sipstore: adds sipstore implementation

Signed-off-by: Ioannis Tsanaktsidis <ioannis.tsanaktsidis@cern.ch>

Author: ioannistsanaktsidis

cap/config.py

@@ -642,3 +642,6 @@ def _(x):
 # ================
 REANA_ACCESS_TOKEN = os.environ.get(
     'APP_REANA_ACCESS_TOKEN', None)
+
+SIPSTORE_DEFAULT_AGENT_JSONSCHEMA = 'sipstore/agent-v0.0.1.json'
+SIPSTORE_DEFAULT_BAGIT_JSONSCHEMA = 'sipstore/bagit-v0.0.1.json'

cap/jsonschemas/sipstore/agent-v0.0.1.json

@@ -0,0 +1,22 @@
+{
+  "allow_all": true,
+  "experiment": null,
+  "fullname": null,
+  "is_deposit": false,
+  "jsonschema": {
+    "type": "object",
+    "title": "SIPStore Agent schema.",
+    "description": "User agent information making the SIP.",
+    "properties": {
+      "orcid": {
+        "type": "string"
+      },
+      "email": {
+        "type": "string"
+      },
+      "ip_address": {
+        "type": "string"
+      }
+    }
+  }
+}

cap/jsonschemas/sipstore/bagit-v0.0.1.json

@@ -0,0 +1,77 @@
+{
+  "allow_all": true,
+  "experiment": null,
+  "fullname": null,
+  "is_deposit": false,
+  "jsonschema": {
+    "definitions": {
+      "file": {
+        "type": "object",
+        "title": "Archived file information.",
+        "description": "JSON describing a single file.",
+        "additionalProperties": false,
+        "properties": {
+          "filepath": {
+            "description":
+              "Filepath to the archived file, relative to the archived directory root.",
+            "type": "string"
+          },
+          "fullpath": {
+            "description":
+              "Absolute filepath to the file in the archive file system.",
+            "type": "string"
+          },
+          "size": {
+            "description": "Size of the file in bytes.",
+            "type": "number"
+          },
+          "checksum": {
+            "description":
+              "MD5 checksum of the file. Always starts with 'md5:' prefix.",
+            "type": "string"
+          },
+          "file_uuid": {
+            "description":
+              "UUID of the related FileInstance object. Used for Record's data files only.",
+            "type": "string"
+          },
+          "metadata_id": {
+            "description":
+              "ID of the type (SIPMetadataType.id) of the related SIPMetadata object. Used for Record's metadata files only.",
+            "type": "number"
+          },
+          "sipfilepath": {
+            "description":
+              "Original SIPFile.filepath value. Used for Record's data files only.",
+            "type": "string"
+          },
+          "filename": {
+            "description":
+              "Filename of the SIPFile in the archive. Used for Record's data files only.",
+            "type": "string"
+          },
+          "content": {
+            "description":
+              "Text-content of the file. Used for BagIt metadata files only.",
+            "type": "string"
+          },
+          "fetched": {
+            "description":
+              "Marks whether given file is fetched from another bag (specified in 'fetch.txt'). If the key does not exist or is set to false, it is assumed that the file is written down in the bag, hence NOT fetched. Used for Record's data files only.",
+            "type": "boolean"
+          }
+        },
+        "required": ["filepath", "fullpath", "size", "checksum"]
+      }
+    },
+    "properties": {
+      "files": {
+        "description": "All files stored in this archive package.",
+        "type": "array",
+        "items": {
+          "$ref": "#/definitions/file"
+        }
+      }
+    }
+  }
+}

