def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
impc._add_assertion_provenance(self.assoc_curie, self.evidence_curie)
triples = """
MONARCH:test_association SEPIO:0000015 <https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> .
<https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> a SEPIO:0000001 ;
SEPIO:0000018 <https://www.mousephenotype.org/> ;
SEPIO:0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<https://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
"""
# dbg
LOG.info(
"Assertion graph:\n %s\n", impc.graph.serialize(
format="turtle").decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(triples, impc.graph))
def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
impc._add_assertion_provenance(self.assoc_curie,
self.evidence_curie, impc_map)
sparql_query = """
SELECT *
WHERE {
MONARCH:test_association OBO:SEPIO_0000015 ?assertion.
?assertion a OBO:SEPIO_0000001 ;
OBO:SEPIO_0000018 <http://www.mousephenotype.org/> ;
OBO:SEPIO_0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<http://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
}
"""
sparql_output = impc.graph.query(sparql_query)
# Test that query passes and returns one row
self.assertEqual(len(list(sparql_output)), 1)
def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
impc._add_assertion_provenance(
self.assoc_curie, self.evidence_curie, impc_map)
triples = """
MONARCH:test_association SEPIO:0000015 <https://monarchinitiative.org/.well-known/genid/bcb2c00a5c2f9c43> .
<https://monarchinitiative.org/.well-known/genid/bcb2c00a5c2f9c43> a SEPIO:0000001 ;
SEPIO:0000018 <http://www.mousephenotype.org/> ;
SEPIO:0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<http://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
"""
# dbg
logger.debug("Reference graph: %s",
impc.graph.serialize(format="turtle")
.decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(
triples, impc.graph))
def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
impc._add_assertion_provenance(self.assoc_curie, self.evidence_curie)
triples = """
MONARCH:test_association SEPIO:0000015 <https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> .
<https://monarchinitiative.org/.well-known/genid/bf92df374a884963e805> a SEPIO:0000001 ;
SEPIO:0000018 <https://www.mousephenotype.org/> ;
SEPIO:0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<https://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
"""
# dbg
logger.info(
"Assertion graph:\n %s\n", impc.graph.serialize(
format="turtle").decode("utf-8")
)
self.assertTrue(self.test_util.test_graph_equality(triples, impc.graph))
def test_assertion_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
impc._add_assertion_provenance(self.assoc_curie, self.evidence_curie,
impc_map)
sparql_query = """
SELECT *
WHERE {
MONARCH:test_association OBO:SEPIO_0000015 ?assertion.
?assertion a OBO:SEPIO_0000001 ;
OBO:SEPIO_0000018 <http://www.mousephenotype.org/> ;
OBO:SEPIO_0000111 <https://monarchinitiative.org/.well-known/genid/evidence> .
<http://www.mousephenotype.org/> a foaf:organization ;
rdfs:label "International Mouse Phenotyping Consortium" .
}
"""
sparql_output = impc.graph.query(sparql_query)
# Test that query passes and returns one row
self.assertEqual(len(list(sparql_output)), 1)
