diff options
Diffstat (limited to 'bh20sequploader/qc_metadata.py')
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 13 |
1 files changed, 12 insertions, 1 deletions
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) |