b7a21323e + id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f destination - + prov:Dictionary wfprov:Artifact - id:069bb313-b651-474e-9a28-fdc7af0fc87b - id:0ce61ea3-fb0f-4338-b021-b0feb31f7b64 - id:66fde9d0-4440-4811-8b03-ae8c34cfebb6 - id:792b7ecd-597e-41ad-ac59-b0767919b4b7 - id:79566035-3dfd-4779-837a-344529381251 - id:97939793-b619-47e0-8ec3-d3baf5965151 - id:ace28a14-6cc4-4efc-adcb-4668dcc9cd60 - id:c0c38d7d-cd18-4050-b5e8-0faf10393207 - id:d5ba27cc-fd05-4540-baac-a8e0c6a7de01 - id:f45f9536-1278-4069-8b91-7edd97d3ff80 - id:f67dbd55-b05c-4a56-aea3-4041399b62d1 + id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a + id:3b543d5d-26b4-48f1-8c80-0c288c8df33f + id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783 + id:4b32d7ec-e96f-41ff-8feb-1e43324962da + id:5f9613d6-b39e-40e1-95d2-d26fb37550fe + id:8a2cf341-8042-40bd-8509-b56f1f4161c7 + id:b0586419-dbb7-4757-9cfd-ae55abef3674 + id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01 + id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72 + id:f5199f67-c23f-46de-a504-11e5465e2e8c + id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca wfprov:Artifact auto - + - + prov:KeyEntityPair data:auto ext @@ -235,24 +235,24 @@ ? - + - + prov:KeyEntityPair data:? dbkey - + true - - + + - + prov:KeyEntityPair - id:9e633b9f-343d-4b29-a78a-85afdd8eef53 + id:f23be627-a96d-47ce-b857-30e370a747a9 to_posix_lines @@ -260,10 +260,10 @@ path - + - + prov:KeyEntityPair data:path src @@ -273,49 +273,49 @@ dataset2.txt - + - + prov:KeyEntityPair data:dataset2.txt name - - prov:Collection + + prov:EmptyCollection wfprov:Artifact - + - - + + - + prov:KeyEntityPair - id:780092f0-87bd-42bc-a3d8-50143d44998b + id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1 hashes - + false - - + + - + prov:KeyEntityPair - id:0f5709cc-12f6-430c-a605-fd3e8978f6c4 + id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7 in_place - + false - - + + - + prov:KeyEntityPair - id:87e7e990-d873-4d20-a6ee-b15094940df1 + id:76b51c9a-5a58-43ce-b9a9-7f4459602a11 purge_source @@ -323,125 +323,125 @@ /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - + - + prov:KeyEntityPair data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 path - + 155708 - - + + - + prov:KeyEntityPair - id:bd860612-ca87-49c5-9d5c-d086f706f789 + id:4ed44fba-accb-410c-baef-53d2cb882954 object_id - + wfprov:Artifact - urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 + urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 - - + + - + prov:KeyEntityPair - data:urn:uuid:41848fc9-cfe2-45ee-b2b7-b5a3371232a9 + data:urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 @id - + wfprov:Artifact - - + + - - + + - + prov:KeyEntityPair - id:e7516c89-e4ed-494b-bf16-74b40fa66bd1 + id:56b63fc0-3bb2-448b-8115-c1cb4384d8db elements - + false - - + + - + prov:KeyEntityPair - id:e8c438c4-7544-4049-8d34-f825ecd3b5e1 + id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d auto_decompress - + wfprov:Artifact - urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1 + urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2 - - + + - + prov:KeyEntityPair - data:urn:uuid:641c238b-2832-4fab-b949-f5f4fc01deb1 + data:urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2 @id - + wfprov:Artifact - - + + - - + + - + prov:KeyEntityPair - id:34aa3429-439f-49df-b575-0c7aee2caa81 + id:508b7a80-e3e7-442e-b9e9-4874e2916aad targets - + true - - + + - + prov:KeyEntityPair - id:ffdb63df-93ba-4e67-8097-308bfd9ba39d + id:f715a46b-9eff-48c3-b88f-1f3a009ea573 check_content - + wfprov:Artifact - urn:uuid:594019f6-4154-49a8-be37-3d511a35f066 + urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c - - + + - + prov:KeyEntityPair - data:urn:uuid:594019f6-4154-49a8-be37-3d511a35f066 + data:urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c @id - - - 2022-03-31T15:39:11.762940 + + + 2022-04-04T16:59:09.406855 wf:main/__DATA_FETCH__/request_json @@ -449,42 +449,42 @@ 1 - + - 2022-03-31T15:39:11.762994 + 2022-04-04T16:59:09.406936 wf:main/__DATA_FETCH__/request_version - + 2021-06-23T10:20:00.981702 2021-06-23T10:20:22.202678 Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ wfprov:ProcessRun - - + + - - + + 2021-06-23T10:20:00.981702 wfprov:Artifact 7c1d8e3101dbcdba - + wfprov:Artifact - + - - - 2022-03-31T15:39:11.763447 + + + 2022-04-04T16:59:09.407566 wf:main/__DATA_FETCH__/output0 @@ -492,28 +492,28 @@ 1 - + - 2022-03-31T15:39:11.763491 + 2022-04-04T16:59:09.407631 wf:main/__DATA_FETCH__/file_count - + prov:Dictionary wfprov:Artifact - id:88aa880c-c240-4877-b1e7-a0c20e29ef3e - id:d3a55e5b-c1fb-4523-b77d-993b00128b05 - id:ef96000b-e230-40a1-a36a-a45f4ca78a0e + id:7c60b838-dd41-4166-aa41-6e652e5ef63b + id:e0524eed-ea77-413b-b0db-5f72e16c365e + id:f8f974ae-cd55-4986-8a9e-1d987b76fd34 - + 0 - - + + - + prov:KeyEntityPair - id:8cb4f8a5-cc3c-45f4-ae31-5dcdca6b5ab4 + id:5d7467bd-1ab8-46ea-8a56-0998f42b079c __index__ @@ -521,38 +521,38 @@ /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - + - + prov:KeyEntityPair data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a file_data - + wfprov:Artifact - urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568 + urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7 - - + + - + prov:KeyEntityPair - data:urn:uuid:5ab542a0-7a79-4f00-b120-b14b0542e568 + data:urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7 @id - + wfprov:Artifact - - + + - - - 2022-03-31T15:39:11.763772 + + + 2022-04-04T16:59:09.408037 wf:main/__DATA_FETCH__/files @@ -560,91 +560,91 @@ - + - 2022-03-31T15:39:11.763813 + 2022-04-04T16:59:09.408097 wf:main/__DATA_FETCH__/paramfile - + prov:Dictionary wfprov:Artifact - id:68c6bdfd-f17d-41b8-bdba-eb3a46749940 - id:6d29c983-528d-46cf-b420-1c9210619f0d - id:a75e7105-d7f0-4a77-865c-2ff5b3162e47 + id:3f52ff7d-9aa8-45c7-8af1-1f7f474c6ad7 + id:689d969e-0df7-40c8-b733-b4e39fd49d34 + id:9baabbde-52d6-4728-8ef7-738960d2a86f - + prov:Dictionary wfprov:Artifact - id:34523c4b-aa54-4d13-8d25-76acadcc8df7 - id:3ca2018c-86dd-4db8-bd27-51575f6fa4e4 - id:9e45fea1-39c5-4b99-be26-72b06a5e8786 - id:eaf445c5-a30d-41ff-aeb6-40c4a1598f8e + id:0c415611-9c31-47d4-82f9-a6330b980a8e + id:2d384308-e0b1-4f82-811c-4bba81b92067 + id:788acdf9-5e3a-4774-aa66-3068819b5cae + id:cc8b2ec1-0c34-4d44-bce6-9dfb3efd9298 - + prov:Dictionary wfprov:Artifact - id:43509e98-23c6-4f3c-94fc-5a5e9a11f1be - id:93b6a52a-f266-4837-9e8e-ed928fbd2775 + id:3ad229e9-064d-4398-8617-d802f10ac40b + id:70fb9ca7-9038-4874-bbda-0f12fad1627a wfprov:Artifact hdas - + - + prov:KeyEntityPair data:hdas type - + wfprov:Artifact - urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2 + urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24 - - + + - + prov:KeyEntityPair - data:urn:uuid:4fa4bb93-f67a-414c-8420-9272773cb5e2 + data:urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24 @id - - + + - + prov:KeyEntityPair - id:4fa4bb93-f67a-414c-8420-9272773cb5e2 + id:9ae42623-faf1-431a-acd3-bce4a4c24a24 destination - + prov:Dictionary wfprov:Artifact - id:286ffa7a-a1f3-424c-90cf-f36d112b13f0 - id:38d925a2-053b-4bdd-bc21-b9d2c4238fb1 - id:4745fa68-123c-4afb-9176-dcf61732f695 - id:63d1e8b3-4ec7-4ce1-b4dc-22216683dfe6 - id:8ced01f6-47ea-4320-b65a-6af7a668fbe9 - id:98a55032-1c60-4303-8ca0-5cff21b96b9d - id:ab51fb43-4e4d-459e-ae56-672b92ac89ea - id:b6e76be2-6e91-40d4-9f7c-32a1c0a809d5 - id:d9811e1d-402f-4343-bc31-7dd5643dbdac - id:fbca4ec6-e519-477f-84ce-23e70dddcc8b - id:feb54146-911b-4d39-90cf-ef6d66b46fe4 + id:06db435a-b77f-424b-8301-acb7e18cc2ce + id:08ffc626-141c-4214-8d71-746a1218f209 + id:23fe35b3-2a01-4edf-952a-5769462abc6c + id:46ce5c94-417b-4bcf-a9af-fb60912d385a + id:7dc6f8f5-cce3-4da9-b386-0a18314af498 + id:919c8f14-f4f3-4151-b936-d7502f64caa4 + id:a05e1e9a-74e5-4efc-ad75-96c15f4a83ce + id:bab1f03d-7ca6-4bb7-a57d-563c0e70808b + id:bb0b8464-83db-421e-9566-a31da915d209 + id:c256e77e-7189-430a-8c59-03fa703dce07 + id:d281fed1-869b-4451-8fda-95b26856a918 wfprov:Artifact auto - + - + prov:KeyEntityPair data:auto ext @@ -654,24 +654,24 @@ ? - + - + prov:KeyEntityPair data:? dbkey - + true - - + + - + prov:KeyEntityPair - id:03d9f2a8-6e48-40b3-84e4-f13e161decf1 + id:493493b1-836f-404c-9084-95086d7ba06a to_posix_lines @@ -679,10 +679,10 @@ path - + - + prov:KeyEntityPair data:path src @@ -692,49 +692,49 @@ dataset1.txt - + - + prov:KeyEntityPair data:dataset1.txt name - - prov:Collection + + prov:EmptyCollection wfprov:Artifact - + - - + + - + prov:KeyEntityPair - id:8bae3361-cfbe-4b69-bfa0-34901d319a21 + id:addafc7d-4439-49fb-9870-b6b0ed7415c3 hashes - + false - - + + - + prov:KeyEntityPair - id:368b85e6-a18c-4452-90ef-32ee5ccd0308 + id:721f1551-f868-4e7d-8cb4-6f196df24a97 in_place - + false - - + + - + prov:KeyEntityPair - id:f350a230-ff86-44a3-8560-e35c1ba07b59 + id:87697625-c033-4483-b5fa-d00140b03808 purge_source @@ -742,125 +742,125 @@ /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - + - + prov:KeyEntityPair data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a path - + 155707 - - + + - + prov:KeyEntityPair - id:d7865c65-4cfe-4723-bd41-8bd7f69b1f0a + id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80 object_id - + wfprov:Artifact - urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266 + urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa - - + + - + prov:KeyEntityPair - data:urn:uuid:6d494d29-2bc7-4da4-ba43-e816ee0b1266 + data:urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa @id - + wfprov:Artifact - - + + - - + + - + prov:KeyEntityPair - id:8dbadfd6-d421-4d18-95ae-36fc4defb317 + id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea elements - + false - - + + - + prov:KeyEntityPair - id:65dace90-ed17-46f9-b809-d98a90563655 + id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f auto_decompress - + wfprov:Artifact - urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0 + urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b - - + + - + prov:KeyEntityPair - data:urn:uuid:7fc57149-e802-47ce-bf01-348e6e787dd0 + data:urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b @id - + wfprov:Artifact - - + + - - + + - + prov:KeyEntityPair - id:a35be1e8-a91b-4c48-8fd5-6d388f6b24b1 + id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab targets - + true - - + + - + prov:KeyEntityPair - id:fc84f9f8-5bb4-402d-ba90-697df02824ca + id:016238d2-8ca1-4335-b232-acae7f43ed72 check_content - + wfprov:Artifact - urn:uuid:71e28368-850b-441f-a008-8b6173a866d7 + urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f - - + + - + prov:KeyEntityPair - data:urn:uuid:71e28368-850b-441f-a008-8b6173a866d7 + data:urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f @id - - - 2022-03-31T15:39:11.765267 + + + 2022-04-04T16:59:09.410250 wf:main/__DATA_FETCH__/request_json @@ -868,76 +868,76 @@ 1 - + - 2022-03-31T15:39:11.765313 + 2022-04-04T16:59:09.410320 wf:main/__DATA_FETCH__/request_version - + 2021-06-23T10:46:28.351123 2021-06-23T10:46:44.738703 Run of ga_export/jobs_attrs.txt#cat1 wfprov:ProcessRun - - + + - - + + 2021-06-23T10:46:28.351123 wfprov:Artifact 7ca3de8f49293d1a - + wfprov:Artifact - + - - - 2022-03-31T15:39:11.765700 + + + 2022-04-04T16:59:09.410900 wf:main/cat1/input1 wfprov:Artifact 2e789aae2475b7da - + wfprov:Artifact - + - - - 2022-03-31T15:39:11.765788 + + + 2022-04-04T16:59:09.411016 wf:main/cat1/queries_0_input2 wfprov:Artifact fd7fec473f1e6c6b - + wfprov:Artifact - + - - - 2022-03-31T15:39:11.765900 + + + 2022-04-04T16:59:09.411131 wf:main/cat1/out_file1 @@ -945,9 +945,9 @@ txt - + - 2022-03-31T15:39:11.765965 + 2022-04-04T16:59:09.411190 wf:main/cat1/__input_ext @@ -955,9 +955,9 @@ 42f21c0ad41011eb87defa163eba836f - + - 2022-03-31T15:39:11.766037 + 2022-04-04T16:59:09.411252 wf:main/cat1/__workflow_invocation_uuid__ @@ -965,9 +965,9 @@ /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - + - 2022-03-31T15:39:11.766105 + 2022-04-04T16:59:09.411312 wf:main/cat1/chromInfo @@ -975,33 +975,33 @@ ? - + - 2022-03-31T15:39:11.766169 + 2022-04-04T16:59:09.411369 wf:main/cat1/dbkey - + prov:Dictionary wfprov:Artifact - id:57844284-ccc8-45f3-a7fa-6ce0246cf99b - id:e9967a89-6747-4067-95ed-5160b763f0b1 + id:4ee5e287-4b5d-4d40-be38-1bf1c3236934 + id:551327a9-e8db-4d46-8ec4-cde270df080b - + prov:Dictionary wfprov:Artifact - id:2e6f9bcd-ecc4-4000-90b2-8fd4683c9c99 - id:3803c3d0-41d3-4e9d-9dda-7ddcbaa2a813 - id:f3ef5dcc-06a9-4ed7-bfb8-eb2dc13ba74d + id:49e48096-0a9e-4ebd-8d9b-2b3647acb1b5 + id:9fb40382-f182-481e-90e6-0e24006c71c5 + id:c0fce355-42ca-41f4-88b0-ccc3b4fec7d2 wfprov:Artifact 7ca3de8f49293d1a - + - + prov:KeyEntityPair data:7ca3de8f49293d1a id @@ -1011,103 +1011,103 @@ hda - + - + prov:KeyEntityPair data:hda src - + wfprov:Artifact - urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 + urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0 - - + + - + prov:KeyEntityPair - data:urn:uuid:d346895c-e12a-4eff-80d8-ecd5e0f1dbc0 + data:urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0 @id - + wfprov:Artifact - - + + - - + + - + prov:KeyEntityPair - id:7827651a-85f5-48a4-8f9d-1427fc02bda4 + id:f8915280-6e26-4eef-b378-cf27df3f8f1d values - + wfprov:Artifact - urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b + urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a - - + + - + prov:KeyEntityPair - data:urn:uuid:a9607900-c633-4837-a4a7-eaee6edcaf3b + data:urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a @id - - - 2022-03-31T15:39:11.766787 + + + 2022-04-04T16:59:09.411964 wf:main/cat1/input1 - + prov:Dictionary wfprov:Artifact - id:4529ad17-6e7b-4493-bba5-475a60c4a11a - id:951bb963-10a7-4234-8119-1b13921f9629 - id:9578a96e-6635-4000-9c81-2951341b65c8 + id:92b2afc9-fc96-4764-adbe-73d014ba2357 + id:b397cf2b-901a-454c-bfc2-e966b6838269 + id:dc09c4fe-c4a9-4cc5-9770-0a4f19369ac0 - + 0 - - + + - + prov:KeyEntityPair - id:f40fd446-41cb-442e-bbb7-9a23d27296e5 + id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a __index__ - + prov:Dictionary wfprov:Artifact - id:8170c31b-5a5f-4150-8531-8b0adac0f282 - id:ff80c261-0171-44d9-86fa-546f8aea6cd8 + id:70e6aab8-ec0d-4ff2-a2d6-03a4ce5062fd + id:d22a3287-f5fa-4465-8383-a6b1a3b0f242 - + prov:Dictionary wfprov:Artifact - id:51656ecb-5b39-4ad7-9888-d7b93ca28266 - id:a26f2ebd-20b2-4760-b1b9-a9ca804bb747 - id:a5dd2be3-47c4-4b8a-b6d5-a98d9620f748 + id:10f720aa-40e7-4c83-9ad1-02ffc26a7944 + id:34e6b60d-4d4a-496d-bb9c-a4d34040155c + id:ebaa0943-a400-4daf-a2e7-f781b714a666 wfprov:Artifact 2e789aae2475b7da - + - + prov:KeyEntityPair data:2e789aae2475b7da id @@ -1117,139 +1117,139 @@ hda - + - + prov:KeyEntityPair data:hda src - + wfprov:Artifact - urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672 + urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470 - - + + - + prov:KeyEntityPair - data:urn:uuid:062d0748-7b74-4d45-98f3-80bd22ed2672 + data:urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470 @id - + wfprov:Artifact - - + + - - + + - + prov:KeyEntityPair - id:55af6a73-efbe-4e5c-8b47-6ff94872e6de + id:351d875a-c130-42f7-ba2f-735780ea4ca8 values - + wfprov:Artifact - urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c + urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c - - + + - + prov:KeyEntityPair - data:urn:uuid:e6248791-d7c3-49a7-9660-5cb622189a3c + data:urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c @id - - + + - + prov:KeyEntityPair - id:e6248791-d7c3-49a7-9660-5cb622189a3c + id:ac40b633-8521-462b-aea0-bea86dcaef7c input2 - + wfprov:Artifact - urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0 + urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98 - - + + - + prov:KeyEntityPair - data:urn:uuid:f39be690-c7d7-4911-be28-6afc1abe40b0 + data:urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98 @id - + wfprov:Artifact - - + + - - - 2022-03-31T15:39:11.767885 + + + 2022-04-04T16:59:09.412881 wf:main/cat1/queries - + 2021-06-23T10:46:28.526901 2021-06-23T10:47:04.837750 Run of ga_export/jobs_attrs.txt#random_lines1 wfprov:ProcessRun - - + + - - + + 2021-06-23T10:46:28.526901 wfprov:Artifact fd7fec473f1e6c6b - + wfprov:Artifact - + - - - 2022-03-31T15:39:11.768651 + + + 2022-04-04T16:59:09.413468 wf:main/random_lines1/input wfprov:Artifact 775bc9b3c1750167 - + wfprov:Artifact - + - - - 2022-03-31T15:39:11.768810 + + + 2022-04-04T16:59:09.413588 wf:main/random_lines1/out_file1 @@ -1257,9 +1257,9 @@ txt - + - 2022-03-31T15:39:11.768884 + 2022-04-04T16:59:09.413652 wf:main/random_lines1/__input_ext @@ -1267,9 +1267,9 @@ 42f21c0ad41011eb87defa163eba836f - + - 2022-03-31T15:39:11.768956 + 2022-04-04T16:59:09.413710 wf:main/random_lines1/__workflow_invocation_uuid__ @@ -1277,9 +1277,9 @@ /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - + - 2022-03-31T15:39:11.769026 + 2022-04-04T16:59:09.413770 wf:main/random_lines1/chromInfo @@ -1287,33 +1287,33 @@ ? - + - 2022-03-31T15:39:11.769116 + 2022-04-04T16:59:09.413826 wf:main/random_lines1/dbkey - + prov:Dictionary wfprov:Artifact - id:279428d4-794f-42cd-9419-0c8c71385b78 - id:81d81eab-2874-43f4-9d2e-ce5ad6236054 + id:298c9e09-232d-4854-bf61-8116b1323f5b + id:838aa24d-f8b4-4ddd-a76c-82460c5b6391 - + prov:Dictionary wfprov:Artifact - id:1a5e9eaa-ef75-4886-8870-7cc60e0e2a94 - id:96981ec2-dac6-4477-9ac3-431cdc24f7ac - id:c40c9210-5155-480f-ba36-5f86aaa39d77 + id:947491c9-a106-4578-b804-16c3100e0111 + id:994bb2e3-42f8-4fd1-9d6f-aff742a0b9b0 + id:ad223424-b8ff-4704-a618-0a033ceaf3ea wfprov:Artifact fd7fec473f1e6c6b - + - + prov:KeyEntityPair data:fd7fec473f1e6c6b id @@ -1323,60 +1323,60 @@ hda - + - + prov:KeyEntityPair data:hda src - + wfprov:Artifact - urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40 + urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa - - + + - + prov:KeyEntityPair - data:urn:uuid:24d7454e-9885-40b1-8a85-cc272df4fa40 + data:urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa @id - + wfprov:Artifact - - + + - - + + - + prov:KeyEntityPair - id:23fbeb5c-eebc-41ef-a966-be8a191c7ede + id:663c25a0-9302-4b8f-aa89-765f3284aeca values - + wfprov:Artifact - urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5 + urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a - - + + - + prov:KeyEntityPair - data:urn:uuid:fd40a61e-108c-42c4-8b49-c20815d2d9e5 + data:urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a @id - - - 2022-03-31T15:39:11.769772 + + + 2022-04-04T16:59:09.414376 wf:main/random_lines1/input @@ -1384,29 +1384,29 @@ 3 - + - 2022-03-31T15:39:11.769848 + 2022-04-04T16:59:09.414444 wf:main/random_lines1/num_lines - + prov:Dictionary wfprov:Artifact - id:0f0f39b2-4d72-4163-b3be-eaf5acab40b9 - id:5ba613ce-6eaa-412d-89bf-eb8f580823a3 - id:903792cc-566c-4ffe-ade9-be65cf4f1fb4 - id:9fe8424c-7f09-4ae6-b6b3-64fa7408975e + id:1b548405-6990-454a-98a6-128dccf12014 + id:3f28e37f-bba8-4b0d-b4d8-ad4749630604 + id:7884960e-a973-4e8f-bb01-58005de82366 + id:c753b9e4-3908-491a-a7a8-a0d4e1543e34 - + 1 - - + + - + prov:KeyEntityPair - id:cb430f8b-bd1c-4b48-bfaa-bf4970f9b8ad + id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd __current_case__ @@ -1414,10 +1414,10 @@ 0 - + - + prov:KeyEntityPair data:0 seed @@ -1427,31 +1427,31 @@ set_seed - + - + prov:KeyEntityPair data:set_seed seed_source_selector - + wfprov:Artifact - urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d + urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948 - - + + - + prov:KeyEntityPair - data:urn:uuid:7e6d530d-6c05-48b1-8d69-879b6e790c9d + data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948 @id - - - 2022-03-31T15:39:11.770390 + + + 2022-04-04T16:59:09.414862 wf:main/random_lines1/seed_source diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt new file mode 100644 index 00000000..8b3f00b0 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt @@ -0,0 +1,4 @@ +hello +universe! +hello +world diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt new file mode 100644 index 00000000..94954abd --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt @@ -0,0 +1,2 @@ +hello +world diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt new file mode 100644 index 00000000..718e715c --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt @@ -0,0 +1,2 @@ +hello +universe! diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json new file mode 100644 index 00000000..aa9ef83a --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json @@ -0,0 +1,2862 @@ +{ + "prefix": { + "wfprov": "http://purl.org/wf4ever/wfprov#", + "wfdesc": 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"2022-04-04T16:59:09.803689"^^ . + . + diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn new file mode 100644 index 00000000..c26f61ae --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn @@ -0,0 +1,330 @@ +document + prefix wfprov + prefix wfdesc + prefix cwlprov + prefix foaf + prefix schema + prefix orcid + prefix id + prefix data + prefix provenance + prefix wf + prefix input + + agent(id:027f7717-78d8-4f9a-a887-87813339b23e) + agent(id:8124e339-e638-4fc3-b421-6367e3682c50, [prov:type='wfprov:WorkflowEngine', prov:type='prov:SoftwareAgent', prov:label="galaxy_version_placeholder"]) + wasStartedBy(id:8124e339-e638-4fc3-b421-6367e3682c50, -, id:027f7717-78d8-4f9a-a887-87813339b23e, 2022-04-04T16:59:09.795855) + activity(id:b02505bb-6b95-4e97-8043-d0823b00b7f4, 2022-04-04T16:59:09.795894, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of galaxy workflow"]) + wasAssociatedWith(id:b02505bb-6b95-4e97-8043-d0823b00b7f4, id:8124e339-e638-4fc3-b421-6367e3682c50, wf:main) + wasStartedBy(id:b02505bb-6b95-4e97-8043-d0823b00b7f4, -, id:8124e339-e638-4fc3-b421-6367e3682c50, 2022-04-04T16:59:09.795971) + activity(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, 2021-06-23T10:20:22.770291, 2021-06-23T10:20:42.041319, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) + wasAssociatedWith(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, id:8124e339-e638-4fc3-b421-6367e3682c50, wf:main/__DATA_FETCH__) + wasStartedBy(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, -, id:b02505bb-6b95-4e97-8043-d0823b00b7f4, 2021-06-23T10:20:22.770291) + entity(data:2524d3d3b68ad39a, [prov:type='wfprov:Artifact', prov:value="2524d3d3b68ad39a"]) + entity(id:2119440c-63be-46a9-bbb7-2b104033b8f2, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:2119440c-63be-46a9-bbb7-2b104033b8f2, data:2524d3d3b68ad39a) + used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, id:2119440c-63be-46a9-bbb7-2b104033b8f2, 2022-04-04T16:59:09.796590, [prov:role='wf:main/__DATA_FETCH__/output0']) + entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) + used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, data:1, 2022-04-04T16:59:09.796656, [prov:role='wf:main/__DATA_FETCH__/file_count']) + entity(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:2301b8b5-528f-4802-bd81-a4a3ca8534f4', prov:hadDictionaryMember='id:00e0f888-71d8-49f9-ba39-dcaed5a91c56', prov:hadDictionaryMember='id:1605ad9c-1b56-4055-a8d0-866f49da1687']) + entity(id:f4d07c61-fb2b-42eb-a7c5-1820900166f3, [prov:value=0]) + hadMember(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, id:f4d07c61-fb2b-42eb-a7c5-1820900166f3) + entity(id:1605ad9c-1b56-4055-a8d0-866f49da1687, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:f4d07c61-fb2b-42eb-a7c5-1820900166f3']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) + hadMember(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:2301b8b5-528f-4802-bd81-a4a3ca8534f4, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b, [prov:type='wfprov:Artifact', prov:value="urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b"]) + hadMember(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b) + entity(id:00e0f888-71d8-49f9-ba39-dcaed5a91c56, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b']) + entity(id:6572947b-c3fd-4c6f-bdff-7aa191bc5546, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:6572947b-c3fd-4c6f-bdff-7aa191bc5546, id:e9693b34-04fb-4b31-a78c-7d089fd6558b) + used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, id:6572947b-c3fd-4c6f-bdff-7aa191bc5546, 2022-04-04T16:59:09.797234, [prov:role='wf:main/__DATA_FETCH__/files']) + entity(data:, [prov:type='wfprov:Artifact', prov:value=""]) + used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, data:, 2022-04-04T16:59:09.797298, [prov:role='wf:main/__DATA_FETCH__/paramfile']) + entity(id:34e943f0-5027-47b0-ba7b-05fca46da136, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:e25dce0d-bf63-414f-a0cd-2663e7a44d50', prov:hadDictionaryMember='id:a15754e6-26b6-4269-96b6-7d35515d1c02', prov:hadDictionaryMember='id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885']) + entity(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:000e294f-576c-469b-8965-4e279bebc880', prov:hadDictionaryMember='id:f89aaeef-0313-42af-b87e-7b519d494be7', prov:hadDictionaryMember='id:e84e01b6-0126-4b79-90d5-99d22e8dde7c', prov:hadDictionaryMember='id:a6d080a6-7c60-46f2-85c8-2519f4d803ea']) + entity(id:e46be7d4-c0c3-489f-86dd-0c8148d86858, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6', prov:hadDictionaryMember='id:7b40bdfc-aacc-4947-a8d8-d13db0419365']) + entity(data:hdas, [prov:type='wfprov:Artifact', prov:value="hdas"]) + hadMember(id:e46be7d4-c0c3-489f-86dd-0c8148d86858, data:hdas) + entity(id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6, [prov:type='prov:KeyEntityPair', prov:pairKey="type", prov:pairEntity='data:hdas']) + entity(data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858, [prov:type='wfprov:Artifact', prov:value="urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858"]) + hadMember(id:e46be7d4-c0c3-489f-86dd-0c8148d86858, data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858) + entity(id:7b40bdfc-aacc-4947-a8d8-d13db0419365, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858']) + hadMember(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, id:e46be7d4-c0c3-489f-86dd-0c8148d86858) + entity(id:a6d080a6-7c60-46f2-85c8-2519f4d803ea, [prov:type='prov:KeyEntityPair', prov:pairKey="destination", prov:pairEntity='id:e46be7d4-c0c3-489f-86dd-0c8148d86858']) + entity(id:1c90cc92-4948-4b69-a163-f63e41891f7a, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:0592876b-ce23-4b6a-a8cf-32a46f7aedea', prov:hadDictionaryMember='id:b1aad576-0af0-43c0-948d-df79e52df6b7', prov:hadDictionaryMember='id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103', prov:hadDictionaryMember='id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38', prov:hadDictionaryMember='id:8232048b-b457-45cb-932e-a5cf8f8be6e1', prov:hadDictionaryMember='id:ed8aaa9a-567f-4893-b432-fa6e49547650', prov:hadDictionaryMember='id:3e26cc6f-1f3b-438d-ada9-a55bead88b03', prov:hadDictionaryMember='id:5ab39f26-7656-40f1-826f-38f40ed09f10', prov:hadDictionaryMember='id:29b40ddc-e592-4aa9-989f-ed4ac9be59af', prov:hadDictionaryMember='id:912f104e-1517-492e-abe3-f931fe47438b', prov:hadDictionaryMember='id:587e2872-6ae3-4716-b99e-12c5db1f8e56']) + entity(data:auto, [prov:type='wfprov:Artifact', prov:value="auto"]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:auto) + entity(id:5ab39f26-7656-40f1-826f-38f40ed09f10, [prov:type='prov:KeyEntityPair', prov:pairKey="ext", prov:pairEntity='data:auto']) + entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:?) + entity(id:0592876b-ce23-4b6a-a8cf-32a46f7aedea, [prov:type='prov:KeyEntityPair', prov:pairKey="dbkey", prov:pairEntity='data:?']) + entity(id:512093ee-9853-484f-9a93-aea928098062, [prov:value="1" %% xsd:boolean]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:512093ee-9853-484f-9a93-aea928098062) + entity(id:3e26cc6f-1f3b-438d-ada9-a55bead88b03, [prov:type='prov:KeyEntityPair', prov:pairKey="to_posix_lines", prov:pairEntity='id:512093ee-9853-484f-9a93-aea928098062']) + entity(data:path, [prov:type='wfprov:Artifact', prov:value="path"]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:path) + entity(id:29b40ddc-e592-4aa9-989f-ed4ac9be59af, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:path']) + entity(data:dataset2.txt, [prov:type='wfprov:Artifact', prov:value="dataset2.txt"]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:dataset2.txt) + entity(id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103, [prov:type='prov:KeyEntityPair', prov:pairKey="name", prov:pairEntity='data:dataset2.txt']) + entity(id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b, [prov:type='prov:Collection', prov:type='wfprov:Artifact', prov:type='prov:EmptyCollection']) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b) + entity(id:587e2872-6ae3-4716-b99e-12c5db1f8e56, [prov:type='prov:KeyEntityPair', prov:pairKey="hashes", prov:pairEntity='id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b']) + entity(id:03827a8b-50a4-463b-876a-742652bb3049, [prov:value="0" %% xsd:boolean]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:03827a8b-50a4-463b-876a-742652bb3049) + entity(id:912f104e-1517-492e-abe3-f931fe47438b, [prov:type='prov:KeyEntityPair', prov:pairKey="in_place", prov:pairEntity='id:03827a8b-50a4-463b-876a-742652bb3049']) + entity(id:16597142-0745-4b4c-80c7-5755b2d087a7, [prov:value="0" %% xsd:boolean]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:16597142-0745-4b4c-80c7-5755b2d087a7) + entity(id:b1aad576-0af0-43c0-948d-df79e52df6b7, [prov:type='prov:KeyEntityPair', prov:pairKey="purge_source", prov:pairEntity='id:16597142-0745-4b4c-80c7-5755b2d087a7']) + entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) + entity(id:8232048b-b457-45cb-932e-a5cf8f8be6e1, [prov:type='prov:KeyEntityPair', prov:pairKey="path", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) + entity(id:cdcc006a-91e4-4f29-8c14-1f91eef044dd, [prov:value=155708]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:cdcc006a-91e4-4f29-8c14-1f91eef044dd) + entity(id:ed8aaa9a-567f-4893-b432-fa6e49547650, [prov:type='prov:KeyEntityPair', prov:pairKey="object_id", prov:pairEntity='id:cdcc006a-91e4-4f29-8c14-1f91eef044dd']) + entity(data:urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a, [prov:type='wfprov:Artifact', prov:value="urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a"]) + hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a) + entity(id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a']) + entity(id:9d27fd2e-c728-420a-86ba-fc92df98dd6c, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:9d27fd2e-c728-420a-86ba-fc92df98dd6c, id:1c90cc92-4948-4b69-a163-f63e41891f7a) + hadMember(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, id:9d27fd2e-c728-420a-86ba-fc92df98dd6c) + entity(id:f89aaeef-0313-42af-b87e-7b519d494be7, [prov:type='prov:KeyEntityPair', prov:pairKey="elements", prov:pairEntity='id:9d27fd2e-c728-420a-86ba-fc92df98dd6c']) + entity(id:040d2761-5df7-4905-a289-3fed059729f3, [prov:value="0" %% xsd:boolean]) + hadMember(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, id:040d2761-5df7-4905-a289-3fed059729f3) + entity(id:e84e01b6-0126-4b79-90d5-99d22e8dde7c, [prov:type='prov:KeyEntityPair', prov:pairKey="auto_decompress", prov:pairEntity='id:040d2761-5df7-4905-a289-3fed059729f3']) + entity(data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe, [prov:type='wfprov:Artifact', prov:value="urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe"]) + hadMember(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe) + entity(id:000e294f-576c-469b-8965-4e279bebc880, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe']) + entity(id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066, id:8d86a2e6-482b-41b3-ac34-acc0b74014fe) + hadMember(id:34e943f0-5027-47b0-ba7b-05fca46da136, id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066) + entity(id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885, [prov:type='prov:KeyEntityPair', prov:pairKey="targets", prov:pairEntity='id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066']) + entity(id:074d9f95-5294-4f33-98a4-a37b8ce802cb, [prov:value="1" %% xsd:boolean]) + hadMember(id:34e943f0-5027-47b0-ba7b-05fca46da136, id:074d9f95-5294-4f33-98a4-a37b8ce802cb) + entity(id:a15754e6-26b6-4269-96b6-7d35515d1c02, [prov:type='prov:KeyEntityPair', prov:pairKey="check_content", prov:pairEntity='id:074d9f95-5294-4f33-98a4-a37b8ce802cb']) + entity(data:urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136, [prov:type='wfprov:Artifact', prov:value="urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136"]) + hadMember(id:34e943f0-5027-47b0-ba7b-05fca46da136, data:urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136) + entity(id:e25dce0d-bf63-414f-a0cd-2663e7a44d50, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136']) + used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, 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prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:37923bc7-fd48-4521-98e4-19a33c90b663', prov:hadDictionaryMember='id:311ea826-fd60-4dc1-a729-af0412613824', prov:hadDictionaryMember='id:36c37981-8a3c-45e8-82fb-1b367dd30899']) + entity(data:fd7fec473f1e6c6b, [prov:type='wfprov:Artifact', prov:value="fd7fec473f1e6c6b"]) + hadMember(id:d34c2c77-9bf0-4850-9f4c-3929c61d4266, data:fd7fec473f1e6c6b) + entity(id:37923bc7-fd48-4521-98e4-19a33c90b663, [prov:type='prov:KeyEntityPair', prov:pairKey="id", prov:pairEntity='data:fd7fec473f1e6c6b']) + entity(data:hda, [prov:type='wfprov:Artifact', prov:value="hda"]) + hadMember(id:d34c2c77-9bf0-4850-9f4c-3929c61d4266, data:hda) + entity(id:311ea826-fd60-4dc1-a729-af0412613824, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:hda']) + entity(data:urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266, [prov:type='wfprov:Artifact', prov:value="urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266"]) + hadMember(id:d34c2c77-9bf0-4850-9f4c-3929c61d4266, data:urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266) + entity(id:36c37981-8a3c-45e8-82fb-1b367dd30899, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266']) + entity(id:0ce5a422-abcb-4f41-a191-0a6068e14574, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) + hadMember(id:0ce5a422-abcb-4f41-a191-0a6068e14574, id:d34c2c77-9bf0-4850-9f4c-3929c61d4266) + hadMember(id:1d62001e-4526-468c-b34a-ef88dcc11ac3, id:0ce5a422-abcb-4f41-a191-0a6068e14574) + entity(id:0f92ffd8-540e-4bd6-8f6c-3c2d3df4f995, [prov:type='prov:KeyEntityPair', prov:pairKey="values", prov:pairEntity='id:0ce5a422-abcb-4f41-a191-0a6068e14574']) + entity(data:urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3, [prov:type='wfprov:Artifact', prov:value="urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3"]) + hadMember(id:1d62001e-4526-468c-b34a-ef88dcc11ac3, data:urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3) + entity(id:838e9760-cb17-4896-9c13-184164aa0c08, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3']) + used(id:a4be0d2e-38dd-4dfd-97de-414781a691ad, id:1d62001e-4526-468c-b34a-ef88dcc11ac3, 2022-04-04T16:59:09.806986, [prov:role='wf:main/random_lines1/input']) + entity(data:3, [prov:type='wfprov:Artifact', prov:value="3"]) + used(id:a4be0d2e-38dd-4dfd-97de-414781a691ad, data:3, 