cap/jsonschemas/sipstore/file-v0.0.1.json

@@ -0,0 +1,55 @@
+{
+  "allow_all": true,
+  "experiment": null,
+  "fullname": null,
+  "is_deposit": false,
+  "jsonschema": {
+    "properties": {
+      "filepath": {
+        "description":
+          "Filepath to the archived file, relative to the archived directory root.",
+        "type": "string"
+      },
+      "fullpath": {
+        "description":
+          "Absolute filepath to the file in the archive file system.",
+        "type": "string"
+      },
+      "size": {
+        "description": "Size of the file in bytes.",
+        "type": "number"
+      },
+      "checksum": {
+        "description":
+          "MD5 checksum of the file. Always starts with 'md5:' prefix.",
+        "type": "string"
+      },
+      "file_uuid": {
+        "description":
+          "UUID of the related FileInstance object. Used for Record's data files only.",
+        "type": "string"
+      },
+      "metadata_id": {
+        "description":
+          "ID of the type (SIPMetadataType.id) of the related SIPMetadata object. Used for Record's metadata files only.",
+        "type": "number"
+      },
+      "sipfilepath": {
+        "description":
+          "Original SIPFile.filepath value. Used for Record's data files only.",
+        "type": "string"
+      },
+      "filename": {
+        "description":
+          "Filename of the SIPFile in the archive. Used for Record's data files only.",
+        "type": "string"
+      },
+      "content": {
+        "description":
+          "Text-content of the file. Used for BagIt metadata files only.",
+        "type": "string"
+      }
+    },
+    "required": ["filepath", "fullpath", "size", "checksum"]
+  }
+}

cap/modules/deposit/api.py

@@ -27,8 +27,6 @@
 from __future__ import absolute_import, print_function
 
 import copy
-import shutil
-import tempfile
 from copy import deepcopy
 from functools import wraps
 
@@ -43,29 +41,36 @@
 from invenio_files_rest.errors import MultipartMissingParts
 from invenio_files_rest.models import Bucket, FileInstance, ObjectVersion
 from invenio_jsonschemas.errors import JSONSchemaNotFound
+from invenio_pidstore.errors import PIDDoesNotExistError
 from invenio_records.models import RecordMetadata
 from invenio_records_files.models import RecordsBuckets
 from invenio_rest.errors import FieldError
+
+from invenio_sipstore.api import RecordSIP, SIP as SIPApi
+from invenio_sipstore.archivers import BagItArchiver
+from invenio_sipstore.models import SIP as SIPModel, \
+    RecordSIP as RecordSIPModel
+
 from jsonschema.validators import Draft4Validator, RefResolutionError
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm.exc import NoResultFound
 from werkzeug.local import LocalProxy
 
-from cap.config import FILES_URL_MAX_SIZE
 from cap.modules.records.api import CAPRecord
 from cap.modules.repoimporter.repo_importer import RepoImporter
 from cap.modules.schemas.models import Schema
 from cap.modules.user.errors import DoesNotExistInLDAP
 from cap.modules.user.utils import (get_existing_or_register_role,
                                     get_existing_or_register_user)
 
-from .errors import (DepositValidationError, FileUploadError,
+from .errors import (ArchivingError, DepositValidationError, FileUploadError,
                      UpdateDepositPermissionsError)
 from .fetchers import cap_deposit_fetcher
 from .minters import cap_deposit_minter
 from .permissions import (AdminDepositPermission, CloneDepositPermission,
                           DepositAdminActionNeed, DepositReadActionNeed,
                           DepositUpdateActionNeed, UpdateDepositPermission)
+from .utils import compare_files, task_commit, ensure_content_length
 
 _datastore = LocalProxy(lambda: current_app.extensions['security'].datastore)
 
@@ -197,7 +202,52 @@ def publish(self, *args, **kwargs):
                 if file_.data['checksum'] is None:
                     raise MultipartMissingParts()
 
