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_evidence_model(self):
"""
Functional test for _add_evidence()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True) # Reset graph
# Test graph is empty
self.assertTrue(len(list(impc.graph)) == 0)
(p_value, percentage_change, effect_size) = self.test_set_1[23:26]
impc._add_evidence(
self.assoc_curie, self.eco_id, p_value, percentage_change, effect_size,
self.study_curie)
triples = """
:MONARCH_test_association SEPIO:0000007 <https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> .
<https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> a ECO:0000015 ;
SEPIO:0000084 <https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888>,
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> ;
SEPIO:0000085 <https://monarchinitiative.org/.well-known/genid/study> .
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> a OBI:0000175 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 1.637023e-10 .
<https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888> a STATO:0000085 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 "8.885439E-007" .
"""
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_evidence_model(self):
"""
Functional test for _add_evidence()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True) # Reset graph
# Test graph is empty
self.assertTrue(len(list(impc.graph)) == 0)
(p_value, percentage_change, effect_size) = self.test_set_1[23:26]
impc._add_evidence(
self.assoc_curie, self.eco_id, p_value, percentage_change, effect_size,
self.study_curie)
triples = """
:MONARCH_test_association SEPIO:0000007 <https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> .
<https://monarchinitiative.org/.well-known/genid/b97a98087df7a99d8a38> a ECO:0000015 ;
SEPIO:0000084 <https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888>,
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> ;
SEPIO:0000085 <https://monarchinitiative.org/.well-known/genid/study> .
<https://monarchinitiative.org/.well-known/genid/b216606de82749b03956> a OBI:0000175 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 1.637023e-10 .
<https://monarchinitiative.org/.well-known/genid/b41ad2bfd375c9de8888> a STATO:0000085 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 "8.885439E-007" .
"""
self.assertTrue(self.test_util.test_graph_equality(
triples, impc.graph))
def test_evidence_model(self):
"""
Functional test for _add_evidence()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True) # Reset graph
# Test graph is empty
self.assertTrue(len(list(impc.graph)) == 0)
impc_map = impc.open_and_parse_yaml(impc.map_files['impc_map'])
(p_value, percentage_change, effect_size) = self.test_set_1[23:26]
impc._add_evidence(self.assoc_curie, self.eco_id, impc_map, p_value,
percentage_change, effect_size, self.study_curie)
triples = """
:MONARCH_test_association SEPIO:0000007 <https://monarchinitiative.org/.well-known/genid/b097a98087df7a99> .
<https://monarchinitiative.org/.well-known/genid/b097a98087df7a99> a ECO:0000015 ;
SEPIO:0000084 <https://monarchinitiative.org/.well-known/genid/b89ee584330837c9>,
<https://monarchinitiative.org/.well-known/genid/bc0eeccdea27a1d8> ;
SEPIO:0000085 <https://monarchinitiative.org/.well-known/genid/study> .
<https://monarchinitiative.org/.well-known/genid/bc0eeccdea27a1d8> a OBI:0000175 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 1.637023e-10 .
<https://monarchinitiative.org/.well-known/genid/b89ee584330837c9> a STATO:0000085 ;
RO:0002353 <https://monarchinitiative.org/.well-known/genid/study> ;
STATO:0000129 "8.885439E-007" .
"""
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_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_provenance_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
(phenotyping_center, colony) = self.test_set_1[2:4]
(project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name, parameter_stable_id,
parameter_name) = self.test_set_1[12:19]
(statistical_method, resource_name) = self.test_set_1[26:28]
impc._add_study_provenance(phenotyping_center, colony,
project_fullname, pipeline_name,
pipeline_stable_id, procedure_stable_id,
procedure_name, parameter_stable_id,
parameter_name, statistical_method,
resource_name)
# dbg
LOG.info("Provenance graph as turtle:\n%s\n",
impc.graph.serialize(format="turtle").decode("utf-8"))
triples = """
<https://monarchinitiative.org/.well-known/genid/bdd05a8ca155ddaf415e> a OBI:0000471 ;
BFO:0000051 OBO:STATO_0000076,
<https://www.mousephenotype.org/impress/protocol/175/15> ;
BFO:0000050 IMPRESS-procedure:15 ,
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> ;
SEPIO:0000114 <https://www.mousephenotype.org/impress/parameterontologies/1867/91> ;
SEPIO:0000017 <http://www.sanger.ac.uk/> .
<https://monarchinitiative.org/.well-known/genid/b0b26361b8687b5ad9ef> a owl:NamedIndividual ;
rdfs:label "MEFW" .
<http://www.sanger.ac.uk/> a foaf:organization ;
rdfs:label "WTSI" .
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> a VIVO:Project ;
rdfs:label "Wellcome Trust Sanger Institute Mouse Genetics Project" .