2022-04-04T16:59:09.807046, [prov:role='wf:main/random_lines1/num_lines']) + entity(id:8456e304-ef4f-4f40-a818-00b01407f6a2, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:0080be3e-2011-44c6-a391-3e151894b43e', prov:hadDictionaryMember='id:6de1750c-1612-4740-87a3-7d000e40c4b2', prov:hadDictionaryMember='id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91', prov:hadDictionaryMember='id:d13aa4a9-9029-4a4a-959b-4e2a3bd0aa3d']) + entity(id:fc4a126f-25bd-4d12-bde7-c41dadf135c6, [prov:value=1]) + hadMember(id:8456e304-ef4f-4f40-a818-00b01407f6a2, id:fc4a126f-25bd-4d12-bde7-c41dadf135c6) + entity(id:0080be3e-2011-44c6-a391-3e151894b43e, [prov:type='prov:KeyEntityPair', prov:pairKey="__current_case__", prov:pairEntity='id:fc4a126f-25bd-4d12-bde7-c41dadf135c6']) + entity(data:0, [prov:type='wfprov:Artifact', prov:value="0"]) + hadMember(id:8456e304-ef4f-4f40-a818-00b01407f6a2, data:0) + entity(id:6de1750c-1612-4740-87a3-7d000e40c4b2, [prov:type='prov:KeyEntityPair', prov:pairKey="seed", prov:pairEntity='data:0']) + entity(data:set_seed, [prov:type='wfprov:Artifact', prov:value="set_seed"]) + hadMember(id:8456e304-ef4f-4f40-a818-00b01407f6a2, data:set_seed) + entity(id:d13aa4a9-9029-4a4a-959b-4e2a3bd0aa3d, [prov:type='prov:KeyEntityPair', prov:pairKey="seed_source_selector", prov:pairEntity='data:set_seed']) + entity(data:urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2, [prov:type='wfprov:Artifact', prov:value="urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2"]) + hadMember(id:8456e304-ef4f-4f40-a818-00b01407f6a2, data:urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2) + entity(id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2']) + used(id:a4be0d2e-38dd-4dfd-97de-414781a691ad, id:8456e304-ef4f-4f40-a818-00b01407f6a2, 2022-04-04T16:59:09.807432, [prov:role='wf:main/random_lines1/seed_source']) +endDocument \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl new file mode 100644 index 00000000..2ef85a57 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl @@ -0,0 +1,1070 @@ +@prefix data: . +@prefix id: . +@prefix prov: . +@prefix rdfs: . +@prefix wf: . +@prefix wfprov: . +@prefix xsd: . + +id:0ffbc8ad-a3f1-4c5a-90a7-c0cba2037931 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.800503"^^xsd:dateTime ; + prov:entity id:202eb0cc-f08e-4946-be23-0b6f195a0997 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.799938"^^xsd:dateTime ; + prov:entity id:78b8eb8f-2594-4af0-9448-9ca96c3fc116 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.800010"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.802972"^^xsd:dateTime ; + prov:entity id:0fd972f6-10e7-42ee-a514-02ed749f9494 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.803053"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.800579"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; + prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . + +id:4e5feb15-2e9a-47c9-90df-18749a56c0d6 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.803927"^^xsd:dateTime ; + prov:entity id:af880c02-79fa-4624-a45c-8f0277838663 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.804768"^^xsd:dateTime ; + prov:entity id:8c884aa2-99c2-4588-9d49-eff12441e6c0 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.803988"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.804112"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.803689"^^xsd:dateTime ; + prov:entity id:cb03c73e-30e1-4184-93e7-ad075995d89f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.804048"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.804169"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.803812"^^xsd:dateTime ; + prov:entity id:e88d7b49-c96b-4e54-92f2-410aa9268df2 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.805613"^^xsd:dateTime ; + prov:entity id:9c04f4c2-683e-4729-938f-ffb2063bcd63 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; + prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . + +id:a4be0d2e-38dd-4dfd-97de-414781a691ad a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.806986"^^xsd:dateTime ; + prov:entity id:1d62001e-4526-468c-b34a-ef88dcc11ac3 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.806121"^^xsd:dateTime ; + prov:entity id:fe8b9a54-02f9-40d5-b3be-d14352b6b76b ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.806350"^^xsd:dateTime ; + prov:entity data:42f21c0ad41011eb87defa163eba836f ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.806236"^^xsd:dateTime ; + prov:entity id:c38cd06f-2a47-441f-8677-9b944c5d49b5 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.806293"^^xsd:dateTime ; + prov:entity data:txt ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.807432"^^xsd:dateTime ; + prov:entity id:8456e304-ef4f-4f40-a818-00b01407f6a2 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.807046"^^xsd:dateTime ; + prov:entity data:3 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.806458"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.806405"^^xsd:dateTime ; + prov:entity ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; + prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . + +id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; + prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.797298"^^xsd:dateTime ; + prov:entity data: ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.799249"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.799177"^^xsd:dateTime ; + prov:entity id:34e943f0-5027-47b0-ba7b-05fca46da136 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.797234"^^xsd:dateTime ; + prov:entity id:6572947b-c3fd-4c6f-bdff-7aa191bc5546 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.796656"^^xsd:dateTime ; + prov:entity data:1 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2022-04-04T16:59:09.796590"^^xsd:dateTime ; + prov:entity id:2119440c-63be-46a9-bbb7-2b104033b8f2 ; + prov:hadRole ] ; + prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; + prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . + +data:2524d3d3b68ad39a a wfprov:Artifact, + prov:Entity ; + prov:value "2524d3d3b68ad39a"^^xsd:string . + +data:3 a wfprov:Artifact, + prov:Entity ; + prov:value "3"^^xsd:string . + +data:775bc9b3c1750167 a wfprov:Artifact, + prov:Entity ; + prov:value "775bc9b3c1750167"^^xsd:string . + +data:7c1d8e3101dbcdba a wfprov:Artifact, + prov:Entity ; + prov:value "7c1d8e3101dbcdba"^^xsd:string . + +id:000e294f-576c-469b-8965-4e279bebc880 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:0080be3e-2011-44c6-a391-3e151894b43e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:fc4a126f-25bd-4d12-bde7-c41dadf135c6 ; + prov:pairKey "__current_case__"^^xsd:string . + +id:00e0f888-71d8-49f9-ba39-dcaed5a91c56 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:02094080-ba1e-458f-8b75-5741f7f9a72b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:2a48c6c5-b7ba-482e-808e-b07d48c0bec7 ; + prov:pairKey "elements"^^xsd:string . + +id:027f7717-78d8-4f9a-a887-87813339b23e a prov:Agent . + +id:0592876b-ce23-4b6a-a8cf-32a46f7aedea a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 ; + prov:pairKey "targets"^^xsd:string . + +id:0ce829aa-f4ff-4f70-804d-09e05aa7a764 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:86fce97c-a524-4a88-a6fb-cf26b95536d2 ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:0f92ffd8-540e-4bd6-8f6c-3c2d3df4f995 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:0ce5a422-abcb-4f41-a191-0a6068e14574 ; + prov:pairKey "values"^^xsd:string . + +id:0fd972f6-10e7-42ee-a514-02ed749f9494 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:100daec7-1e65-4bc5-814b-622b8d197b78, + id:578fa382-6aec-49cf-a1ee-b3f65cc63dc0, + id:a465c657-53e0-49bf-a7b0-665b53baafbf ; + prov:hadMember , + id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59, + id:7225c876-9def-4725-8512-f1e8cedf1d78 . + +id:100daec7-1e65-4bc5-814b-622b8d197b78 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:7225c876-9def-4725-8512-f1e8cedf1d78 ; + prov:pairKey "targets"^^xsd:string . + +id:11a7af4f-7df4-4a99-ba83-6d0418b6f7df a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:1605ad9c-1b56-4055-a8d0-866f49da1687 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:f4d07c61-fb2b-42eb-a7c5-1820900166f3 ; + prov:pairKey "__index__"^^xsd:string . + +id:1c90cc92-4948-4b69-a163-f63e41891f7a a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:0592876b-ce23-4b6a-a8cf-32a46f7aedea, + id:29b40ddc-e592-4aa9-989f-ed4ac9be59af, + id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38, + id:3e26cc6f-1f3b-438d-ada9-a55bead88b03, + id:587e2872-6ae3-4716-b99e-12c5db1f8e56, + id:5ab39f26-7656-40f1-826f-38f40ed09f10, + id:8232048b-b457-45cb-932e-a5cf8f8be6e1, + id:912f104e-1517-492e-abe3-f931fe47438b, + id:b1aad576-0af0-43c0-948d-df79e52df6b7, + id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103, + id:ed8aaa9a-567f-4893-b432-fa6e49547650 ; + prov:hadMember , + , + data:auto, + data:dataset2.txt, + data:path, + , + id:03827a8b-50a4-463b-876a-742652bb3049, + id:16597142-0745-4b4c-80c7-5755b2d087a7, + id:512093ee-9853-484f-9a93-aea928098062, + id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b, + id:cdcc006a-91e4-4f29-8c14-1f91eef044dd . + +id:1d62001e-4526-468c-b34a-ef88dcc11ac3 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:0f92ffd8-540e-4bd6-8f6c-3c2d3df4f995, + id:838e9760-cb17-4896-9c13-184164aa0c08 ; + prov:hadMember , + id:0ce5a422-abcb-4f41-a191-0a6068e14574 . + +id:202eb0cc-f08e-4946-be23-0b6f195a0997 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:34422e4d-9f35-46dc-bbf6-f819ae20a341 . + +id:2119440c-63be-46a9-bbb7-2b104033b8f2 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2524d3d3b68ad39a . + +id:2301b8b5-528f-4802-bd81-a4a3ca8534f4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:2326e0c6-2608-432a-934a-dc26b09dabcd a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c ; + prov:pairKey "__index__"^^xsd:string . + +id:2605025b-6018-4473-b1f2-10ffa81c469a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:28f039db-5706-4cf6-96ce-321fbfd994f8 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:fd39387a-478e-4380-8597-2a544a032b8c ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:29b40ddc-e592-4aa9-989f-ed4ac9be59af a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:2e397e93-13e6-4ce4-bced-ed3008a1b0db a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:2e7982bf-5cce-44ac-9547-a552c8964d5a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:311ea826-fd60-4dc1-a729-af0412613824 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:34422e4d-9f35-46dc-bbf6-f819ae20a341 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:86e5e11c-8ad1-4659-8fc4-85b4c2b57230, + id:a5be47a1-5d66-4f63-b71e-f7eacb04da10, + id:da1f3881-ca92-447f-b7fd-992e43d9536c ; + prov:hadMember , + , + id:6d83fa63-70b3-4a8d-9234-8e9f01d8e89a . + +id:34e943f0-5027-47b0-ba7b-05fca46da136 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885, + id:a15754e6-26b6-4269-96b6-7d35515d1c02, + id:e25dce0d-bf63-414f-a0cd-2663e7a44d50 ; + prov:hadMember , + id:074d9f95-5294-4f33-98a4-a37b8ce802cb, + id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 . + +id:36c37981-8a3c-45e8-82fb-1b367dd30899 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:37923bc7-fd48-4521-98e4-19a33c90b663 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:fd7fec473f1e6c6b ; + prov:pairKey "id"^^xsd:string . + +id:3e26cc6f-1f3b-438d-ada9-a55bead88b03 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:512093ee-9853-484f-9a93-aea928098062 ; + prov:pairKey "to_posix_lines"^^xsd:string . + +id:450f4c3b-e384-42b0-8090-47cc2e4691fb a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:2e789aae2475b7da ; + prov:pairKey "id"^^xsd:string . + +id:45cbe10d-9998-43f0-910f-646eb2c4dbca a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset1.txt ; + prov:pairKey "name"^^xsd:string . + +id:4cea125d-b4d1-454b-982e-6bb7b393022e a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:578fa382-6aec-49cf-a1ee-b3f65cc63dc0 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59 ; + prov:pairKey "check_content"^^xsd:string . + +id:587e2872-6ae3-4716-b99e-12c5db1f8e56 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b ; + prov:pairKey "hashes"^^xsd:string . + +id:5ab39f26-7656-40f1-826f-38f40ed09f10 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:60e283d2-d89f-4235-8d61-2600cb5717c4 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:3d532d55-2434-4449-9fd3-aae8eca62c1b ; + prov:pairKey "input2"^^xsd:string . + +id:633b83e5-3fa9-41be-b2e4-52381339221a a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:63446d8e-78fe-4025-a69a-c5ca6f8a0bea ; + prov:pairKey "values"^^xsd:string . + +id:651a06c8-c920-42d6-98ca-71dcd610322f a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:6572947b-c3fd-4c6f-bdff-7aa191bc5546 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:e9693b34-04fb-4b31-a78c-7d089fd6558b . + +id:67c9330c-aef5-4d94-ad77-f38d191198a2 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:6c9b6d77-2863-4fe0-a703-5ff0d53a7504 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:02094080-ba1e-458f-8b75-5741f7f9a72b, + id:28f039db-5706-4cf6-96ce-321fbfd994f8, + id:aab81666-8ccd-45a7-99e8-b4519ce85496, + id:c5939a58-b121-40a2-b972-7f2fb66a5f03 ; + prov:hadMember , + id:2a48c6c5-b7ba-482e-808e-b07d48c0bec7, + id:4304771d-432a-48d3-b461-e84b2972ee0a, + id:fd39387a-478e-4380-8597-2a544a032b8c . + +id:6de1750c-1612-4740-87a3-7d000e40c4b2 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:0 ; + prov:pairKey "seed"^^xsd:string . + +id:708a0ca4-2972-467e-9443-52a37e9d0bf1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hda ; + prov:pairKey "src"^^xsd:string . + +id:78b8eb8f-2594-4af0-9448-9ca96c3fc116 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7c1d8e3101dbcdba . + +id:7b40bdfc-aacc-4947-a8d8-d13db0419365 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:7cbde64f-8934-42ab-af87-2044c3e092ce a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:7ca3de8f49293d1a ; + prov:pairKey "id"^^xsd:string . + +id:7cd3eabc-b445-4a44-baea-fade541b56d7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "dbkey"^^xsd:string . + +id:80c39113-024d-45a2-9e33-e8216a8fc6d7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:path ; + prov:pairKey "src"^^xsd:string . + +id:8232048b-b457-45cb-932e-a5cf8f8be6e1 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:838e9760-cb17-4896-9c13-184164aa0c08 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:8456e304-ef4f-4f40-a818-00b01407f6a2 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:0080be3e-2011-44c6-a391-3e151894b43e, + id:6de1750c-1612-4740-87a3-7d000e40c4b2, + id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91, + id:d13aa4a9-9029-4a4a-959b-4e2a3bd0aa3d ; + prov:hadMember data:0, + data:set_seed, + , + id:fc4a126f-25bd-4d12-bde7-c41dadf135c6 . + +id:86e5e11c-8ad1-4659-8fc4-85b4c2b57230 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:6d83fa63-70b3-4a8d-9234-8e9f01d8e89a ; + prov:pairKey "__index__"^^xsd:string . + +id:8c884aa2-99c2-4588-9d49-eff12441e6c0 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:2e397e93-13e6-4ce4-bced-ed3008a1b0db, + id:633b83e5-3fa9-41be-b2e4-52381339221a ; + prov:hadMember , + id:63446d8e-78fe-4025-a69a-c5ca6f8a0bea . + +id:8d86a2e6-482b-41b3-ac34-acc0b74014fe a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:000e294f-576c-469b-8965-4e279bebc880, + id:a6d080a6-7c60-46f2-85c8-2519f4d803ea, + id:e84e01b6-0126-4b79-90d5-99d22e8dde7c, + id:f89aaeef-0313-42af-b87e-7b519d494be7 ; + prov:hadMember , + id:040d2761-5df7-4905-a289-3fed059729f3, + id:9d27fd2e-c728-420a-86ba-fc92df98dd6c, + id:e46be7d4-c0c3-489f-86dd-0c8148d86858 . + +id:912f104e-1517-492e-abe3-f931fe47438b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:03827a8b-50a4-463b-876a-742652bb3049 ; + prov:pairKey "in_place"^^xsd:string . + +id:9c04f4c2-683e-4729-938f-ffb2063bcd63 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:e66c4859-3380-4705-b3bb-2c650dfb7888 . + +id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:11a7af4f-7df4-4a99-ba83-6d0418b6f7df, + id:67c9330c-aef5-4d94-ad77-f38d191198a2, + id:7cbde64f-8934-42ab-af87-2044c3e092ce ; + prov:hadMember data:7ca3de8f49293d1a, + data:hda, + . + +id:a15754e6-26b6-4269-96b6-7d35515d1c02 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:074d9f95-5294-4f33-98a4-a37b8ce802cb ; + prov:pairKey "check_content"^^xsd:string . + +id:a465c657-53e0-49bf-a7b0-665b53baafbf a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a5be47a1-5d66-4f63-b71e-f7eacb04da10 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:a6d080a6-7c60-46f2-85c8-2519f4d803ea a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e46be7d4-c0c3-489f-86dd-0c8148d86858 ; + prov:pairKey "destination"^^xsd:string . + +id:aab81666-8ccd-45a7-99e8-b4519ce85496 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:4304771d-432a-48d3-b461-e84b2972ee0a ; + prov:pairKey "destination"^^xsd:string . + +id:af880c02-79fa-4624-a45c-8f0277838663 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +id:b1aad576-0af0-43c0-948d-df79e52df6b7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:16597142-0745-4b4c-80c7-5755b2d087a7 ; + prov:pairKey "purge_source"^^xsd:string . + +id:b468ef66-ed86-4002-acd9-32c459e7f565 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:5605777b-6f2c-46cb-a64a-189695ee3693 ; + prov:pairKey "object_id"^^xsd:string . + +id:b4f8420d-99cf-4b6a-bd7f-7ffb549e16c9 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "path"^^xsd:string . + +id:b785b0a5-c798-49f4-b1a1-8be87a4bda8b a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:hdas ; + prov:pairKey "type"^^xsd:string . + +id:bb92fa6f-500c-493b-9107-5d9837a294ba a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:c4933233-a84f-4ce0-840e-e5577b27c96c ; + prov:pairKey "purge_source"^^xsd:string . + +id:c38cd06f-2a47-441f-8677-9b944c5d49b5 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:775bc9b3c1750167 . + +id:c5939a58-b121-40a2-b972-7f2fb66a5f03 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:ca085eb3-7628-4fd6-98be-09f5a23547b9 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:auto ; + prov:pairKey "ext"^^xsd:string . + +id:cb03c73e-30e1-4184-93e7-ad075995d89f a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:7ca3de8f49293d1a . + +id:d13aa4a9-9029-4a4a-959b-4e2a3bd0aa3d a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:set_seed ; + prov:pairKey "seed_source_selector"^^xsd:string . + +id:d34c2c77-9bf0-4850-9f4c-3929c61d4266 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:311ea826-fd60-4dc1-a729-af0412613824, + id:36c37981-8a3c-45e8-82fb-1b367dd30899, + id:37923bc7-fd48-4521-98e4-19a33c90b663 ; + prov:hadMember data:fd7fec473f1e6c6b, + data:hda, + . + +id:d530cc8c-b67b-4e1d-8992-bca7f8454520 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:e1cda342-b856-423e-aa58-5485505a0d28 ; + prov:pairKey "values"^^xsd:string . + +id:da1f3881-ca92-447f-b7fd-992e43d9536c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "file_data"^^xsd:string . + +id:de072b7b-d692-4453-9af4-9975a3742a44 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:450f4c3b-e384-42b0-8090-47cc2e4691fb, + id:708a0ca4-2972-467e-9443-52a37e9d0bf1, + id:eedcc56e-086a-42dc-a5d4-212bee28b594 ; + prov:hadMember data:2e789aae2475b7da, + data:hda, + . + +id:e25dce0d-bf63-414f-a0cd-2663e7a44d50 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity data:dataset2.txt ; + prov:pairKey "name"^^xsd:string . + +id:e66c4859-3380-4705-b3bb-2c650dfb7888 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:2326e0c6-2608-432a-934a-dc26b09dabcd, + id:60e283d2-d89f-4235-8d61-2600cb5717c4, + id:651a06c8-c920-42d6-98ca-71dcd610322f ; + prov:hadMember , + id:3d532d55-2434-4449-9fd3-aae8eca62c1b, + id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c . + +id:e84e01b6-0126-4b79-90d5-99d22e8dde7c a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:040d2761-5df7-4905-a289-3fed059729f3 ; + prov:pairKey "auto_decompress"^^xsd:string . + +id:e88d7b49-c96b-4e54-92f2-410aa9268df2 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:2e789aae2475b7da . + +id:e9693b34-04fb-4b31-a78c-7d089fd6558b a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:00e0f888-71d8-49f9-ba39-dcaed5a91c56, + id:1605ad9c-1b56-4055-a8d0-866f49da1687, + id:2301b8b5-528f-4802-bd81-a4a3ca8534f4 ; + prov:hadMember , + , + id:f4d07c61-fb2b-42eb-a7c5-1820900166f3 . + +id:ed8aaa9a-567f-4893-b432-fa6e49547650 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:cdcc006a-91e4-4f29-8c14-1f91eef044dd ; + prov:pairKey "object_id"^^xsd:string . + +id:eedcc56e-086a-42dc-a5d4-212bee28b594 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity ; + prov:pairKey "@id"^^xsd:string . + +id:f149acac-0ee5-4588-887f-d7ee04e430cb a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:0ce829aa-f4ff-4f70-804d-09e05aa7a764, + id:45cbe10d-9998-43f0-910f-646eb2c4dbca, + id:4cea125d-b4d1-454b-982e-6bb7b393022e, + id:7cd3eabc-b445-4a44-baea-fade541b56d7, + id:80c39113-024d-45a2-9e33-e8216a8fc6d7, + id:b468ef66-ed86-4002-acd9-32c459e7f565, + id:b4f8420d-99cf-4b6a-bd7f-7ffb549e16c9, + id:bb92fa6f-500c-493b-9107-5d9837a294ba, + id:ca085eb3-7628-4fd6-98be-09f5a23547b9, + id:f9c2956e-46cf-4b27-bc2a-2c4ae74dc704, + id:fa1a58d9-9489-4cc8-9f75-0fe047e1d970 ; + prov:hadMember , + , + data:auto, + data:dataset1.txt, + data:path, + , + id:5605777b-6f2c-46cb-a64a-189695ee3693, + id:86fce97c-a524-4a88-a6fb-cf26b95536d2, + id:c4933233-a84f-4ce0-840e-e5577b27c96c, + id:de67df28-2fa8-46d5-901f-9b72a3ff6949, + id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 . + +id:f89aaeef-0313-42af-b87e-7b519d494be7 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:9d27fd2e-c728-420a-86ba-fc92df98dd6c ; + prov:pairKey "elements"^^xsd:string . + +id:f9c2956e-46cf-4b27-bc2a-2c4ae74dc704 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:de67df28-2fa8-46d5-901f-9b72a3ff6949 ; + prov:pairKey "hashes"^^xsd:string . + +id:fa1a58d9-9489-4cc8-9f75-0fe047e1d970 a prov:Entity, + prov:KeyEntityPair ; + prov:pairEntity id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 ; + prov:pairKey "in_place"^^xsd:string . + +id:fe8b9a54-02f9-40d5-b3be-d14352b6b76b a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember data:fd7fec473f1e6c6b . + +data: a wfprov:Artifact, + prov:Entity ; + prov:value ""^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^xsd:string . + +data:0 a wfprov:Artifact, + prov:Entity ; + prov:value "0"^^xsd:string . + +data:42f21c0ad41011eb87defa163eba836f a wfprov:Artifact, + prov:Entity ; + prov:value "42f21c0ad41011eb87defa163eba836f"^^xsd:string . + +data:dataset1.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset1.txt"^^xsd:string . + +data:dataset2.txt a wfprov:Artifact, + prov:Entity ; + prov:value "dataset2.txt"^^xsd:string . + +data:set_seed a wfprov:Artifact, + prov:Entity ; + prov:value "set_seed"^^xsd:string . + +data:txt a wfprov:Artifact, + prov:Entity ; + prov:value "txt"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:0fd972f6-10e7-42ee-a514-02ed749f9494"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:34422e4d-9f35-46dc-bbf6-f819ae20a341"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:3d532d55-2434-4449-9fd3-aae8eca62c1b"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:4304771d-432a-48d3-b461-e84b2972ee0a"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:6c9b6d77-2863-4fe0-a703-5ff0d53a7504"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:8c884aa2-99c2-4588-9d49-eff12441e6c0"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:de072b7b-d692-4453-9af4-9975a3742a44"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:e66c4859-3380-4705-b3bb-2c650dfb7888"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "urn:uuid:f149acac-0ee5-4588-887f-d7ee04e430cb"^^xsd:string . + +id:03827a8b-50a4-463b-876a-742652bb3049 a prov:Entity ; + prov:value false . + +id:040d2761-5df7-4905-a289-3fed059729f3 a prov:Entity ; + prov:value false . + +id:074d9f95-5294-4f33-98a4-a37b8ce802cb a prov:Entity ; + prov:value true . + +id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59 a prov:Entity ; + prov:value true . + +id:0ce5a422-abcb-4f41-a191-0a6068e14574 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:d34c2c77-9bf0-4850-9f4c-3929c61d4266 . + +id:16597142-0745-4b4c-80c7-5755b2d087a7 a prov:Entity ; + prov:value false . + +id:2a48c6c5-b7ba-482e-808e-b07d48c0bec7 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:f149acac-0ee5-4588-887f-d7ee04e430cb . + +id:3d532d55-2434-4449-9fd3-aae8eca62c1b a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:2605025b-6018-4473-b1f2-10ffa81c469a, + id:d530cc8c-b67b-4e1d-8992-bca7f8454520 ; + prov:hadMember , + id:e1cda342-b856-423e-aa58-5485505a0d28 . + +id:4304771d-432a-48d3-b461-e84b2972ee0a a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:2e7982bf-5cce-44ac-9547-a552c8964d5a, + id:b785b0a5-c798-49f4-b1a1-8be87a4bda8b ; + prov:hadMember data:hdas, + . + +id:512093ee-9853-484f-9a93-aea928098062 a prov:Entity ; + prov:value true . + +id:5605777b-6f2c-46cb-a64a-189695ee3693 a prov:Entity ; + prov:value "155707"^^xsd:int . + +id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c a prov:Entity ; + prov:value "0"^^xsd:int . + +id:63446d8e-78fe-4025-a69a-c5ca6f8a0bea a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114 . + +id:6d83fa63-70b3-4a8d-9234-8e9f01d8e89a a prov:Entity ; + prov:value "0"^^xsd:int . + +id:7225c876-9def-4725-8512-f1e8cedf1d78 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:6c9b6d77-2863-4fe0-a703-5ff0d53a7504 . + +id:86fce97c-a524-4a88-a6fb-cf26b95536d2 a prov:Entity ; + prov:value true . + +id:9d27fd2e-c728-420a-86ba-fc92df98dd6c a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:1c90cc92-4948-4b69-a163-f63e41891f7a . + +id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:8d86a2e6-482b-41b3-ac34-acc0b74014fe . + +id:c4933233-a84f-4ce0-840e-e5577b27c96c a prov:Entity ; + prov:value false . + +id:cdcc006a-91e4-4f29-8c14-1f91eef044dd a prov:Entity ; + prov:value "155708"^^xsd:int . + +id:de67df28-2fa8-46d5-901f-9b72a3ff6949 a wfprov:Artifact, + prov:Collection, + prov:EmptyCollection, + prov:Entity . + +id:e1cda342-b856-423e-aa58-5485505a0d28 a wfprov:Artifact, + prov:Collection, + prov:Entity ; + prov:hadMember id:de072b7b-d692-4453-9af4-9975a3742a44 . + +id:e46be7d4-c0c3-489f-86dd-0c8148d86858 a wfprov:Artifact, + prov:Collection, + prov:Dictionary, + prov:Entity ; + prov:hadDictionaryMember id:7b40bdfc-aacc-4947-a8d8-d13db0419365, + id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6 ; + prov:hadMember data:hdas, + . + +id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 a prov:Entity ; + prov:value false . + +id:f4d07c61-fb2b-42eb-a7c5-1820900166f3 a prov:Entity ; + prov:value "0"^^xsd:int . + +id:fc4a126f-25bd-4d12-bde7-c41dadf135c6 a prov:Entity ; + prov:value "1"^^xsd:int . + +id:fd39387a-478e-4380-8597-2a544a032b8c a prov:Entity ; + prov:value false . + +data:2e789aae2475b7da a wfprov:Artifact, + prov:Entity ; + prov:value "2e789aae2475b7da"^^xsd:string . + +data:7ca3de8f49293d1a a wfprov:Artifact, + prov:Entity ; + prov:value "7ca3de8f49293d1a"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"^^xsd:string . + + a wfprov:Artifact, + prov:Entity ; + prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"^^xsd:string . + +data:1 a wfprov:Artifact, + prov:Entity ; + prov:value "1"^^xsd:string . + +data:auto a wfprov:Artifact, + prov:Entity ; + prov:value "auto"^^xsd:string . + +data:fd7fec473f1e6c6b a wfprov:Artifact, + prov:Entity ; + prov:value "fd7fec473f1e6c6b"^^xsd:string . + +data:hdas a wfprov:Artifact, + prov:Entity ; + prov:value "hdas"^^xsd:string . + +data:path a wfprov:Artifact, + prov:Entity ; + prov:value "path"^^xsd:string . + +id:b02505bb-6b95-4e97-8043-d0823b00b7f4 a wfprov:WorkflowRun, + prov:Activity ; + rdfs:label "Run of galaxy workflow"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan wf:main ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-04-04T16:59:09.795971"^^xsd:dateTime ; + prov:hadActivity id:8124e339-e638-4fc3-b421-6367e3682c50 ] ; + prov:startedAtTime "2022-04-04T16:59:09.795894"^^xsd:dateTime ; + prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . + + a wfprov:Artifact, + prov:Entity ; + prov:value "?"^^xsd:string . + +data:hda a wfprov:Artifact, + prov:Entity ; + prov:value "hda"^^xsd:string . + +id:8124e339-e638-4fc3-b421-6367e3682c50 a wfprov:WorkflowEngine, + prov:Agent, + prov:SoftwareAgent ; + rdfs:label "galaxy_version_placeholder"^^xsd:string ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2022-04-04T16:59:09.795855"^^xsd:dateTime ; + prov:hadActivity id:027f7717-78d8-4f9a-a887-87813339b23e ] . + diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml new file mode 100644 index 00000000..6f14c1e6 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml @@ -0,0 +1,1447 @@ + + + + + galaxy_version_placeholder + wfprov:WorkflowEngine + + + + + 2022-04-04T16:59:09.795855 + + + 2022-04-04T16:59:09.795894 + Run of galaxy workflow + wfprov:WorkflowRun + + + + + + + + + + 2022-04-04T16:59:09.795971 + + + 2021-06-23T10:20:22.770291 + 2021-06-23T10:20:42.041319 + Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:20:22.770291 + + + wfprov:Artifact + 2524d3d3b68ad39a + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.796590 + wf:main/__DATA_FETCH__/output0 + + + wfprov:Artifact + 1 + + + + + 2022-04-04T16:59:09.796656 + wf:main/__DATA_FETCH__/file_count + + + prov:Dictionary + wfprov:Artifact + id:00e0f888-71d8-49f9-ba39-dcaed5a91c56 + id:1605ad9c-1b56-4055-a8d0-866f49da1687 + id:2301b8b5-528f-4802-bd81-a4a3ca8534f4 + + + 0 + + + + + + + prov:KeyEntityPair + id:f4d07c61-fb2b-42eb-a7c5-1820900166f3 + __index__ + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + file_data + + + wfprov:Artifact + urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b + + + + + + + prov:KeyEntityPair + data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b + @id + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.797234 + wf:main/__DATA_FETCH__/files + + + wfprov:Artifact + + + + + + 2022-04-04T16:59:09.797298 + wf:main/__DATA_FETCH__/paramfile + + + prov:Dictionary + wfprov:Artifact + id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885 + id:a15754e6-26b6-4269-96b6-7d35515d1c02 + id:e25dce0d-bf63-414f-a0cd-2663e7a44d50 + + + prov:Dictionary + wfprov:Artifact + id:000e294f-576c-469b-8965-4e279bebc880 + id:a6d080a6-7c60-46f2-85c8-2519f4d803ea + id:e84e01b6-0126-4b79-90d5-99d22e8dde7c + id:f89aaeef-0313-42af-b87e-7b519d494be7 + + + prov:Dictionary + wfprov:Artifact + id:7b40bdfc-aacc-4947-a8d8-d13db0419365 + id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6 + + + wfprov:Artifact + hdas + + + + + + + prov:KeyEntityPair + data:hdas + type + + + wfprov:Artifact + urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858 + + + + + + + prov:KeyEntityPair + data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858 + @id + + + + + + + prov:KeyEntityPair + id:e46be7d4-c0c3-489f-86dd-0c8148d86858 + destination + + + prov:Dictionary + wfprov:Artifact + id:0592876b-ce23-4b6a-a8cf-32a46f7aedea + id:29b40ddc-e592-4aa9-989f-ed4ac9be59af + id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38 + id:3e26cc6f-1f3b-438d-ada9-a55bead88b03 + id:587e2872-6ae3-4716-b99e-12c5db1f8e56 + id:5ab39f26-7656-40f1-826f-38f40ed09f10 + id:8232048b-b457-45cb-932e-a5cf8f8be6e1 + id:912f104e-1517-492e-abe3-f931fe47438b + id:b1aad576-0af0-43c0-948d-df79e52df6b7 + id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103 + id:ed8aaa9a-567f-4893-b432-fa6e49547650 + + + wfprov:Artifact + auto + + + + + + + prov:KeyEntityPair + data:auto + ext + + + wfprov:Artifact + ? + + + + + + + prov:KeyEntityPair + data:? + dbkey + + + true + + + + + + + prov:KeyEntityPair + id:512093ee-9853-484f-9a93-aea928098062 + to_posix_lines + + + wfprov:Artifact + path + + + + + + + prov:KeyEntityPair + data:path + src + + + wfprov:Artifact + dataset2.txt + + + + + + + prov:KeyEntityPair + data:dataset2.txt + name + + + prov:EmptyCollection + wfprov:Artifact + + + + + + + prov:KeyEntityPair + id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b + hashes + + + false + + + + + + + prov:KeyEntityPair + id:03827a8b-50a4-463b-876a-742652bb3049 + in_place + + + false + + + + + + + prov:KeyEntityPair + id:16597142-0745-4b4c-80c7-5755b2d087a7 + purge_source + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 + path + + + 155708 + + + + + + + prov:KeyEntityPair + id:cdcc006a-91e4-4f29-8c14-1f91eef044dd + object_id + + + wfprov:Artifact + urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a + + + + + + + prov:KeyEntityPair + data:urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:9d27fd2e-c728-420a-86ba-fc92df98dd6c + elements + + + false + + + + + + + prov:KeyEntityPair + id:040d2761-5df7-4905-a289-3fed059729f3 + auto_decompress + + + wfprov:Artifact + urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe + + + + + + + prov:KeyEntityPair + data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 + targets + + + true + + + + + + + prov:KeyEntityPair + id:074d9f95-5294-4f33-98a4-a37b8ce802cb + check_content + + + wfprov:Artifact + urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136 + + + + + + + prov:KeyEntityPair + data:urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136 + @id + + + + + 2022-04-04T16:59:09.799177 + wf:main/__DATA_FETCH__/request_json + + + wfprov:Artifact + 1 + + + + + 2022-04-04T16:59:09.799249 + wf:main/__DATA_FETCH__/request_version + + + 2021-06-23T10:20:00.981702 + 2021-06-23T10:20:22.202678 + Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:20:00.981702 + + + wfprov:Artifact + 7c1d8e3101dbcdba + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.799938 + wf:main/__DATA_FETCH__/output0 + + + wfprov:Artifact + 1 + + + + + 2022-04-04T16:59:09.800010 + wf:main/__DATA_FETCH__/file_count + + + prov:Dictionary + wfprov:Artifact + id:86e5e11c-8ad1-4659-8fc4-85b4c2b57230 + id:a5be47a1-5d66-4f63-b71e-f7eacb04da10 + id:da1f3881-ca92-447f-b7fd-992e43d9536c + + + 0 + + + + + + + prov:KeyEntityPair + id:6d83fa63-70b3-4a8d-9234-8e9f01d8e89a + __index__ + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + file_data + + + wfprov:Artifact + urn:uuid:34422e4d-9f35-46dc-bbf6-f819ae20a341 + + + + + + + prov:KeyEntityPair + data:urn:uuid:34422e4d-9f35-46dc-bbf6-f819ae20a341 + @id + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.800503 + wf:main/__DATA_FETCH__/files + + + wfprov:Artifact + + + + + + 2022-04-04T16:59:09.800579 + wf:main/__DATA_FETCH__/paramfile + + + prov:Dictionary + wfprov:Artifact + id:100daec7-1e65-4bc5-814b-622b8d197b78 + id:578fa382-6aec-49cf-a1ee-b3f65cc63dc0 + id:a465c657-53e0-49bf-a7b0-665b53baafbf + + + prov:Dictionary + wfprov:Artifact + id:02094080-ba1e-458f-8b75-5741f7f9a72b + id:28f039db-5706-4cf6-96ce-321fbfd994f8 + id:aab81666-8ccd-45a7-99e8-b4519ce85496 + id:c5939a58-b121-40a2-b972-7f2fb66a5f03 + + + prov:Dictionary + wfprov:Artifact + id:2e7982bf-5cce-44ac-9547-a552c8964d5a + id:b785b0a5-c798-49f4-b1a1-8be87a4bda8b + + + wfprov:Artifact + hdas + + + + + + + prov:KeyEntityPair + data:hdas + type + + + wfprov:Artifact + urn:uuid:4304771d-432a-48d3-b461-e84b2972ee0a + + + + + + + prov:KeyEntityPair + data:urn:uuid:4304771d-432a-48d3-b461-e84b2972ee0a + @id + + + + + + + prov:KeyEntityPair + id:4304771d-432a-48d3-b461-e84b2972ee0a + destination + + + prov:Dictionary + wfprov:Artifact + id:0ce829aa-f4ff-4f70-804d-09e05aa7a764 + id:45cbe10d-9998-43f0-910f-646eb2c4dbca + id:4cea125d-b4d1-454b-982e-6bb7b393022e + id:7cd3eabc-b445-4a44-baea-fade541b56d7 + id:80c39113-024d-45a2-9e33-e8216a8fc6d7 + id:b468ef66-ed86-4002-acd9-32c459e7f565 + id:b4f8420d-99cf-4b6a-bd7f-7ffb549e16c9 + id:bb92fa6f-500c-493b-9107-5d9837a294ba + id:ca085eb3-7628-4fd6-98be-09f5a23547b9 + id:f9c2956e-46cf-4b27-bc2a-2c4ae74dc704 + id:fa1a58d9-9489-4cc8-9f75-0fe047e1d970 + + + wfprov:Artifact + auto + + + + + + + prov:KeyEntityPair + data:auto + ext + + + wfprov:Artifact + ? + + + + + + + prov:KeyEntityPair + data:? + dbkey + + + true + + + + + + + prov:KeyEntityPair + id:86fce97c-a524-4a88-a6fb-cf26b95536d2 + to_posix_lines + + + wfprov:Artifact + path + + + + + + + prov:KeyEntityPair + data:path + src + + + wfprov:Artifact + dataset1.txt + + + + + + + prov:KeyEntityPair + data:dataset1.txt + name + + + prov:EmptyCollection + wfprov:Artifact + + + + + + + prov:KeyEntityPair + id:de67df28-2fa8-46d5-901f-9b72a3ff6949 + hashes + + + false + + + + + + + prov:KeyEntityPair + id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 + in_place + + + false + + + + + + + prov:KeyEntityPair + id:c4933233-a84f-4ce0-840e-e5577b27c96c + purge_source + + + wfprov:Artifact + /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + + + + + + + prov:KeyEntityPair + data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a + path + + + 155707 + + + + + + + prov:KeyEntityPair + id:5605777b-6f2c-46cb-a64a-189695ee3693 + object_id + + + wfprov:Artifact + urn:uuid:f149acac-0ee5-4588-887f-d7ee04e430cb + + + + + + + prov:KeyEntityPair + data:urn:uuid:f149acac-0ee5-4588-887f-d7ee04e430cb + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:2a48c6c5-b7ba-482e-808e-b07d48c0bec7 + elements + + + false + + + + + + + prov:KeyEntityPair + id:fd39387a-478e-4380-8597-2a544a032b8c + auto_decompress + + + wfprov:Artifact + urn:uuid:6c9b6d77-2863-4fe0-a703-5ff0d53a7504 + + + + + + + prov:KeyEntityPair + data:urn:uuid:6c9b6d77-2863-4fe0-a703-5ff0d53a7504 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:7225c876-9def-4725-8512-f1e8cedf1d78 + targets + + + true + + + + + + + prov:KeyEntityPair + id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59 + check_content + + + wfprov:Artifact + urn:uuid:0fd972f6-10e7-42ee-a514-02ed749f9494 + + + + + + + prov:KeyEntityPair + data:urn:uuid:0fd972f6-10e7-42ee-a514-02ed749f9494 + @id + + + + + 2022-04-04T16:59:09.802972 + wf:main/__DATA_FETCH__/request_json + + + wfprov:Artifact + 1 + + + + + 2022-04-04T16:59:09.803053 + wf:main/__DATA_FETCH__/request_version + + + 2021-06-23T10:46:28.351123 + 2021-06-23T10:46:44.738703 + Run of ga_export/jobs_attrs.txt#cat1 + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:46:28.351123 + + + wfprov:Artifact + 7ca3de8f49293d1a + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.803689 + wf:main/cat1/input1 + + + wfprov:Artifact + 2e789aae2475b7da + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.803812 + wf:main/cat1/queries_0_input2 + + + wfprov:Artifact + fd7fec473f1e6c6b + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.803927 + wf:main/cat1/out_file1 + + + wfprov:Artifact + txt + + + + + 2022-04-04T16:59:09.803988 + wf:main/cat1/__input_ext + + + wfprov:Artifact + 42f21c0ad41011eb87defa163eba836f + + + + + 2022-04-04T16:59:09.804048 + wf:main/cat1/__workflow_invocation_uuid__ + + + wfprov:Artifact + /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len + + + + + 2022-04-04T16:59:09.804112 + wf:main/cat1/chromInfo + + + wfprov:Artifact + ? + + + + + 2022-04-04T16:59:09.804169 + wf:main/cat1/dbkey + + + prov:Dictionary + wfprov:Artifact + id:2e397e93-13e6-4ce4-bced-ed3008a1b0db + id:633b83e5-3fa9-41be-b2e4-52381339221a + + + prov:Dictionary + wfprov:Artifact + id:11a7af4f-7df4-4a99-ba83-6d0418b6f7df + id:67c9330c-aef5-4d94-ad77-f38d191198a2 + id:7cbde64f-8934-42ab-af87-2044c3e092ce + + + wfprov:Artifact + 7ca3de8f49293d1a + + + + + + + prov:KeyEntityPair + data:7ca3de8f49293d1a + id + + + wfprov:Artifact + hda + + + + + + + prov:KeyEntityPair + data:hda + src + + + wfprov:Artifact + urn:uuid:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114 + + + + + + + prov:KeyEntityPair + data:urn:uuid:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:63446d8e-78fe-4025-a69a-c5ca6f8a0bea + values + + + wfprov:Artifact + urn:uuid:8c884aa2-99c2-4588-9d49-eff12441e6c0 + + + + + + + prov:KeyEntityPair + data:urn:uuid:8c884aa2-99c2-4588-9d49-eff12441e6c0 + @id + + + + + 2022-04-04T16:59:09.804768 + wf:main/cat1/input1 + + + prov:Dictionary + wfprov:Artifact + id:2326e0c6-2608-432a-934a-dc26b09dabcd + id:60e283d2-d89f-4235-8d61-2600cb5717c4 + id:651a06c8-c920-42d6-98ca-71dcd610322f + + + 0 + + + + + + + prov:KeyEntityPair + id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c + __index__ + + + prov:Dictionary + wfprov:Artifact + id:2605025b-6018-4473-b1f2-10ffa81c469a + id:d530cc8c-b67b-4e1d-8992-bca7f8454520 + + + prov:Dictionary + wfprov:Artifact + id:450f4c3b-e384-42b0-8090-47cc2e4691fb + id:708a0ca4-2972-467e-9443-52a37e9d0bf1 + id:eedcc56e-086a-42dc-a5d4-212bee28b594 + + + wfprov:Artifact + 2e789aae2475b7da + + + + + + + prov:KeyEntityPair + data:2e789aae2475b7da + id + + + wfprov:Artifact + hda + + + + + + + prov:KeyEntityPair + data:hda + src + + + wfprov:Artifact + urn:uuid:de072b7b-d692-4453-9af4-9975a3742a44 + + + + + + + prov:KeyEntityPair + data:urn:uuid:de072b7b-d692-4453-9af4-9975a3742a44 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:e1cda342-b856-423e-aa58-5485505a0d28 + values + + + wfprov:Artifact + urn:uuid:3d532d55-2434-4449-9fd3-aae8eca62c1b + + + + + + + prov:KeyEntityPair + data:urn:uuid:3d532d55-2434-4449-9fd3-aae8eca62c1b + @id + + + + + + + prov:KeyEntityPair + id:3d532d55-2434-4449-9fd3-aae8eca62c1b + input2 + + + wfprov:Artifact + urn:uuid:e66c4859-3380-4705-b3bb-2c650dfb7888 + + + + + + + prov:KeyEntityPair + data:urn:uuid:e66c4859-3380-4705-b3bb-2c650dfb7888 + @id + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.805613 + wf:main/cat1/queries + + + 2021-06-23T10:46:28.526901 + 2021-06-23T10:47:04.837750 + Run of ga_export/jobs_attrs.txt#random_lines1 + wfprov:ProcessRun + + + + + + + + + + 2021-06-23T10:46:28.526901 + + + wfprov:Artifact + fd7fec473f1e6c6b + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.806121 + wf:main/random_lines1/input + + + wfprov:Artifact + 775bc9b3c1750167 + + + wfprov:Artifact + + + + + + + + + 2022-04-04T16:59:09.806236 + wf:main/random_lines1/out_file1 + + + wfprov:Artifact + txt + + + + + 2022-04-04T16:59:09.806293 + wf:main/random_lines1/__input_ext + + + wfprov:Artifact + 42f21c0ad41011eb87defa163eba836f + + + + + 2022-04-04T16:59:09.806350 + wf:main/random_lines1/__workflow_invocation_uuid__ + + + wfprov:Artifact + /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len + + + + + 2022-04-04T16:59:09.806405 + wf:main/random_lines1/chromInfo + + + wfprov:Artifact + ? + + + + + 2022-04-04T16:59:09.806458 + wf:main/random_lines1/dbkey + + + prov:Dictionary + wfprov:Artifact + id:0f92ffd8-540e-4bd6-8f6c-3c2d3df4f995 + id:838e9760-cb17-4896-9c13-184164aa0c08 + + + prov:Dictionary + wfprov:Artifact + id:311ea826-fd60-4dc1-a729-af0412613824 + id:36c37981-8a3c-45e8-82fb-1b367dd30899 + id:37923bc7-fd48-4521-98e4-19a33c90b663 + + + wfprov:Artifact + fd7fec473f1e6c6b + + + + + + + prov:KeyEntityPair + data:fd7fec473f1e6c6b + id + + + wfprov:Artifact + hda + + + + + + + prov:KeyEntityPair + data:hda + src + + + wfprov:Artifact + urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266 + + + + + + + prov:KeyEntityPair + data:urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266 + @id + + + wfprov:Artifact + + + + + + + + + + + prov:KeyEntityPair + id:0ce5a422-abcb-4f41-a191-0a6068e14574 + values + + + wfprov:Artifact + urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3 + + + + + + + prov:KeyEntityPair + data:urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3 + @id + + + + + 2022-04-04T16:59:09.806986 + wf:main/random_lines1/input + + + wfprov:Artifact + 3 + + + + + 2022-04-04T16:59:09.807046 + wf:main/random_lines1/num_lines + + + prov:Dictionary + wfprov:Artifact + id:0080be3e-2011-44c6-a391-3e151894b43e + id:6de1750c-1612-4740-87a3-7d000e40c4b2 + id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91 + id:d13aa4a9-9029-4a4a-959b-4e2a3bd0aa3d + + + 1 + + + + + + + prov:KeyEntityPair + id:fc4a126f-25bd-4d12-bde7-c41dadf135c6 + __current_case__ + + + wfprov:Artifact + 0 + + + + + + + prov:KeyEntityPair + data:0 + seed + + + wfprov:Artifact + set_seed + + + + + + + prov:KeyEntityPair + data:set_seed + seed_source_selector + + + wfprov:Artifact + urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2 + + + + + + + prov:KeyEntityPair + data:urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2 + @id + + + + + 2022-04-04T16:59:09.807432 + wf:main/random_lines1/seed_source + + diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json b/test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json new file mode 100644 index 00000000..ff5daa4f --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json @@ -0,0 +1,123 @@ +{ + "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "datePublished": "2022-04-04T14:59:09+00:00", + "hasPart": [ + { + "@id": "wf_definition.ga" + }, + { + "@id": "wf_definition.cwl" + }, + { + "@id": "provenance/" + }, + { + "@id": "dataset2.txt_1.txt" + }, + { + "@id": "Concatenate_datasets_on_data_2_and_data_1_3.txt" + }, + { + "@id": "tutorial_output.txt_4.txt" + }, + { + "@id": "dataset1.txt_2.txt" + } + ], + "mainEntity": { + "@id": "wf_definition.ga" + } + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "wf_definition.ga", + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], + "name": "wf_definition", + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy" + }, + "subjectOf": { + "@id": "wf_definition.cwl" + } + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://galaxyproject.org/" + }, + "name": "Galaxy", + "url": { + "@id": "https://galaxyproject.org/" + }, + "version": "21.09" + }, + { + "@id": "wf_definition.cwl", + "@type": [ + "File", + "SoftwareSourceCode", + "HowTo" + ], + "name": "wf_definition", + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl" + } + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl", + "@type": "ComputerLanguage", + "alternateName": "CWL", + "identifier": { + "@id": "https://w3id.org/cwl/1.2/" + }, + "name": "Common Workflow Language", + "url": { + "@id": "https://www.commonwl.org/" + }, + "version": "1.2" + }, + { + "@id": "provenance/", + "@type": "Dataset" + }, + { + "@id": "dataset2.txt_1.txt", + "@type": "File" + }, + { + "@id": "Concatenate_datasets_on_data_2_and_data_1_3.txt", + "@type": "File" + }, + { + "@id": "tutorial_output.txt_4.txt", + "@type": "File" + }, + { + "@id": "dataset1.txt_2.txt", + "@type": "File" + } + ] +} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt new file mode 100644 index 00000000..f631dd54 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt @@ -0,0 +1,3 @@ +hello +universe! +world diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl b/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl new file mode 100644 index 00000000..8af43e5e --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl @@ -0,0 +1,50 @@ +class: Workflow +cwlVersion: v1.2.0-dev2 +doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: Workflow + constructed from history ''Minimal-history''' +inputs: + dataset1_txt: + format: data + type: File + dataset2_txt: + format: data + type: File +outputs: {} +steps: + 2_Concatenate datasets: + in: + input1: dataset2_txt + queries_0|input2: dataset1_txt + out: + - out_file1 + run: + class: Operation + id: cat1 + inputs: + input1: + format: Any + type: File + queries_0|input2: + format: Any + type: File + outputs: + out_file1: + doc: input + type: File + 3_Select random lines: + in: + input: 2_Concatenate datasets/out_file1 + out: + - out_file1 + run: + class: Operation + id: random_lines1 + inputs: + input: + format: Any + type: File + outputs: + out_file1: + doc: input + type: File + diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga b/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga new file mode 100644 index 00000000..28194ed4 --- /dev/null +++ b/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga @@ -0,0 +1,131 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Workflow constructed from history 'Minimal-history'", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "dataset2.txt" + } + ], + "label": "dataset2.txt", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 10, + "top": 10 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "8dfb1a60-ac90-4125-b1a4-c674a084bf37", + "workflow_outputs": [] + }, + "1": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "dataset1.txt" + } + ], + "label": "dataset1.txt", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 10, + "top": 130 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "104d6198-2f2e-46f1-8006-1c594f1f091c", + "workflow_outputs": [] + }, + "2": { + "annotation": "", + "content_id": "cat1", + "errors": null, + "id": 2, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "queries_0|input2": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 230, + "top": 10 + }, + "post_job_actions": {}, + "tool_id": "cat1", + "tool_state": "{\"__input_ext\": \"txt\", \"__workflow_invocation_uuid__\": \"42f21c0ad41011eb87defa163eba836f\", \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input1\": null, \"queries\": [{\"__index__\": 0, \"input2\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "821567a8-1edd-4f35-9430-596fd6801ca1", + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "random_lines1", + "errors": null, + "id": 3, + "input_connections": { + "input": { + "id": 2, + "output_name": "out_file1" + } + }, + "inputs": [], + "label": null, + "name": "Select random lines", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 450, + "top": 10 + }, + "post_job_actions": {}, + "tool_id": "random_lines1", + "tool_state": "{\"__input_ext\": \"txt\", \"__workflow_invocation_uuid__\": \"42f21c0ad41011eb87defa163eba836f\", \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": null, \"num_lines\": \"3\", \"seed_source\": {\"seed_source_selector\": \"set_seed\", \"__current_case__\": 1, \"seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.0.2", + "type": "tool", + "uuid": "a6b4dc53-9a0f-4a5c-9311-f9f03238f9dc", + "workflow_outputs": [] + } + }, + "tags": [], + "uuid": "de90339e-0497-49da-a1ce-f7e2dd3080c6", + "version": 0 +} \ No newline at end of file diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index a4cabb17..b2916f77 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -1,4 +1,5 @@ import sys +import os import pytest from typing import ( Tuple, @@ -50,36 +51,30 @@ def test_ga_history_parsing(test_data_dir, tmpdir, helpers): def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): - wf_id = 'test_galaxy_wf.ga' - wf_path = test_data_dir / wf_id - wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy') + # wf_path = base_path + "example-history-export3.ga" + # dataset_path = base_path + "example-history-export3/datasets/" + # wfr_metadata_path = base_path + "example-history-export3" + # files_list = os.listdir(dataset_path) + # files_list = [dataset_path + f for f in files_list] + + export_dir = "test_ga_history_export" + wfr_metadata_path = test_data_dir / export_dir / "history_export" + dataset_path = wfr_metadata_path / "datasets" + files_list = os.listdir(dataset_path) + files_list = [dataset_path / f for f in files_list] + wf_id = 'wf_definition.ga' + wf_path = test_data_dir / export_dir / wf_id + + # wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy') + wf_crate = roc_api.make_workflow_run_rocrate(workflow_path=wf_path, + wfr_metadata_path=wfr_metadata_path, author=None, orcid=None, + wf_type="Galaxy",include_files=files_list, prov_name="test_prov") assert isinstance(wf_crate, ROCrate) - wf = wf_crate.dereference(wf_id) - assert wf._default_type == "ComputationalWorkflow" - assert wf_crate.mainEntity is wf - lang = wf_crate.dereference(f"{WF_CRATE}#galaxy") - assert hasattr(lang, "name") - assert lang.version == GALAXY_DEFAULT_VERSION - assert wf.get("programmingLanguage") is lang - assert wf.get("subjectOf") is not None - assert helpers.WORKFLOW_DESC_TYPES.issubset(wf["subjectOf"].type) + # wf = wf_crate.dereference(wf_id) - out_path = tmpdir / 'ro_crate_out' - out_path.mkdir() + out_path = test_data_dir / export_dir / "history_export_ro_crate" + if not os.path.exists(out_path): + out_path.mkdir() wf_crate.write(out_path) - json_entities = helpers.read_json_entities(out_path) - helpers.check_wf_crate(json_entities, wf_id) - wf_entity = json_entities[wf_id] - assert "subjectOf" in wf_entity - abstract_wf_id = wf_entity["subjectOf"]["@id"] - abstract_wf_entity = json_entities[abstract_wf_id] - assert helpers.WORKFLOW_DESC_TYPES.issubset(abstract_wf_entity["@type"]) - - wf_out_path = out_path / wf_id - assert wf_out_path.exists() - with open(wf_path) as f1, open(wf_out_path) as f2: - assert f1.read() == f2.read() - - abstract_wf_out_path = out_path / abstract_wf_id - assert abstract_wf_out_path.exists() \ No newline at end of file + \ No newline at end of file From 68c958133ee4b7723e1232a63ccc02da61df59ab Mon Sep 17 00:00:00 2001 From: pauldg Date: Mon, 4 Apr 2022 17:13:55 +0200 Subject: [PATCH 12/27] removed local path from test --- test/test_parse_ga_export.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index b2916f77..6ac12565 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -32,7 +32,7 @@ def test_ga_history_loading(test_data_dir, tmpdir, helpers): def test_ga_history_parsing(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" export_path = test_data_dir / export_dir / "history_export" - prov_path = "/home/padge/Elixir/workflow-export/ro-crate-py/test/test-data/test_ga_history_export/history_export/provenance" + prov_path = "provenance" # prov_name = "ga_export.cwlprov" # crate_path = test_data_dir / export_dir / "history_export_crate" From 81b1e1eacccfb3d698d5c808269dae13e7d18c02 Mon Sep 17 00:00:00 2001 From: simleo Date: Tue, 5 Apr 2022 16:58:55 +0200 Subject: [PATCH 13/27] fix requirements and pep8 --- requirements.txt | 2 +- rocrate/provenance_profile.py | 89 +++++++++++++++-------------------- rocrate/rocrate_api.py | 4 +- test/test_parse_ga_export.py | 32 +++++-------- tools/load_ga_export.py | 28 ++++------- 5 files changed, 62 insertions(+), 93 deletions(-) diff --git a/requirements.txt b/requirements.txt index d473ab3d..4003b9dd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,4 +5,4 @@ jinja2 python-dateutil click prov -schema_salad \ No newline at end of file +typing-extensions diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index b2effddc..41d945da 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -1,19 +1,12 @@ -import copy -import pdb import datetime -import logging import urllib import uuid import json -from io import BytesIO from pathlib import PurePath, PurePosixPath -from socket import getfqdn from typing import ( Any, Dict, - Iterable, List, - MutableMapping, MutableSequence, Optional, Tuple, @@ -23,9 +16,7 @@ from prov.identifier import Identifier from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity -from schema_salad.sourceline import SourceLine -from typing_extensions import TYPE_CHECKING -from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset +from tools.load_ga_export import load_ga_history_export, GalaxyJob from ast import literal_eval import os @@ -36,16 +27,12 @@ from rocrate.provenance_constants import ( ACCOUNT_UUID, CWLPROV, - ENCODING, - FOAF, METADATA, ORE, PROVENANCE, RO, SCHEMA, SHA1, - SHA256, - TEXT_PLAIN, UUID, WF4EVER, WFDESC, @@ -59,15 +46,17 @@ # from rocrate.provenance import ResearchObject from pathlib import Path -import rocrate.rocrate as roc + def posix_path(local_path: str) -> str: return str(PurePosixPath(Path(local_path))) + def remove_escapes(s): escapes = ''.join([chr(char) for char in range(1, 32)]) translator = str.maketrans('', '', escapes) - t = s.translate(translator) + s.translate(translator) + def reassign(d): for k, v in d.items(): @@ -78,8 +67,9 @@ def reassign(d): except ValueError: pass + class ProvenanceProfile: - """ + """\ Provenance profile. Populated from a galaxy workflow export. @@ -87,7 +77,7 @@ class ProvenanceProfile: def __init__( self, - ga_export: Dict, + ga_export: Dict, full_name: str = None, orcid: str = None, # prov_name: str = None, @@ -112,12 +102,11 @@ def __init__( self.base_uri = "arcp://uuid,%s/" % self.ro_uuid self.document = ProvDocument() # TODO extract engine_uuid from galaxy, type: str - self.engine_uuid = "urn:uuid:%s" % uuid.uuid4() #type: str + self.engine_uuid = "urn:uuid:%s" % uuid.uuid4() # type: str self.full_name = full_name self.workflow_run_uuid = run_uuid or uuid.uuid4() self.workflow_run_uri = self.workflow_run_uuid.urn # type: str - - # move to separate function + # move to separate function metadata_export = load_ga_history_export(ga_export) self.generate_prov_doc() self.jobs = [] @@ -143,7 +132,7 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: # PROV_TYPE: FOAF["OnlineAccount"], # TODO: change how we register galaxy version, probably a declare_version func # self.galaxy_version = self.ga_export["jobs_attrs"][0]["galaxy_version"] - # TODO: change notation to already imported namespaces? + # TODO: change notation to already imported namespaces? self.document.add_namespace("wfprov", "http://purl.org/wf4ever/wfprov#") # document.add_namespace('prov', 'http://www.w3.org/ns/prov#') self.document.add_namespace("wfdesc", "http://purl.org/wf4ever/wfdesc#") @@ -166,7 +155,7 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: "provenance", self.base_uri + posix_path(PROVENANCE) + "/" ) # TODO: use appropriate refs for ga_export and related inputs - ro_identifier_workflow = self.base_uri + "ga_export" + "/" + ro_identifier_workflow = self.base_uri + "ga_export" + "/" self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow) ro_identifier_input = ( self.base_uri + "ga_export/datasets#" @@ -230,15 +219,15 @@ def declare_process( """Record the start of each Process.""" if process_run_id is None: process_run_id = uuid.uuid4().urn - - cmd = ga_export_jobs_attrs["command_line"] + + # cmd = ga_export_jobs_attrs["command_line"] process_name = ga_export_jobs_attrs["tool_id"] - tool_version = ga_export_jobs_attrs["tool_version"] + # tool_version = ga_export_jobs_attrs["tool_version"] prov_label = "Run of ga_export/jobs_attrs.txt#" + process_name start_time = ga_export_jobs_attrs["create_time"] end_time = ga_export_jobs_attrs["update_time"] - #TODO: Find out how to include commandline as a string + # TODO: Find out how to include commandline as a string # cmd = self.document.entity( # uuid.uuid4().urn, # {PROV_TYPE: WFPROV["Artifact"], PROV_LABEL: ga_export_jobs_attrs["command_line"]} @@ -249,9 +238,9 @@ def declare_process( start_time, end_time, { - PROV_TYPE: WFPROV["ProcessRun"], - PROV_LABEL: prov_label, - #TODO: Find out how to include commandline as a string + PROV_TYPE: WFPROV["ProcessRun"], + PROV_LABEL: prov_label, + # TODO: Find out how to include commandline as a string # PROV_LABEL: cmd }, ) @@ -279,7 +268,7 @@ def used_artefacts( base += "/" + process_name tool_id = process_metadata["tool_id"] base += "/" + tool_id - items = ["inputs","outputs","parameters"] + items = ["inputs", "outputs", "parameters"] # print(process_metadata["params"]) for item in items: # print(item) @@ -293,8 +282,8 @@ def used_artefacts( value = json.loads(value) if isinstance(key, str): key = key.replace("|", "_") - if isinstance(value, str): - val = value.replace("|", "_") + if isinstance(value, str): + value = value.replace("|", "_") prov_role = self.wf_ns[f"{base}/{key}"] @@ -307,7 +296,6 @@ def used_artefacts( # for artefact in value: try: - # pdb.set_trace() entity = self.declare_artefact(value) self.document.used( process_run_id, @@ -346,7 +334,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: # byte_s = BytesIO(value) # data_file = self.research_object.add_data_file(byte_s) # FIXME: Don't naively assume add_data_file uses hash in filename! - data_id = "data:%s" % str(value) #PurePosixPath(data_file).stem + data_id = "data:%s" % str(value) # PurePosixPath(data_file).stem return self.document.entity( data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)}, @@ -383,7 +371,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: ) if value.get("class"): - #_logger.warning("Unknown data class %s.", value["class"]) + # _logger.warning("Unknown data class %s.", value["class"]) # FIXME: The class might be "http://example.com/somethingelse" coll.add_asserted_type(CWLPROV[value["class"]]) @@ -393,7 +381,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: # clean up unwanted characters if isinstance(key, str): key = key.replace("|", "_") - if isinstance(val, str): + if isinstance(val, str): val = val.replace("|", "_") v_ent = self.declare_artefact(val) @@ -440,7 +428,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: # FIXME: list value does not support adding "@id" return coll except TypeError: - #_logger.warning("Unrecognized type %s of %r", type(value), value) + # _logger.warning("Unrecognized type %s of %r", type(value), value) # Let's just fall back to Python repr() entity = self.document.entity(uuid.uuid4().urn, {PROV_LABEL: repr(value)}) # self.research_object.add_uri(entity.identifier.uri) @@ -455,7 +443,7 @@ def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: if "checksum" in value: csum = cast(str, value["checksum"]) (method, checksum) = csum.split("$", 1) - if method == SHA1: # and self.research_object.has_data_file(checksum): + if method == SHA1: # and self.research_object.has_data_file(checksum): entity = self.document.entity("data:" + checksum) if not entity and "location" in value: @@ -502,8 +490,8 @@ def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: # Check for secondaries for sec in cast( - # MutableSequence[CWLObjectType], - value.get("secondaryFiles", []) + # MutableSequence[CWLObjectType], + value.get("secondaryFiles", []) # noqa ): # TODO: Record these in a specializationOf entity with UUID? if sec["class"] == "File": @@ -524,8 +512,10 @@ def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: return file_entity, entity, checksum - def declare_directory(self - # , value: CWLObjectType + def declare_directory( + self, + # value: CWLObjectType + value ) -> ProvEntity: """Register any nested files/directories.""" # FIXME: Calculate a hash-like identifier for directory @@ -636,12 +626,11 @@ def declare_string(self, value: str) -> Tuple[ProvEntity, str]: # checksum = PurePosixPath(data_file).name # FIXME: Don't naively assume add_data_file uses hash in filename! value = str(value).replace("|", "_") - data_id = "data:%s" % str(value) #PurePosixPath(data_file).stem + data_id = "data:%s" % str(value) # PurePosixPath(data_file).stem entity = self.document.entity( data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)} ) # type: ProvEntity - return entity #, checksum - + return entity # , checksum def generate_output_prov( self, @@ -724,7 +713,7 @@ def activity_has_provenance(self, activity, prov_ids): self.document.activity(activity, other_attributes=attribs) # Tip: we can't use https://www.w3.org/TR/prov-links/#term-mention # as prov:mentionOf() is only for entities, not activities - uris = [i.uri for i in prov_ids] + # uris = [i.uri for i in prov_ids] # self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) def finalize_prov_profile(self, name=None, out_path=None): @@ -759,7 +748,7 @@ def finalize_prov_profile(self, name=None, out_path=None): # https://www.w3.org/TR/prov-xml/ # serialized_prov_docs["xml"] = self.document.serialize(format="xml", indent=4) - prov_ids.append(self.provenance_ns[filename + ".xml"]) + prov_ids.append(self.provenance_ns[filename + ".xml"]) with open(basename + ".xml", "w") as provenance_file: self.document.serialize(provenance_file, format="xml", indent=4) @@ -768,7 +757,6 @@ def finalize_prov_profile(self, name=None, out_path=None): prov_ids.append(self.provenance_ns[filename + ".provn"]) with open(basename + ".provn", "w") as provenance_file: self.document.serialize(provenance_file, format="provn", indent=2) - # https://www.w3.org/Submission/prov-json/ # serialized_prov_docs["json"] = self.document.serialize(format="json", indent=2) @@ -799,7 +787,6 @@ def finalize_prov_profile(self, name=None, out_path=None): prov_ids.append(self.provenance_ns[filename + ".jsonld"]) with open(basename + ".jsonld", "w") as provenance_file: self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") - - #_logger.debug("[provenance] added provenance: %s", prov_ids) + # _logger.debug("[provenance] added provenance: %s", prov_ids) return (serialized_prov_docs, prov_ids) diff --git a/rocrate/rocrate_api.py b/rocrate/rocrate_api.py index f6f912ce..3243a6b1 100644 --- a/rocrate/rocrate_api.py +++ b/rocrate/rocrate_api.py @@ -18,7 +18,6 @@ # limitations under the License. from pathlib import Path -import os import rocrate.rocrate as roc from rocrate.provenance_profile import ProvenanceProfile @@ -79,6 +78,7 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], return wf_crate + # WIP def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, author=None, orcid=None, include_files=[], fetch_remote=False, prov_name=None, prov_path=None, cwl=None, diagram=None): @@ -110,4 +110,4 @@ def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, author= for file_entry in include_files: wfr_crate.add_file(file_entry) - return wfr_crate \ No newline at end of file + return wfr_crate diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index 6ac12565..08120be1 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -1,41 +1,34 @@ -import sys import os -import pytest -from typing import ( - Tuple, -) -from prov.model import ProvDocument -sys.path.append('./ro-crate-py') from rocrate.rocrate import ROCrate from rocrate import rocrate_api as roc_api -from rocrate.model.computerlanguage import CWL_DEFAULT_VERSION, GALAXY_DEFAULT_VERSION from rocrate.provenance_profile import ProvenanceProfile -WF_CRATE = "https://w3id.org/workflowhub/workflow-ro-crate" -from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset +from tools.load_ga_export import load_ga_history_export, GalaxyJob + def test_ga_history_loading(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" export_path = test_data_dir / export_dir / "history_export" - + metadata_export = load_ga_history_export(export_path) jobs = [] for job in metadata_export["jobs_attrs"]: job_attrs = GalaxyJob() job_attrs.parse_ga_jobs_attrs(job) jobs.append(job_attrs.attributes) - + assert isinstance(job_attrs, GalaxyJob) # print(jobs[0]) assert len(jobs) == 4 + def test_ga_history_parsing(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" export_path = test_data_dir / export_dir / "history_export" - prov_path = "provenance" + prov_path = tmpdir / "provenance" # prov_name = "ga_export.cwlprov" # crate_path = test_data_dir / export_dir / "history_export_crate" - + # metadata_export = load_ga_history_export(export_path) prov = ProvenanceProfile(export_path, "PDG", "https://orcid.org/0000-0002-8940-4946") @@ -49,14 +42,13 @@ def test_ga_history_parsing(test_data_dir, tmpdir, helpers): # print(serialized_prov_docs.keys()) - def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): # wf_path = base_path + "example-history-export3.ga" # dataset_path = base_path + "example-history-export3/datasets/" # wfr_metadata_path = base_path + "example-history-export3" # files_list = os.listdir(dataset_path) # files_list = [dataset_path + f for f in files_list] - + export_dir = "test_ga_history_export" wfr_metadata_path = test_data_dir / export_dir / "history_export" dataset_path = wfr_metadata_path / "datasets" @@ -66,9 +58,10 @@ def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): wf_path = test_data_dir / export_dir / wf_id # wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy') - wf_crate = roc_api.make_workflow_run_rocrate(workflow_path=wf_path, - wfr_metadata_path=wfr_metadata_path, author=None, orcid=None, - wf_type="Galaxy",include_files=files_list, prov_name="test_prov") + wf_crate = roc_api.make_workflow_run_rocrate( + workflow_path=wf_path, wfr_metadata_path=wfr_metadata_path, author=None, orcid=None, + wf_type="Galaxy", include_files=files_list, prov_name="test_prov" + ) assert isinstance(wf_crate, ROCrate) # wf = wf_crate.dereference(wf_id) @@ -77,4 +70,3 @@ def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): if not os.path.exists(out_path): out_path.mkdir() wf_crate.write(out_path) - \ No newline at end of file diff --git a/tools/load_ga_export.py b/tools/load_ga_export.py index b608c7fa..6bb51dd1 100644 --- a/tools/load_ga_export.py +++ b/tools/load_ga_export.py @@ -2,35 +2,23 @@ import os import re from typing import ( - IO, - Any, - Callable, Dict, - Generator, - Iterable, - List, - MutableMapping, - MutableSequence, - NamedTuple, - Optional, - Set, - Tuple, - Union, - cast, ) + def load_ga_history_export(export_dir): fn_list = os.listdir(export_dir) export_metadata = {} - for f in fn_list : - export_dir_path = os.path.join(export_dir,f) + for f in fn_list: + export_dir_path = os.path.join(export_dir, f) if os.path.isfile(export_dir_path): - with open(export_dir_path,"r") as fh: + with open(export_dir_path, "r") as fh: # create keys for metadata files, removes '.' and 'txt' from fn - key = '_'.join(list(filter(None, re.split('\.|txt',f)))) + key = '_'.join(list(filter(None, re.split(r'\.