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("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml") (document_loader, avsc_names, schema_metadata, metaschema_loader) = metadata_schema print(metadata_schema) assert(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) shex = pkg_resources.resource_stream(__name__, "../bh20sequploader/bh20seq-shex.rdf").read().decode("utf-8") rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") g.serialize(format="ntriples") if not rslt: raise Exception(reason) if __name__ == '__main__': unittest.main()