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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| recursive-include tests * |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,189 @@ | ||
| import json | ||
| import logging | ||
| import os | ||
| import re | ||
| import sys | ||
| from itertools import chain | ||
|
|
||
| import click | ||
|
|
||
| if sys.version_info < (3, 9): | ||
| from importlib_resources import files | ||
| else: | ||
| from importlib.resources import files | ||
|
|
||
| from .rules import regexify_filename_rules | ||
| from .schema import export_schema, load_schema | ||
| from .validator import _bidsignore_check | ||
|
|
||
|
|
||
| @click.group() | ||
| @click.option("-v", "--verbose", count=True) | ||
| @click.option("-q", "--quiet", count=True) | ||
| def cli(verbose, quiet): | ||
| """BIDS Schema Tools""" | ||
| verbose = verbose - quiet | ||
| logging.getLogger("bidsschematools").setLevel(logging.WARNING - verbose * 10) | ||
|
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||
|
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| @cli.command() | ||
| @click.option("--schema") | ||
| @click.option("--output", default="-") | ||
| @click.pass_context | ||
| def export(ctx, schema, output): | ||
| """Export BIDS schema to JSON document""" | ||
| logger = logging.getLogger("bidsschematools") | ||
| schema = load_schema(schema) | ||
| text = export_schema(schema) | ||
| if output == "-": | ||
| logger.debug("Writing to stdout") | ||
| print(text) | ||
| else: | ||
| output = os.path.abspath(output) | ||
| logger.debug(f"Writing to {output}") | ||
| with open(output, "w") as fobj: | ||
| fobj.write(text) | ||
|
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||
|
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| @cli.command() | ||
| @click.option("--output", default="-") | ||
| @click.pass_context | ||
| def export_metaschema(ctx, output): | ||
| """Export BIDS schema to JSON document""" | ||
| metaschema = files("bidsschematools.data").joinpath("metaschema.json").read_text() | ||
| if output == "-": | ||
| print(metaschema, end="") | ||
| else: | ||
| output = os.path.abspath(output) | ||
| with open(output, "w") as fobj: | ||
| fobj.write(metaschema) | ||
|
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||
|
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| @cli.command("pre-receive-hook") | ||
| @click.option("--schema", "-s", type=click.Path(), help="Path to the BIDS schema") | ||
| @click.option( | ||
| "--input", "-i", "input_", default="-", type=click.Path(), help="Input file (default: stdin)" | ||
| ) | ||
| @click.option( | ||
| "--output", | ||
| "-o", | ||
| "output", | ||
| default="-", | ||
| type=click.Path(), | ||
| help="Output file (default: stdout)", | ||
| ) | ||
| def pre_receive_hook(schema, input_, output): | ||
| """Validate filenames from a list of files against the BIDS schema | ||
| The expected input takes the following form: | ||
| ``` | ||
| bids-hook-v2 | ||
| {"Name": "My dataset", "BIDSVersion": "1.9.0", "DatasetType": "raw"} | ||
| ignore-pattern1 | ||
| ... | ||
| ignore-patternN | ||
| 0001 | ||
| .datalad/config | ||
| .gitattributes | ||
| CHANGES | ||
| README | ||
| dataset_description.json | ||
| participants.tsv | ||
| sub-01/anat/sub-01_T1w.nii.gz | ||
| ... | ||
| ``` | ||
| The header identifies the protocol version. For protocol ``bids-hook-v2``, | ||
| the second line MUST be the dataset_description.json file, with any newlines removed. | ||
| The following lines, up to the line containing "0001", are ignore patterns | ||
| from the .bidsignore file. The lines following "0001" are the filenames to | ||
| be validated. | ||
| This is intended to be used in a git pre-receive hook. | ||
| """ | ||
| logger = logging.getLogger("bidsschematools") | ||
| schema = load_schema(schema) | ||
|
|
||
| # Slurp inputs for now; we can think about streaming later | ||
| if input_ == "-": | ||
| stream = sys.stdin | ||
| else: | ||
| stream = open(input_) | ||
|
|
||
| first_line = next(stream) | ||
| if first_line == "bids-hook-v2\n": | ||
| # V2 format: header line, description JSON, followed by legacy format | ||
| description_str = next(stream) | ||
| fail = False | ||
| try: | ||
| description: dict = json.loads(description_str) | ||
| except json.JSONDecodeError: | ||
| fail = True | ||
| if fail or not isinstance(description, dict): | ||
| logger.critical("Protocol error: invalid JSON in description") | ||
| logger.critical( | ||
| "Dataset description must be one JSON object, written to a single line" | ||
| ) | ||
| logger.critical("Received: %s", description_str) | ||
| stream.close() | ||
| sys.exit(2) | ||
| else: | ||
| # Legacy: ignore patterns, followed by "0001", followed by filenames | ||
| stream = chain([first_line], stream) | ||
| description = {} | ||
|
|
||
| dataset_type = description.get("DatasetType", "raw") | ||
| logger.info("Dataset type: %s", dataset_type) | ||
|
|
||
| ignore = [] | ||
| for line in stream: | ||
| if line == "0001\n": | ||
| break | ||
| ignore.append(line.strip()) | ||
| logger.info("Ignore patterns found: %d", len(ignore)) | ||
|
|
||
| all_rules = chain.from_iterable( | ||
| regexify_filename_rules(group, schema, level=2) | ||
| for group in (schema.rules.files.common, schema.rules.files.raw) | ||
| ) | ||
| if dataset_type == "derivative": | ||
| all_rules = chain( | ||
| all_rules, | ||
| regexify_filename_rules(schema.rules.files.derivatives, schema, level=2), | ||
| ) | ||
|
|
||
| regexes = [rule["regex"] for rule in all_rules] | ||
| # XXX Hack for phenotype files - this can be removed once we | ||
| # have a schema definition for them | ||
| regexes.append(r"phenotype/.*\.(tsv|json)") | ||
|
|
||
| output = sys.stdout if output == "-" else open(output, "w") | ||
|
|
||
| rc = 0 | ||
| any_files = False | ||
| valid_files = 0 | ||
| with output: | ||
| for filename in stream: | ||
| if not any_files: | ||
| logger.debug("Validating files, first file: %s", filename) | ||
| any_files = True | ||
| filename = filename.strip() | ||
| if any(_bidsignore_check(pattern, filename, "") for pattern in ignore): | ||
| continue | ||
| if not any(re.match(regex, filename) for regex in regexes): | ||
| print(filename, file=output) | ||
| rc = 1 | ||
| else: | ||
| valid_files += 1 | ||
|
|
||
| if valid_files == 0: | ||
| logger.error("No files to validate") | ||
| rc = 2 | ||
|
|
||
| stream.close() | ||
| sys.exit(rc) | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| cli() |
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