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import sys
import schema_salad.schema
import schema_salad.jsonld_context
from pyshex.evaluate import evaluate
path_yaml = sys.argv[1]
path_schema_yaml = sys.argv[2]
path_shex_rdf = sys.argv[3]
with open(path_schema_yaml, "rb") as f:
cache = {
"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": f.read().decode("utf-8")
}
metadata_schema = schema_salad.schema.load_schema(
"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml",
cache=cache
)
(document_loader, avsc_names, schema_metadata, metaschema_loader) = metadata_schema
if not isinstance(avsc_names, schema_salad.avro.schema.Names):
raise Exception(avsc_names)
with open(path_shex_rdf, "rb") as f:
shex = f.read().decode("utf-8")
doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, path_yaml, 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")
# As part of QC make sure serialization works too, this will raise
# an exception if there are invalid URIs.
g.serialize(format="ntriples")
if not rslt:
raise Exception(reason)
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