bh20sequploader/qc_metadata.py


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import schema_salad.schema
import schema_salad.ref_resolver
import logging
import pkg_resources
import logging
import traceback

def qc_metadata(metadatafile):
    schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml")
    cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")}
    (document_loader,
     avsc_names,
     schema_metadata,
     metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache)

    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
    except Exception as e:
        traceback.print_exc()
        logging.warn(e)
    return False