<https://www.mousephenotype.org/impress/parameterontologies/1867/91> a owl:NamedIndividual ;
rdfs:label "Number of ribs right (X-ray)" .
IMPRESS-procedure:15 a owl:NamedIndividual ;
rdfs:label "MGP Select Pipeline" .
<https://www.mousephenotype.org/impress/protocol/175/15> a owl:NamedIndividual ;
rdfs:label "X-ray" .
"""
# dbg
LOG.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_provenance_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
(phenotyping_center,
colony) = self.test_set_1[2:4]
(project_name,
project_fullname,
pipeline_name,
pipeline_stable_id,
procedure_stable_id,
procedure_name,
parameter_stable_id,
parameter_name) = self.test_set_1[11:19]
(statistical_method, resource_name) = self.test_set_1[26:28]
impc._add_study_provenance(
phenotyping_center, colony,
project_name,
pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name)
# dbg
LOG.info(
"Provenance graph as turtle:\n%s\n",
impc.graph.serialize(format="turtle").decode("utf-8")
)
triples = """
<https://monarchinitiative.org/.well-known/genid/b0b26361b8687b5ad9ef> a owl:NamedIndividual ;
rdfs:label "MEFW" .
<https://monarchinitiative.org/.well-known/genid/b6f14f763c8d0629360e> a OBI:0000471 ;
BFO:0000050 <http://www.sanger.ac.uk/science/data/mouse-genomes-project>,
IMPC-pipe:MGP_001 ;
BFO:0000051 STATO:0000076,
IMPC-proc:MGP_XRY_001 ;
SEPIO:0000017 <http://www.sanger.ac.uk/> ;
SEPIO:0000114 <https://www.mousephenotype.org/impress/OntologyInfo?action=list&procID=MGP_XRY_001#IMPC_XRY_008_001> .
<http://www.sanger.ac.uk/> a foaf:organization ;
rdfs:label "WTSI" .
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> a VIVO:Project ;
rdfs:label "MGP" .
<https://www.mousephenotype.org/impress/OntologyInfo?action=list&procID=MGP_XRY_001#IMPC_XRY_008_001> a owl:NamedIndividual ;
rdfs:label "Number of ribs right (X-ray)" .
IMPC-pipe:MGP_001 a owl:NamedIndividual ;
rdfs:label "MGP Select Pipeline" .
IMPC-proc:MGP_XRY_001 a owl:NamedIndividual ;
rdfs:label "X-ray" .
"""
# dbg
LOG.info(
"Reference graph: %s",
impc.graph.serialize(format="turtle").decode("utf-8")
)
self.assertTrue(
self.test_util.test_graph_equality(triples, impc.graph))
def test_provenance_model(self):
"""
Functional test for _add_study_provenance()
"""
impc = IMPC('rdf_graph', True)
impc.graph = RDFGraph(True)
self.assertTrue(len(list(impc.graph)) == 0)
(phenotyping_center, colony) = self.test_set_1[2:4]
(project_fullname, pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name, parameter_stable_id,
parameter_name) = self.test_set_1[12:19]
(statistical_method, resource_name) = self.test_set_1[26:28]
impc._add_study_provenance(
phenotyping_center, colony,
project_fullname,
pipeline_name, pipeline_stable_id,
procedure_stable_id, procedure_name,
parameter_stable_id, parameter_name,
statistical_method, resource_name, 0)
# dbg
logger.info(
"Provenance graph as turtle:\n%s\n",
impc.graph.serialize(format="turtle").decode("utf-8")
)
triples = """
<https://monarchinitiative.org/.well-known/genid/bdd05a8ca155ddaf415e> a OBI:0000471 ;
BFO:0000051 OBO:STATO_0000076,
<https://www.mousephenotype.org/impress/protocol/175/15> ;
BFO:0000050 IMPRESS-procedure:15 ,
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> ;
SEPIO:0000114 <https://www.mousephenotype.org/impress/parameterontologies/1867/91> ;
SEPIO:0000017 <http://www.sanger.ac.uk/> .
<https://monarchinitiative.org/.well-known/genid/b0b26361b8687b5ad9ef> a owl:NamedIndividual ;
rdfs:label "MEFW" .
<http://www.sanger.ac.uk/> a foaf:organization ;
rdfs:label "WTSI" .
<http://www.sanger.ac.uk/science/data/mouse-genomes-project> a VIVO:Project ;
rdfs:label "Wellcome Trust Sanger Institute Mouse Genetics Project" .
<https://www.mousephenotype.org/impress/parameterontologies/1867/91> a owl:NamedIndividual ;
rdfs:label "Number of ribs right (X-ray)" .
IMPRESS-procedure:15 a owl:NamedIndividual ;
rdfs:label "MGP Select Pipeline" .
<https://www.mousephenotype.org/impress/protocol/175/15> a owl:NamedIndividual ;
rdfs:label "X-ray" .
"""
# 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))