|txt', f)))) export_metadata[key] = json.loads(fh.read()) return export_metadata + class GalaxyJob(Dict): def __init__(self): """ @@ -57,7 +45,9 @@ def parse_ga_jobs_attrs(self, job_attrs): if "params" in key: self.attributes["parameters"].update(job_attrs[key]) + class GalaxyDataset(Dict): + def __init__(self, ga_export_dataset_attrs): """ Initialize the GalaxyDataset object. @@ -75,4 +65,4 @@ def parse_ga_dataset_attrs(self, job_attrs): pass else: if "metadata" in key: - self.attributes["metadata"].update(job_attrs[key]) \ No newline at end of file + self.attributes["metadata"].update(job_attrs[key]) From dac39ad5a1b229061dc15b90d7be5e41d71d899a Mon Sep 17 00:00:00 2001 From: pauldg Date: Fri, 15 Apr 2022 12:00:27 +0200 Subject: [PATCH 14/27] small updates to metadata parsing --- rocrate/provenance_profile.py | 25 ++++++++++++++++++++----- tools/load_ga_export.py | 8 ++++---- 2 files changed, 24 insertions(+), 9 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 41d945da..7f3f5358 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -16,7 +16,7 @@ from prov.identifier import Identifier from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity -from tools.load_ga_export import load_ga_history_export, GalaxyJob +from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset from ast import literal_eval import os @@ -109,12 +109,26 @@ def __init__( # move to separate function metadata_export = load_ga_history_export(ga_export) self.generate_prov_doc() - self.jobs = [] + + self.datasets = {} # print(metadata_export["jobs_attrs"][0]["params"]) - for job in metadata_export["jobs_attrs"]: + for i,dataset in enumerate(metadata_export["datasets_attrs"]): + datasets_attrs = GalaxyDataset() + datasets_attrs.parse_ga_dataset_attrs(dataset) + print(i) + print(datasets_attrs.attributes['encoded_id']) + self.datasets[datasets_attrs.attributes['encoded_id']] = datasets_attrs.attributes + # self.declare_process(ds_attrs.attributes) + + self.jobs = {} + for i,job in enumerate(metadata_export["jobs_attrs"]): job_attrs = GalaxyJob() job_attrs.parse_ga_jobs_attrs(job) - self.jobs.append(job_attrs.attributes) + print(i) + print(job_attrs.attributes.keys()) + # for k,v in job_attrs.attributes['parameters'].items(): + # print(k, " : ",v) + self.jobs[job_attrs.attributes['encoded_id']] = job_attrs.attributes self.declare_process(job_attrs.attributes) def __str__(self) -> str: @@ -223,7 +237,8 @@ def declare_process( # cmd = ga_export_jobs_attrs["command_line"] process_name = ga_export_jobs_attrs["tool_id"] # tool_version = ga_export_jobs_attrs["tool_version"] - prov_label = "Run of ga_export/jobs_attrs.txt#" + process_name + # TODO: insert workflow id + prov_label = "Run of workflow_id_placeholder" + process_name start_time = ga_export_jobs_attrs["create_time"] end_time = ga_export_jobs_attrs["update_time"] diff --git a/tools/load_ga_export.py b/tools/load_ga_export.py index 6bb51dd1..92f94ac8 100644 --- a/tools/load_ga_export.py +++ b/tools/load_ga_export.py @@ -48,16 +48,16 @@ def parse_ga_jobs_attrs(self, job_attrs): class GalaxyDataset(Dict): - def __init__(self, ga_export_dataset_attrs): + def __init__(self): """ Initialize the GalaxyDataset object. """ self.attributes = {} self.attributes["metadata"] = {} - def parse_ga_dataset_attrs(self, job_attrs): + def parse_ga_dataset_attrs(self, dataset_attrs): - for key, value in job_attrs.items(): + for key, value in dataset_attrs.items(): if not isinstance(value, dict): self.attributes[key] = value else: @@ -65,4 +65,4 @@ def parse_ga_dataset_attrs(self, job_attrs): pass else: if "metadata" in key: - self.attributes["metadata"].update(job_attrs[key]) + self.attributes["metadata"].update(dataset_attrs[key]) From 3e85bf5cbb8aad023646c045ced9adfc73d37553 Mon Sep 17 00:00:00 2001 From: pauldg Date: Fri, 15 Apr 2022 13:23:38 +0200 Subject: [PATCH 15/27] fixed whitespaces --- rocrate/provenance_profile.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 7f3f5358..b7a3463c 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -109,19 +109,18 @@ def __init__( # move to separate function metadata_export = load_ga_history_export(ga_export) self.generate_prov_doc() - self.datasets = {} # print(metadata_export["jobs_attrs"][0]["params"]) - for i,dataset in enumerate(metadata_export["datasets_attrs"]): + for i, dataset in enumerate(metadata_export["datasets_attrs"]): datasets_attrs = GalaxyDataset() datasets_attrs.parse_ga_dataset_attrs(dataset) print(i) print(datasets_attrs.attributes['encoded_id']) self.datasets[datasets_attrs.attributes['encoded_id']] = datasets_attrs.attributes # self.declare_process(ds_attrs.attributes) - + self.jobs = {} - for i,job in enumerate(metadata_export["jobs_attrs"]): + for i, job in enumerate(metadata_export["jobs_attrs"]): job_attrs = GalaxyJob() job_attrs.parse_ga_jobs_attrs(job) print(i) @@ -237,7 +236,7 @@ def declare_process( # cmd = ga_export_jobs_attrs["command_line"] process_name = ga_export_jobs_attrs["tool_id"] # tool_version = ga_export_jobs_attrs["tool_version"] - # TODO: insert workflow id + # TODO: insert workflow id prov_label = "Run of workflow_id_placeholder" + process_name start_time = ga_export_jobs_attrs["create_time"] end_time = ga_export_jobs_attrs["update_time"] @@ -325,7 +324,8 @@ def used_artefacts( def declare_artefact(self, value: Any) -> ProvEntity: """Create data artefact entities for all file objects.""" if value is None: - # FIXME: If this can happen we'll need a better way to represent this in PROV + # FIXME: If this can happen we'll need a better way to + # represent this in PROV return self.document.entity(CWLPROV["None"], {PROV_LABEL: "None"}) if isinstance(value, (bool, int, float)): @@ -357,7 +357,8 @@ def declare_artefact(self, value: Any) -> ProvEntity: if isinstance(value, Dict): if "@id" in value: - # Already processed this value, but it might not be in this PROV + # Already processed this value, + # but it might not be in this PROV entities = self.document.get_record(value["@id"]) if entities: return entities[0] From 642c3e1e7d7e3794e94a9b624e497e3305ff5f2f Mon Sep 17 00:00:00 2001 From: pauldg Date: Tue, 26 Apr 2022 18:58:52 +0200 Subject: [PATCH 16/27] added dataset registration in prov doc --- rocrate/provenance_profile.py | 211 +++++++++++++++++++--------------- tools/load_ga_export.py | 14 ++- 2 files changed, 131 insertions(+), 94 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index b7a3463c..dbfbe976 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -1,8 +1,7 @@ import datetime import urllib import uuid -import json -from pathlib import PurePath, PurePosixPath +from pathlib import PurePosixPath from typing import ( Any, Dict, @@ -32,7 +31,7 @@ PROVENANCE, RO, SCHEMA, - SHA1, + # SHA1, UUID, WF4EVER, WFDESC, @@ -109,25 +108,33 @@ def __init__( # move to separate function metadata_export = load_ga_history_export(ga_export) self.generate_prov_doc() - self.datasets = {} + self.datasets = [] # print(metadata_export["jobs_attrs"][0]["params"]) for i, dataset in enumerate(metadata_export["datasets_attrs"]): datasets_attrs = GalaxyDataset() datasets_attrs.parse_ga_dataset_attrs(dataset) - print(i) - print(datasets_attrs.attributes['encoded_id']) - self.datasets[datasets_attrs.attributes['encoded_id']] = datasets_attrs.attributes + # print(i) + # print(datasets_attrs.attributes['encoded_id']) + self.datasets.append(datasets_attrs.attributes) # self.declare_process(ds_attrs.attributes) + # print(self.datasets) + + # print([[d['encoded_id']]+d['copied_from_history_dataset_association_id_chain'] for d in self.datasets]) + self.jobs = {} for i, job in enumerate(metadata_export["jobs_attrs"]): job_attrs = GalaxyJob() job_attrs.parse_ga_jobs_attrs(job) - print(i) - print(job_attrs.attributes.keys()) - # for k,v in job_attrs.attributes['parameters'].items(): - # print(k, " : ",v) + # print(i) + print(job_attrs.attributes) + # for k, v in job_attrs.attributes['parameters'].items(): + # print(k, " : ", v) self.jobs[job_attrs.attributes['encoded_id']] = job_attrs.attributes + # print("inputs") + # print(job_attrs.attributes["inputs"]) + # print("outputs") + # print(job_attrs.attributes["outputs"]) self.declare_process(job_attrs.attributes) def __str__(self) -> str: @@ -230,6 +237,7 @@ def declare_process( process_run_id: Optional[str] = None, ) -> str: """Record the start of each Process.""" + # TODO: change to workflow invocation id? if process_run_id is None: process_run_id = uuid.uuid4().urn @@ -276,7 +284,8 @@ def used_artefacts( process_name: Optional[str] = None, ) -> None: """Add used() for each data artefact.""" - # FIXME: Use workflow name if available, "main" is wrong for nested workflows + # FIXME: Use workflow name if available, + # "main" is wrong for nested workflows base = "main" if process_name is not None: base += "/" + process_name @@ -288,12 +297,11 @@ def used_artefacts( # print(item) # print("-----------") # print(process_metadata[item]) - for key, value in process_metadata[item].items(): if not value: value = "" - if "json" in key: - value = json.loads(value) + # if "json" in key: + # value = json.loads(value) if isinstance(key, str): key = key.replace("|", "_") if isinstance(value, str): @@ -301,25 +309,40 @@ def used_artefacts( prov_role = self.wf_ns[f"{base}/{key}"] - # print("key : ",key) - # print("-----------") - # print("value: ",value) - # print("-----------") - # print("type : ",type(value)) - # print("-----------") - - # for artefact in value: - try: - entity = self.declare_artefact(value) - self.document.used( - process_run_id, - entity, - datetime.datetime.now(), - None, - {"prov:role": prov_role}, - ) - except OSError: - pass + if item in ("inputs", "outputs"): + for v in value: + for d in self.datasets: + print([d['encoded_id']]) + print(d['copied_from_history_dataset_association_id_chain']) + if v in ([d['encoded_id']] + d['copied_from_history_dataset_association_id_chain']): + self.declare_entity(process_run_id, d, prov_role) + else: + self.declare_entity(process_run_id, value, prov_role) + + print("key : ", key) + print("-----------") + print("value: ", value) + print("-----------") + print("type : ", type(value)) + print("-----------") + + def declare_entity( + self, + process_run_id, + value, + prov_role + ) -> None: + try: + entity = self.declare_artefact(value) + self.document.used( + process_run_id, + entity, + datetime.datetime.now(), + None, + {"prov:role": prov_role}, + ) + except OSError: + pass def declare_artefact(self, value: Any) -> ProvEntity: """Create data artefact entities for all file objects.""" @@ -366,7 +389,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: # Base case - we found a File we need to update if value.get("class") == "File": - (entity, _, _) = self.declare_file(value) + entity = self.declare_file(value) value["@id"] = entity.identifier.uri return entity @@ -454,79 +477,81 @@ def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: if value["class"] != "File": raise ValueError("Must have class:File: %s" % value) # Need to determine file hash aka RO filename + # TODO: do we need a checksum value? entity = None # type: Optional[ProvEntity] checksum = None - if "checksum" in value: - csum = cast(str, value["checksum"]) - (method, checksum) = csum.split("$", 1) - if method == SHA1: # and self.research_object.has_data_file(checksum): - entity = self.document.entity("data:" + checksum) - - if not entity and "location" in value: - location = str(value["location"]) - # If we made it here, we'll have to add it to the RO - with self.fsaccess.open(location, "rb") as fhandle: - relative_path = self.research_object.add_data_file(fhandle) - # FIXME: This naively relies on add_data_file setting hash as filename - checksum = PurePath(relative_path).name - entity = self.document.entity( - "data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]} - ) - if "checksum" not in value: - value["checksum"] = f"{SHA1}${checksum}" - - if not entity and "contents" in value: - # Anonymous file, add content as string - entity, checksum = self.declare_string(cast(str, value["contents"])) - - # By here one of them should have worked! - if not entity or not checksum: - raise ValueError( - "class:File but missing checksum/location/content: %r" % value - ) + # if "checksum" in value: + # csum = cast(str, value["checksum"]) + # (method, checksum) = csum.split("$", 1) + # if method == SHA1: # and self.research_object.has_data_file(checksum): + # entity = self.document.entity("data:" + checksum) + + # if not entity and "location" in value: + # location = str(value["location"]) + # # If we made it here, we'll have to add it to the RO + # with self.fsaccess.open(location, "rb") as fhandle: + # relative_path = self.research_object.add_data_file(fhandle) + # # FIXME: This naively relies on add_data_file setting hash as filename + # checksum = PurePath(relative_path).name + # entity = self.document.entity( + # "data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]} + # ) + # if "checksum" not in value: + # value["checksum"] = f"{SHA1}${checksum}" + + # if not entity and "contents" in value: + # # Anonymous file, add content as string + # entity, checksum = self.declare_string(cast(str, value["contents"])) + + # # By here one of them should have worked! + # if not entity or not checksum: + # raise ValueError( + # "class:File but missing checksum/location/content: %r" % value + # ) # Track filename and extension, this is generally useful only for # secondaryFiles. Note that multiple uses of a file might thus record # different names for the same entity, so we'll # make/track a specialized entity by UUID - file_id = value.setdefault("@id", uuid.uuid4().urn) + file_id = value.setdefault("@id", uuid.UUID(value["dataset_uuid"]).urn) # A specialized entity that has just these names file_entity = self.document.entity( file_id, [(PROV_TYPE, WFPROV["Artifact"]), (PROV_TYPE, WF4EVER["File"])], ) # type: ProvEntity - if "basename" in value: - file_entity.add_attributes({CWLPROV["basename"]: value["basename"]}) - if "nameroot" in value: - file_entity.add_attributes({CWLPROV["nameroot"]: value["nameroot"]}) - if "nameext" in value: - file_entity.add_attributes({CWLPROV["nameext"]: value["nameext"]}) - self.document.specializationOf(file_entity, entity) + if "name" in value: + file_entity.add_attributes({CWLPROV["basename"]: value["name"]}) + # if "nameroot" in value: + # file_entity.add_attributes({CWLPROV["nameroot"]: value["nameroot"]}) + if "extension" in value: + file_entity.add_attributes({CWLPROV["nameext"]: value["extension"]}) + # self.document.specializationOf(file_entity, entity) + # TODO: figure out if we need to keep track of derived files # Check for secondaries - for sec in cast( - # MutableSequence[CWLObjectType], - value.get("secondaryFiles", []) # noqa - ): - # TODO: Record these in a specializationOf entity with UUID? - if sec["class"] == "File": - (sec_entity, _, _) = self.declare_file(sec) - elif sec["class"] == "Directory": - sec_entity = self.declare_directory(sec) - else: - raise ValueError(f"Got unexpected secondaryFiles value: {sec}") - # We don't know how/when/where the secondary file was generated, - # but CWL convention is a kind of summary/index derived - # from the original file. As its generally in a different format - # then prov:Quotation is not appropriate. - self.document.derivation( - sec_entity, - file_entity, - other_attributes={PROV["type"]: CWLPROV["SecondaryFile"]}, - ) + # for sec in cast( + # # MutableSequence[CWLObjectType], + # value.get("secondaryFiles", []) # noqa + # ): + # # TODO: Record these in a specializationOf entity with UUID? + # if sec["class"] == "File": + # (sec_entity, _, _) = self.declare_file(sec) + # elif sec["class"] == "Directory": + # sec_entity = self.declare_directory(sec) + # else: + # raise ValueError(f"Got unexpected secondaryFiles value: {sec}") + # # We don't know how/when/where the secondary file was generated, + # # but CWL convention is a kind of summary/index derived + # # from the original file. As its generally in a different format + # # then prov:Quotation is not appropriate. + # self.document.derivation( + # sec_entity, + # file_entity, + # other_attributes={PROV["type"]: CWLPROV["SecondaryFile"]}, + # ) - return file_entity, entity, checksum + return file_entity # , entity, checksum def declare_directory( self, @@ -756,7 +781,7 @@ def finalize_prov_profile(self, name=None, out_path=None): if not os.path.exists(out_path): os.makedirs(out_path) - print(basename) + # print(basename) # serialized prov documents serialized_prov_docs = {} # list of prov identifiers of provenance files diff --git a/tools/load_ga_export.py b/tools/load_ga_export.py index 92f94ac8..1358c5ed 100644 --- a/tools/load_ga_export.py +++ b/tools/load_ga_export.py @@ -43,7 +43,13 @@ def parse_ga_jobs_attrs(self, job_attrs): if "output" in key: self.attributes["outputs"].update(job_attrs[key]) if "params" in key: - self.attributes["parameters"].update(job_attrs[key]) + tmp_dict = {} + for k, v in job_attrs[key].items(): + if "json" in k: + v = json.loads(v) + tmp_dict[k] = str(v) + + self.attributes["parameters"].update(tmp_dict) class GalaxyDataset(Dict): @@ -54,6 +60,7 @@ def __init__(self): """ self.attributes = {} self.attributes["metadata"] = {} + self.attributes["class"] = "File" def parse_ga_dataset_attrs(self, dataset_attrs): @@ -66,3 +73,8 @@ def parse_ga_dataset_attrs(self, dataset_attrs): else: if "metadata" in key: self.attributes["metadata"].update(dataset_attrs[key]) + # self.attributes["used_encoded_id"] = \ + # next( + # iter(self.attributes["copied_from_history_dataset_association_id_chain"]), + # self.attributes["encoded_id"] + # ) From af8eac2fa920030b91809d5e12ae26061378ebe1 Mon Sep 17 00:00:00 2001 From: pauldg Date: Wed, 27 Apr 2022 10:42:46 +0200 Subject: [PATCH 17/27] resolved flake8 errors --- rocrate/provenance_profile.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index dbfbe976..0a96f4e5 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -284,7 +284,7 @@ def used_artefacts( process_name: Optional[str] = None, ) -> None: """Add used() for each data artefact.""" - # FIXME: Use workflow name if available, + # FIXME: Use workflow name if available, # "main" is wrong for nested workflows base = "main" if process_name is not None: @@ -327,11 +327,11 @@ def used_artefacts( print("-----------") def declare_entity( - self, - process_run_id, - value, - prov_role - ) -> None: + self, + process_run_id, + value, + prov_role + ) -> None: try: entity = self.declare_artefact(value) self.document.used( @@ -478,8 +478,8 @@ def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: raise ValueError("Must have class:File: %s" % value) # Need to determine file hash aka RO filename # TODO: do we need a checksum value? - entity = None # type: Optional[ProvEntity] - checksum = None + # entity = None # type: Optional[ProvEntity] + # checksum = None # if "checksum" in value: # csum = cast(str, value["checksum"]) # (method, checksum) = csum.split("$", 1) From bb9675af1c1781bf01850fb8ed02eed30f9961fd Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 23 Jun 2022 15:21:56 +0200 Subject: [PATCH 18/27] updates to prov creation --- rocrate/provenance_profile.py | 178 +- rocrate/rocrate_api.py | 49 +- rocrate/utils.py | 15 + .../provenance/ga_export.cwlprov.json | 2883 ------------ .../provenance/ga_export.cwlprov.jsonld | 3869 ----------------- .../provenance/ga_export.cwlprov.nt | 942 ---- .../provenance/ga_export.cwlprov.provn | 332 -- .../provenance/ga_export.cwlprov.ttl | 1081 ----- .../provenance/ga_export.cwlprov.xml | 1457 ------- ...tenate_datasets_on_data_2_and_data_1_3.txt | 4 - .../dataset1.txt_2.txt | 2 - .../dataset2.txt_1.txt | 2 - .../provenance/ga_export.cwlprov.json | 2862 ------------ .../provenance/ga_export.cwlprov.jsonld | 3841 ---------------- .../provenance/ga_export.cwlprov.nt | 935 ---- .../provenance/ga_export.cwlprov.provn | 330 -- .../provenance/ga_export.cwlprov.ttl | 1070 ----- .../provenance/ga_export.cwlprov.xml | 1447 ------ .../ro-crate-metadata.json | 123 - .../tutorial_output.txt_4.txt | 3 - .../history_export_ro_crate/wf_definition.cwl | 50 - .../history_export_ro_crate/wf_definition.ga | 131 - test/test_parse_ga_export.py | 17 +- tools/load_ga_export.py | 17 +- 24 files changed, 178 insertions(+), 21462 deletions(-) delete mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json delete mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.jsonld delete mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.nt delete mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn delete mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl delete mode 100644 test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.jsonld delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.nt delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl delete mode 100644 test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 0a96f4e5..c7fffba0 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -1,6 +1,10 @@ import datetime +# from tokenize import String +from io import StringIO import urllib import uuid +from io import BytesIO +from hashlib import md5 from pathlib import PurePosixPath from typing import ( Any, @@ -12,9 +16,11 @@ Union, cast, ) +from xmlrpc.client import Boolean from prov.identifier import Identifier from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity +from prov.dot import prov_to_dot from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset from ast import literal_eval import os @@ -29,6 +35,8 @@ METADATA, ORE, PROVENANCE, + ENCODING, + # TEXT_PLAIN, RO, SCHEMA, # SHA1, @@ -76,7 +84,7 @@ class ProvenanceProfile: def __init__( self, - ga_export: Dict, + ga_export_dir: Path, full_name: str = None, orcid: str = None, # prov_name: str = None, @@ -88,6 +96,7 @@ def __init__( Initialize the provenance profile. Keyword arguments: ga_export -- the galaxy metadata export (Dict) + outpath -- full_name -- author name (optional) orcid -- orcid (optional) prov_name -- provenance file name @@ -95,7 +104,11 @@ def __init__( """ # self.fsaccess = fsaccess self.orcid = orcid - self.ga_export = ga_export + self.ga_export_dir = ga_export_dir + # TODO: does it make sense to write all outputs to a tmp dir + # chance that temp dir doesnt get removed properly + # if out_path is None: + # self.out_path = tempfile.mkdtemp() self.ro_uuid = uuid.uuid4() # TODO: should be connected to a ro_crate? self.base_uri = "arcp://uuid,%s/" % self.ro_uuid @@ -103,11 +116,11 @@ def __init__( # TODO extract engine_uuid from galaxy, type: str self.engine_uuid = "urn:uuid:%s" % uuid.uuid4() # type: str self.full_name = full_name - self.workflow_run_uuid = run_uuid or uuid.uuid4() - self.workflow_run_uri = self.workflow_run_uuid.urn # type: str - # move to separate function - metadata_export = load_ga_history_export(ga_export) - self.generate_prov_doc() + # TODO move to separate function + metadata_export = load_ga_history_export(ga_export_dir) + # self.tmp_dir = tempfile.mkdtemp() + self.declared_strings_s = {} + self.datasets = [] # print(metadata_export["jobs_attrs"][0]["params"]) for i, dataset in enumerate(metadata_export["datasets_attrs"]): @@ -121,21 +134,39 @@ def __init__( # print(self.datasets) # print([[d['encoded_id']]+d['copied_from_history_dataset_association_id_chain'] for d in self.datasets]) - + self.workflow_invocation_uuid = set() self.jobs = {} for i, job in enumerate(metadata_export["jobs_attrs"]): job_attrs = GalaxyJob() job_attrs.parse_ga_jobs_attrs(job) # print(i) - print(job_attrs.attributes) + # print(job_attrs.attributes) # for k, v in job_attrs.attributes['parameters'].items(): # print(k, " : ", v) self.jobs[job_attrs.attributes['encoded_id']] = job_attrs.attributes + try: + self.workflow_invocation_uuid.add(job_attrs.attributes['parameters']['__workflow_invocation_uuid__']) + except KeyError: + pass + # print('set:') + # print(self.workflow_invocation_uuid) # print("inputs") # print(job_attrs.attributes["inputs"]) # print("outputs") # print(job_attrs.attributes["outputs"]) - self.declare_process(job_attrs.attributes) + + if self.workflow_invocation_uuid: + self.workflow_run_uuid = uuid.UUID(next(iter(self.workflow_invocation_uuid))) + self.workflow_run_uri = self.workflow_run_uuid.urn # type: str + else: + self.workflow_run_uuid = run_uuid or uuid.uuid4() + self.workflow_run_uri = self.workflow_run_uuid.urn # type: str + + self.generate_prov_doc() + for v in self.jobs.values(): + self.declare_process(v) + + # print(os.listdir(tempfile.gettempdir())) def __str__(self) -> str: """Represent this Provenvance profile as a string.""" @@ -245,7 +276,7 @@ def declare_process( process_name = ga_export_jobs_attrs["tool_id"] # tool_version = ga_export_jobs_attrs["tool_version"] # TODO: insert workflow id - prov_label = "Run of workflow_id_placeholder" + process_name + prov_label = "Run of " + process_name start_time = ga_export_jobs_attrs["create_time"] end_time = ga_export_jobs_attrs["update_time"] @@ -299,7 +330,7 @@ def used_artefacts( # print(process_metadata[item]) for key, value in process_metadata[item].items(): if not value: - value = "" + pass # if "json" in key: # value = json.loads(value) if isinstance(key, str): @@ -309,23 +340,24 @@ def used_artefacts( prov_role = self.wf_ns[f"{base}/{key}"] + # if not value or len(value) == 0: + # print("key : ", key) + # print("-----------") + # print("value: ", value) + # print("-----------") + # print("type : ", type(value)) + # print("-----------") + if item in ("inputs", "outputs"): for v in value: for d in self.datasets: - print([d['encoded_id']]) - print(d['copied_from_history_dataset_association_id_chain']) + # print([d['encoded_id']]) + # print(d['copied_from_history_dataset_association_id_chain']) if v in ([d['encoded_id']] + d['copied_from_history_dataset_association_id_chain']): self.declare_entity(process_run_id, d, prov_role) else: self.declare_entity(process_run_id, value, prov_role) - print("key : ", key) - print("-----------") - print("value: ", value) - print("-----------") - print("type : ", type(value)) - print("-----------") - def declare_entity( self, process_run_id, @@ -334,6 +366,8 @@ def declare_entity( ) -> None: try: entity = self.declare_artefact(value) + # print("test2") + # print(entity) self.document.used( process_run_id, entity, @@ -353,6 +387,7 @@ def declare_artefact(self, value: Any) -> ProvEntity: if isinstance(value, (bool, int, float)): # Typically used in job documents for flags + # print(value) # FIXME: Make consistent hash URIs for these # that somehow include the type @@ -361,10 +396,10 @@ def declare_artefact(self, value: Any) -> ProvEntity: # self.research_object.add_uri(entity.identifier.uri) return entity - if isinstance(value, (str)): + if isinstance(value, str): # clean up unwanted characters - value = value.replace("|", "_") - entity = self.declare_string(value) + # value = value.replace("|", "_") + (entity, _) = self.declare_string(value) return entity if isinstance(value, bytes): @@ -379,6 +414,9 @@ def declare_artefact(self, value: Any) -> ProvEntity: ) if isinstance(value, Dict): + # print("value: ", value) + # print("-----------") + # print("type : ", type(value)) if "@id" in value: # Already processed this value, # but it might not be in this PROV @@ -662,16 +700,18 @@ def declare_directory( def declare_string(self, value: str) -> Tuple[ProvEntity, str]: """Save as string in UTF-8.""" - # byte_s = BytesIO(str(value).encode(ENCODING)) + value = str(value).replace("|", "_") + byte_s = BytesIO(str(value).encode(ENCODING)) # data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN) - # checksum = PurePosixPath(data_file).name + checksum = md5(byte_s.getbuffer()).hexdigest() + self.declared_strings_s[checksum] = byte_s + # FIXME: Don't naively assume add_data_file uses hash in filename! - value = str(value).replace("|", "_") - data_id = "data:%s" % str(value) # PurePosixPath(data_file).stem + data_id = "data:%s" % checksum # PurePosixPath(data_file).stem entity = self.document.entity( data_id, {PROV_TYPE: WFPROV["Artifact"], PROV_VALUE: str(value)} ) # type: ProvEntity - return entity # , checksum + return entity, checksum # , data_file def generate_output_prov( self, @@ -757,7 +797,8 @@ def activity_has_provenance(self, activity, prov_ids): # uris = [i.uri for i in prov_ids] # self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) - def finalize_prov_profile(self, name=None, out_path=None): + def finalize_prov_profile(self, out_path: Path = None, + serialize: Boolean = False, name=None): # type: (Optional[str],Optional[str]) -> Tuple[Dict,List[Identifier]] """Transfer the provenance related files to the RO-crate""" # NOTE: Relative posix path @@ -765,7 +806,8 @@ def finalize_prov_profile(self, name=None, out_path=None): # main workflow, fixed filenames filename = "ga_export.cwlprov" else: - # ASCII-friendly filename, avoiding % as we don't want %2520 in manifest.json + # ASCII-friendly filename, + # avoiding % as we don't want %2520 in manifest.json wf_name = urllib.parse.quote(str(name), safe="").replace("%", "_") # Note that the above could cause overlaps for similarly named # workflows, but that's OK as we'll also include run uuid @@ -773,61 +815,69 @@ def finalize_prov_profile(self, name=None, out_path=None): # multiple places or iterations filename = f"{wf_name}.{self.workflow_run_uuid}.cwlprov" - if out_path is not None: - basename = str(PurePosixPath(out_path) / filename) - # else: - # basename = filename - - if not os.path.exists(out_path): - os.makedirs(out_path) - # print(basename) # serialized prov documents serialized_prov_docs = {} # list of prov identifiers of provenance files prov_ids = [] - # https://www.w3.org/TR/prov-xml/ - # serialized_prov_docs["xml"] = self.document.serialize(format="xml", indent=4) + serialized_prov_docs[filename + ".xml"] = StringIO(self.document.serialize(format="xml", indent=4)) prov_ids.append(self.provenance_ns[filename + ".xml"]) - with open(basename + ".xml", "w") as provenance_file: - self.document.serialize(provenance_file, format="xml", indent=4) - # https://www.w3.org/TR/prov-n/ - # serialized_prov_docs["provn"] = self.document.serialize(format="provn", indent=2) + serialized_prov_docs[filename + ".provn"] = StringIO(self.document.serialize(format="provn", indent=2)) prov_ids.append(self.provenance_ns[filename + ".provn"]) - with open(basename + ".provn", "w") as provenance_file: - self.document.serialize(provenance_file, format="provn", indent=2) - # https://www.w3.org/Submission/prov-json/ - # serialized_prov_docs["json"] = self.document.serialize(format="json", indent=2) + serialized_prov_docs[filename + ".json"] = StringIO(self.document.serialize(format="json", indent=2)) prov_ids.append(self.provenance_ns[filename + ".json"]) - with open(basename + ".json", "w") as provenance_file: - self.document.serialize(provenance_file, format="json", indent=2) # "rdf" aka https://www.w3.org/TR/prov-o/ # which can be serialized to ttl/nt/jsonld (and more!) # https://www.w3.org/TR/turtle/ - # serialized_prov_docs["turtle"] = self.document.serialize(format="rdf", rdf_format="turtle") + serialized_prov_docs[filename + ".ttl"] = StringIO(self.document.serialize(format="rdf", rdf_format="turtle")) prov_ids.append(self.provenance_ns[filename + ".ttl"]) - with open(basename + ".ttl", "w") as provenance_file: - self.document.serialize(provenance_file, format="rdf", rdf_format="turtle") - # https://www.w3.org/TR/n-triples/ - # serialized_prov_docs["ntriples"] = self.document.serialize(format="rdf", rdf_format="ntriples") + serialized_prov_docs[filename + ".nt"] = StringIO(self.document.serialize(format="rdf", rdf_format="ntriples")) prov_ids.append(self.provenance_ns[filename + ".nt"]) - with open(basename + ".nt", "w") as provenance_file: - self.document.serialize(provenance_file, format="rdf", rdf_format="ntriples") - # https://www.w3.org/TR/json-ld/ # TODO: Use a nice JSON-LD context # see also https://eprints.soton.ac.uk/395985/ # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld : - # serialized_prov_docs["jsonld"] = self.document.serialize(format="rdf", rdf_format="json-ld") + serialized_prov_docs[filename + ".jsonld"] = StringIO(self.document.serialize(format="rdf", rdf_format="json-ld")) prov_ids.append(self.provenance_ns[filename + ".jsonld"]) - with open(basename + ".jsonld", "w") as provenance_file: - self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") - # _logger.debug("[provenance] added provenance: %s", prov_ids) - return (serialized_prov_docs, prov_ids) + graph_dot = prov_to_dot(self.document) + png_b = graph_dot.create_png() + graph_b = BytesIO() + graph_b.write(png_b) + # dot.write_png(basename + '.png') + + if serialize: + if out_path is not None: + basename = str(PurePosixPath(out_path) / filename) + else: + basename = filename + + if not os.path.exists(out_path): + os.makedirs(out_path) + + with open(basename + ".xml", "w") as provenance_file: + self.document.serialize(provenance_file, format="xml", indent=4) + + with open(basename + ".provn", "w") as provenance_file: + self.document.serialize(provenance_file, format="provn", indent=2) + + with open(basename + ".json", "w") as provenance_file: + self.document.serialize(provenance_file, format="json", indent=2) + + with open(basename + ".ttl", "w") as provenance_file: + self.document.serialize(provenance_file, format="rdf", rdf_format="turtle") + + with open(basename + ".nt", "w") as provenance_file: + self.document.serialize(provenance_file, format="rdf", rdf_format="ntriples") + + with open(basename + ".jsonld", "w") as provenance_file: + self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") + + # _logger.debug("[provenance] added provenance: %s", prov_ids) + return (serialized_prov_docs, prov_ids, graph_b) diff --git a/rocrate/rocrate_api.py b/rocrate/rocrate_api.py index 40247ee6..c49ffbbc 100644 --- a/rocrate/rocrate_api.py +++ b/rocrate/rocrate_api.py @@ -19,6 +19,8 @@ # limitations under the License. from pathlib import Path +import os +import tempfile import rocrate.rocrate as roc from rocrate.provenance_profile import ProvenanceProfile @@ -81,34 +83,51 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], # WIP -def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, author=None, orcid=None, - include_files=[], fetch_remote=False, prov_name=None, prov_path=None, cwl=None, diagram=None): +def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, + author=None, orcid=None, include_files=[], + fetch_remote=False, prov_name=None, cwl=None, + diagram=None): wfr_crate = roc.ROCrate() workflow_path = Path(workflow_path) + print(workflow_path) wf_file = wfr_crate.add_workflow( workflow_path, workflow_path.name, fetch_remote=fetch_remote, main=True, lang=wf_type, gen_cwl=(cwl is None) ) + if 'url' in wf_file.properties(): + wf_file['codeRepository'] = wf_file['url'] + + # add extra files + datasets = Path('datasets') + wfr_crate.add_dataset(datasets) + for file_entry in include_files: + print(os.path.basename(file_entry)) + # print(file_entry) + wfr_crate.add_file(file_entry, datasets / os.path.basename(file_entry)) + wfr_metadata_path = Path(wfr_metadata_path) + prov = ProvenanceProfile(wfr_metadata_path, author, orcid) - prov_path = "provenance" - prov.finalize_prov_profile(out_path=wfr_metadata_path / prov_path) - # add serialized provenance documents - wfr_crate.add_directory(wfr_metadata_path / prov_path) - # for doc in serialized_prov_docs.values(): - # # print(doc) - # wfr_crate.add_file(doc) + artifacts = Path('artifacts') + wfr_crate.add_dataset(artifacts) + for key, value in prov.declared_strings_s.items(): + dest = artifacts / key + wfr_crate.add_file(value, dest) + + prov_docs, _, graph = prov.finalize_prov_profile() + # add output files to ro-crate + provenance = Path('provenance') + wfr_crate.add_dataset(provenance) + for key, value in prov_docs.items(): + dest = provenance / key + wfr_crate.add_file(value, dest) + + wfr_crate.add_file(graph, provenance / "graph.png") # if the source is a remote URL then add https://schema.org/codeRepository # property to it this can be checked by checking if the source is a URL # instead of a local path - if 'url' in wf_file.properties(): - wf_file['codeRepository'] = wf_file['url'] - - # add extra files - for file_entry in include_files: - wfr_crate.add_file(file_entry) return wfr_crate diff --git a/rocrate/utils.py b/rocrate/utils.py index 7768804e..b2a4f699 100644 --- a/rocrate/utils.py +++ b/rocrate/utils.py @@ -22,6 +22,21 @@ import os from datetime import datetime, timezone from urllib.parse import urlsplit +from typing import ( + IO, + Any, + BinaryIO, + Callable, + Dict, + List, + MutableMapping, + MutableSequence, + Optional, + Set, + Tuple, + Union, + cast, +) def first(iterable): diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json deleted file mode 100644 index 9708344f..00000000 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.json +++ /dev/null @@ -1,2883 +0,0 @@ -{ - "prefix": { - "wfprov": "http://purl.org/wf4ever/wfprov#", - "wfdesc": "http://purl.org/wf4ever/wfdesc#", - "cwlprov": "https://w3id.org/cwl/prov#", - "foaf": "http://xmlns.com/foaf/0.1/", - "schema": "http://schema.org/", - "orcid": "https://orcid.org/", - "id": "urn:uuid:", - "data": "urn:hash::sha1:", - "provenance": "arcp://uuid,ebd18716-e481-43ab-8721-a7a8e342efb3/metadata/provenance/", - "wf": "arcp://uuid,ebd18716-e481-43ab-8721-a7a8e342efb3/ga_export/", - "input": "arcp://uuid,ebd18716-e481-43ab-8721-a7a8e342efb3/ga_export/datasets#" - }, - "agent": { - "id:027f7717-78d8-4f9a-a887-87813339b23e": {}, - "orcid:0000-0002-8940-4946": { - "prov:type": [ - { - "$": "prov:Person", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "schema:Person", - "type": "prov:QUALIFIED_NAME" - } - ], - "prov:label": "PDG", - "foaf:name": "PDG", - "schema:name": "PDG" - }, - "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec": { - "prov:type": [ - { - "$": "wfprov:WorkflowEngine", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "prov:SoftwareAgent", - "type": "prov:QUALIFIED_NAME" - } - ], - "prov:label": "galaxy_version_placeholder" - } - }, - "actedOnBehalfOf": { - "_:id1": { - "prov:delegate": "id:027f7717-78d8-4f9a-a887-87813339b23e", - "prov:responsible": "orcid:0000-0002-8940-4946" - } - }, - "wasStartedBy": { - "_:id2": { - "prov:activity": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", - "prov:starter": "id:027f7717-78d8-4f9a-a887-87813339b23e", - "prov:time": "2022-04-04T16:59:09.402992" - }, - "_:id4": { - "prov:activity": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", - "prov:starter": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", - "prov:time": "2022-04-04T16:59:09.403118" - }, - "_:id6": { - "prov:activity": "id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c", - "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", - "prov:time": "2021-06-23T10:20:22.770291" - }, - "_:id41": { - "prov:activity": "id:b7a0ab16-c370-48aa-924b-74d57ab7d542", - "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", - "prov:time": "2021-06-23T10:20:00.981702" - }, - "_:id76": { - "prov:activity": "id:290068a6-8ef9-4718-800b-cb22efbdfd62", - "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", - "prov:time": "2021-06-23T10:46:28.351123" - }, - "_:id106": { - "prov:activity": "id:1747ea92-6d32-4175-9aef-2893fc71c7a5", - "prov:starter": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", - "prov:time": "2021-06-23T10:46:28.526901" - } - }, - "activity": { - "id:b9177644-871b-492a-ae5f-3ee833ba0ae5": { - "prov:startTime": "2022-04-04T16:59:09.403029", - "prov:type": { - "$": "wfprov:WorkflowRun", - "type": "prov:QUALIFIED_NAME" - }, - "prov:label": "Run of galaxy workflow" - }, - "id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c": { - "prov:startTime": "2021-06-23T10:20:22.770291", - "prov:endTime": "2021-06-23T10:20:42.041319", - "prov:type": { - "$": "wfprov:ProcessRun", - "type": "prov:QUALIFIED_NAME" - }, - "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" - }, - "id:b7a0ab16-c370-48aa-924b-74d57ab7d542": { - "prov:startTime": "2021-06-23T10:20:00.981702", - "prov:endTime": "2021-06-23T10:20:22.202678", - "prov:type": { - "$": "wfprov:ProcessRun", - "type": "prov:QUALIFIED_NAME" - }, - "prov:label": "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__" - }, - "id:290068a6-8ef9-4718-800b-cb22efbdfd62": { - "prov:startTime": "2021-06-23T10:46:28.351123", - "prov:endTime": "2021-06-23T10:46:44.738703", - "prov:type": { - "$": "wfprov:ProcessRun", - "type": "prov:QUALIFIED_NAME" - }, - "prov:label": "Run of ga_export/jobs_attrs.txt#cat1" - }, - "id:1747ea92-6d32-4175-9aef-2893fc71c7a5": { - "prov:startTime": "2021-06-23T10:46:28.526901", - "prov:endTime": "2021-06-23T10:47:04.837750", - "prov:type": { - "$": "wfprov:ProcessRun", - "type": "prov:QUALIFIED_NAME" - }, - "prov:label": "Run of ga_export/jobs_attrs.txt#random_lines1" - } - }, - "wasAssociatedWith": { - "_:id3": { - "prov:activity": "id:b9177644-871b-492a-ae5f-3ee833ba0ae5", - "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", - "prov:plan": "wf:main" - }, - "_:id5": { - "prov:activity": "id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c", - "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", - "prov:plan": "wf:main/__DATA_FETCH__" - }, - "_:id40": { - "prov:activity": "id:b7a0ab16-c370-48aa-924b-74d57ab7d542", - "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", - "prov:plan": "wf:main/__DATA_FETCH__" - }, - "_:id75": { - "prov:activity": "id:290068a6-8ef9-4718-800b-cb22efbdfd62", - "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", - "prov:plan": "wf:main/cat1" - }, - "_:id105": { - "prov:activity": "id:1747ea92-6d32-4175-9aef-2893fc71c7a5", - "prov:agent": "id:ade93562-cbf5-453b-a445-cc9a5f95f0ec", - "prov:plan": "wf:main/random_lines1" - } - }, - "entity": { - "data:2524d3d3b68ad39a": { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - }, - "prov:value": "2524d3d3b68ad39a" - }, - "id:e13acf9b-83e9-40f0-adc1-a7195e612fa3": { - "prov:type": [ - { - "$": "prov:Collection", - "type": "prov:QUALIFIED_NAME" - 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}, - { - "$": "id:a92435e7-0621-4629-80fa-d73aa1989363", - "type": "prov:QUALIFIED_NAME" - } - ] - }, - "id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc": { - "prov:value": { - "$": 0, - "type": "xsd:int" - } - }, - "id:a92435e7-0621-4629-80fa-d73aa1989363": { - "prov:type": { - "$": "prov:KeyEntityPair", - "type": "prov:QUALIFIED_NAME" - }, - "prov:pairKey": "__index__", - "prov:pairEntity": { - "$": "id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc", - "type": "prov:QUALIFIED_NAME" - } - }, - "data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2": [ - { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - }, - "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" - }, - { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - }, - "prov:value": "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2" - } - ], - "id:f268cc7a-3474-404e-892f-8af376e98ae3": { - "prov:type": { - "$": "prov:KeyEntityPair", - "type": "prov:QUALIFIED_NAME" - 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}, - "prov:value": "hdas" - } - ], - "id:b17c488e-30c3-42cb-b2f0-092b0efe2427": { - "prov:type": { - "$": "prov:KeyEntityPair", - "type": "prov:QUALIFIED_NAME" - }, - "prov:pairKey": "type", - "prov:pairEntity": { - "$": "data:hdas", - "type": "prov:QUALIFIED_NAME" - } - }, - "data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f": { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - }, - "prov:value": "urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f" - }, - "id:e1829e51-7947-4db2-99a0-1ea7703ee764": { - "prov:type": { - "$": "prov:KeyEntityPair", - "type": "prov:QUALIFIED_NAME" - }, - "prov:pairKey": "@id", - "prov:pairEntity": { - "$": "data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f", - "type": "prov:QUALIFIED_NAME" - } - }, - "id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a": { - "prov:type": { - "$": "prov:KeyEntityPair", - "type": "prov:QUALIFIED_NAME" - }, - "prov:pairKey": "destination", - "prov:pairEntity": { - "$": "id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f", - "type": "prov:QUALIFIED_NAME" - } - }, - "id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551": { - "prov:type": [ - { - "$": "prov:Collection", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "prov:Dictionary", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - } - ], - "prov:hadDictionaryMember": [ - { - "$": "id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:b0586419-dbb7-4757-9cfd-ae55abef3674", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:3b543d5d-26b4-48f1-8c80-0c288c8df33f", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:5f9613d6-b39e-40e1-95d2-d26fb37550fe", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:8a2cf341-8042-40bd-8509-b56f1f4161c7", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:4b32d7ec-e96f-41ff-8feb-1e43324962da", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:f5199f67-c23f-46de-a504-11e5465e2e8c", - "type": "prov:QUALIFIED_NAME" - }, - { - "$": "id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01", - "type": "prov:QUALIFIED_NAME" - } - ] - }, - "data:auto": [ - { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - }, - "prov:value": "auto" - }, - { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - }, - "prov:value": "auto" - } - ], - "id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca": { - "prov:type": { - "$": "prov:KeyEntityPair", - "type": "prov:QUALIFIED_NAME" - }, - "prov:pairKey": "ext", - "prov:pairEntity": { - "$": "data:auto", - "type": "prov:QUALIFIED_NAME" - } - }, - "data:?": [ - { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - }, - "prov:value": "?" - }, - { - "prov:type": { - "$": "wfprov:Artifact", - "type": "prov:QUALIFIED_NAME" - 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. - . - . - . - diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn deleted file mode 100644 index 5aae4048..00000000 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.provn +++ /dev/null @@ -1,332 +0,0 @@ -document - prefix wfprov - prefix wfdesc - prefix cwlprov - prefix foaf - prefix schema - prefix orcid - prefix id - prefix data - prefix provenance - prefix wf - prefix input - - agent(id:027f7717-78d8-4f9a-a887-87813339b23e) - agent(orcid:0000-0002-8940-4946, [prov:type='prov:Person', prov:type='schema:Person', prov:label="PDG", foaf:name="PDG", schema:name="PDG"]) - actedOnBehalfOf(id:027f7717-78d8-4f9a-a887-87813339b23e, orcid:0000-0002-8940-4946, -) - agent(id:ade93562-cbf5-453b-a445-cc9a5f95f0ec, [prov:type='wfprov:WorkflowEngine', prov:type='prov:SoftwareAgent', prov:label="galaxy_version_placeholder"]) - 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entity(id:e13acf9b-83e9-40f0-adc1-a7195e612fa3, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) - hadMember(id:e13acf9b-83e9-40f0-adc1-a7195e612fa3, data:2524d3d3b68ad39a) - used(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, id:e13acf9b-83e9-40f0-adc1-a7195e612fa3, 2022-04-04T16:59:09.403801, [prov:role='wf:main/__DATA_FETCH__/output0']) - entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) - used(id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c, data:1, 2022-04-04T16:59:09.403870, [prov:role='wf:main/__DATA_FETCH__/file_count']) - entity(id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:e311b33d-139a-4e92-a5c1-3a04530b9128', prov:hadDictionaryMember='id:f268cc7a-3474-404e-892f-8af376e98ae3', prov:hadDictionaryMember='id:a92435e7-0621-4629-80fa-d73aa1989363']) - entity(id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc, [prov:value=0]) - hadMember(id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a, id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc) - 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entity(id:838aa24d-f8b4-4ddd-a76c-82460c5b6391, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a']) - used(id:1747ea92-6d32-4175-9aef-2893fc71c7a5, id:db786d1e-928b-4b0f-b118-bd235731ea9a, 2022-04-04T16:59:09.414376, [prov:role='wf:main/random_lines1/input']) - entity(data:3, [prov:type='wfprov:Artifact', prov:value="3"]) - used(id:1747ea92-6d32-4175-9aef-2893fc71c7a5, data:3, 2022-04-04T16:59:09.414444, [prov:role='wf:main/random_lines1/num_lines']) - entity(id:cb9975e1-3882-4cc3-9995-9352d37f1948, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:1b548405-6990-454a-98a6-128dccf12014', prov:hadDictionaryMember='id:3f28e37f-bba8-4b0d-b4d8-ad4749630604', prov:hadDictionaryMember='id:7884960e-a973-4e8f-bb01-58005de82366', prov:hadDictionaryMember='id:c753b9e4-3908-491a-a7a8-a0d4e1543e34']) - entity(id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd, [prov:value=1]) - hadMember(id:cb9975e1-3882-4cc3-9995-9352d37f1948, id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd) - entity(id:1b548405-6990-454a-98a6-128dccf12014, [prov:type='prov:KeyEntityPair', prov:pairKey="__current_case__", prov:pairEntity='id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd']) - entity(data:0, [prov:type='wfprov:Artifact', prov:value="0"]) - hadMember(id:cb9975e1-3882-4cc3-9995-9352d37f1948, data:0) - entity(id:3f28e37f-bba8-4b0d-b4d8-ad4749630604, [prov:type='prov:KeyEntityPair', prov:pairKey="seed", prov:pairEntity='data:0']) - entity(data:set_seed, [prov:type='wfprov:Artifact', prov:value="set_seed"]) - hadMember(id:cb9975e1-3882-4cc3-9995-9352d37f1948, data:set_seed) - entity(id:7884960e-a973-4e8f-bb01-58005de82366, [prov:type='prov:KeyEntityPair', prov:pairKey="seed_source_selector", prov:pairEntity='data:set_seed']) - entity(data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948, [prov:type='wfprov:Artifact', prov:value="urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948"]) - hadMember(id:cb9975e1-3882-4cc3-9995-9352d37f1948, data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948) - entity(id:c753b9e4-3908-491a-a7a8-a0d4e1543e34, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948']) - used(id:1747ea92-6d32-4175-9aef-2893fc71c7a5, id:cb9975e1-3882-4cc3-9995-9352d37f1948, 2022-04-04T16:59:09.414862, [prov:role='wf:main/random_lines1/seed_source']) -endDocument \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl deleted file mode 100644 index c7b80cee..00000000 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.ttl +++ /dev/null @@ -1,1081 +0,0 @@ -@prefix data: . -@prefix foaf: . -@prefix id: . -@prefix orcid: . -@prefix prov: . -@prefix rdfs: . -@prefix schema: . -@prefix wf: . -@prefix wfprov: . -@prefix xsd: . - -id:1747ea92-6d32-4175-9aef-2893fc71c7a5 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.414376"^^xsd:dateTime ; - prov:entity id:db786d1e-928b-4b0f-b118-bd235731ea9a ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.413468"^^xsd:dateTime ; - prov:entity id:c857b436-a405-4bf1-9b58-1f2d255d91b5 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.413652"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.414444"^^xsd:dateTime ; - prov:entity data:3 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.413710"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.413826"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.413588"^^xsd:dateTime ; - prov:entity id:a8ba8607-96e1-4d6f-a17e-3e4d3a1168c8 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.413770"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.414862"^^xsd:dateTime ; - prov:entity id:cb9975e1-3882-4cc3-9995-9352d37f1948 ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . - -id:290068a6-8ef9-4718-800b-cb22efbdfd62 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.411252"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.411312"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.411016"^^xsd:dateTime ; - prov:entity id:6c4049ff-bf0b-4c3e-829d-16e5ece01b8e ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.411369"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.412881"^^xsd:dateTime ; - prov:entity id:67c5d8ae-be1d-41a2-85c9-d0543a97dd3e ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.411131"^^xsd:dateTime ; - prov:entity id:90923c5c-2bd8-4aa7-a029-817e8b57037a ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.411190"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.410900"^^xsd:dateTime ; - prov:entity id:d731fa25-6b69-4910-80ab-897579cd74ba ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.411964"^^xsd:dateTime ; - prov:entity id:b040da72-a0ee-4309-ad1e-353be140b04a ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . - -id:b7a0ab16-c370-48aa-924b-74d57ab7d542 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.410250"^^xsd:dateTime ; - prov:entity id:ce5712eb-9c70-401d-811e-a01bfdbf3b3f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.410320"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.407631"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.408037"^^xsd:dateTime ; - prov:entity id:c00decaf-ac43-4246-8705-8c1bb0defce1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.407566"^^xsd:dateTime ; - prov:entity id:fb247085-dfc8-42bc-bee7-a7475ce9289a ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.408097"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . - -id:c9d9fd80-24e9-4f17-91ff-a2336fbc1d3c a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:hadActivity id:b9177644-871b-492a-ae5f-3ee833ba0ae5 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.406936"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.403801"^^xsd:dateTime ; - prov:entity id:e13acf9b-83e9-40f0-adc1-a7195e612fa3 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.406855"^^xsd:dateTime ; - prov:entity id:b148f9da-c287-4a2b-a6ee-41a95cf23d1c ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.404363"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.404286"^^xsd:dateTime ; - prov:entity id:bef03503-1c1f-4f05-9a58-56449dcc9ac3 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.403870"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . - -orcid:0000-0002-8940-4946 a schema:Person, - prov:Agent, - prov:Person ; - rdfs:label "PDG"^^xsd:string ; - schema:name "PDG"^^xsd:string ; - foaf:name "PDG"^^xsd:string . - -data:2524d3d3b68ad39a a wfprov:Artifact, - prov:Entity ; - prov:value "2524d3d3b68ad39a"^^xsd:string . - -data:3 a wfprov:Artifact, - prov:Entity ; - prov:value "3"^^xsd:string . - -data:775bc9b3c1750167 a wfprov:Artifact, - prov:Entity ; - prov:value "775bc9b3c1750167"^^xsd:string . - -data:7c1d8e3101dbcdba a wfprov:Artifact, - prov:Entity ; - prov:value "7c1d8e3101dbcdba"^^xsd:string . - -id:0196242d-cfb9-45f3-965c-8fa2a037f104 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d ; - prov:pairKey "auto_decompress"^^xsd:string . - -id:027f7717-78d8-4f9a-a887-87813339b23e a prov:Agent ; - prov:actedOnBehalfOf orcid:0000-0002-8940-4946 . - -id:02bb9d1c-f248-47fb-ac2c-9985301385a7 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:7c60b838-dd41-4166-aa41-6e652e5ef63b, - id:e0524eed-ea77-413b-b0db-5f72e16c365e, - id:f8f974ae-cd55-4986-8a9e-1d987b76fd34 ; - prov:hadMember , - , - id:5d7467bd-1ab8-46ea-8a56-0998f42b079c . - -id:06db435a-b77f-424b-8301-acb7e18cc2ce a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "dbkey"^^xsd:string . - -id:08ffc626-141c-4214-8d71-746a1218f209 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "path"^^xsd:string . - -id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:0c415611-9c31-47d4-82f9-a6330b980a8e a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea ; - prov:pairKey "elements"^^xsd:string . - -id:0fba80f8-6eff-4909-b5b4-78ddf1f2794a a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:a92435e7-0621-4629-80fa-d73aa1989363, - id:e311b33d-139a-4e92-a5c1-3a04530b9128, - id:f268cc7a-3474-404e-892f-8af376e98ae3 ; - prov:hadMember , - , - id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc . - -id:0ff29d35-01d6-471f-84e8-a1fc63c05daa a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:06db435a-b77f-424b-8301-acb7e18cc2ce, - id:08ffc626-141c-4214-8d71-746a1218f209, - id:23fe35b3-2a01-4edf-952a-5769462abc6c, - id:46ce5c94-417b-4bcf-a9af-fb60912d385a, - id:7dc6f8f5-cce3-4da9-b386-0a18314af498, - id:919c8f14-f4f3-4151-b936-d7502f64caa4, - id:a05e1e9a-74e5-4efc-ad75-96c15f4a83ce, - id:bab1f03d-7ca6-4bb7-a57d-563c0e70808b, - id:bb0b8464-83db-421e-9566-a31da915d209, - id:c256e77e-7189-430a-8c59-03fa703dce07, - id:d281fed1-869b-4451-8fda-95b26856a918 ; - prov:hadMember , - , - data:auto, - data:dataset1.txt, - data:path, - , - id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80, - id:493493b1-836f-404c-9084-95086d7ba06a, - id:721f1551-f868-4e7d-8cb4-6f196df24a97, - id:87697625-c033-4483-b5fa-d00140b03808, - id:addafc7d-4439-49fb-9870-b6b0ed7415c3 . - -id:10f720aa-40e7-4c83-9ad1-02ffc26a7944 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:15212ae6-d7ff-4660-870e-34f3caa32ceb a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:508b7a80-e3e7-442e-b9e9-4874e2916aad ; - prov:pairKey "targets"^^xsd:string . - -id:1b548405-6990-454a-98a6-128dccf12014 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd ; - prov:pairKey "__current_case__"^^xsd:string . - -id:23fe35b3-2a01-4edf-952a-5769462abc6c a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:493493b1-836f-404c-9084-95086d7ba06a ; - prov:pairKey "to_posix_lines"^^xsd:string . - -id:298c9e09-232d-4854-bf61-8116b1323f5b a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:663c25a0-9302-4b8f-aa89-765f3284aeca ; - prov:pairKey "values"^^xsd:string . - -id:2d384308-e0b1-4f82-811c-4bba81b92067 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f ; - prov:pairKey "auto_decompress"^^xsd:string . - -id:34e6b60d-4d4a-496d-bb9c-a4d34040155c a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . - -id:38113d6d-950c-4c1a-826d-636d3c6fa3ea a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:3ad229e9-064d-4398-8617-d802f10ac40b a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hdas ; - prov:pairKey "type"^^xsd:string . - -id:3b543d5d-26b4-48f1-8c80-0c288c8df33f a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:76b51c9a-5a58-43ce-b9a9-7f4459602a11 ; - prov:pairKey "purge_source"^^xsd:string . - -id:3f28e37f-bba8-4b0d-b4d8-ad4749630604 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:0 ; - 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-id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a, - id:3b543d5d-26b4-48f1-8c80-0c288c8df33f, - id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783, - id:4b32d7ec-e96f-41ff-8feb-1e43324962da, - id:5f9613d6-b39e-40e1-95d2-d26fb37550fe, - id:8a2cf341-8042-40bd-8509-b56f1f4161c7, - id:b0586419-dbb7-4757-9cfd-ae55abef3674, - id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01, - id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72, - id:f5199f67-c23f-46de-a504-11e5465e2e8c, - id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca ; - prov:hadMember , - , - data:auto, - data:dataset2.txt, - data:path, - , - id:4ed44fba-accb-410c-baef-53d2cb882954, - id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7, - id:76b51c9a-5a58-43ce-b9a9-7f4459602a11, - id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1, - id:f23be627-a96d-47ce-b857-30e370a747a9 . - -id:ebaa0943-a400-4daf-a2e7-f781b714a666 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:2e789aae2475b7da ; - 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prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:49e48096-0a9e-4ebd-8d9b-2b3647acb1b5, - id:9fb40382-f182-481e-90e6-0e24006c71c5, - id:c0fce355-42ca-41f4-88b0-ccc3b4fec7d2 ; - prov:hadMember data:7ca3de8f49293d1a, - data:hda, - . - -data: a wfprov:Artifact, - prov:Entity ; - prov:value ""^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^xsd:string . - -data:0 a wfprov:Artifact, - prov:Entity ; - prov:value "0"^^xsd:string . - -data:42f21c0ad41011eb87defa163eba836f a wfprov:Artifact, - prov:Entity ; - prov:value "42f21c0ad41011eb87defa163eba836f"^^xsd:string . - -data:dataset1.txt a wfprov:Artifact, - prov:Entity ; - prov:value "dataset1.txt"^^xsd:string . - -data:dataset2.txt a wfprov:Artifact, - prov:Entity ; - prov:value "dataset2.txt"^^xsd:string . - -data:set_seed a wfprov:Artifact, - prov:Entity ; - prov:value "set_seed"^^xsd:string . - -data:txt a wfprov:Artifact, - prov:Entity ; - prov:value "txt"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0"^^xsd:string . - -id:016238d2-8ca1-4335-b232-acae7f43ed72 a prov:Entity ; - prov:value true . - -id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f a prov:Entity ; - prov:value false . - -id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80 a prov:Entity ; - prov:value "155707"^^xsd:int . - -id:351d875a-c130-42f7-ba2f-735780ea4ca8 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:c9198eaf-36fb-42c4-bf4b-d740591fe470 . - -id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:b17c488e-30c3-42cb-b2f0-092b0efe2427, - id:e1829e51-7947-4db2-99a0-1ea7703ee764 ; - prov:hadMember data:hdas, - . - -id:493493b1-836f-404c-9084-95086d7ba06a a prov:Entity ; - prov:value true . - -id:4ed44fba-accb-410c-baef-53d2cb882954 a prov:Entity ; - prov:value "155708"^^xsd:int . - -id:508b7a80-e3e7-442e-b9e9-4874e2916aad a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2 . - -id:56b63fc0-3bb2-448b-8115-c1cb4384d8db a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 . - -id:5d7467bd-1ab8-46ea-8a56-0998f42b079c a prov:Entity ; - prov:value "0"^^xsd:int . - -id:663c25a0-9302-4b8f-aa89-765f3284aeca a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:abbdd009-c520-4098-baf6-6400cf916ffa . - -id:721f1551-f868-4e7d-8cb4-6f196df24a97 a prov:Entity ; - prov:value false . - -id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7 a prov:Entity ; - prov:value false . - -id:76b51c9a-5a58-43ce-b9a9-7f4459602a11 a prov:Entity ; - prov:value false . - -id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a a prov:Entity ; - prov:value "0"^^xsd:int . - -id:87697625-c033-4483-b5fa-d00140b03808 a prov:Entity ; - prov:value false . - -id:9ae42623-faf1-431a-acd3-bce4a4c24a24 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:3ad229e9-064d-4398-8617-d802f10ac40b, - id:70fb9ca7-9038-4874-bbda-0f12fad1627a ; - prov:hadMember data:hdas, - . - -id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:0ff29d35-01d6-471f-84e8-a1fc63c05daa . - -id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc a prov:Entity ; - prov:value "0"^^xsd:int . - -id:ac40b633-8521-462b-aea0-bea86dcaef7c a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:70e6aab8-ec0d-4ff2-a2d6-03a4ce5062fd, - id:d22a3287-f5fa-4465-8383-a6b1a3b0f242 ; - prov:hadMember , - id:351d875a-c130-42f7-ba2f-735780ea4ca8 . - -id:addafc7d-4439-49fb-9870-b6b0ed7415c3 a wfprov:Artifact, - prov:Collection, - prov:EmptyCollection, - prov:Entity . - -id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:6102b40f-814e-41b4-8e21-caee1eab126b . - -id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d a prov:Entity ; - prov:value false . - -id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1 a wfprov:Artifact, - prov:Collection, - prov:EmptyCollection, - prov:Entity . - -id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd a prov:Entity ; - prov:value "1"^^xsd:int . - -id:f23be627-a96d-47ce-b857-30e370a747a9 a prov:Entity ; - prov:value true . - -id:f715a46b-9eff-48c3-b88f-1f3a009ea573 a prov:Entity ; - prov:value true . - -id:f8915280-6e26-4eef-b378-cf27df3f8f1d a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0 . - -data:2e789aae2475b7da a wfprov:Artifact, - prov:Entity ; - prov:value "2e789aae2475b7da"^^xsd:string . - -data:7ca3de8f49293d1a a wfprov:Artifact, - prov:Entity ; - prov:value "7ca3de8f49293d1a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"^^xsd:string . - -data:1 a wfprov:Artifact, - prov:Entity ; - prov:value "1"^^xsd:string . - -data:auto a wfprov:Artifact, - prov:Entity ; - prov:value "auto"^^xsd:string . - -data:fd7fec473f1e6c6b a wfprov:Artifact, - prov:Entity ; - prov:value "fd7fec473f1e6c6b"^^xsd:string . - -data:hdas a wfprov:Artifact, - prov:Entity ; - prov:value "hdas"^^xsd:string . - -data:path a wfprov:Artifact, - prov:Entity ; - prov:value "path"^^xsd:string . - -id:b9177644-871b-492a-ae5f-3ee833ba0ae5 a wfprov:WorkflowRun, - prov:Activity ; - rdfs:label "Run of galaxy workflow"^^xsd:string ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan wf:main ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-04-04T16:59:09.403118"^^xsd:dateTime ; - prov:hadActivity id:ade93562-cbf5-453b-a445-cc9a5f95f0ec ] ; - prov:startedAtTime "2022-04-04T16:59:09.403029"^^xsd:dateTime ; - prov:wasAssociatedWith id:ade93562-cbf5-453b-a445-cc9a5f95f0ec . - - a wfprov:Artifact, - prov:Entity ; - prov:value "?"^^xsd:string . - -data:hda a wfprov:Artifact, - prov:Entity ; - prov:value "hda"^^xsd:string . - -id:ade93562-cbf5-453b-a445-cc9a5f95f0ec a wfprov:WorkflowEngine, - prov:Agent, - prov:SoftwareAgent ; - rdfs:label "galaxy_version_placeholder"^^xsd:string ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-04-04T16:59:09.402992"^^xsd:dateTime ; - prov:hadActivity id:027f7717-78d8-4f9a-a887-87813339b23e ] . - diff --git a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml b/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml deleted file mode 100644 index 68097876..00000000 --- a/test/test-data/test_ga_history_export/history_export/provenance/ga_export.cwlprov.xml +++ /dev/null @@ -1,1457 +0,0 @@ - - - - - PDG - schema:Person - PDG - PDG - - - - - - - galaxy_version_placeholder - wfprov:WorkflowEngine - - - - - 2022-04-04T16:59:09.402992 - - - 2022-04-04T16:59:09.403029 - Run of galaxy workflow - wfprov:WorkflowRun - - - - - - - - - - 2022-04-04T16:59:09.403118 - - - 2021-06-23T10:20:22.770291 - 2021-06-23T10:20:42.041319 - Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:20:22.770291 - - - wfprov:Artifact - 2524d3d3b68ad39a - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.403801 - wf:main/__DATA_FETCH__/output0 - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.403870 - wf:main/__DATA_FETCH__/file_count - - - prov:Dictionary - wfprov:Artifact - id:a92435e7-0621-4629-80fa-d73aa1989363 - id:e311b33d-139a-4e92-a5c1-3a04530b9128 - id:f268cc7a-3474-404e-892f-8af376e98ae3 - - - 0 - - - - - - - prov:KeyEntityPair - id:a6f4a351-1c15-472c-b6f4-5d7a38e817cc - __index__ - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - file_data - - - wfprov:Artifact - urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a - - - - - - - prov:KeyEntityPair - data:urn:uuid:0fba80f8-6eff-4909-b5b4-78ddf1f2794a - @id - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.404286 - wf:main/__DATA_FETCH__/files - - - wfprov:Artifact - - - - - - 2022-04-04T16:59:09.404363 - wf:main/__DATA_FETCH__/paramfile - - - prov:Dictionary - wfprov:Artifact - id:15212ae6-d7ff-4660-870e-34f3caa32ceb - id:441a9ce2-fada-464f-84fb-6dfd01a6379e - id:9af37a24-65f9-41cd-8191-228ec8108418 - - - prov:Dictionary - wfprov:Artifact - id:0196242d-cfb9-45f3-965c-8fa2a037f104 - id:38113d6d-950c-4c1a-826d-636d3c6fa3ea - id:a2e3fcfb-922a-4b10-8c50-f6715c7bf86a - id:d9d0779c-b85e-47b9-8aff-caf7cc16b1ce - - - prov:Dictionary - wfprov:Artifact - id:b17c488e-30c3-42cb-b2f0-092b0efe2427 - id:e1829e51-7947-4db2-99a0-1ea7703ee764 - - - wfprov:Artifact - hdas - - - - - - - prov:KeyEntityPair - data:hdas - type - - - wfprov:Artifact - urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f - - - - - - - prov:KeyEntityPair - data:urn:uuid:40755d93-d65b-4fb3-bb40-e052a5ea6d4f - @id - - - - - - - prov:KeyEntityPair - id:40755d93-d65b-4fb3-bb40-e052a5ea6d4f - destination - - - prov:Dictionary - wfprov:Artifact - id:0bb99b2c-055b-4f0f-88ce-d36d3a77fd3a - id:3b543d5d-26b4-48f1-8c80-0c288c8df33f - id:46e9c6f5-8a4e-42e7-9fd6-2b366e1f3783 - id:4b32d7ec-e96f-41ff-8feb-1e43324962da - id:5f9613d6-b39e-40e1-95d2-d26fb37550fe - id:8a2cf341-8042-40bd-8509-b56f1f4161c7 - id:b0586419-dbb7-4757-9cfd-ae55abef3674 - id:de8c8cf1-a3dd-4fd0-9feb-901eb5b77a01 - id:ed2f097b-344c-4f9e-bf0c-ada2ec9e4c72 - id:f5199f67-c23f-46de-a504-11e5465e2e8c - id:fa3c9ec4-7c90-43f8-b23b-7a0a66e85dca - - - wfprov:Artifact - auto - - - - - - - prov:KeyEntityPair - data:auto - ext - - - wfprov:Artifact - ? - - - - - - - prov:KeyEntityPair - data:? - dbkey - - - true - - - - - - - prov:KeyEntityPair - id:f23be627-a96d-47ce-b857-30e370a747a9 - to_posix_lines - - - wfprov:Artifact - path - - - - - - - prov:KeyEntityPair - data:path - src - - - wfprov:Artifact - dataset2.txt - - - - - - - prov:KeyEntityPair - data:dataset2.txt - name - - - prov:EmptyCollection - wfprov:Artifact - - - - - - - prov:KeyEntityPair - id:be70b3ea-6658-46fd-aa73-3abe8d7fd1f1 - hashes - - - false - - - - - - - prov:KeyEntityPair - id:73e6bc82-81b8-4ae4-bc9d-1eb89e451bd7 - in_place - - - false - - - - - - - prov:KeyEntityPair - id:76b51c9a-5a58-43ce-b9a9-7f4459602a11 - purge_source - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - path - - - 155708 - - - - - - - prov:KeyEntityPair - id:4ed44fba-accb-410c-baef-53d2cb882954 - object_id - - - wfprov:Artifact - urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 - - - - - - - prov:KeyEntityPair - data:urn:uuid:e46f93fb-b0ec-4ed7-b4ec-2ebb719a1551 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:56b63fc0-3bb2-448b-8115-c1cb4384d8db - elements - - - false - - - - - - - prov:KeyEntityPair - id:b1bd43cc-60dd-464c-bc17-13d4ad78be9d - auto_decompress - - - wfprov:Artifact - urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2 - - - - - - - prov:KeyEntityPair - data:urn:uuid:85ddd8ea-0da6-4f63-9ed0-b736abedc2c2 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:508b7a80-e3e7-442e-b9e9-4874e2916aad - targets - - - true - - - - - - - prov:KeyEntityPair - id:f715a46b-9eff-48c3-b88f-1f3a009ea573 - check_content - - - wfprov:Artifact - urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c - - - - - - - prov:KeyEntityPair - data:urn:uuid:b148f9da-c287-4a2b-a6ee-41a95cf23d1c - @id - - - - - 2022-04-04T16:59:09.406855 - wf:main/__DATA_FETCH__/request_json - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.406936 - wf:main/__DATA_FETCH__/request_version - - - 2021-06-23T10:20:00.981702 - 2021-06-23T10:20:22.202678 - Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:20:00.981702 - - - wfprov:Artifact - 7c1d8e3101dbcdba - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.407566 - wf:main/__DATA_FETCH__/output0 - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.407631 - wf:main/__DATA_FETCH__/file_count - - - prov:Dictionary - wfprov:Artifact - id:7c60b838-dd41-4166-aa41-6e652e5ef63b - id:e0524eed-ea77-413b-b0db-5f72e16c365e - id:f8f974ae-cd55-4986-8a9e-1d987b76fd34 - - - 0 - - - - - - - prov:KeyEntityPair - id:5d7467bd-1ab8-46ea-8a56-0998f42b079c - __index__ - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - file_data - - - wfprov:Artifact - urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7 - - - - - - - prov:KeyEntityPair - data:urn:uuid:02bb9d1c-f248-47fb-ac2c-9985301385a7 - @id - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.408037 - wf:main/__DATA_FETCH__/files - - - wfprov:Artifact - - - - - - 2022-04-04T16:59:09.408097 - wf:main/__DATA_FETCH__/paramfile - - - prov:Dictionary - wfprov:Artifact - id:3f52ff7d-9aa8-45c7-8af1-1f7f474c6ad7 - id:689d969e-0df7-40c8-b733-b4e39fd49d34 - id:9baabbde-52d6-4728-8ef7-738960d2a86f - - - prov:Dictionary - wfprov:Artifact - id:0c415611-9c31-47d4-82f9-a6330b980a8e - id:2d384308-e0b1-4f82-811c-4bba81b92067 - id:788acdf9-5e3a-4774-aa66-3068819b5cae - id:cc8b2ec1-0c34-4d44-bce6-9dfb3efd9298 - - - prov:Dictionary - wfprov:Artifact - id:3ad229e9-064d-4398-8617-d802f10ac40b - id:70fb9ca7-9038-4874-bbda-0f12fad1627a - - - wfprov:Artifact - hdas - - - - - - - prov:KeyEntityPair - data:hdas - type - - - wfprov:Artifact - urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24 - - - - - - - prov:KeyEntityPair - data:urn:uuid:9ae42623-faf1-431a-acd3-bce4a4c24a24 - @id - - - - - - - prov:KeyEntityPair - id:9ae42623-faf1-431a-acd3-bce4a4c24a24 - destination - - - prov:Dictionary - wfprov:Artifact - id:06db435a-b77f-424b-8301-acb7e18cc2ce - id:08ffc626-141c-4214-8d71-746a1218f209 - id:23fe35b3-2a01-4edf-952a-5769462abc6c - id:46ce5c94-417b-4bcf-a9af-fb60912d385a - id:7dc6f8f5-cce3-4da9-b386-0a18314af498 - id:919c8f14-f4f3-4151-b936-d7502f64caa4 - id:a05e1e9a-74e5-4efc-ad75-96c15f4a83ce - id:bab1f03d-7ca6-4bb7-a57d-563c0e70808b - id:bb0b8464-83db-421e-9566-a31da915d209 - id:c256e77e-7189-430a-8c59-03fa703dce07 - id:d281fed1-869b-4451-8fda-95b26856a918 - - - wfprov:Artifact - auto - - - - - - - prov:KeyEntityPair - data:auto - ext - - - wfprov:Artifact - ? - - - - - - - prov:KeyEntityPair - data:? - dbkey - - - true - - - - - - - prov:KeyEntityPair - id:493493b1-836f-404c-9084-95086d7ba06a - to_posix_lines - - - wfprov:Artifact - path - - - - - - - prov:KeyEntityPair - data:path - src - - - wfprov:Artifact - dataset1.txt - - - - - - - prov:KeyEntityPair - data:dataset1.txt - name - - - prov:EmptyCollection - wfprov:Artifact - - - - - - - prov:KeyEntityPair - id:addafc7d-4439-49fb-9870-b6b0ed7415c3 - hashes - - - false - - - - - - - prov:KeyEntityPair - id:721f1551-f868-4e7d-8cb4-6f196df24a97 - in_place - - - false - - - - - - - prov:KeyEntityPair - id:87697625-c033-4483-b5fa-d00140b03808 - purge_source - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - path - - - 155707 - - - - - - - prov:KeyEntityPair - id:1478aab0-2721-45d5-8a99-6ae0ae2ccd80 - object_id - - - wfprov:Artifact - urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa - - - - - - - prov:KeyEntityPair - data:urn:uuid:0ff29d35-01d6-471f-84e8-a1fc63c05daa - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:a1d976ed-02eb-43c7-a2f6-fa8c9447ddea - elements - - - false - - - - - - - prov:KeyEntityPair - id:13cd8c51-e771-4474-9a85-8a5eee6d2f4f - auto_decompress - - - wfprov:Artifact - urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b - - - - - - - prov:KeyEntityPair - data:urn:uuid:6102b40f-814e-41b4-8e21-caee1eab126b - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:b0b957a4-3167-4dee-a4ac-f9e4f0b1afab - targets - - - true - - - - - - - prov:KeyEntityPair - id:016238d2-8ca1-4335-b232-acae7f43ed72 - check_content - - - wfprov:Artifact - urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f - - - - - - - prov:KeyEntityPair - data:urn:uuid:ce5712eb-9c70-401d-811e-a01bfdbf3b3f - @id - - - - - 2022-04-04T16:59:09.410250 - wf:main/__DATA_FETCH__/request_json - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.410320 - wf:main/__DATA_FETCH__/request_version - - - 2021-06-23T10:46:28.351123 - 2021-06-23T10:46:44.738703 - Run of ga_export/jobs_attrs.txt#cat1 - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:46:28.351123 - - - wfprov:Artifact - 7ca3de8f49293d1a - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.410900 - wf:main/cat1/input1 - - - wfprov:Artifact - 2e789aae2475b7da - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.411016 - wf:main/cat1/queries_0_input2 - - - wfprov:Artifact - fd7fec473f1e6c6b - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.411131 - wf:main/cat1/out_file1 - - - wfprov:Artifact - txt - - - - - 2022-04-04T16:59:09.411190 - wf:main/cat1/__input_ext - - - wfprov:Artifact - 42f21c0ad41011eb87defa163eba836f - - - - - 2022-04-04T16:59:09.411252 - wf:main/cat1/__workflow_invocation_uuid__ - - - wfprov:Artifact - /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - - - - - 2022-04-04T16:59:09.411312 - wf:main/cat1/chromInfo - - - wfprov:Artifact - ? - - - - - 2022-04-04T16:59:09.411369 - wf:main/cat1/dbkey - - - prov:Dictionary - wfprov:Artifact - id:4ee5e287-4b5d-4d40-be38-1bf1c3236934 - id:551327a9-e8db-4d46-8ec4-cde270df080b - - - prov:Dictionary - wfprov:Artifact - id:49e48096-0a9e-4ebd-8d9b-2b3647acb1b5 - id:9fb40382-f182-481e-90e6-0e24006c71c5 - id:c0fce355-42ca-41f4-88b0-ccc3b4fec7d2 - - - wfprov:Artifact - 7ca3de8f49293d1a - - - - - - - prov:KeyEntityPair - data:7ca3de8f49293d1a - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0 - - - - - - - prov:KeyEntityPair - data:urn:uuid:fee3b98e-6c76-4d2d-b80d-47e4655bf9e0 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:f8915280-6e26-4eef-b378-cf27df3f8f1d - values - - - wfprov:Artifact - urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a - - - - - - - prov:KeyEntityPair - data:urn:uuid:b040da72-a0ee-4309-ad1e-353be140b04a - @id - - - - - 2022-04-04T16:59:09.411964 - wf:main/cat1/input1 - - - prov:Dictionary - wfprov:Artifact - id:92b2afc9-fc96-4764-adbe-73d014ba2357 - id:b397cf2b-901a-454c-bfc2-e966b6838269 - id:dc09c4fe-c4a9-4cc5-9770-0a4f19369ac0 - - - 0 - - - - - - - prov:KeyEntityPair - id:7e30574b-3aba-44ce-b8ee-f9df06a3ab4a - __index__ - - - prov:Dictionary - wfprov:Artifact - id:70e6aab8-ec0d-4ff2-a2d6-03a4ce5062fd - id:d22a3287-f5fa-4465-8383-a6b1a3b0f242 - - - prov:Dictionary - wfprov:Artifact - id:10f720aa-40e7-4c83-9ad1-02ffc26a7944 - id:34e6b60d-4d4a-496d-bb9c-a4d34040155c - id:ebaa0943-a400-4daf-a2e7-f781b714a666 - - - wfprov:Artifact - 2e789aae2475b7da - - - - - - - prov:KeyEntityPair - data:2e789aae2475b7da - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470 - - - - - - - prov:KeyEntityPair - data:urn:uuid:c9198eaf-36fb-42c4-bf4b-d740591fe470 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:351d875a-c130-42f7-ba2f-735780ea4ca8 - values - - - wfprov:Artifact - urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c - - - - - - - prov:KeyEntityPair - data:urn:uuid:ac40b633-8521-462b-aea0-bea86dcaef7c - @id - - - - - - - prov:KeyEntityPair - id:ac40b633-8521-462b-aea0-bea86dcaef7c - input2 - - - wfprov:Artifact - urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98 - - - - - - - prov:KeyEntityPair - data:urn:uuid:7519c8b1-64da-4255-9960-acb3dda9ab98 - @id - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.412881 - wf:main/cat1/queries - - - 2021-06-23T10:46:28.526901 - 2021-06-23T10:47:04.837750 - Run of ga_export/jobs_attrs.txt#random_lines1 - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:46:28.526901 - - - wfprov:Artifact - fd7fec473f1e6c6b - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.413468 - wf:main/random_lines1/input - - - wfprov:Artifact - 775bc9b3c1750167 - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.413588 - wf:main/random_lines1/out_file1 - - - wfprov:Artifact - txt - - - - - 2022-04-04T16:59:09.413652 - wf:main/random_lines1/__input_ext - - - wfprov:Artifact - 42f21c0ad41011eb87defa163eba836f - - - - - 2022-04-04T16:59:09.413710 - wf:main/random_lines1/__workflow_invocation_uuid__ - - - wfprov:Artifact - /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - - - - - 2022-04-04T16:59:09.413770 - wf:main/random_lines1/chromInfo - - - wfprov:Artifact - ? - - - - - 2022-04-04T16:59:09.413826 - wf:main/random_lines1/dbkey - - - prov:Dictionary - wfprov:Artifact - id:298c9e09-232d-4854-bf61-8116b1323f5b - id:838aa24d-f8b4-4ddd-a76c-82460c5b6391 - - - prov:Dictionary - wfprov:Artifact - id:947491c9-a106-4578-b804-16c3100e0111 - id:994bb2e3-42f8-4fd1-9d6f-aff742a0b9b0 - id:ad223424-b8ff-4704-a618-0a033ceaf3ea - - - wfprov:Artifact - fd7fec473f1e6c6b - - - - - - - prov:KeyEntityPair - data:fd7fec473f1e6c6b - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa - - - - - - - prov:KeyEntityPair - data:urn:uuid:abbdd009-c520-4098-baf6-6400cf916ffa - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:663c25a0-9302-4b8f-aa89-765f3284aeca - values - - - wfprov:Artifact - urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a - - - - - - - prov:KeyEntityPair - data:urn:uuid:db786d1e-928b-4b0f-b118-bd235731ea9a - @id - - - - - 2022-04-04T16:59:09.414376 - wf:main/random_lines1/input - - - wfprov:Artifact - 3 - - - - - 2022-04-04T16:59:09.414444 - wf:main/random_lines1/num_lines - - - prov:Dictionary - wfprov:Artifact - id:1b548405-6990-454a-98a6-128dccf12014 - id:3f28e37f-bba8-4b0d-b4d8-ad4749630604 - id:7884960e-a973-4e8f-bb01-58005de82366 - id:c753b9e4-3908-491a-a7a8-a0d4e1543e34 - - - 1 - - - - - - - prov:KeyEntityPair - id:e51d7946-1b09-4d47-946b-cb7b1bb8a8dd - __current_case__ - - - wfprov:Artifact - 0 - - - - - - - prov:KeyEntityPair - data:0 - seed - - - wfprov:Artifact - set_seed - - - - - - - prov:KeyEntityPair - data:set_seed - seed_source_selector - - - wfprov:Artifact - urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948 - - - - - - - prov:KeyEntityPair - data:urn:uuid:cb9975e1-3882-4cc3-9995-9352d37f1948 - @id - - - - - 2022-04-04T16:59:09.414862 - wf:main/random_lines1/seed_source - - diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt deleted file mode 100644 index 8b3f00b0..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/Concatenate_datasets_on_data_2_and_data_1_3.txt +++ /dev/null @@ -1,4 +0,0 @@ -hello -universe! -hello -world diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt deleted file mode 100644 index 94954abd..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/dataset1.txt_2.txt +++ /dev/null @@ -1,2 +0,0 @@ -hello -world diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt deleted file mode 100644 index 718e715c..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/dataset2.txt_1.txt +++ /dev/null @@ -1,2 +0,0 @@ -hello -universe! diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json deleted file mode 100644 index aa9ef83a..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.json +++ /dev/null @@ -1,2862 +0,0 @@ -{ - 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} - ], - "http://www.w3.org/ns/prov#pairKey": [ - { - "@value": "file_data" - } - ] - } -] \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.nt b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.nt deleted file mode 100644 index ac23c67b..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.nt +++ /dev/null @@ -1,935 +0,0 @@ - . - . - _:Nf120d57e510c4e5bb1d02257d12091a0 . - "to_posix_lines"^^ . - . - . - . - "hashes"^^ . - . - . - _:N61cc0850252b4d1cad508659bbcb6996 . - "@id"^^ . - . - . - . -_:N7e13fa1b379e4046b063849344b53a99 . -_:Nf8a5c837264c4fcea460ed4c16d858e7 . - "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^ . - . - . - . -_:N7f3c55d1fb784122b844eef9ba3eaab4 "2022-04-04T16:59:09.795855"^^ . - . - . - . -_:N3054756d153b4da5b13bb453b8cc4085 . - . - . - _:Ncdd6820f5a6f4038a7d97e21a8d54047 . - "/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len"^^ . - 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. - "false"^^ . - . - . - . - . - . - . - . - . -_:Nd49fda34316049d9905e9e97ed294837 . - . - . - . - . - . - . - . - . - . - . - . -_:Nbc294ac99e664954950b7238720820ff . - . - . - . - . - . - . - . - . - "7c1d8e3101dbcdba"^^ . - . -_:N7e13fa1b379e4046b063849344b53a99 . -_:N8826178d654543cba856ba032532b2ce "2022-04-04T16:59:09.797298"^^ . -_:N3ad5c0900e40422c871e0000e977d688 "2022-04-04T16:59:09.803689"^^ . - . - diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn deleted file mode 100644 index c26f61ae..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.provn +++ /dev/null @@ -1,330 +0,0 @@ -document - prefix wfprov - prefix wfdesc - prefix cwlprov - prefix foaf - prefix schema - prefix orcid - prefix id - prefix data - prefix provenance - prefix wf - prefix input - - agent(id:027f7717-78d8-4f9a-a887-87813339b23e) - agent(id:8124e339-e638-4fc3-b421-6367e3682c50, [prov:type='wfprov:WorkflowEngine', prov:type='prov:SoftwareAgent', prov:label="galaxy_version_placeholder"]) - wasStartedBy(id:8124e339-e638-4fc3-b421-6367e3682c50, -, id:027f7717-78d8-4f9a-a887-87813339b23e, 2022-04-04T16:59:09.795855) - activity(id:b02505bb-6b95-4e97-8043-d0823b00b7f4, 2022-04-04T16:59:09.795894, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of galaxy workflow"]) - wasAssociatedWith(id:b02505bb-6b95-4e97-8043-d0823b00b7f4, id:8124e339-e638-4fc3-b421-6367e3682c50, wf:main) - wasStartedBy(id:b02505bb-6b95-4e97-8043-d0823b00b7f4, -, id:8124e339-e638-4fc3-b421-6367e3682c50, 2022-04-04T16:59:09.795971) - activity(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, 2021-06-23T10:20:22.770291, 2021-06-23T10:20:42.041319, [prov:type='wfprov:ProcessRun', prov:label="Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"]) - wasAssociatedWith(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, id:8124e339-e638-4fc3-b421-6367e3682c50, wf:main/__DATA_FETCH__) - wasStartedBy(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, -, id:b02505bb-6b95-4e97-8043-d0823b00b7f4, 2021-06-23T10:20:22.770291) - entity(data:2524d3d3b68ad39a, [prov:type='wfprov:Artifact', prov:value="2524d3d3b68ad39a"]) - entity(id:2119440c-63be-46a9-bbb7-2b104033b8f2, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) - hadMember(id:2119440c-63be-46a9-bbb7-2b104033b8f2, data:2524d3d3b68ad39a) - used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, id:2119440c-63be-46a9-bbb7-2b104033b8f2, 2022-04-04T16:59:09.796590, [prov:role='wf:main/__DATA_FETCH__/output0']) - entity(data:1, [prov:type='wfprov:Artifact', prov:value="1"]) - used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, data:1, 2022-04-04T16:59:09.796656, [prov:role='wf:main/__DATA_FETCH__/file_count']) - entity(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:2301b8b5-528f-4802-bd81-a4a3ca8534f4', prov:hadDictionaryMember='id:00e0f888-71d8-49f9-ba39-dcaed5a91c56', prov:hadDictionaryMember='id:1605ad9c-1b56-4055-a8d0-866f49da1687']) - entity(id:f4d07c61-fb2b-42eb-a7c5-1820900166f3, [prov:value=0]) - hadMember(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, id:f4d07c61-fb2b-42eb-a7c5-1820900166f3) - entity(id:1605ad9c-1b56-4055-a8d0-866f49da1687, [prov:type='prov:KeyEntityPair', prov:pairKey="__index__", prov:pairEntity='id:f4d07c61-fb2b-42eb-a7c5-1820900166f3']) - entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) - hadMember(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) - entity(id:2301b8b5-528f-4802-bd81-a4a3ca8534f4, [prov:type='prov:KeyEntityPair', prov:pairKey="file_data", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) - entity(data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b, [prov:type='wfprov:Artifact', prov:value="urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b"]) - hadMember(id:e9693b34-04fb-4b31-a78c-7d089fd6558b, data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b) - entity(id:00e0f888-71d8-49f9-ba39-dcaed5a91c56, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b']) - entity(id:6572947b-c3fd-4c6f-bdff-7aa191bc5546, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) - hadMember(id:6572947b-c3fd-4c6f-bdff-7aa191bc5546, id:e9693b34-04fb-4b31-a78c-7d089fd6558b) - used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, id:6572947b-c3fd-4c6f-bdff-7aa191bc5546, 2022-04-04T16:59:09.797234, [prov:role='wf:main/__DATA_FETCH__/files']) - entity(data:, [prov:type='wfprov:Artifact', prov:value=""]) - used(id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb, data:, 2022-04-04T16:59:09.797298, [prov:role='wf:main/__DATA_FETCH__/paramfile']) - entity(id:34e943f0-5027-47b0-ba7b-05fca46da136, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:e25dce0d-bf63-414f-a0cd-2663e7a44d50', prov:hadDictionaryMember='id:a15754e6-26b6-4269-96b6-7d35515d1c02', prov:hadDictionaryMember='id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885']) - entity(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:000e294f-576c-469b-8965-4e279bebc880', prov:hadDictionaryMember='id:f89aaeef-0313-42af-b87e-7b519d494be7', prov:hadDictionaryMember='id:e84e01b6-0126-4b79-90d5-99d22e8dde7c', prov:hadDictionaryMember='id:a6d080a6-7c60-46f2-85c8-2519f4d803ea']) - entity(id:e46be7d4-c0c3-489f-86dd-0c8148d86858, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6', prov:hadDictionaryMember='id:7b40bdfc-aacc-4947-a8d8-d13db0419365']) - entity(data:hdas, [prov:type='wfprov:Artifact', prov:value="hdas"]) - hadMember(id:e46be7d4-c0c3-489f-86dd-0c8148d86858, data:hdas) - entity(id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6, [prov:type='prov:KeyEntityPair', prov:pairKey="type", prov:pairEntity='data:hdas']) - entity(data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858, [prov:type='wfprov:Artifact', prov:value="urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858"]) - hadMember(id:e46be7d4-c0c3-489f-86dd-0c8148d86858, data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858) - entity(id:7b40bdfc-aacc-4947-a8d8-d13db0419365, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858']) - hadMember(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, id:e46be7d4-c0c3-489f-86dd-0c8148d86858) - entity(id:a6d080a6-7c60-46f2-85c8-2519f4d803ea, [prov:type='prov:KeyEntityPair', prov:pairKey="destination", prov:pairEntity='id:e46be7d4-c0c3-489f-86dd-0c8148d86858']) - entity(id:1c90cc92-4948-4b69-a163-f63e41891f7a, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:0592876b-ce23-4b6a-a8cf-32a46f7aedea', prov:hadDictionaryMember='id:b1aad576-0af0-43c0-948d-df79e52df6b7', prov:hadDictionaryMember='id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103', prov:hadDictionaryMember='id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38', prov:hadDictionaryMember='id:8232048b-b457-45cb-932e-a5cf8f8be6e1', prov:hadDictionaryMember='id:ed8aaa9a-567f-4893-b432-fa6e49547650', prov:hadDictionaryMember='id:3e26cc6f-1f3b-438d-ada9-a55bead88b03', prov:hadDictionaryMember='id:5ab39f26-7656-40f1-826f-38f40ed09f10', prov:hadDictionaryMember='id:29b40ddc-e592-4aa9-989f-ed4ac9be59af', prov:hadDictionaryMember='id:912f104e-1517-492e-abe3-f931fe47438b', prov:hadDictionaryMember='id:587e2872-6ae3-4716-b99e-12c5db1f8e56']) - entity(data:auto, [prov:type='wfprov:Artifact', prov:value="auto"]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:auto) - entity(id:5ab39f26-7656-40f1-826f-38f40ed09f10, [prov:type='prov:KeyEntityPair', prov:pairKey="ext", prov:pairEntity='data:auto']) - entity(data:?, [prov:type='wfprov:Artifact', prov:value="?"]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:?) - entity(id:0592876b-ce23-4b6a-a8cf-32a46f7aedea, [prov:type='prov:KeyEntityPair', prov:pairKey="dbkey", prov:pairEntity='data:?']) - entity(id:512093ee-9853-484f-9a93-aea928098062, [prov:value="1" %% xsd:boolean]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:512093ee-9853-484f-9a93-aea928098062) - entity(id:3e26cc6f-1f3b-438d-ada9-a55bead88b03, [prov:type='prov:KeyEntityPair', prov:pairKey="to_posix_lines", prov:pairEntity='id:512093ee-9853-484f-9a93-aea928098062']) - entity(data:path, [prov:type='wfprov:Artifact', prov:value="path"]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:path) - entity(id:29b40ddc-e592-4aa9-989f-ed4ac9be59af, [prov:type='prov:KeyEntityPair', prov:pairKey="src", prov:pairEntity='data:path']) - entity(data:dataset2.txt, [prov:type='wfprov:Artifact', prov:value="dataset2.txt"]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:dataset2.txt) - entity(id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103, [prov:type='prov:KeyEntityPair', prov:pairKey="name", prov:pairEntity='data:dataset2.txt']) - entity(id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b, [prov:type='prov:Collection', prov:type='wfprov:Artifact', prov:type='prov:EmptyCollection']) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b) - entity(id:587e2872-6ae3-4716-b99e-12c5db1f8e56, [prov:type='prov:KeyEntityPair', prov:pairKey="hashes", prov:pairEntity='id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b']) - entity(id:03827a8b-50a4-463b-876a-742652bb3049, [prov:value="0" %% xsd:boolean]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:03827a8b-50a4-463b-876a-742652bb3049) - entity(id:912f104e-1517-492e-abe3-f931fe47438b, [prov:type='prov:KeyEntityPair', prov:pairKey="in_place", prov:pairEntity='id:03827a8b-50a4-463b-876a-742652bb3049']) - entity(id:16597142-0745-4b4c-80c7-5755b2d087a7, [prov:value="0" %% xsd:boolean]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, id:16597142-0745-4b4c-80c7-5755b2d087a7) - entity(id:b1aad576-0af0-43c0-948d-df79e52df6b7, [prov:type='prov:KeyEntityPair', prov:pairKey="purge_source", prov:pairEntity='id:16597142-0745-4b4c-80c7-5755b2d087a7']) - entity(data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2, [prov:type='wfprov:Artifact', prov:value="/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"]) - hadMember(id:1c90cc92-4948-4b69-a163-f63e41891f7a, data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2) - entity(id:8232048b-b457-45cb-932e-a5cf8f8be6e1, [prov:type='prov:KeyEntityPair', prov:pairKey="path", prov:pairEntity='data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2']) - 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entity(id:f89aaeef-0313-42af-b87e-7b519d494be7, [prov:type='prov:KeyEntityPair', prov:pairKey="elements", prov:pairEntity='id:9d27fd2e-c728-420a-86ba-fc92df98dd6c']) - entity(id:040d2761-5df7-4905-a289-3fed059729f3, [prov:value="0" %% xsd:boolean]) - hadMember(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, id:040d2761-5df7-4905-a289-3fed059729f3) - entity(id:e84e01b6-0126-4b79-90d5-99d22e8dde7c, [prov:type='prov:KeyEntityPair', prov:pairKey="auto_decompress", prov:pairEntity='id:040d2761-5df7-4905-a289-3fed059729f3']) - entity(data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe, [prov:type='wfprov:Artifact', prov:value="urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe"]) - hadMember(id:8d86a2e6-482b-41b3-ac34-acc0b74014fe, data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe) - entity(id:000e294f-576c-469b-8965-4e279bebc880, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe']) - entity(id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066, [prov:type='prov:Collection', prov:type='wfprov:Artifact']) - 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entity(id:838e9760-cb17-4896-9c13-184164aa0c08, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3']) - used(id:a4be0d2e-38dd-4dfd-97de-414781a691ad, id:1d62001e-4526-468c-b34a-ef88dcc11ac3, 2022-04-04T16:59:09.806986, [prov:role='wf:main/random_lines1/input']) - entity(data:3, [prov:type='wfprov:Artifact', prov:value="3"]) - used(id:a4be0d2e-38dd-4dfd-97de-414781a691ad, data:3, 2022-04-04T16:59:09.807046, [prov:role='wf:main/random_lines1/num_lines']) - entity(id:8456e304-ef4f-4f40-a818-00b01407f6a2, [prov:type='prov:Collection', prov:type='prov:Dictionary', prov:type='wfprov:Artifact', prov:hadDictionaryMember='id:0080be3e-2011-44c6-a391-3e151894b43e', prov:hadDictionaryMember='id:6de1750c-1612-4740-87a3-7d000e40c4b2', prov:hadDictionaryMember='id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91', prov:hadDictionaryMember='id:d13aa4a9-9029-4a4a-959b-4e2a3bd0aa3d']) - entity(id:fc4a126f-25bd-4d12-bde7-c41dadf135c6, [prov:value=1]) - 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entity(id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91, [prov:type='prov:KeyEntityPair', prov:pairKey="@id", prov:pairEntity='data:urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2']) - used(id:a4be0d2e-38dd-4dfd-97de-414781a691ad, id:8456e304-ef4f-4f40-a818-00b01407f6a2, 2022-04-04T16:59:09.807432, [prov:role='wf:main/random_lines1/seed_source']) -endDocument \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl deleted file mode 100644 index 2ef85a57..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.ttl +++ /dev/null @@ -1,1070 +0,0 @@ -@prefix data: . -@prefix id: . -@prefix prov: . -@prefix rdfs: . -@prefix wf: . -@prefix wfprov: . -@prefix xsd: . - -id:0ffbc8ad-a3f1-4c5a-90a7-c0cba2037931 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:22.202678"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.800503"^^xsd:dateTime ; - prov:entity id:202eb0cc-f08e-4946-be23-0b6f195a0997 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.799938"^^xsd:dateTime ; - prov:entity id:78b8eb8f-2594-4af0-9448-9ca96c3fc116 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.800010"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.802972"^^xsd:dateTime ; - prov:entity id:0fd972f6-10e7-42ee-a514-02ed749f9494 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.803053"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.800579"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:00.981702"^^xsd:dateTime ; - prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . - -id:4e5feb15-2e9a-47c9-90df-18749a56c0d6 a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#cat1"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:46:44.738703"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.803927"^^xsd:dateTime ; - prov:entity id:af880c02-79fa-4624-a45c-8f0277838663 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.804768"^^xsd:dateTime ; - prov:entity id:8c884aa2-99c2-4588-9d49-eff12441e6c0 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.803988"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.804112"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.803689"^^xsd:dateTime ; - prov:entity id:cb03c73e-30e1-4184-93e7-ad075995d89f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.804048"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.804169"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.803812"^^xsd:dateTime ; - prov:entity id:e88d7b49-c96b-4e54-92f2-410aa9268df2 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.805613"^^xsd:dateTime ; - prov:entity id:9c04f4c2-683e-4729-938f-ffb2063bcd63 ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:46:28.351123"^^xsd:dateTime ; - prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . - -id:a4be0d2e-38dd-4dfd-97de-414781a691ad a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#random_lines1"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:47:04.837750"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.806986"^^xsd:dateTime ; - prov:entity id:1d62001e-4526-468c-b34a-ef88dcc11ac3 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.806121"^^xsd:dateTime ; - prov:entity id:fe8b9a54-02f9-40d5-b3be-d14352b6b76b ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.806350"^^xsd:dateTime ; - prov:entity data:42f21c0ad41011eb87defa163eba836f ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.806236"^^xsd:dateTime ; - prov:entity id:c38cd06f-2a47-441f-8677-9b944c5d49b5 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.806293"^^xsd:dateTime ; - prov:entity data:txt ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.807432"^^xsd:dateTime ; - prov:entity id:8456e304-ef4f-4f40-a818-00b01407f6a2 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.807046"^^xsd:dateTime ; - prov:entity data:3 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.806458"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.806405"^^xsd:dateTime ; - prov:entity ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:46:28.526901"^^xsd:dateTime ; - prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . - -id:fd4bf69f-d083-4309-892e-41a1b3d7bdfb a wfprov:ProcessRun, - prov:Activity ; - rdfs:label "Run of ga_export/jobs_attrs.txt#__DATA_FETCH__"^^xsd:string ; - prov:endedAtTime "2021-06-23T10:20:42.041319"^^xsd:dateTime ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:hadActivity id:b02505bb-6b95-4e97-8043-d0823b00b7f4 ] ; - prov:qualifiedUsage [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.797298"^^xsd:dateTime ; - prov:entity data: ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.799249"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.799177"^^xsd:dateTime ; - prov:entity id:34e943f0-5027-47b0-ba7b-05fca46da136 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.797234"^^xsd:dateTime ; - prov:entity id:6572947b-c3fd-4c6f-bdff-7aa191bc5546 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.796656"^^xsd:dateTime ; - prov:entity data:1 ; - prov:hadRole ], - [ a prov:Usage ; - prov:atTime "2022-04-04T16:59:09.796590"^^xsd:dateTime ; - prov:entity id:2119440c-63be-46a9-bbb7-2b104033b8f2 ; - prov:hadRole ] ; - prov:startedAtTime "2021-06-23T10:20:22.770291"^^xsd:dateTime ; - prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . - -data:2524d3d3b68ad39a a wfprov:Artifact, - prov:Entity ; - prov:value "2524d3d3b68ad39a"^^xsd:string . - -data:3 a wfprov:Artifact, - prov:Entity ; - prov:value "3"^^xsd:string . - -data:775bc9b3c1750167 a wfprov:Artifact, - prov:Entity ; - prov:value "775bc9b3c1750167"^^xsd:string . - -data:7c1d8e3101dbcdba a wfprov:Artifact, - prov:Entity ; - prov:value "7c1d8e3101dbcdba"^^xsd:string . - -id:000e294f-576c-469b-8965-4e279bebc880 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:0080be3e-2011-44c6-a391-3e151894b43e a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:fc4a126f-25bd-4d12-bde7-c41dadf135c6 ; - prov:pairKey "__current_case__"^^xsd:string . - -id:00e0f888-71d8-49f9-ba39-dcaed5a91c56 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:02094080-ba1e-458f-8b75-5741f7f9a72b a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:2a48c6c5-b7ba-482e-808e-b07d48c0bec7 ; - prov:pairKey "elements"^^xsd:string . - -id:027f7717-78d8-4f9a-a887-87813339b23e a prov:Agent . - -id:0592876b-ce23-4b6a-a8cf-32a46f7aedea a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "dbkey"^^xsd:string . - -id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 ; - prov:pairKey "targets"^^xsd:string . - -id:0ce829aa-f4ff-4f70-804d-09e05aa7a764 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:86fce97c-a524-4a88-a6fb-cf26b95536d2 ; - prov:pairKey "to_posix_lines"^^xsd:string . - -id:0f92ffd8-540e-4bd6-8f6c-3c2d3df4f995 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:0ce5a422-abcb-4f41-a191-0a6068e14574 ; - prov:pairKey "values"^^xsd:string . - -id:0fd972f6-10e7-42ee-a514-02ed749f9494 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:100daec7-1e65-4bc5-814b-622b8d197b78, - id:578fa382-6aec-49cf-a1ee-b3f65cc63dc0, - id:a465c657-53e0-49bf-a7b0-665b53baafbf ; - prov:hadMember , - id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59, - id:7225c876-9def-4725-8512-f1e8cedf1d78 . - -id:100daec7-1e65-4bc5-814b-622b8d197b78 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:7225c876-9def-4725-8512-f1e8cedf1d78 ; - prov:pairKey "targets"^^xsd:string . - -id:11a7af4f-7df4-4a99-ba83-6d0418b6f7df a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . - -id:1605ad9c-1b56-4055-a8d0-866f49da1687 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:f4d07c61-fb2b-42eb-a7c5-1820900166f3 ; - prov:pairKey "__index__"^^xsd:string . - -id:1c90cc92-4948-4b69-a163-f63e41891f7a a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:0592876b-ce23-4b6a-a8cf-32a46f7aedea, - id:29b40ddc-e592-4aa9-989f-ed4ac9be59af, - id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38, - id:3e26cc6f-1f3b-438d-ada9-a55bead88b03, - id:587e2872-6ae3-4716-b99e-12c5db1f8e56, - id:5ab39f26-7656-40f1-826f-38f40ed09f10, - id:8232048b-b457-45cb-932e-a5cf8f8be6e1, - id:912f104e-1517-492e-abe3-f931fe47438b, - id:b1aad576-0af0-43c0-948d-df79e52df6b7, - id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103, - id:ed8aaa9a-567f-4893-b432-fa6e49547650 ; - prov:hadMember , - , - data:auto, - data:dataset2.txt, - data:path, - , - id:03827a8b-50a4-463b-876a-742652bb3049, - id:16597142-0745-4b4c-80c7-5755b2d087a7, - id:512093ee-9853-484f-9a93-aea928098062, - id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b, - id:cdcc006a-91e4-4f29-8c14-1f91eef044dd . - -id:1d62001e-4526-468c-b34a-ef88dcc11ac3 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:0f92ffd8-540e-4bd6-8f6c-3c2d3df4f995, - id:838e9760-cb17-4896-9c13-184164aa0c08 ; - prov:hadMember , - id:0ce5a422-abcb-4f41-a191-0a6068e14574 . - -id:202eb0cc-f08e-4946-be23-0b6f195a0997 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:34422e4d-9f35-46dc-bbf6-f819ae20a341 . - -id:2119440c-63be-46a9-bbb7-2b104033b8f2 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:2524d3d3b68ad39a . - -id:2301b8b5-528f-4802-bd81-a4a3ca8534f4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "file_data"^^xsd:string . - -id:2326e0c6-2608-432a-934a-dc26b09dabcd a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c ; - prov:pairKey "__index__"^^xsd:string . - -id:2605025b-6018-4473-b1f2-10ffa81c469a a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:28f039db-5706-4cf6-96ce-321fbfd994f8 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:fd39387a-478e-4380-8597-2a544a032b8c ; - prov:pairKey "auto_decompress"^^xsd:string . - -id:29b40ddc-e592-4aa9-989f-ed4ac9be59af a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:path ; - prov:pairKey "src"^^xsd:string . - -id:2e397e93-13e6-4ce4-bced-ed3008a1b0db a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:2e7982bf-5cce-44ac-9547-a552c8964d5a a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:311ea826-fd60-4dc1-a729-af0412613824 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:hda ; - prov:pairKey "src"^^xsd:string . - -id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:34422e4d-9f35-46dc-bbf6-f819ae20a341 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:86e5e11c-8ad1-4659-8fc4-85b4c2b57230, - id:a5be47a1-5d66-4f63-b71e-f7eacb04da10, - id:da1f3881-ca92-447f-b7fd-992e43d9536c ; - prov:hadMember , - , - id:6d83fa63-70b3-4a8d-9234-8e9f01d8e89a . - -id:34e943f0-5027-47b0-ba7b-05fca46da136 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885, - id:a15754e6-26b6-4269-96b6-7d35515d1c02, - id:e25dce0d-bf63-414f-a0cd-2663e7a44d50 ; - prov:hadMember , - id:074d9f95-5294-4f33-98a4-a37b8ce802cb, - id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 . - -id:36c37981-8a3c-45e8-82fb-1b367dd30899 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:37923bc7-fd48-4521-98e4-19a33c90b663 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:fd7fec473f1e6c6b ; - prov:pairKey "id"^^xsd:string . - -id:3e26cc6f-1f3b-438d-ada9-a55bead88b03 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:512093ee-9853-484f-9a93-aea928098062 ; - prov:pairKey "to_posix_lines"^^xsd:string . - -id:450f4c3b-e384-42b0-8090-47cc2e4691fb a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:2e789aae2475b7da ; - prov:pairKey "id"^^xsd:string . - -id:45cbe10d-9998-43f0-910f-646eb2c4dbca a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:dataset1.txt ; - prov:pairKey "name"^^xsd:string . - -id:4cea125d-b4d1-454b-982e-6bb7b393022e a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "@id"^^xsd:string . - -id:578fa382-6aec-49cf-a1ee-b3f65cc63dc0 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59 ; - prov:pairKey "check_content"^^xsd:string . - -id:587e2872-6ae3-4716-b99e-12c5db1f8e56 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b ; - prov:pairKey "hashes"^^xsd:string . - -id:5ab39f26-7656-40f1-826f-38f40ed09f10 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:auto ; - prov:pairKey "ext"^^xsd:string . - -id:60e283d2-d89f-4235-8d61-2600cb5717c4 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:3d532d55-2434-4449-9fd3-aae8eca62c1b ; - prov:pairKey "input2"^^xsd:string . - -id:633b83e5-3fa9-41be-b2e4-52381339221a a prov:Entity, - prov:KeyEntityPair ; - 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prov:pairEntity id:e46be7d4-c0c3-489f-86dd-0c8148d86858 ; - prov:pairKey "destination"^^xsd:string . - -id:aab81666-8ccd-45a7-99e8-b4519ce85496 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:4304771d-432a-48d3-b461-e84b2972ee0a ; - prov:pairKey "destination"^^xsd:string . - -id:af880c02-79fa-4624-a45c-8f0277838663 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:fd7fec473f1e6c6b . - -id:b1aad576-0af0-43c0-948d-df79e52df6b7 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:16597142-0745-4b4c-80c7-5755b2d087a7 ; - prov:pairKey "purge_source"^^xsd:string . - -id:b468ef66-ed86-4002-acd9-32c459e7f565 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:5605777b-6f2c-46cb-a64a-189695ee3693 ; - prov:pairKey "object_id"^^xsd:string . - -id:b4f8420d-99cf-4b6a-bd7f-7ffb549e16c9 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity ; - prov:pairKey "path"^^xsd:string . - -id:b785b0a5-c798-49f4-b1a1-8be87a4bda8b a prov:Entity, - prov:KeyEntityPair ; - 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prov:pairKey "@id"^^xsd:string . - -id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity data:dataset2.txt ; - prov:pairKey "name"^^xsd:string . - -id:e66c4859-3380-4705-b3bb-2c650dfb7888 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:2326e0c6-2608-432a-934a-dc26b09dabcd, - id:60e283d2-d89f-4235-8d61-2600cb5717c4, - id:651a06c8-c920-42d6-98ca-71dcd610322f ; - prov:hadMember , - id:3d532d55-2434-4449-9fd3-aae8eca62c1b, - id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c . - -id:e84e01b6-0126-4b79-90d5-99d22e8dde7c a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:040d2761-5df7-4905-a289-3fed059729f3 ; - prov:pairKey "auto_decompress"^^xsd:string . - -id:e88d7b49-c96b-4e54-92f2-410aa9268df2 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember data:2e789aae2475b7da . - -id:e9693b34-04fb-4b31-a78c-7d089fd6558b a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - 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id:ca085eb3-7628-4fd6-98be-09f5a23547b9, - id:f9c2956e-46cf-4b27-bc2a-2c4ae74dc704, - id:fa1a58d9-9489-4cc8-9f75-0fe047e1d970 ; - prov:hadMember , - , - data:auto, - data:dataset1.txt, - data:path, - , - id:5605777b-6f2c-46cb-a64a-189695ee3693, - id:86fce97c-a524-4a88-a6fb-cf26b95536d2, - id:c4933233-a84f-4ce0-840e-e5577b27c96c, - id:de67df28-2fa8-46d5-901f-9b72a3ff6949, - id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 . - -id:f89aaeef-0313-42af-b87e-7b519d494be7 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:9d27fd2e-c728-420a-86ba-fc92df98dd6c ; - prov:pairKey "elements"^^xsd:string . - -id:f9c2956e-46cf-4b27-bc2a-2c4ae74dc704 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:de67df28-2fa8-46d5-901f-9b72a3ff6949 ; - prov:pairKey "hashes"^^xsd:string . - -id:fa1a58d9-9489-4cc8-9f75-0fe047e1d970 a prov:Entity, - prov:KeyEntityPair ; - prov:pairEntity id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 ; - prov:pairKey "in_place"^^xsd:string . - -id:fe8b9a54-02f9-40d5-b3be-d14352b6b76b a wfprov:Artifact, - 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prov:value "urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:34422e4d-9f35-46dc-bbf6-f819ae20a341"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:3d532d55-2434-4449-9fd3-aae8eca62c1b"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:4304771d-432a-48d3-b461-e84b2972ee0a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:6c9b6d77-2863-4fe0-a703-5ff0d53a7504"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:8c884aa2-99c2-4588-9d49-eff12441e6c0"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:de072b7b-d692-4453-9af4-9975a3742a44"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:e66c4859-3380-4705-b3bb-2c650dfb7888"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "urn:uuid:f149acac-0ee5-4588-887f-d7ee04e430cb"^^xsd:string . - -id:03827a8b-50a4-463b-876a-742652bb3049 a prov:Entity ; - prov:value false . - -id:040d2761-5df7-4905-a289-3fed059729f3 a prov:Entity ; - prov:value false . - -id:074d9f95-5294-4f33-98a4-a37b8ce802cb a prov:Entity ; - prov:value true . - -id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59 a prov:Entity ; - prov:value true . - -id:0ce5a422-abcb-4f41-a191-0a6068e14574 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:d34c2c77-9bf0-4850-9f4c-3929c61d4266 . - -id:16597142-0745-4b4c-80c7-5755b2d087a7 a prov:Entity ; - prov:value false . - -id:2a48c6c5-b7ba-482e-808e-b07d48c0bec7 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:f149acac-0ee5-4588-887f-d7ee04e430cb . - -id:3d532d55-2434-4449-9fd3-aae8eca62c1b a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:2605025b-6018-4473-b1f2-10ffa81c469a, - id:d530cc8c-b67b-4e1d-8992-bca7f8454520 ; - prov:hadMember , - id:e1cda342-b856-423e-aa58-5485505a0d28 . - -id:4304771d-432a-48d3-b461-e84b2972ee0a a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:2e7982bf-5cce-44ac-9547-a552c8964d5a, - id:b785b0a5-c798-49f4-b1a1-8be87a4bda8b ; - prov:hadMember data:hdas, - . - -id:512093ee-9853-484f-9a93-aea928098062 a prov:Entity ; - prov:value true . - -id:5605777b-6f2c-46cb-a64a-189695ee3693 a prov:Entity ; - prov:value "155707"^^xsd:int . - -id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c a prov:Entity ; - prov:value "0"^^xsd:int . - -id:63446d8e-78fe-4025-a69a-c5ca6f8a0bea a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114 . - -id:6d83fa63-70b3-4a8d-9234-8e9f01d8e89a a prov:Entity ; - prov:value "0"^^xsd:int . - -id:7225c876-9def-4725-8512-f1e8cedf1d78 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:6c9b6d77-2863-4fe0-a703-5ff0d53a7504 . - -id:86fce97c-a524-4a88-a6fb-cf26b95536d2 a prov:Entity ; - prov:value true . - -id:9d27fd2e-c728-420a-86ba-fc92df98dd6c a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:1c90cc92-4948-4b69-a163-f63e41891f7a . - -id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b a wfprov:Artifact, - prov:Collection, - prov:EmptyCollection, - prov:Entity . - -id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:8d86a2e6-482b-41b3-ac34-acc0b74014fe . - -id:c4933233-a84f-4ce0-840e-e5577b27c96c a prov:Entity ; - prov:value false . - -id:cdcc006a-91e4-4f29-8c14-1f91eef044dd a prov:Entity ; - prov:value "155708"^^xsd:int . - -id:de67df28-2fa8-46d5-901f-9b72a3ff6949 a wfprov:Artifact, - prov:Collection, - prov:EmptyCollection, - prov:Entity . - -id:e1cda342-b856-423e-aa58-5485505a0d28 a wfprov:Artifact, - prov:Collection, - prov:Entity ; - prov:hadMember id:de072b7b-d692-4453-9af4-9975a3742a44 . - -id:e46be7d4-c0c3-489f-86dd-0c8148d86858 a wfprov:Artifact, - prov:Collection, - prov:Dictionary, - prov:Entity ; - prov:hadDictionaryMember id:7b40bdfc-aacc-4947-a8d8-d13db0419365, - id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6 ; - prov:hadMember data:hdas, - . - -id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 a prov:Entity ; - prov:value false . - -id:f4d07c61-fb2b-42eb-a7c5-1820900166f3 a prov:Entity ; - prov:value "0"^^xsd:int . - -id:fc4a126f-25bd-4d12-bde7-c41dadf135c6 a prov:Entity ; - prov:value "1"^^xsd:int . - -id:fd39387a-478e-4380-8597-2a544a032b8c a prov:Entity ; - prov:value false . - -data:2e789aae2475b7da a wfprov:Artifact, - prov:Entity ; - prov:value "2e789aae2475b7da"^^xsd:string . - -data:7ca3de8f49293d1a a wfprov:Artifact, - prov:Entity ; - prov:value "7ca3de8f49293d1a"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2"^^xsd:string . - - a wfprov:Artifact, - prov:Entity ; - prov:value "/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a"^^xsd:string . - -data:1 a wfprov:Artifact, - prov:Entity ; - prov:value "1"^^xsd:string . - -data:auto a wfprov:Artifact, - prov:Entity ; - prov:value "auto"^^xsd:string . - -data:fd7fec473f1e6c6b a wfprov:Artifact, - prov:Entity ; - prov:value "fd7fec473f1e6c6b"^^xsd:string . - -data:hdas a wfprov:Artifact, - prov:Entity ; - prov:value "hdas"^^xsd:string . - -data:path a wfprov:Artifact, - prov:Entity ; - prov:value "path"^^xsd:string . - -id:b02505bb-6b95-4e97-8043-d0823b00b7f4 a wfprov:WorkflowRun, - prov:Activity ; - rdfs:label "Run of galaxy workflow"^^xsd:string ; - prov:qualifiedAssociation [ a prov:Association ; - prov:hadPlan wf:main ] ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-04-04T16:59:09.795971"^^xsd:dateTime ; - prov:hadActivity id:8124e339-e638-4fc3-b421-6367e3682c50 ] ; - prov:startedAtTime "2022-04-04T16:59:09.795894"^^xsd:dateTime ; - prov:wasAssociatedWith id:8124e339-e638-4fc3-b421-6367e3682c50 . - - a wfprov:Artifact, - prov:Entity ; - prov:value "?"^^xsd:string . - -data:hda a wfprov:Artifact, - prov:Entity ; - prov:value "hda"^^xsd:string . - -id:8124e339-e638-4fc3-b421-6367e3682c50 a wfprov:WorkflowEngine, - prov:Agent, - prov:SoftwareAgent ; - rdfs:label "galaxy_version_placeholder"^^xsd:string ; - prov:qualifiedStart [ a prov:Start ; - prov:atTime "2022-04-04T16:59:09.795855"^^xsd:dateTime ; - prov:hadActivity id:027f7717-78d8-4f9a-a887-87813339b23e ] . - diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml b/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml deleted file mode 100644 index 6f14c1e6..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/provenance/ga_export.cwlprov.xml +++ /dev/null @@ -1,1447 +0,0 @@ - - - - - galaxy_version_placeholder - wfprov:WorkflowEngine - - - - - 2022-04-04T16:59:09.795855 - - - 2022-04-04T16:59:09.795894 - Run of galaxy workflow - wfprov:WorkflowRun - - - - - - - - - - 2022-04-04T16:59:09.795971 - - - 2021-06-23T10:20:22.770291 - 2021-06-23T10:20:42.041319 - Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:20:22.770291 - - - wfprov:Artifact - 2524d3d3b68ad39a - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.796590 - wf:main/__DATA_FETCH__/output0 - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.796656 - wf:main/__DATA_FETCH__/file_count - - - prov:Dictionary - wfprov:Artifact - id:00e0f888-71d8-49f9-ba39-dcaed5a91c56 - id:1605ad9c-1b56-4055-a8d0-866f49da1687 - id:2301b8b5-528f-4802-bd81-a4a3ca8534f4 - - - 0 - - - - - - - prov:KeyEntityPair - id:f4d07c61-fb2b-42eb-a7c5-1820900166f3 - __index__ - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - file_data - - - wfprov:Artifact - urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b - - - - - - - prov:KeyEntityPair - data:urn:uuid:e9693b34-04fb-4b31-a78c-7d089fd6558b - @id - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.797234 - wf:main/__DATA_FETCH__/files - - - wfprov:Artifact - - - - - - 2022-04-04T16:59:09.797298 - wf:main/__DATA_FETCH__/paramfile - - - prov:Dictionary - wfprov:Artifact - id:05eb4f15-1d7f-4b6f-8bc6-5919f1254885 - id:a15754e6-26b6-4269-96b6-7d35515d1c02 - id:e25dce0d-bf63-414f-a0cd-2663e7a44d50 - - - prov:Dictionary - wfprov:Artifact - id:000e294f-576c-469b-8965-4e279bebc880 - id:a6d080a6-7c60-46f2-85c8-2519f4d803ea - id:e84e01b6-0126-4b79-90d5-99d22e8dde7c - id:f89aaeef-0313-42af-b87e-7b519d494be7 - - - prov:Dictionary - wfprov:Artifact - id:7b40bdfc-aacc-4947-a8d8-d13db0419365 - id:833d1ed9-d6f4-4afa-b577-de6314c3a6e6 - - - wfprov:Artifact - hdas - - - - - - - prov:KeyEntityPair - data:hdas - type - - - wfprov:Artifact - urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858 - - - - - - - prov:KeyEntityPair - data:urn:uuid:e46be7d4-c0c3-489f-86dd-0c8148d86858 - @id - - - - - - - prov:KeyEntityPair - id:e46be7d4-c0c3-489f-86dd-0c8148d86858 - destination - - - prov:Dictionary - wfprov:Artifact - id:0592876b-ce23-4b6a-a8cf-32a46f7aedea - id:29b40ddc-e592-4aa9-989f-ed4ac9be59af - id:316b0cad-c5b8-405a-8452-d3d1bc7c3d38 - id:3e26cc6f-1f3b-438d-ada9-a55bead88b03 - id:587e2872-6ae3-4716-b99e-12c5db1f8e56 - id:5ab39f26-7656-40f1-826f-38f40ed09f10 - id:8232048b-b457-45cb-932e-a5cf8f8be6e1 - id:912f104e-1517-492e-abe3-f931fe47438b - id:b1aad576-0af0-43c0-948d-df79e52df6b7 - id:e63a6a8f-d53e-49da-a9f0-cb2bbe2f5103 - id:ed8aaa9a-567f-4893-b432-fa6e49547650 - - - wfprov:Artifact - auto - - - - - - - prov:KeyEntityPair - data:auto - ext - - - wfprov:Artifact - ? - - - - - - - prov:KeyEntityPair - data:? - dbkey - - - true - - - - - - - prov:KeyEntityPair - id:512093ee-9853-484f-9a93-aea928098062 - to_posix_lines - - - wfprov:Artifact - path - - - - - - - prov:KeyEntityPair - data:path - src - - - wfprov:Artifact - dataset2.txt - - - - - - - prov:KeyEntityPair - data:dataset2.txt - name - - - prov:EmptyCollection - wfprov:Artifact - - - - - - - prov:KeyEntityPair - id:b61cfd8e-28b9-4e95-a4dc-bdc9be3fb39b - hashes - - - false - - - - - - - prov:KeyEntityPair - id:03827a8b-50a4-463b-876a-742652bb3049 - in_place - - - false - - - - - - - prov:KeyEntityPair - id:16597142-0745-4b4c-80c7-5755b2d087a7 - purge_source - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_85x51jn2 - path - - - 155708 - - - - - - - prov:KeyEntityPair - id:cdcc006a-91e4-4f29-8c14-1f91eef044dd - object_id - - - wfprov:Artifact - urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a - - - - - - - prov:KeyEntityPair - data:urn:uuid:1c90cc92-4948-4b69-a163-f63e41891f7a - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:9d27fd2e-c728-420a-86ba-fc92df98dd6c - elements - - - false - - - - - - - prov:KeyEntityPair - id:040d2761-5df7-4905-a289-3fed059729f3 - auto_decompress - - - wfprov:Artifact - urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe - - - - - - - prov:KeyEntityPair - data:urn:uuid:8d86a2e6-482b-41b3-ac34-acc0b74014fe - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:c3e536ce-dbe1-4fe9-ad9e-41f3e5b2b066 - targets - - - true - - - - - - - prov:KeyEntityPair - id:074d9f95-5294-4f33-98a4-a37b8ce802cb - check_content - - - wfprov:Artifact - urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136 - - - - - - - prov:KeyEntityPair - data:urn:uuid:34e943f0-5027-47b0-ba7b-05fca46da136 - @id - - - - - 2022-04-04T16:59:09.799177 - wf:main/__DATA_FETCH__/request_json - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.799249 - wf:main/__DATA_FETCH__/request_version - - - 2021-06-23T10:20:00.981702 - 2021-06-23T10:20:22.202678 - Run of ga_export/jobs_attrs.txt#__DATA_FETCH__ - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:20:00.981702 - - - wfprov:Artifact - 7c1d8e3101dbcdba - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.799938 - wf:main/__DATA_FETCH__/output0 - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.800010 - wf:main/__DATA_FETCH__/file_count - - - prov:Dictionary - wfprov:Artifact - id:86e5e11c-8ad1-4659-8fc4-85b4c2b57230 - id:a5be47a1-5d66-4f63-b71e-f7eacb04da10 - id:da1f3881-ca92-447f-b7fd-992e43d9536c - - - 0 - - - - - - - prov:KeyEntityPair - id:6d83fa63-70b3-4a8d-9234-8e9f01d8e89a - __index__ - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - file_data - - - wfprov:Artifact - urn:uuid:34422e4d-9f35-46dc-bbf6-f819ae20a341 - - - - - - - prov:KeyEntityPair - data:urn:uuid:34422e4d-9f35-46dc-bbf6-f819ae20a341 - @id - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.800503 - wf:main/__DATA_FETCH__/files - - - wfprov:Artifact - - - - - - 2022-04-04T16:59:09.800579 - wf:main/__DATA_FETCH__/paramfile - - - prov:Dictionary - wfprov:Artifact - id:100daec7-1e65-4bc5-814b-622b8d197b78 - id:578fa382-6aec-49cf-a1ee-b3f65cc63dc0 - id:a465c657-53e0-49bf-a7b0-665b53baafbf - - - prov:Dictionary - wfprov:Artifact - id:02094080-ba1e-458f-8b75-5741f7f9a72b - id:28f039db-5706-4cf6-96ce-321fbfd994f8 - id:aab81666-8ccd-45a7-99e8-b4519ce85496 - id:c5939a58-b121-40a2-b972-7f2fb66a5f03 - - - prov:Dictionary - wfprov:Artifact - id:2e7982bf-5cce-44ac-9547-a552c8964d5a - id:b785b0a5-c798-49f4-b1a1-8be87a4bda8b - - - wfprov:Artifact - hdas - - - - - - - prov:KeyEntityPair - data:hdas - type - - - wfprov:Artifact - urn:uuid:4304771d-432a-48d3-b461-e84b2972ee0a - - - - - - - prov:KeyEntityPair - data:urn:uuid:4304771d-432a-48d3-b461-e84b2972ee0a - @id - - - - - - - prov:KeyEntityPair - id:4304771d-432a-48d3-b461-e84b2972ee0a - destination - - - prov:Dictionary - wfprov:Artifact - id:0ce829aa-f4ff-4f70-804d-09e05aa7a764 - id:45cbe10d-9998-43f0-910f-646eb2c4dbca - id:4cea125d-b4d1-454b-982e-6bb7b393022e - id:7cd3eabc-b445-4a44-baea-fade541b56d7 - id:80c39113-024d-45a2-9e33-e8216a8fc6d7 - id:b468ef66-ed86-4002-acd9-32c459e7f565 - id:b4f8420d-99cf-4b6a-bd7f-7ffb549e16c9 - id:bb92fa6f-500c-493b-9107-5d9837a294ba - id:ca085eb3-7628-4fd6-98be-09f5a23547b9 - id:f9c2956e-46cf-4b27-bc2a-2c4ae74dc704 - id:fa1a58d9-9489-4cc8-9f75-0fe047e1d970 - - - wfprov:Artifact - auto - - - - - - - prov:KeyEntityPair - data:auto - ext - - - wfprov:Artifact - ? - - - - - - - prov:KeyEntityPair - data:? - dbkey - - - true - - - - - - - prov:KeyEntityPair - id:86fce97c-a524-4a88-a6fb-cf26b95536d2 - to_posix_lines - - - wfprov:Artifact - path - - - - - - - prov:KeyEntityPair - data:path - src - - - wfprov:Artifact - dataset1.txt - - - - - - - prov:KeyEntityPair - data:dataset1.txt - name - - - prov:EmptyCollection - wfprov:Artifact - - - - - - - prov:KeyEntityPair - id:de67df28-2fa8-46d5-901f-9b72a3ff6949 - hashes - - - false - - - - - - - prov:KeyEntityPair - id:ea67e5d5-59fe-40db-9000-0610ab97a7e7 - in_place - - - false - - - - - - - prov:KeyEntityPair - id:c4933233-a84f-4ce0-840e-e5577b27c96c - purge_source - - - wfprov:Artifact - /srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - - - - - - - prov:KeyEntityPair - data:/srv/galaxy/shared/etc/tmpdir/tmp/upload_file_data_asmrlj6a - path - - - 155707 - - - - - - - prov:KeyEntityPair - id:5605777b-6f2c-46cb-a64a-189695ee3693 - object_id - - - wfprov:Artifact - urn:uuid:f149acac-0ee5-4588-887f-d7ee04e430cb - - - - - - - prov:KeyEntityPair - data:urn:uuid:f149acac-0ee5-4588-887f-d7ee04e430cb - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:2a48c6c5-b7ba-482e-808e-b07d48c0bec7 - elements - - - false - - - - - - - prov:KeyEntityPair - id:fd39387a-478e-4380-8597-2a544a032b8c - auto_decompress - - - wfprov:Artifact - urn:uuid:6c9b6d77-2863-4fe0-a703-5ff0d53a7504 - - - - - - - prov:KeyEntityPair - data:urn:uuid:6c9b6d77-2863-4fe0-a703-5ff0d53a7504 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:7225c876-9def-4725-8512-f1e8cedf1d78 - targets - - - true - - - - - - - prov:KeyEntityPair - id:0a43a146-d6f8-4566-b1bc-7cd1116f2d59 - check_content - - - wfprov:Artifact - urn:uuid:0fd972f6-10e7-42ee-a514-02ed749f9494 - - - - - - - prov:KeyEntityPair - data:urn:uuid:0fd972f6-10e7-42ee-a514-02ed749f9494 - @id - - - - - 2022-04-04T16:59:09.802972 - wf:main/__DATA_FETCH__/request_json - - - wfprov:Artifact - 1 - - - - - 2022-04-04T16:59:09.803053 - wf:main/__DATA_FETCH__/request_version - - - 2021-06-23T10:46:28.351123 - 2021-06-23T10:46:44.738703 - Run of ga_export/jobs_attrs.txt#cat1 - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:46:28.351123 - - - wfprov:Artifact - 7ca3de8f49293d1a - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.803689 - wf:main/cat1/input1 - - - wfprov:Artifact - 2e789aae2475b7da - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.803812 - wf:main/cat1/queries_0_input2 - - - wfprov:Artifact - fd7fec473f1e6c6b - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.803927 - wf:main/cat1/out_file1 - - - wfprov:Artifact - txt - - - - - 2022-04-04T16:59:09.803988 - wf:main/cat1/__input_ext - - - wfprov:Artifact - 42f21c0ad41011eb87defa163eba836f - - - - - 2022-04-04T16:59:09.804048 - wf:main/cat1/__workflow_invocation_uuid__ - - - wfprov:Artifact - /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - - - - - 2022-04-04T16:59:09.804112 - wf:main/cat1/chromInfo - - - wfprov:Artifact - ? - - - - - 2022-04-04T16:59:09.804169 - wf:main/cat1/dbkey - - - prov:Dictionary - wfprov:Artifact - id:2e397e93-13e6-4ce4-bced-ed3008a1b0db - id:633b83e5-3fa9-41be-b2e4-52381339221a - - - prov:Dictionary - wfprov:Artifact - id:11a7af4f-7df4-4a99-ba83-6d0418b6f7df - id:67c9330c-aef5-4d94-ad77-f38d191198a2 - id:7cbde64f-8934-42ab-af87-2044c3e092ce - - - wfprov:Artifact - 7ca3de8f49293d1a - - - - - - - prov:KeyEntityPair - data:7ca3de8f49293d1a - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114 - - - - - - - prov:KeyEntityPair - data:urn:uuid:9ee5b3b1-dbd7-4bf2-b7c9-ac8a1c6b1114 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:63446d8e-78fe-4025-a69a-c5ca6f8a0bea - values - - - wfprov:Artifact - urn:uuid:8c884aa2-99c2-4588-9d49-eff12441e6c0 - - - - - - - prov:KeyEntityPair - data:urn:uuid:8c884aa2-99c2-4588-9d49-eff12441e6c0 - @id - - - - - 2022-04-04T16:59:09.804768 - wf:main/cat1/input1 - - - prov:Dictionary - wfprov:Artifact - id:2326e0c6-2608-432a-934a-dc26b09dabcd - id:60e283d2-d89f-4235-8d61-2600cb5717c4 - id:651a06c8-c920-42d6-98ca-71dcd610322f - - - 0 - - - - - - - prov:KeyEntityPair - id:5fcce4fe-5161-4161-8d0a-cbdb1b874e7c - __index__ - - - prov:Dictionary - wfprov:Artifact - id:2605025b-6018-4473-b1f2-10ffa81c469a - id:d530cc8c-b67b-4e1d-8992-bca7f8454520 - - - prov:Dictionary - wfprov:Artifact - id:450f4c3b-e384-42b0-8090-47cc2e4691fb - id:708a0ca4-2972-467e-9443-52a37e9d0bf1 - id:eedcc56e-086a-42dc-a5d4-212bee28b594 - - - wfprov:Artifact - 2e789aae2475b7da - - - - - - - prov:KeyEntityPair - data:2e789aae2475b7da - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:de072b7b-d692-4453-9af4-9975a3742a44 - - - - - - - prov:KeyEntityPair - data:urn:uuid:de072b7b-d692-4453-9af4-9975a3742a44 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:e1cda342-b856-423e-aa58-5485505a0d28 - values - - - wfprov:Artifact - urn:uuid:3d532d55-2434-4449-9fd3-aae8eca62c1b - - - - - - - prov:KeyEntityPair - data:urn:uuid:3d532d55-2434-4449-9fd3-aae8eca62c1b - @id - - - - - - - prov:KeyEntityPair - id:3d532d55-2434-4449-9fd3-aae8eca62c1b - input2 - - - wfprov:Artifact - urn:uuid:e66c4859-3380-4705-b3bb-2c650dfb7888 - - - - - - - prov:KeyEntityPair - data:urn:uuid:e66c4859-3380-4705-b3bb-2c650dfb7888 - @id - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.805613 - wf:main/cat1/queries - - - 2021-06-23T10:46:28.526901 - 2021-06-23T10:47:04.837750 - Run of ga_export/jobs_attrs.txt#random_lines1 - wfprov:ProcessRun - - - - - - - - - - 2021-06-23T10:46:28.526901 - - - wfprov:Artifact - fd7fec473f1e6c6b - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.806121 - wf:main/random_lines1/input - - - wfprov:Artifact - 775bc9b3c1750167 - - - wfprov:Artifact - - - - - - - - - 2022-04-04T16:59:09.806236 - wf:main/random_lines1/out_file1 - - - wfprov:Artifact - txt - - - - - 2022-04-04T16:59:09.806293 - wf:main/random_lines1/__input_ext - - - wfprov:Artifact - 42f21c0ad41011eb87defa163eba836f - - - - - 2022-04-04T16:59:09.806350 - wf:main/random_lines1/__workflow_invocation_uuid__ - - - wfprov:Artifact - /srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len - - - - - 2022-04-04T16:59:09.806405 - wf:main/random_lines1/chromInfo - - - wfprov:Artifact - ? - - - - - 2022-04-04T16:59:09.806458 - wf:main/random_lines1/dbkey - - - prov:Dictionary - wfprov:Artifact - id:0f92ffd8-540e-4bd6-8f6c-3c2d3df4f995 - id:838e9760-cb17-4896-9c13-184164aa0c08 - - - prov:Dictionary - wfprov:Artifact - id:311ea826-fd60-4dc1-a729-af0412613824 - id:36c37981-8a3c-45e8-82fb-1b367dd30899 - id:37923bc7-fd48-4521-98e4-19a33c90b663 - - - wfprov:Artifact - fd7fec473f1e6c6b - - - - - - - prov:KeyEntityPair - data:fd7fec473f1e6c6b - id - - - wfprov:Artifact - hda - - - - - - - prov:KeyEntityPair - data:hda - src - - - wfprov:Artifact - urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266 - - - - - - - prov:KeyEntityPair - data:urn:uuid:d34c2c77-9bf0-4850-9f4c-3929c61d4266 - @id - - - wfprov:Artifact - - - - - - - - - - - prov:KeyEntityPair - id:0ce5a422-abcb-4f41-a191-0a6068e14574 - values - - - wfprov:Artifact - urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3 - - - - - - - prov:KeyEntityPair - data:urn:uuid:1d62001e-4526-468c-b34a-ef88dcc11ac3 - @id - - - - - 2022-04-04T16:59:09.806986 - wf:main/random_lines1/input - - - wfprov:Artifact - 3 - - - - - 2022-04-04T16:59:09.807046 - wf:main/random_lines1/num_lines - - - prov:Dictionary - wfprov:Artifact - id:0080be3e-2011-44c6-a391-3e151894b43e - id:6de1750c-1612-4740-87a3-7d000e40c4b2 - id:9daa05b2-1eaf-4e8b-9c59-48967c5ffc91 - id:d13aa4a9-9029-4a4a-959b-4e2a3bd0aa3d - - - 1 - - - - - - - prov:KeyEntityPair - id:fc4a126f-25bd-4d12-bde7-c41dadf135c6 - __current_case__ - - - wfprov:Artifact - 0 - - - - - - - prov:KeyEntityPair - data:0 - seed - - - wfprov:Artifact - set_seed - - - - - - - prov:KeyEntityPair - data:set_seed - seed_source_selector - - - wfprov:Artifact - urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2 - - - - - - - prov:KeyEntityPair - data:urn:uuid:8456e304-ef4f-4f40-a818-00b01407f6a2 - @id - - - - - 2022-04-04T16:59:09.807432 - wf:main/random_lines1/seed_source - - diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json b/test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json deleted file mode 100644 index ff5daa4f..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/ro-crate-metadata.json +++ /dev/null @@ -1,123 +0,0 @@ -{ - "@context": "https://w3id.org/ro/crate/1.1/context", - "@graph": [ - { - "@id": "./", - "@type": "Dataset", - "datePublished": "2022-04-04T14:59:09+00:00", - "hasPart": [ - { - "@id": "wf_definition.ga" - }, - { - "@id": "wf_definition.cwl" - }, - { - "@id": "provenance/" - }, - { - "@id": "dataset2.txt_1.txt" - }, - { - "@id": "Concatenate_datasets_on_data_2_and_data_1_3.txt" - }, - { - "@id": "tutorial_output.txt_4.txt" - }, - { - "@id": "dataset1.txt_2.txt" - } - ], - "mainEntity": { - "@id": "wf_definition.ga" - } - }, - { - "@id": "ro-crate-metadata.json", - "@type": "CreativeWork", - "about": { - "@id": "./" - }, - "conformsTo": [ - { - "@id": "https://w3id.org/ro/crate/1.1" - }, - { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" - } - ] - }, - { - "@id": "wf_definition.ga", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], - "name": "wf_definition", - "programmingLanguage": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy" - }, - "subjectOf": { - "@id": "wf_definition.cwl" - } - }, - { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate#galaxy", - "@type": "ComputerLanguage", - "identifier": { - "@id": "https://galaxyproject.org/" - }, - "name": "Galaxy", - "url": { - "@id": "https://galaxyproject.org/" - }, - "version": "21.09" - }, - { - "@id": "wf_definition.cwl", - "@type": [ - "File", - "SoftwareSourceCode", - "HowTo" - ], - "name": "wf_definition", - "programmingLanguage": { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl" - } - }, - { - "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl", - "@type": "ComputerLanguage", - "alternateName": "CWL", - "identifier": { - "@id": "https://w3id.org/cwl/1.2/" - }, - "name": "Common Workflow Language", - "url": { - "@id": "https://www.commonwl.org/" - }, - "version": "1.2" - }, - { - "@id": "provenance/", - "@type": "Dataset" - }, - { - "@id": "dataset2.txt_1.txt", - "@type": "File" - }, - { - "@id": "Concatenate_datasets_on_data_2_and_data_1_3.txt", - "@type": "File" - }, - { - "@id": "tutorial_output.txt_4.txt", - "@type": "File" - }, - { - "@id": "dataset1.txt_2.txt", - "@type": "File" - } - ] -} \ No newline at end of file diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt b/test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt deleted file mode 100644 index f631dd54..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/tutorial_output.txt_4.txt +++ /dev/null @@ -1,3 +0,0 @@ -hello -universe! -world diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl b/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl deleted file mode 100644 index 8af43e5e..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.cwl +++ /dev/null @@ -1,50 +0,0 @@ -class: Workflow -cwlVersion: v1.2.0-dev2 -doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: Workflow - constructed from history ''Minimal-history''' -inputs: - dataset1_txt: - format: data - type: File - dataset2_txt: - format: data - type: File -outputs: {} -steps: - 2_Concatenate datasets: - in: - input1: dataset2_txt - queries_0|input2: dataset1_txt - out: - - out_file1 - run: - class: Operation - id: cat1 - inputs: - input1: - format: Any - type: File - queries_0|input2: - format: Any - type: File - outputs: - out_file1: - doc: input - type: File - 3_Select random lines: - in: - input: 2_Concatenate datasets/out_file1 - out: - - out_file1 - run: - class: Operation - id: random_lines1 - inputs: - input: - format: Any - type: File - outputs: - out_file1: - doc: input - type: File - diff --git a/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga b/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga deleted file mode 100644 index 28194ed4..00000000 --- a/test/test-data/test_ga_history_export/history_export_ro_crate/wf_definition.ga +++ /dev/null @@ -1,131 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "Workflow constructed from history 'Minimal-history'", - "steps": { - "0": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "dataset2.txt" - } - ], - "label": "dataset2.txt", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 10, - "top": 10 - }, - "tool_id": null, - "tool_state": "{\"optional\": false}", - "tool_version": null, - "type": "data_input", - "uuid": "8dfb1a60-ac90-4125-b1a4-c674a084bf37", - "workflow_outputs": [] - }, - "1": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "", - "name": "dataset1.txt" - } - ], - "label": "dataset1.txt", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 10, - "top": 130 - }, - "tool_id": null, - "tool_state": "{\"optional\": false}", - "tool_version": null, - "type": "data_input", - "uuid": "104d6198-2f2e-46f1-8006-1c594f1f091c", - "workflow_outputs": [] - }, - "2": { - "annotation": "", - "content_id": "cat1", - "errors": null, - "id": 2, - "input_connections": { - "input1": { - "id": 0, - "output_name": "output" - }, - "queries_0|input2": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Concatenate datasets", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 230, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "cat1", - "tool_state": "{\"__input_ext\": \"txt\", \"__workflow_invocation_uuid__\": \"42f21c0ad41011eb87defa163eba836f\", \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input1\": null, \"queries\": [{\"__index__\": 0, \"input2\": null}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0", - "type": "tool", - "uuid": "821567a8-1edd-4f35-9430-596fd6801ca1", - "workflow_outputs": [] - }, - "3": { - "annotation": "", - "content_id": "random_lines1", - "errors": null, - "id": 3, - "input_connections": { - "input": { - "id": 2, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "Select random lines", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 450, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "random_lines1", - "tool_state": "{\"__input_ext\": \"txt\", \"__workflow_invocation_uuid__\": \"42f21c0ad41011eb87defa163eba836f\", \"chromInfo\": \"/srv/galaxy/mutable-config/tool-data/shared/ucsc/chrom/?.len\", \"input\": null, \"num_lines\": \"3\", \"seed_source\": {\"seed_source_selector\": \"set_seed\", \"__current_case__\": 1, \"seed\": \"0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0.2", - "type": "tool", - "uuid": "a6b4dc53-9a0f-4a5c-9311-f9f03238f9dc", - "workflow_outputs": [] - } - }, - "tags": [], - "uuid": "de90339e-0497-49da-a1ce-f7e2dd3080c6", - "version": 0 -} \ No newline at end of file diff --git a/test/test_parse_ga_export.py b/test/test_parse_ga_export.py index 08120be1..96f7717e 100644 --- a/test/test_parse_ga_export.py +++ b/test/test_parse_ga_export.py @@ -18,7 +18,7 @@ def test_ga_history_loading(test_data_dir, tmpdir, helpers): jobs.append(job_attrs.attributes) assert isinstance(job_attrs, GalaxyJob) - # print(jobs[0]) + assert len(jobs) == 4 @@ -26,28 +26,14 @@ def test_ga_history_parsing(test_data_dir, tmpdir, helpers): export_dir = "test_ga_history_export" export_path = test_data_dir / export_dir / "history_export" prov_path = tmpdir / "provenance" - # prov_name = "ga_export.cwlprov" - # crate_path = test_data_dir / export_dir / "history_export_crate" - - # metadata_export = load_ga_history_export(export_path) prov = ProvenanceProfile(export_path, "PDG", "https://orcid.org/0000-0002-8940-4946") - # print(len(metadata_export['jobs_attrs'])) - # print(prov.document.serialize(format="rdf", rdf_format="turtle")) - # with open("test_prov.ttl","w") as provenance_file: - # prov.document.serialize(provenance_file,format="rdf", rdf_format="turtle") assert isinstance(prov, ProvenanceProfile) prov.finalize_prov_profile(out_path=prov_path) - # print(serialized_prov_docs.keys()) def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): - # wf_path = base_path + "example-history-export3.ga" - # dataset_path = base_path + "example-history-export3/datasets/" - # wfr_metadata_path = base_path + "example-history-export3" - # files_list = os.listdir(dataset_path) - # files_list = [dataset_path + f for f in files_list] export_dir = "test_ga_history_export" wfr_metadata_path = test_data_dir / export_dir / "history_export" @@ -57,7 +43,6 @@ def test_create_wf_run_ro_crate(test_data_dir, tmpdir, helpers): wf_id = 'wf_definition.ga' wf_path = test_data_dir / export_dir / wf_id - # wf_crate = roc_api.make_workflow_rocrate(wf_path, wf_type='Galaxy') wf_crate = roc_api.make_workflow_run_rocrate( workflow_path=wf_path, wfr_metadata_path=wfr_metadata_path, author=None, orcid=None, wf_type="Galaxy", include_files=files_list, prov_name="test_prov" diff --git a/tools/load_ga_export.py b/tools/load_ga_export.py index 1358c5ed..b5dca540 100644 --- a/tools/load_ga_export.py +++ b/tools/load_ga_export.py @@ -35,8 +35,8 @@ def parse_ga_jobs_attrs(self, job_attrs): if not isinstance(value, dict): self.attributes[key] = value else: - if len(value) == 0: - pass + if not value or len(value) == 0: + continue else: if "input" in key: self.attributes["inputs"].update(job_attrs[key]) @@ -45,9 +45,20 @@ def parse_ga_jobs_attrs(self, job_attrs): if "params" in key: tmp_dict = {} for k, v in job_attrs[key].items(): + if not v or len(v) == 0: + continue + try: + v = int(v) + except (TypeError, ValueError): + pass # it was a string, not an int. + # print(k, v) + # print(type(v)) + if "json" in k: v = json.loads(v) - tmp_dict[k] = str(v) + if isinstance(v, dict) or isinstance(v, list): + v = str(v) + tmp_dict[k] = v self.attributes["parameters"].update(tmp_dict) From 350433dfbab910aab5ecf697778fa7bb2d7e8767 Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 23 Jun 2022 15:27:14 +0200 Subject: [PATCH 19/27] example ro-crate notebook --- notebooks/ROcrate-example.