Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

1 files changed, 36 insertions, 0 deletions

diff --git a/test/test_shex.py b/test/test_shex.py
new file mode 100644
index 0000000..728bfdc
--- /dev/null
+++ b/test/test_shex.py
@@ -0,0 +1,36 @@
+# Run with python3 test/test_shex.py
+
+import schema_salad.schema
+import schema_salad.ref_resolver
+import schema_salad.jsonld_context
+from pyshex.evaluate import evaluate
+import unittest
+
+class TestShexMethods(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()