1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
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()
|