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/ROcrate-example.ipynb b/notebooks/ROcrate-example.ipynb index ca290661..07b07352 100644 --- a/notebooks/ROcrate-example.ipynb +++ b/notebooks/ROcrate-example.ipynb @@ -151,7 +151,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.5" + "version": "3.9.10" }, "orig_nbformat": 4 }, From 73324f5a18b9dd94728d279a90e8c3957f46eac0 Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 23 Jun 2022 16:30:53 +0200 Subject: [PATCH 20/27] resolved more conflicts --- rocrate/rocrate.py | 78 ---------------------------------------------- rocrate/utils.py | 15 --------- 2 files changed, 93 deletions(-) diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py index 38a29f10..264e8948 100644 --- a/rocrate/rocrate.py +++ b/rocrate/rocrate.py @@ -46,7 +46,6 @@ from .utils import is_url, subclasses, get_norm_value, walk from .metadata import read_metadata, find_root_entity_id -from .provenance_profile import ProvenanceProfile def pick_type(json_entity, type_map, fallback=None): @@ -461,39 +460,6 @@ def add_workflow( workflow.subjectOf = cwl_workflow return workflow - def add_workflow_run( - self, source=None, dest_path=None, fetch_remote=False, validate_url=True, properties=None, - main=False, lang="cwl", lang_version=None, gen_cwl=False, cls=ComputationalWorkflow - ): - workflow_run = self.add(cls( - self, source=source, dest_path=dest_path, fetch_remote=fetch_remote, - validate_url=validate_url, properties=properties - )) - if isinstance(lang, ComputerLanguage): - assert lang.crate is self - else: - kwargs = {"version": lang_version} if lang_version else {} - lang = get_lang(self, lang, **kwargs) - self.add(lang) - lang_str = lang.id.rsplit("#", 1)[1] - workflow_run.lang = lang - if main: - self.mainEntity = workflow_run - profiles = set(_.rstrip("/") for _ in get_norm_value(self.metadata, "conformsTo")) - profiles.add(WORKFLOW_PROFILE) - self.metadata["conformsTo"] = [{"@id": _} for _ in sorted(profiles)] - if gen_cwl and lang_str != "cwl": - if lang_str != "galaxy": - raise ValueError(f"conversion from {lang.name} to abstract CWL not supported") - cwl_source = galaxy_to_abstract_cwl(source) - cwl_dest_path = Path(source).with_suffix(".cwl").name - cwl_workflow = self.add_workflow_run( - source=cwl_source, dest_path=cwl_dest_path, fetch_remote=fetch_remote, properties=properties, - main=False, lang="cwl", gen_cwl=False, cls=WorkflowDescription - ) - workflow_run.subjectOf = cwl_workflow - return workflow_run - def add_test_suite(self, identifier=None, name=None, main_entity=None): test_ref_prop = "mentions" if not main_entity: @@ -568,47 +534,3 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], for file_entry in include_files: wf_crate.add_file(file_entry) return wf_crate - - -# WIP -def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, - author=None, orcid=None, include_files=[], - fetch_remote=False, prov_name=None, cwl=None, - diagram=None): - - wfr_crate = ROCrate() - workflow_path = Path(workflow_path) - print(workflow_path) - wf_file = wfr_crate.add_workflow( - workflow_path, workflow_path.name, fetch_remote=fetch_remote, - main=True, lang=wf_type, gen_cwl=(cwl is None) - ) - if 'url' in wf_file.properties(): - wf_file['codeRepository'] = wf_file['url'] - - # add extra files - datasets = Path('datasets') - wfr_crate.add_dataset(datasets) - for file_entry in include_files: - wfr_crate.add_file(file_entry, datasets / file_entry.name) - - wfr_metadata_path = Path(wfr_metadata_path) - - prov = ProvenanceProfile(wfr_metadata_path, author, orcid) - - artifacts = Path('artifacts') - wfr_crate.add_dataset(artifacts) - for key, value in prov.declared_strings_s.items(): - dest = artifacts / key - wfr_crate.add_file(value, dest) - - prov_docs, _, graph = prov.finalize_prov_profile() - # add output files to ro-crate - provenance = Path('provenance') - wfr_crate.add_dataset(provenance) - for key, value in prov_docs.items(): - dest = provenance / key - wfr_crate.add_file(value, dest) - - wfr_crate.add_file(graph, provenance / "graph.png") - return wfr_crate diff --git a/rocrate/utils.py b/rocrate/utils.py index 6f9a58d5..1107a479 100644 --- a/rocrate/utils.py +++ b/rocrate/utils.py @@ -21,21 +21,6 @@ import os from datetime import datetime, timezone from urllib.parse import urlsplit -from typing import ( - IO, - Any, - BinaryIO, - Callable, - Dict, - List, - MutableMapping, - MutableSequence, - Optional, - Set, - Tuple, - Union, - cast, -) def is_url(string): From cf41846a6fec12b99756757ed869bad7f4e9bce4 Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 23 Jun 2022 16:36:53 +0200 Subject: [PATCH 21/27] added add_workflow_run_ro_crate function to rocrate.py --- rocrate/rocrate.py | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py index 264e8948..b14b3b48 100644 --- a/rocrate/rocrate.py +++ b/rocrate/rocrate.py @@ -46,6 +46,7 @@ from .utils import is_url, subclasses, get_norm_value, walk from .metadata import read_metadata, find_root_entity_id +from .provenance_profile import ProvenanceProfile def pick_type(json_entity, type_map, fallback=None): @@ -534,3 +535,47 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], for file_entry in include_files: wf_crate.add_file(file_entry) return wf_crate + + +# WIP +def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, + author=None, orcid=None, include_files=[], + fetch_remote=False, prov_name=None, cwl=None, + diagram=None): + + wfr_crate = ROCrate() + workflow_path = Path(workflow_path) + print(workflow_path) + wf_file = wfr_crate.add_workflow( + workflow_path, workflow_path.name, fetch_remote=fetch_remote, + main=True, lang=wf_type, gen_cwl=(cwl is None) + ) + if 'url' in wf_file.properties(): + wf_file['codeRepository'] = wf_file['url'] + + # add extra files + datasets = Path('datasets') + wfr_crate.add_dataset(datasets) + for file_entry in include_files: + wfr_crate.add_file(file_entry, datasets / file_entry.name) + + wfr_metadata_path = Path(wfr_metadata_path) + + prov = ProvenanceProfile(wfr_metadata_path, author, orcid) + + artifacts = Path('artifacts') + wfr_crate.add_dataset(artifacts) + for key, value in prov.declared_strings_s.items(): + dest = artifacts / key + wfr_crate.add_file(value, dest) + + prov_docs, _, graph = prov.finalize_prov_profile() + # add output files to ro-crate + provenance = Path('provenance') + wfr_crate.add_dataset(provenance) + for key, value in prov_docs.items(): + dest = provenance / key + wfr_crate.add_file(value, dest) + + wfr_crate.add_file(graph, provenance / "graph.png") + return wfr_crate From 53d6c8daa0a4e65cc6b55b78b4c599fffdfb49cc Mon Sep 17 00:00:00 2001 From: pauldg Date: Thu, 23 Jun 2022 17:03:26 +0200 Subject: [PATCH 22/27] included pydot and graphviz to requirements --- requirements.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/requirements.txt b/requirements.txt index 4003b9dd..09fd4360 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,3 +6,5 @@ python-dateutil click prov typing-extensions +pydot +graphviz \ No newline at end of file From b2c3ffb85a902e8b9895f81402d7ac1442d310c8 Mon Sep 17 00:00:00 2001 From: pauldg Date: Wed, 29 Jun 2022 15:15:59 +0200 Subject: [PATCH 23/27] reformat using black, exclude prov graph creation (to avoid installing graphviz) --- requirements.txt | 3 +- rocrate/provenance_profile.py | 94 ++++++++++++++++++++++------------- rocrate/rocrate.py | 37 +++++++++----- 3 files changed, 85 insertions(+), 49 deletions(-) diff --git a/requirements.txt b/requirements.txt index 09fd4360..a161f22b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,5 +6,4 @@ python-dateutil click prov typing-extensions -pydot -graphviz \ No newline at end of file +pydot \ No newline at end of file diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index c7fffba0..1c6b9a2e 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -1,4 +1,5 @@ import datetime + # from tokenize import String from io import StringIO import urllib @@ -20,6 +21,8 @@ from prov.identifier import Identifier from prov.model import PROV, PROV_LABEL, PROV_TYPE, PROV_VALUE, ProvDocument, ProvEntity + +# import graphviz from prov.dot import prov_to_dot from tools.load_ga_export import load_ga_history_export, GalaxyJob, GalaxyDataset from ast import literal_eval @@ -45,6 +48,7 @@ WFDESC, WFPROV, ) + # from .stdfsaccess import StdFsAccess # from rocrate.utils_cwl import CWLObjectType, JobsType, get_listing, posix_path, versionstring # from .workflow_job import WorkflowJob @@ -60,8 +64,8 @@ def posix_path(local_path: str) -> str: def remove_escapes(s): - escapes = ''.join([chr(char) for char in range(1, 32)]) - translator = str.maketrans('', '', escapes) + escapes = "".join([chr(char) for char in range(1, 32)]) + translator = str.maketrans("", "", escapes) s.translate(translator) @@ -143,9 +147,11 @@ def __init__( # print(job_attrs.attributes) # for k, v in job_attrs.attributes['parameters'].items(): # print(k, " : ", v) - self.jobs[job_attrs.attributes['encoded_id']] = job_attrs.attributes + self.jobs[job_attrs.attributes["encoded_id"]] = job_attrs.attributes try: - self.workflow_invocation_uuid.add(job_attrs.attributes['parameters']['__workflow_invocation_uuid__']) + self.workflow_invocation_uuid.add( + job_attrs.attributes["parameters"]["__workflow_invocation_uuid__"] + ) except KeyError: pass # print('set:') @@ -156,7 +162,9 @@ def __init__( # print(job_attrs.attributes["outputs"]) if self.workflow_invocation_uuid: - self.workflow_run_uuid = uuid.UUID(next(iter(self.workflow_invocation_uuid))) + self.workflow_run_uuid = uuid.UUID( + next(iter(self.workflow_invocation_uuid)) + ) self.workflow_run_uri = self.workflow_run_uuid.urn # type: str else: self.workflow_run_uuid = run_uuid or uuid.uuid4() @@ -208,9 +216,7 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: # TODO: use appropriate refs for ga_export and related inputs ro_identifier_workflow = self.base_uri + "ga_export" + "/" self.wf_ns = self.document.add_namespace("wf", ro_identifier_workflow) - ro_identifier_input = ( - self.base_uri + "ga_export/datasets#" - ) + ro_identifier_input = self.base_uri + "ga_export/datasets#" self.document.add_namespace("input", ro_identifier_input) # More info about the account (e.g. username, fullname) @@ -353,17 +359,15 @@ def used_artefacts( for d in self.datasets: # print([d['encoded_id']]) # print(d['copied_from_history_dataset_association_id_chain']) - if v in ([d['encoded_id']] + d['copied_from_history_dataset_association_id_chain']): + if v in ( + [d["encoded_id"]] + + d["copied_from_history_dataset_association_id_chain"] + ): self.declare_entity(process_run_id, d, prov_role) else: self.declare_entity(process_run_id, value, prov_role) - def declare_entity( - self, - process_run_id, - value, - prov_role - ) -> None: + def declare_entity(self, process_run_id, value, prov_role) -> None: try: entity = self.declare_artefact(value) # print("test2") @@ -592,9 +596,9 @@ def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: return file_entity # , entity, checksum def declare_directory( - self, - # value: CWLObjectType - value + self, + # value: CWLObjectType + value, ) -> ProvEntity: """Register any nested files/directories.""" # FIXME: Calculate a hash-like identifier for directory @@ -797,9 +801,10 @@ def activity_has_provenance(self, activity, prov_ids): # uris = [i.uri for i in prov_ids] # self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) - def finalize_prov_profile(self, out_path: Path = None, - serialize: Boolean = False, name=None): - # type: (Optional[str],Optional[str]) -> Tuple[Dict,List[Identifier]] + def finalize_prov_profile( + self, out_path: Path = None, serialize: Boolean = False, name=None + ): + # type: (Optional[str],Optional[bool],Optional[str]) -> Tuple[Dict,List[Identifier]] """Transfer the provenance related files to the RO-crate""" # NOTE: Relative posix path if name is None: @@ -821,35 +826,48 @@ def finalize_prov_profile(self, out_path: Path = None, # list of prov identifiers of provenance files prov_ids = [] # https://www.w3.org/TR/prov-xml/ - serialized_prov_docs[filename + ".xml"] = StringIO(self.document.serialize(format="xml", indent=4)) + serialized_prov_docs[filename + ".xml"] = StringIO( + self.document.serialize(format="xml", indent=4) + ) prov_ids.append(self.provenance_ns[filename + ".xml"]) # https://www.w3.org/TR/prov-n/ - serialized_prov_docs[filename + ".provn"] = StringIO(self.document.serialize(format="provn", indent=2)) + serialized_prov_docs[filename + ".provn"] = StringIO( + self.document.serialize(format="provn", indent=2) + ) prov_ids.append(self.provenance_ns[filename + ".provn"]) # https://www.w3.org/Submission/prov-json/ - serialized_prov_docs[filename + ".json"] = StringIO(self.document.serialize(format="json", indent=2)) + serialized_prov_docs[filename + ".json"] = StringIO( + self.document.serialize(format="json", indent=2) + ) prov_ids.append(self.provenance_ns[filename + ".json"]) # "rdf" aka https://www.w3.org/TR/prov-o/ # which can be serialized to ttl/nt/jsonld (and more!) # https://www.w3.org/TR/turtle/ - serialized_prov_docs[filename + ".ttl"] = StringIO(self.document.serialize(format="rdf", rdf_format="turtle")) + serialized_prov_docs[filename + ".ttl"] = StringIO( + self.document.serialize(format="rdf", rdf_format="turtle") + ) prov_ids.append(self.provenance_ns[filename + ".ttl"]) # https://www.w3.org/TR/n-triples/ - serialized_prov_docs[filename + ".nt"] = StringIO(self.document.serialize(format="rdf", rdf_format="ntriples")) + serialized_prov_docs[filename + ".nt"] = StringIO( + self.document.serialize(format="rdf", rdf_format="ntriples") + ) prov_ids.append(self.provenance_ns[filename + ".nt"]) # https://www.w3.org/TR/json-ld/ # TODO: Use a nice JSON-LD context # see also https://eprints.soton.ac.uk/395985/ # 404 Not Found on https://provenance.ecs.soton.ac.uk/prov.jsonld : - serialized_prov_docs[filename + ".jsonld"] = StringIO(self.document.serialize(format="rdf", rdf_format="json-ld")) + serialized_prov_docs[filename + ".jsonld"] = StringIO( + self.document.serialize(format="rdf", rdf_format="json-ld") + ) prov_ids.append(self.provenance_ns[filename + ".jsonld"]) - graph_dot = prov_to_dot(self.document) - png_b = graph_dot.create_png() - graph_b = BytesIO() - graph_b.write(png_b) + graph = prov_to_dot(self.document).to_string() + # graph_s = graph_dot + # print(type(graph)) + graph_s = StringIO() + graph_s.write(graph) # dot.write_png(basename + '.png') if serialize: @@ -871,13 +889,19 @@ def finalize_prov_profile(self, out_path: Path = None, self.document.serialize(provenance_file, format="json", indent=2) with open(basename + ".ttl", "w") as provenance_file: - self.document.serialize(provenance_file, format="rdf", rdf_format="turtle") + self.document.serialize( + provenance_file, format="rdf", rdf_format="turtle" + ) with open(basename + ".nt", "w") as provenance_file: - self.document.serialize(provenance_file, format="rdf", rdf_format="ntriples") + self.document.serialize( + provenance_file, format="rdf", rdf_format="ntriples" + ) with open(basename + ".jsonld", "w") as provenance_file: - self.document.serialize(provenance_file, format="rdf", rdf_format="json-ld") + self.document.serialize( + provenance_file, format="rdf", rdf_format="json-ld" + ) # _logger.debug("[provenance] added provenance: %s", prov_ids) - return (serialized_prov_docs, prov_ids, graph_b) + return (serialized_prov_docs, prov_ids, graph_s) diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py index b14b3b48..cd817804 100644 --- a/rocrate/rocrate.py +++ b/rocrate/rocrate.py @@ -538,23 +538,35 @@ def make_workflow_rocrate(workflow_path, wf_type, include_files=[], # WIP -def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, - author=None, orcid=None, include_files=[], - fetch_remote=False, prov_name=None, cwl=None, - diagram=None): +def make_workflow_run_rocrate( + workflow_path, + wf_type, + wfr_metadata_path, + author=None, + orcid=None, + include_files=[], + fetch_remote=False, + prov_name=None, + cwl=None, + diagram=None, +): wfr_crate = ROCrate() workflow_path = Path(workflow_path) print(workflow_path) wf_file = wfr_crate.add_workflow( - workflow_path, workflow_path.name, fetch_remote=fetch_remote, - main=True, lang=wf_type, gen_cwl=(cwl is None) + workflow_path, + workflow_path.name, + fetch_remote=fetch_remote, + main=True, + lang=wf_type, + gen_cwl=(cwl is None), ) - if 'url' in wf_file.properties(): - wf_file['codeRepository'] = wf_file['url'] + if "url" in wf_file.properties(): + wf_file["codeRepository"] = wf_file["url"] # add extra files - datasets = Path('datasets') + datasets = Path("datasets") wfr_crate.add_dataset(datasets) for file_entry in include_files: wfr_crate.add_file(file_entry, datasets / file_entry.name) @@ -563,19 +575,20 @@ def make_workflow_run_rocrate(workflow_path, wf_type, wfr_metadata_path, prov = ProvenanceProfile(wfr_metadata_path, author, orcid) - artifacts = Path('artifacts') + artifacts = Path("artifacts") wfr_crate.add_dataset(artifacts) for key, value in prov.declared_strings_s.items(): dest = artifacts / key wfr_crate.add_file(value, dest) prov_docs, _, graph = prov.finalize_prov_profile() + print(graph) # add output files to ro-crate - provenance = Path('provenance') + provenance = Path("provenance") wfr_crate.add_dataset(provenance) for key, value in prov_docs.items(): dest = provenance / key wfr_crate.add_file(value, dest) - wfr_crate.add_file(graph, provenance / "graph.png") + wfr_crate.add_file(graph, provenance / "graph.dot") return wfr_crate From efe25a8d3c6ccfeb6cc94d77de22a30025b170b1 Mon Sep 17 00:00:00 2001 From: pauldg Date: Mon, 5 Sep 2022 15:55:54 +0200 Subject: [PATCH 24/27] simplified output provenance --- rocrate/provenance_profile.py | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 1c6b9a2e..f2e247e1 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -347,14 +347,15 @@ def used_artefacts( prov_role = self.wf_ns[f"{base}/{key}"] # if not value or len(value) == 0: - # print("key : ", key) - # print("-----------") - # print("value: ", value) - # print("-----------") - # print("type : ", type(value)) - # print("-----------") + if item in ("inputs", "outputs"): + print("key : ", key) + print("-----------") + print("value: ", value) + print("-----------") + print("type : ", type(value)) + print("-----------") for v in value: for d in self.datasets: # print([d['encoded_id']]) @@ -364,14 +365,12 @@ def used_artefacts( + d["copied_from_history_dataset_association_id_chain"] ): self.declare_entity(process_run_id, d, prov_role) - else: - self.declare_entity(process_run_id, value, prov_role) + # else: + # self.declare_entity(process_run_id, value, prov_role) def declare_entity(self, process_run_id, value, prov_role) -> None: try: entity = self.declare_artefact(value) - # print("test2") - # print(entity) self.document.used( process_run_id, entity, From af2ffb8a7923f4d1c27fc88e312ffc9fcda870f1 Mon Sep 17 00:00:00 2001 From: pauldg Date: Mon, 5 Sep 2022 16:22:22 +0200 Subject: [PATCH 25/27] resolved flake8 issues --- rocrate/provenance_profile.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index f2e247e1..dfb2397b 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -347,8 +347,6 @@ def used_artefacts( prov_role = self.wf_ns[f"{base}/{key}"] # if not value or len(value) == 0: - - if item in ("inputs", "outputs"): print("key : ", key) print("-----------") From e4ea3b32d128e920a6f455d3c3ba0e00743b0f5c Mon Sep 17 00:00:00 2001 From: pauldg Date: Fri, 9 Sep 2022 17:07:25 +0200 Subject: [PATCH 26/27] first cleanup of code --- rocrate/provenance_profile.py | 56 ++--------------------------------- tools/load_ga_export.py | 2 -- 2 files changed, 3 insertions(+), 55 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index dfb2397b..2a6c2082 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -91,9 +91,6 @@ def __init__( ga_export_dir: Path, full_name: str = None, orcid: str = None, - # prov_name: str = None, - # prov_path: Path = None, - # fsaccess: StdFsAccess, run_uuid: Optional[uuid.UUID] = None, ) -> None: """ @@ -106,13 +103,8 @@ def __init__( prov_name -- provenance file name run_uuid -- uuid for the workflow run """ - # self.fsaccess = fsaccess self.orcid = orcid self.ga_export_dir = ga_export_dir - # TODO: does it make sense to write all outputs to a tmp dir - # chance that temp dir doesnt get removed properly - # if out_path is None: - # self.out_path = tempfile.mkdtemp() self.ro_uuid = uuid.uuid4() # TODO: should be connected to a ro_crate? self.base_uri = "arcp://uuid,%s/" % self.ro_uuid @@ -120,33 +112,22 @@ def __init__( # TODO extract engine_uuid from galaxy, type: str self.engine_uuid = "urn:uuid:%s" % uuid.uuid4() # type: str self.full_name = full_name - # TODO move to separate function + # import galaxy history metadata metadata_export = load_ga_history_export(ga_export_dir) - # self.tmp_dir = tempfile.mkdtemp() + self.declared_strings_s = {} self.datasets = [] - # print(metadata_export["jobs_attrs"][0]["params"]) for i, dataset in enumerate(metadata_export["datasets_attrs"]): datasets_attrs = GalaxyDataset() datasets_attrs.parse_ga_dataset_attrs(dataset) - # print(i) - # print(datasets_attrs.attributes['encoded_id']) self.datasets.append(datasets_attrs.attributes) - # self.declare_process(ds_attrs.attributes) - - # print(self.datasets) - # print([[d['encoded_id']]+d['copied_from_history_dataset_association_id_chain'] for d in self.datasets]) self.workflow_invocation_uuid = set() self.jobs = {} for i, job in enumerate(metadata_export["jobs_attrs"]): job_attrs = GalaxyJob() job_attrs.parse_ga_jobs_attrs(job) - # print(i) - # print(job_attrs.attributes) - # for k, v in job_attrs.attributes['parameters'].items(): - # print(k, " : ", v) self.jobs[job_attrs.attributes["encoded_id"]] = job_attrs.attributes try: self.workflow_invocation_uuid.add( @@ -154,12 +135,6 @@ def __init__( ) except KeyError: pass - # print('set:') - # print(self.workflow_invocation_uuid) - # print("inputs") - # print(job_attrs.attributes["inputs"]) - # print("outputs") - # print(job_attrs.attributes["outputs"]) if self.workflow_invocation_uuid: self.workflow_run_uuid = uuid.UUID( @@ -174,8 +149,6 @@ def __init__( for v in self.jobs.values(): self.declare_process(v) - # print(os.listdir(tempfile.gettempdir())) - def __str__(self) -> str: """Represent this Provenvance profile as a string.""" return "ProvenanceProfile <{}>".format( @@ -206,10 +179,7 @@ def generate_prov_doc(self) -> Tuple[str, ProvDocument]: # TODO: Change to nih:sha-256; hashes # https://tools.ietf.org/html/rfc6920#section-7 self.document.add_namespace("data", "urn:hash::sha1:") - # Also needed for docker images - # self.document.add_namespace(SHA256, "nih:sha-256;") - # Pre-register provenance directory so we can refer to its files self.provenance_ns = self.document.add_namespace( "provenance", self.base_uri + posix_path(PROVENANCE) + "/" ) @@ -274,11 +244,9 @@ def declare_process( process_run_id: Optional[str] = None, ) -> str: """Record the start of each Process.""" - # TODO: change to workflow invocation id? if process_run_id is None: process_run_id = uuid.uuid4().urn - # cmd = ga_export_jobs_attrs["command_line"] process_name = ga_export_jobs_attrs["tool_id"] # tool_version = ga_export_jobs_attrs["tool_version"] # TODO: insert workflow id @@ -287,6 +255,7 @@ def declare_process( end_time = ga_export_jobs_attrs["update_time"] # TODO: Find out how to include commandline as a string + # cmd = ga_export_jobs_attrs["command_line"] # cmd = self.document.entity( # uuid.uuid4().urn, # {PROV_TYPE: WFPROV["Artifact"], PROV_LABEL: ga_export_jobs_attrs["command_line"]} @@ -299,7 +268,6 @@ def declare_process( { PROV_TYPE: WFPROV["ProcessRun"], PROV_LABEL: prov_label, - # TODO: Find out how to include commandline as a string # PROV_LABEL: cmd }, ) @@ -310,8 +278,6 @@ def declare_process( process_run_id, None, self.workflow_run_uri, start_time, None, None ) self.used_artefacts(process_run_id, ga_export_jobs_attrs) - # self.generate_output_prov(outputs, process_run_id, process_name) - # self.document.wasEndedBy(process_run_id, None, self.workflow_run_uri, when) return process_run_id def used_artefacts( @@ -329,11 +295,7 @@ def used_artefacts( tool_id = process_metadata["tool_id"] base += "/" + tool_id items = ["inputs", "outputs", "parameters"] - # print(process_metadata["params"]) for item in items: - # print(item) - # print("-----------") - # print(process_metadata[item]) for key, value in process_metadata[item].items(): if not value: pass @@ -348,16 +310,8 @@ def used_artefacts( # if not value or len(value) == 0: if item in ("inputs", "outputs"): - print("key : ", key) - print("-----------") - print("value: ", value) - print("-----------") - print("type : ", type(value)) - print("-----------") for v in value: for d in self.datasets: - # print([d['encoded_id']]) - # print(d['copied_from_history_dataset_association_id_chain']) if v in ( [d["encoded_id"]] + d["copied_from_history_dataset_association_id_chain"] @@ -388,7 +342,6 @@ def declare_artefact(self, value: Any) -> ProvEntity: if isinstance(value, (bool, int, float)): # Typically used in job documents for flags - # print(value) # FIXME: Make consistent hash URIs for these # that somehow include the type @@ -415,9 +368,6 @@ def declare_artefact(self, value: Any) -> ProvEntity: ) if isinstance(value, Dict): - # print("value: ", value) - # print("-----------") - # print("type : ", type(value)) if "@id" in value: # Already processed this value, # but it might not be in this PROV diff --git a/tools/load_ga_export.py b/tools/load_ga_export.py index b5dca540..9799edb0 100644 --- a/tools/load_ga_export.py +++ b/tools/load_ga_export.py @@ -51,8 +51,6 @@ def parse_ga_jobs_attrs(self, job_attrs): v = int(v) except (TypeError, ValueError): pass # it was a string, not an int. - # print(k, v) - # print(type(v)) if "json" in k: v = json.loads(v) From 791ba5c04adfb7c241984d5ecae333d7cdfb6a2e Mon Sep 17 00:00:00 2001 From: pauldg Date: Tue, 13 Sep 2022 22:08:40 +0200 Subject: [PATCH 27/27] second cleanup of code --- rocrate/provenance_profile.py | 274 +--------------------------------- 1 file changed, 1 insertion(+), 273 deletions(-) diff --git a/rocrate/provenance_profile.py b/rocrate/provenance_profile.py index 2a6c2082..378448aa 100644 --- a/rocrate/provenance_profile.py +++ b/rocrate/provenance_profile.py @@ -401,102 +401,11 @@ def declare_artefact(self, value: Any) -> ProvEntity: if value.get("class"): # _logger.warning("Unknown data class %s.", value["class"]) # FIXME: The class might be "http://example.com/somethingelse" - coll.add_asserted_type(CWLPROV[value["class"]]) - - # Let's iterate and recurse - coll_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] - for (key, val) in value.items(): - # clean up unwanted characters - if isinstance(key, str): - key = key.replace("|", "_") - if isinstance(val, str): - val = val.replace("|", "_") - - v_ent = self.declare_artefact(val) - self.document.membership(coll, v_ent) - m_entity = self.document.entity(uuid.uuid4().urn) - # Note: only support PROV-O style dictionary - # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition - # as prov.py do not easily allow PROV-N extensions - m_entity.add_asserted_type(PROV["KeyEntityPair"]) - m_entity.add_attributes( - {PROV["pairKey"]: str(key), PROV["pairEntity"]: v_ent} - ) - coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) - coll.add_attributes(coll_attribs) - # self.research_object.add_uri(coll.identifier.uri) - return coll - - # some other kind of Collection? - # TODO: also save as JSON - try: - members = [] - for each_input_obj in iter(value): - # Recurse and register any nested objects - e = self.declare_artefact(each_input_obj) - members.append(e) - - # If we reached this, then we were allowed to iterate - coll = self.document.entity( - uuid.uuid4().urn, - [ - (PROV_TYPE, WFPROV["Artifact"]), - (PROV_TYPE, PROV["Collection"]), - ], - ) - if not members: - coll.add_asserted_type(PROV["EmptyCollection"]) - else: - for member in members: - # FIXME: This won't preserve order, for that - # we would need to use PROV.Dictionary - # with numeric keys - self.document.membership(coll, member) - # self.research_object.add_uri(coll.identifier.uri) - # FIXME: list value does not support adding "@id" - return coll - except TypeError: - # _logger.warning("Unrecognized type %s of %r", type(value), value) - # Let's just fall back to Python repr() - entity = self.document.entity(uuid.uuid4().urn, {PROV_LABEL: repr(value)}) - # self.research_object.add_uri(entity.identifier.uri) - return entity + coll.add_asserted_type(CWLPROV[value["class"]])q def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: if value["class"] != "File": raise ValueError("Must have class:File: %s" % value) - # Need to determine file hash aka RO filename - # TODO: do we need a checksum value? - # entity = None # type: Optional[ProvEntity] - # checksum = None - # if "checksum" in value: - # csum = cast(str, value["checksum"]) - # (method, checksum) = csum.split("$", 1) - # if method == SHA1: # and self.research_object.has_data_file(checksum): - # entity = self.document.entity("data:" + checksum) - - # if not entity and "location" in value: - # location = str(value["location"]) - # # If we made it here, we'll have to add it to the RO - # with self.fsaccess.open(location, "rb") as fhandle: - # relative_path = self.research_object.add_data_file(fhandle) - # # FIXME: This naively relies on add_data_file setting hash as filename - # checksum = PurePath(relative_path).name - # entity = self.document.entity( - # "data:" + checksum, {PROV_TYPE: WFPROV["Artifact"]} - # ) - # if "checksum" not in value: - # value["checksum"] = f"{SHA1}${checksum}" - - # if not entity and "contents" in value: - # # Anonymous file, add content as string - # entity, checksum = self.declare_string(cast(str, value["contents"])) - - # # By here one of them should have worked! - # if not entity or not checksum: - # raise ValueError( - # "class:File but missing checksum/location/content: %r" % value - # ) # Track filename and extension, this is generally useful only for # secondaryFiles. Note that multiple uses of a file might thus record @@ -517,138 +426,8 @@ def declare_file(self, value: Dict) -> Tuple[ProvEntity, ProvEntity, str]: file_entity.add_attributes({CWLPROV["nameext"]: value["extension"]}) # self.document.specializationOf(file_entity, entity) - # TODO: figure out if we need to keep track of derived files - # Check for secondaries - # for sec in cast( - # # MutableSequence[CWLObjectType], - # value.get("secondaryFiles", []) # noqa - # ): - # # TODO: Record these in a specializationOf entity with UUID? - # if sec["class"] == "File": - # (sec_entity, _, _) = self.declare_file(sec) - # elif sec["class"] == "Directory": - # sec_entity = self.declare_directory(sec) - # else: - # raise ValueError(f"Got unexpected secondaryFiles value: {sec}") - # # We don't know how/when/where the secondary file was generated, - # # but CWL convention is a kind of summary/index derived - # # from the original file. As its generally in a different format - # # then prov:Quotation is not appropriate. - # self.document.derivation( - # sec_entity, - # file_entity, - # other_attributes={PROV["type"]: CWLPROV["SecondaryFile"]}, - # ) - return file_entity # , entity, checksum - def declare_directory( - self, - # value: CWLObjectType - value, - ) -> ProvEntity: - """Register any nested files/directories.""" - # FIXME: Calculate a hash-like identifier for directory - # so we get same value if it's the same filenames/hashes - # in a different location. - # For now, mint a new UUID to identify this directory, but - # attempt to keep it inside the value dictionary - dir_id = cast(str, value.setdefault("@id", uuid.uuid4().urn)) - - # New annotation file to keep the ORE Folder listing - ore_doc_fn = dir_id.replace("urn:uuid:", "directory-") + ".ttl" - dir_bundle = self.document.bundle(self.metadata_ns[ore_doc_fn]) - - coll = self.document.entity( - dir_id, - [ - (PROV_TYPE, WFPROV["Artifact"]), - (PROV_TYPE, PROV["Collection"]), - (PROV_TYPE, PROV["Dictionary"]), - (PROV_TYPE, RO["Folder"]), - ], - ) - # ORE description of ro:Folder, saved separately - coll_b = dir_bundle.entity( - dir_id, - [(PROV_TYPE, RO["Folder"]), (PROV_TYPE, ORE["Aggregation"])], - ) - self.document.mentionOf(dir_id + "#ore", dir_id, dir_bundle.identifier) - - # dir_manifest = dir_bundle.entity( - # dir_bundle.identifier, {PROV["type"]: ORE["ResourceMap"], - # ORE["describes"]: coll_b.identifier}) - - coll_attribs = [(ORE["isDescribedBy"], dir_bundle.identifier)] - coll_b_attribs = [] # type: List[Tuple[Identifier, ProvEntity]] - - # FIXME: .listing might not be populated yet - hopefully - # a later call to this method will sort that - is_empty = True - - # if "listing" not in value: - # get_listing(self.fsaccess, value) - for entry in cast(Dict, value.get("listing", [])): - is_empty = False - # Declare child-artifacts - entity = self.declare_artefact(entry) - self.document.membership(coll, entity) - # Membership relation aka our ORE Proxy - m_id = uuid.uuid4().urn - m_entity = self.document.entity(m_id) - m_b = dir_bundle.entity(m_id) - - # PROV-O style Dictionary - # https://www.w3.org/TR/prov-dictionary/#dictionary-ontological-definition - # ..as prov.py do not currently allow PROV-N extensions - # like hadDictionaryMember(..) - m_entity.add_asserted_type(PROV["KeyEntityPair"]) - - m_entity.add_attributes( - { - PROV["pairKey"]: entry["basename"], - PROV["pairEntity"]: entity, - } - ) - - # As well as a being a - # http://wf4ever.github.io/ro/2016-01-28/ro/#FolderEntry - m_b.add_asserted_type(RO["FolderEntry"]) - m_b.add_asserted_type(ORE["Proxy"]) - m_b.add_attributes( - { - RO["entryName"]: entry["basename"], - ORE["proxyIn"]: coll, - ORE["proxyFor"]: entity, - } - ) - coll_attribs.append((PROV["hadDictionaryMember"], m_entity)) - coll_b_attribs.append((ORE["aggregates"], m_b)) - - coll.add_attributes(coll_attribs) - coll_b.add_attributes(coll_b_attribs) - - # Also Save ORE Folder as annotation metadata - ore_doc = ProvDocument() - ore_doc.add_namespace(ORE) - ore_doc.add_namespace(RO) - ore_doc.add_namespace(UUID) - ore_doc.add_bundle(dir_bundle) - ore_doc = ore_doc.flattened() - ore_doc_path = str(PurePosixPath(METADATA, ore_doc_fn)) - with self.research_object.write_bag_file(ore_doc_path) as provenance_file: - ore_doc.serialize(provenance_file, format="rdf", rdf_format="turtle") - self.research_object.add_annotation( - dir_id, [ore_doc_fn], ORE["isDescribedBy"].uri - ) - - if is_empty: - # Empty directory - coll.add_asserted_type(PROV["EmptyCollection"]) - coll.add_asserted_type(PROV["EmptyDictionary"]) - # self.research_object.add_uri(coll.identifier.uri) - return coll - def declare_string(self, value: str) -> Tuple[ProvEntity, str]: """Save as string in UTF-8.""" value = str(value).replace("|", "_") @@ -697,57 +476,6 @@ def generate_output_prov( entity, process_run_id, timestamp, None, {"prov:role": role} ) - def prospective_prov(self, job: GalaxyJob) -> None: - """Create prospective prov recording as wfdesc prov:Plan.""" - if not isinstance(job, GalaxyJob): - # direct command line tool execution - self.document.entity( - "wf:main", - { - PROV_TYPE: WFDESC["Process"], - "prov:type": PROV["Plan"], - "prov:label": "Prospective provenance", - }, - ) - return - - self.document.entity( - "wf:main", - { - PROV_TYPE: WFDESC["Workflow"], - "prov:type": PROV["Plan"], - "prov:label": "Prospective provenance", - }, - ) - - for step in job.steps: - stepnametemp = "wf:main/" + str(step.name)[5:] - stepname = urllib.parse.quote(stepnametemp, safe=":/,#") - provstep = self.document.entity( - stepname, - {PROV_TYPE: WFDESC["Process"], "prov:type": PROV["Plan"]}, - ) - self.document.entity( - "wf:main", - { - "wfdesc:hasSubProcess": provstep, - "prov:label": "Prospective provenance", - }, - ) - # TODO: Declare roles/parameters as well - - def activity_has_provenance(self, activity, prov_ids): - # type: (str, List[Identifier]) -> None - """Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files.""" - # NOTE: The below will only work if the corresponding metadata/provenance arcp URI - # is a pre-registered namespace in the PROV Document - attribs = [(PROV["has_provenance"], prov_id) for prov_id in prov_ids] - self.document.activity(activity, other_attributes=attribs) - # Tip: we can't use https://www.w3.org/TR/prov-links/#term-mention - # as prov:mentionOf() is only for entities, not activities - # uris = [i.uri for i in prov_ids] - # self.research_object.add_annotation(activity, uris, PROV["has_provenance"].uri) - def finalize_prov_profile( self, out_path: Path = None, serialize: Boolean = False, name=None ):