def test_all_nodes(self):
outf = StringIO()
with (redirect_stderr(outf)):
evaluate_cli(
f"{rdffile} {shexfile} -s http://example.org/shapes/S".split())
self.assertEqual(
'Error: You must specify one or more graph focus nodes, supply a SPARQL query, '
'or use the "-A" option',
outf.getvalue().strip())
outf = StringIO()
with (redirect_stdout(outf)):
evaluate_cli(
f"{rdffile} {shexfile} -A -s http://example.org/shapes/S".
split())
self.assertEqual(
"""Errors:
Focus: http://a.example/s1
Start: http://example.org/shapes/S
Reason: Testing :s1 against shape http://example.org/shapes/S
No matching triples found for predicate :s4
Focus: http://a.example/s2
Start: http://example.org/shapes/S
Reason: Testing :s2 against shape http://example.org/shapes/S
No matching triples found for predicate :s4
Focus: http://a.example/s3
Start: http://example.org/shapes/S
Reason: Testing :s3 against shape http://example.org/shapes/S
No matching triples found for predicate :s4""",
outf.getvalue().strip())
def test_nostart(self):
outf = StringIO()
with (redirect_stdout(outf)):
evaluate_cli(f"{rdffile} {shexfile} -A".split())
self.assertEqual(
"""Errors:
Focus: None
Start: None
Reason: START node is not specified""",
outf.getvalue().strip())
def test_inline_rdf(self):
""" Issue #28. Make sure inline SPARQL with no carriage return works """
shex = os.path.join(data_dir, 'biolink-model.shex')
sparql = 'select ?item where{graph ?g {?item a <http://w3id.org/biolink/vocab/Protein>}}'
# This raises an InvalidSchema error
messages = StringIO()
with redirect_stdout(messages):
evaluate_cli((['-ss', '-sq', sparql, 'http://graphdb.dumontierlab.com/repositories/ncats-red-kg',
shex, '-ut', '-pb']))
print(messages.getvalue())
def test_messages(self):
""" Test failures with no reasons supplied """
shex = os.path.join(data_dir, 'biolink-model.shex')
sparql = os.path.join(data_dir, 'biolink_model.sparql')
messages = StringIO()
with redirect_stdout(messages):
evaluate_cli(
f'-ss -sq {sparql} http://graphdb.dumontierlab.com/repositories/ncats-red-kg {shex} -ut -pb'
)
for line in messages.getvalue().split('\n'):
self.assertFalse(line.strip().endswith('Reason:'))
def test_observation_online(self):
""" Test online FHIR example """
source_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)),
'data')
result = os.path.join(source_dir, 'example-haplotype2.results')
outf = StringIO()
with (redirect_stdout(outf)):
evaluate_cli(
"http://build.fhir.org/observation-example-haplotype2.ttl "
"http://build.fhir.org/observation.shex "
"-fn http://hl7.org/fhir/Observation/example-haplotype2")
with open(result) as f:
self.assertEqual(f.read(), outf.getvalue())
def test_obseration(self):
""" Test of local FHIR example """
source_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'data')
rdf = os.path.join(source_dir, 'example-haplotype2.ttl')
shex = os.path.join(source_dir, 'observation.shex')
result = os.path.join(source_dir, 'example-haplotype2.results')
outf = StringIO()
with(redirect_stdout(outf)):
evaluate_cli(f"{rdf} {shex} -fn http://hl7.org/fhir/Observation/example-haplotype2")
if not os.path.exists(result):
with open(result, 'w') as f:
f.write(outf.getvalue())
self.assertTrue(False, "Created test file -- rerun ")
with open(result) as f:
self.assertEqual(f.read(), outf.getvalue())
def test_fail(self):
""" Test max cardinality of 0 AND error reporting """
datadir = os.path.abspath(
os.path.join(os.path.dirname(__file__), 'data'))
shexpath = os.path.join(datadir, 'issue_20.shex')
rdfpath = os.path.join(datadir, 'issue_20.ttl')
expectedpath = os.path.join(datadir, 'issue_20.errors')
pl = PrefixLibrary(rdfpath)
output = StringIO()
with redirect_stdout(output):
evaluate_cli(f"{rdfpath} {shexpath} -fn {pl.EX.BPM1}")
evaluate_cli(f"{rdfpath} {shexpath} -fn {pl.EX.BPM2}")
if not os.path.exists(expectedpath):
with open(expectedpath, 'w') as f:
f.write(output.getvalue())
self.assertTrue(False, "Output created, rerun")
with open(expectedpath) as f:
expected = f.read()
self.maxDiff = None
self.assertEqual(expected, output.getvalue())
def prog_ep(self, argv: List[str]) -> bool:
return bool(evaluate_cli(argv, prog=self.testprog))
def test_anon_start(self):
self.assertEqual(0, evaluate_cli(f"{rdffile} {shexfile} -A"))