BIDS validation

docs/bids_app/workflow.rst

@@ -14,10 +14,10 @@ To get access to these additions, the base Snakefile for a snakebids workflow sh
     inputs = snakebids.generate_inputs(
         bids_dir=config["bids_dir"],
         pybids_inputs=config["pybids_inputs"],
+        skip_bids_validation=config["skip_bids_validation"],
         derivatives=config.get("derivatives", None),
         participant_label=config.get("participant_label", None),
         exclude_participant_label=config.get("exclude_participant_label", None)
-
     )
 
     #this adds constraints to the bids naming

docs/running_snakebids/overview.md

@@ -19,6 +19,8 @@ Indexing of large datasets can be a time-consuming process. Snakebids, through `
 1. Uncomment the lines in `snakebids.yml` containing `pybids_db_dir` and `pybids_db_reset`.
 1. The variables can be updated directly in this file or through the CLI by using `-pybidsdb-dir {dir}` to specify the database path and `--reset-db` to indicate that the database should be updated. _Note: CLI arguments take precendence if both CLI and config variables are set._
 
+Input BIDS datasets are also validated via the bids-validator. By default, this feature uses the command-line (node.js) version of the [validator](https://www.npmjs.com/package/bids-validator). If this is not found to be installed on the system, the `pybids` version of validation will be performed instead. To opt-out validation, one can invoke `--skip-bids-validation`. 
+
 Workflow mode
 =============
 

snakebids/app.py

@@ -20,6 +20,7 @@
     parse_snakebids_args,
 )
 from snakebids.exceptions import ConfigError, RunError
+from snakebids.plugins.validation import bids_validate
 from snakebids.utils.output import (
     prepare_bidsapp_output,
     write_config_file,

snakebids/cli.py

@@ -55,12 +55,16 @@ class SnakebidsArgs:
         Directory to place outputs
     pybidsdb_dir : Path
         Directory to place pybids database
+    reset_db : bool
+        Update the pybids database
     snakemake_args : list of strings
         Arguments to pass on to Snakemake
     args_dict : Dict[str, Any]
         Contains all the snakebids specific args. Meant to contain custom user args
         defined in config, as well as dynamic --filter-xx and --wildcard-xx args.
         These will eventually be printed in the new config.
+    skip_bids_validation : bool
+        Skip bids validation of input dataset
     """
 
     force: bool
@@ -69,6 +73,7 @@ class SnakebidsArgs:
     args_dict: Dict[str, Any]
     pybidsdb_dir: Optional[Path] = None
     reset_db: bool = False
+    skip_bids_validation: bool = False
 
 
 def create_parser(include_snakemake=False):
@@ -141,6 +146,13 @@ def create_parser(include_snakemake=False):
         help="Force output in a new directory that already has contents",
     )
 
+    standard_group.add_argument(
+        "--skip-bids-validation",
+        "--skip_bids-validation",
+        action="store_true",
+        help=("Skip bids validation of input dataset"),
+    )
+
     standard_group.add_argument(
         "--retrofit",
         action="store_true",
@@ -271,6 +283,7 @@ def parse_snakebids_args(parser: argparse.ArgumentParser):
             else Path(all_args[0].pybidsdb_dir).resolve()
         ),
         reset_db=all_args[0].reset_db,
+        skip_bids_validation=all_args[0].skip_bids_validation,
     )
 
 

snakebids/core/input_generation.py

@@ -34,6 +34,7 @@ def generate_inputs(
     limit_to=...,
     participant_label=...,
     exclude_participant_label=...,
+    skip_bids_validation=...,
     use_bids_inputs: Union[Literal[False], None] = ...,
 ) -> BidsDatasetDict:
     ...
@@ -51,6 +52,7 @@ def generate_inputs(
     limit_to=...,
     participant_label=...,
     exclude_participant_label=...,
+    skip_bids_validation=...,
     use_bids_inputs: Literal[True] = ...,
 ) -> BidsDataset:
     ...
@@ -67,6 +69,7 @@ def generate_inputs(
     limit_to=None,
     participant_label=None,
     exclude_participant_label=None,
+    skip_bids_validation=False,
     use_bids_inputs=None,
 ):
     """Dynamically generate snakemake inputs using pybids_inputs
@@ -129,6 +132,12 @@ def generate_inputs(
         cause errors if subject filters are also specified in pybids_inputs. It may not
         be specified if participant_label is specified
 
+    skip_bids_validation : bool, optional
+        If True, will not perform validation of the input dataset. Otherwise,
+        validation is first attempted by performing a system call to `bids-validator`
+        (e.g. node version), which is has more comprehensive coverage, before falling
+        back on the python version of the validator.
+
     use_bids_inputs : bool, optional
         If True, opts in to the new :class:`BidsDataset` output, otherwise returns the
         classic dict. Currently, the classic dict will be returned by default, however,
@@ -257,7 +266,6 @@ def generate_inputs(
         participant_label, exclude_participant_label
     )
 
