import schema_salad.schema import schema_salad.ref_resolver import schema_salad.jsonld_context # import pkg_resources import logging # import traceback # from rdflib import Graph, Namespace from pyshex.evaluate import evaluate import unittest class TestStringMethods(unittest.TestCase): def test_schema(self): with open("bh20sequploader/bh20seq-schema.yml") as schema_resource: metadata_schema = schema_salad.schema.load_schema("bh20sequploader/bh20seq-schema.yml") (document_loader, avsc_names, schema_metadata, metaschema_loader) = metadata_schema # print(metadata_schema) self.assertTrue(isinstance(avsc_names, schema_salad.avro.schema.Names)) metadatafile = "test/data/input/TN_UT2.yaml" doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) print(doc) g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx) with open("bh20sequploader/bh20seq-shex.rdf") as f: shex = f.read() # Note the https link simply acts as a URI descriptor (it does not fetch) rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") with open("test/data/regression/TN_UT2.rdf","w") as f: f.write(g.serialize(format="ntriples").decode("utf-8")) if not rslt: raise Exception(reason) if __name__ == '__main__': unittest.main()