diff options
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf (renamed from bh20sequploader/validation_shape.rdf) | 2 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 11 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 13 | ||||
| -rw-r--r-- | example/metadata.yaml | 2 | ||||
| -rw-r--r-- | setup.py | 7 |
5 files changed, 29 insertions, 6 deletions
diff --git a/bh20sequploader/validation_shape.rdf b/bh20sequploader/bh20seq-shex.rdf index dd34fa9..8d3f5fc 100644 --- a/bh20sequploader/validation_shape.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -1,4 +1,4 @@ -PREFIX : <http://whatever/> +PREFIX : <https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#> PREFIX MainSchema: <http://biohackathon.org/bh20-seq-schema#MainSchema/> PREFIX hostSchema: <http://biohackathon.org/bh20-seq-schema#hostSchema/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index e0a6a9a..49d012d 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -21,16 +21,25 @@ def main(): parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ') parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') + parser.add_argument("--validate", action="store_true", help="Dry run, validate only") args = parser.parse_args() api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) - target = qc_fasta(args.sequence) + try: + target = qc_fasta(args.sequence) + except ValueError as e: + print(e) + exit(1) if not qc_metadata(args.metadata.name): print("Failed metadata qc") exit(1) + if args.validate: + print("Valid") + exit(0) + col = arvados.collection.Collection(api_client=api) with col.open(target, "w") as f: diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index e477f21..fbfd286 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -1,9 +1,12 @@ import schema_salad.schema import schema_salad.ref_resolver +import schema_salad.jsonld_context import logging import pkg_resources import logging import traceback +from rdflib import Graph, Namespace +from pyshex.evaluate import evaluate def qc_metadata(metadatafile): schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") @@ -13,13 +16,21 @@ def qc_metadata(metadatafile): schema_metadata, metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) + shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8") + if not isinstance(avsc_names, schema_salad.avro.schema.Names): print(avsc_names) return False try: doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) - return True + g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx) + rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") + + if not rslt: + print(reason) + + return rslt except Exception as e: traceback.print_exc() logging.warn(e) diff --git a/example/metadata.yaml b/example/metadata.yaml index 8bbf980..1e83400 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -17,7 +17,7 @@ sample: collecting_institution: Institute that was responsible of sampeling specimen_source: http://purl.obolibrary.org/obo/NCIT_C155831 specimen_source2: http://purl.obolibrary.org/obo/NCIT_C155835 - collection_date: 2020-01-01 + collection_date: "2020-01-01" collection_location: http://www.wikidata.org/entity/Q148 sample_storage_conditions: XXX additional_collection_information: XXX diff --git a/setup.py b/setup.py index 0e91274..4ab6329 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ try: except ImportError: tagger = egg_info_cmd.egg_info -install_requires = ["arvados-python-client", "schema-salad", "python-magic"] +install_requires = ["arvados-python-client", "schema-salad", "python-magic", "pyshex"] web_requires = ["flask", "pyyaml"] needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv) @@ -31,7 +31,10 @@ setup( author_email="peter.amstutz@curii.com", license="Apache 2.0", packages=["bh20sequploader", "bh20seqanalyzer", "bh20simplewebuploader"], - package_data={"bh20sequploader": ["bh20seq-schema.yml", "bh20seq-options.yml", "validation/formats"], + package_data={"bh20sequploader": ["bh20seq-schema.yml", + "bh20seq-options.yml", + "bh20seq-shex.rdf", + "validation/formats"], }, install_requires=install_requires, extras_require={ |