-    # Generates a BIDSLayout
     layout = (
         _gen_bids_layout(
             bids_dir=bids_dir,
@@ -360,11 +368,10 @@ def _gen_bids_layout(
     return BIDSLayout(
         bids_dir,
         derivatives=derivatives,
-        validate=False,
         config=pybids_config,
         database_path=pybids_database_dir,
         reset_database=pybids_reset_database,
-        indexer=BIDSLayoutIndexer(validate=False, index_metadata=False),
+        indexer=BIDSLayoutIndexer(index_metadata=False),
     )
 
 

snakebids/plugins/__init__.py

@@ -0,0 +1,6 @@
+__submodules__ = []
+
+# <AUTOGEN_INIT>
+__all__ = []
+
+# </AUTOGEN_INIT>

snakebids/plugins/validation.py

@@ -0,0 +1,48 @@
+import json
+import logging
+import subprocess
+import tempfile
+
+from snakebids.app import SnakeBidsApp
+
+_logger = logging.getLogger(__name__)
+
+
+class InvalidBidsError(Exception):
+    """Error raised if an input BIDS dataset is invalid."""
+
+
+def bids_validate(app: SnakeBidsApp, bids_dir: str) -> None:
+    """Perform validation of dataset. Initial attempt at validation performed
+    with node-version of bids-validator. If not found, will fall back to Python
+    version of validation (same as pybids).
+
+    Parameters
+    ----------
+    app
+        Snakebids application to be run
+    bids_dir
+        BIDS organized directory to be validated
+    """
+
+    # Skip bids validation
+    if app.config["skip_bids_validation"]:
+        return
+
+    try:
+        validator_config_dict = {"ignoredFiles": ["/participants.tsv"]}
+
+        with tempfile.NamedTemporaryFile(mode="w+", suffix=".json") as temp:
+            temp.write(json.dumps(validator_config_dict))
+            temp.flush()
+
+        subprocess.check_call(["bids-validator", str(bids_dir), "-c", temp.name])
+    # If the bids-validator call can't be made
+    except FileNotFoundError:
+        _logger.warning(
+            "Bids-validator does not appear to be installed - will use python "
+            "validation."
+        )
+    # Any other bids-validator error
+    except subprocess.CalledProcessError as err:
+        raise InvalidBidsError from err

snakebids/project_template/{{cookiecutter.app_name}}/config/snakebids.yml

@@ -40,6 +40,9 @@ pybids_inputs:
 # pybids_db_dir: '/path/to/db_dir' # Leave blank if you do not wish to use this
 # pybids_db_reset: False # Change this to true to update the database
 
+# Skipping of bids validation
+skip_bids_validation: False
+
 #configuration for the command-line parameters to make available
 # passed on the argparse add_argument()
 parse_args:

snakebids/project_template/{{cookiecutter.app_name}}/workflow/Snakefile

@@ -14,6 +14,7 @@ inputs = snakebids.generate_inputs(
     derivatives=config.get("derivatives", None),
     participant_label=config.get("participant_label", None),
     exclude_participant_label=config.get("exclude_participant_label", None),
+    skip_bids_validation=config.get("skip_bids_validation", False),
     use_bids_inputs=True,
 )
 

snakebids/tests/data/dataset_description.json

@@ -0,0 +1,4 @@
+{
+    "Name": "Snakebids - test dataset",
+    "BIDSVersion": "1.8.0"
+}

snakebids/tests/mock/config.yaml

@@ -22,6 +22,8 @@ pybids_inputs:
 pybids_db_dir: '/path/to/db_dir'
 pybids_db_reset: False
 
+skip_bids_validation: False
+
 targets_by_analysis_level:
   participant:
     - ''  # if '', then the first rule is run

snakebids/tests/test_generate_inputs.py

@@ -15,6 +15,7 @@
 import more_itertools as itx
 import pytest
 from bids import BIDSLayout
+from bids.exceptions import BIDSValidationError
 from hypothesis import HealthCheck, assume, example, given, settings
 from hypothesis import strategies as st
 from pyfakefs.fake_filesystem import FakeFilesystem
@@ -914,11 +915,11 @@ def bids_fs(self, bids_fs: Optional[FakeFilesystem]):
     def test_gen_layout_returns_valid_dataset(self, tmpdir: Path):
         dataset = sb_st.datasets().example()
         create_dataset(tmpdir, dataset)
-        assert _gen_bids_layout(tmpdir, False, None, False, None)
+        assert _gen_bids_layout(tmpdir, False, False, None, False, None)
 
     def test_invalid_path_raises_error(self, tmpdir: Path):
         with pytest.raises(ValueError):
-            _gen_bids_layout(tmpdir / "foo", False, None, False)
+            _gen_bids_layout(tmpdir / "foo", False, False, None, False)
 
 
 @pytest.mark.parametrize("count", tuple(range(6)))