-            return super(CAPDeposit, self).publish(*args, **kwargs)
+            try:
+                _, last_record = self.fetch_published()
+                is_first_publishing = False
+                fetched_files = last_record.files
+                create_sip_files = not compare_files(fetched_files, self.files)
+            except (PIDDoesNotExistError, KeyError):
+                is_first_publishing = True
+                create_sip_files = True if self.files else False
+
+            deposit = super(CAPDeposit, self).publish(*args, **kwargs)
+            recid, record = deposit.fetch_published()
+            sip_patch_of = None
+            if not is_first_publishing:
+                sip_recid = recid
+
+                sip_patch_of = (
+                    db.session.query(SIPModel)
+                    .join(RecordSIPModel, RecordSIPModel.sip_id == SIPModel.id)
+                    .filter(RecordSIPModel.pid_id == sip_recid.id)
+                    .order_by(SIPModel.created.desc())
+                    .first()
+                )
+
+            recordsip = RecordSIP.create(
+                recid, record, archivable=True,
+                create_sip_files=create_sip_files,
+                sip_metadata_type='json',
+                user_id=current_user.id,
+                agent=None)
+
+            archiver = BagItArchiver(
+                recordsip.sip, include_all_previous=(not is_first_publishing),
+                patch_of=sip_patch_of)
+
+            archiver.save_bagit_metadata()
+
+            sip = (
+                RecordSIPModel.query
+                .filter_by(pid_id=recid.id)
+                .order_by(RecordSIPModel.created.desc())
+                .first().sip
+            )
+
+            archive_sip.delay(str(sip.id))
+
+            return deposit
 
     @mark_as_action
     def upload(self, pid=None, *args, **kwargs):
@@ -601,32 +651,31 @@ def download_repo(pid, url, filename):
     task_commit(record, response.raw, filename, total)
 
 
-def task_commit(record, response, filename, total):
-    """Commit file to the record."""
-    record.files[filename].file.set_contents(
-        response,
-        default_location=record.files.bucket.location.uri,
-        size=total
-    )
-    db.session.commit()
-
-
-def ensure_content_length(
-        url, method='GET',
-        session=None,
-        max_size=FILES_URL_MAX_SIZE or 2**20,
-        *args, **kwargs):
-    """Add Content-Length when no present."""
-    kwargs['stream'] = True
-    session = session or requests.Session()
-    r = session.request(method, url, *args, **kwargs)
-    if 'Content-Length' not in r.headers:
-        # stream content into a temporary file so we can get the real size
-        spool = tempfile.SpooledTemporaryFile(max_size)
-        shutil.copyfileobj(r.raw, spool)
-        r.headers['Content-Length'] = str(spool.tell())
-        spool.seek(0)
-        # replace the original socket with our temporary file
-        r.raw._fp.close()
-        r.raw._fp = spool
-    return r
+@shared_task(ignore_result=True, max_retries=6,
+             default_retry_delay=4 * 60 * 60)
+def archive_sip(sip_uuid):
+    """Send the SIP for archiving.
+
+    Retries every 4 hours, six times, which should work for up to 24 hours
+    archiving system downtime.
+    :param sip_uuid: UUID of the SIP for archiving.
+    :type sip_uuid: str
+    """
+    try:
+        sip = SIPApi(SIPModel.query.get(sip_uuid))
+        archiver = BagItArchiver(sip)
+        bagmeta = archiver.get_bagit_metadata(sip)
+        if bagmeta is None:
+            raise ArchivingError(
+                'Bagit metadata does not exist for SIP: {0}.'.format(sip.id))
+        if sip.archived:
+            raise ArchivingError(
+                'SIP was already archived {0}.'.format(sip.id))
+        archiver.write_all_files()
+        sip.archived = True
+        db.session.commit()
+    except Exception as exc:
+        # On ArchivingError (see above), do not retry, but re-raise
+        if not isinstance(exc, ArchivingError):
+            archive_sip.retry(exc=exc)
+        raise

cap/modules/deposit/errors.py

@@ -28,6 +28,10 @@
 from invenio_rest.errors import RESTException
 
 
+class ArchivingError(Exception):
+    """Represents a SIP archiving error that can occur during task."""
+
+
 class DepositDoesNotExist(Exception):
     """Deposit with given key does not exist exception."""