def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
self.orphanet.rawdir = os.path.join(os.path.dirname(__file__),
'resources/orphanet')
class OrphanetTestCase(SourceTestCase):
def setUp(self):
self.source = Orphanet('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
def tearDown(self):
self.source = None
return
class OrphanetTestCase(SourceTestCase):
def setUp(self):
self.source = Orphanet('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
def tearDown(self):
self.source = None
return
def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
# Override so tests don't break when we update terms
self.globaltt = self.orphanet.open_and_parse_yaml(
os.path.join(os.path.dirname(__file__),
'./resources/test_terms.yaml'))
self.orphanet.rawdir = os.path.join(os.path.dirname(__file__),
'resources/orphanet')
class GeneVariantDiseaseTest(unittest.TestCase):
def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
self.orphanet.rawdir = os.path.join(os.path.dirname(__file__),
'resources/orphanet')
def tearDown(self):
self.orphanet = None
return
def test_germline_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:ba2ac5d2153c70e2bb98 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0004013 ;
OBAN:association_has_subject HGNC:30497 .
ENSEMBL:ENSG00000166813 a owl:Class .
HGNC:30497 a owl:Class ;
RO:0004013 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" ;
owl:equivalentClass ENSEMBL:ENSG00000166813,
ORPHA:268061 .
ORPHA:268061 a owl:Class .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
ENSEMBL:ENSG00000166813 biolink:category biolink:Gene .
ECO:0000322 biolink:category biolink:EvidenceType .
HGNC:30497 biolink:category biolink:Genotype .
HGNC:30497 biolink:category biolink:Gene .
ORPHA:268061 biolink:category biolink:Gene .
ORPHA:938475 biolink:category biolink:Disease .
MONARCH:ba2ac5d2153c70e2bb98 biolink:category biolink:Association .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
return
def test_germline_lof_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline-lof.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b9ad1b0c562ad4db3f1e a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0004012 ;
OBAN:association_has_subject ORPHA:268061 .
ORPHA:268061 RO:0004012 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
ECO:0000322 biolink:category biolink:EvidenceType .
ORPHA:268061 biolink:category biolink:Gene .
ORPHA:268061 biolink:category biolink:Genotype .
ORPHA:938475 biolink:category biolink:Disease .
MONARCH:b9ad1b0c562ad4db3f1e biolink:category biolink:Association .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
return
def test_gene_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-variant.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:bdbeb077e365ddedda20 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0004015 ;
OBAN:association_has_subject ORPHA:268061 .
ORPHA:268061 RO:0004015 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
ECO:0000322 biolink:category biolink:EvidenceType .
ORPHA:268061 biolink:category biolink:Gene .
ORPHA:268061 biolink:category biolink:Genotype .
ORPHA:938475 biolink:category biolink:Disease .
MONARCH:bdbeb077e365ddedda20 biolink:category biolink:Association .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
return
def test_unmapped_disease_assoc_type(self):
"""
Test that a gene disease type that we have
not mapped in translationtable/orphanet.yaml
raises a ValueError
"""
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-mapping.xml'
self.assertRaises(
KeyError, lambda: self.orphanet._process_diseasegene(limit=None))
return
def setUp(self):
self.source = Orphanet('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
def setUp(self):
self.source = Orphanet()
self.source.settestonly(True)
self.source.setnobnodes(True)
self._setDirToSource()
return
class GeneVariantDiseaseTest(unittest.TestCase):
def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
# Override so tests don't break when we update terms
self.globaltt = self.orphanet.open_and_parse_yaml(
os.path.join(os.path.dirname(__file__),
'./resources/test_terms.yaml'))
self.orphanet.rawdir = os.path.join(os.path.dirname(__file__),
'resources/orphanet')
def tearDown(self):
self.orphanet = None
return
def test_germline_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline.xml'
self.orphanet._process_diseasegene(limit=None)
logger.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b2cd4dfacc21d0e28c39 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object Orphanet:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/b56f798350412a34> .
ENSEMBL:ENSG00000166813 a owl:Class .
HGNC:30497 a owl:Class .
Orphanet:268061 a owl:Class ;
rdfs:label "KS1" ;
dc:description "kinesin family member 7" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf OBO:SO_0001217 ;
owl:equivalentClass ENSEMBL:ENSG00000166813,
HGNC:30497 .
<https://monarchinitiative.org/.well-known/genid/b56f798350412a34> a GENO:0000002 ;
rdfs:label "germline variant of KS1" ;
GENO:0000418 Orphanet:268061 ;
RO:0003303 Orphanet:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 .
Orphanet:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
def test_germline_lof_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline-lof.xml'
self.orphanet._process_diseasegene(limit=None)
logger.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b53dada0eb229a75e705 OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object Orphanet:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> .
Orphanet:268061 a owl:Class ;
rdfs:label "KS1" ;
dc:description "kinesin family member 7" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
<https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> a GENO:0000002 ;
rdfs:label "germline loss of function variant of KS1" ;
GENO:0000418 Orphanet:268061 ;
RO:0003303 Orphanet:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 ;
:has_functional_consequence SO:0002054 .
Orphanet:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
def test_gene_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-variant.xml'
self.orphanet._process_diseasegene(limit=None)
logger.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8"))
expected_triples = """
MONARCH:b64684a0ea6ae59fdb09 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object Orphanet:938475 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject Orphanet:268061 .
Orphanet:268061 a owl:Class ;
rdfs:label "KS1" ;
RO:0003304 Orphanet:938475 ;
dc:description "kinesin family member 7" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
Orphanet:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples,
self.orphanet.graph))
def test_unmapped_disease_assoc_type(self):
"""
Test that a gene disease type that we have
not mapped in translationtable/orphanet.yaml
raises a ValueError
"""
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-mapping.xml'
self.assertRaises(
ValueError, lambda: self.orphanet._process_diseasegene(limit=None))
def setUp(self):
self.source = Orphanet('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
class GeneVariantDiseaseTest(unittest.TestCase):
def setUp(self):
"""
"""
self.test_util = TestUtils()
self.orphanet = Orphanet('rdf_graph', True)
# Override so tests don't break when we update terms
# Note there is no such file ./resources/test_terms.yaml
# self.globaltt = self.orphanet.open_and_parse_yaml(
# os.path.join(os.path.dirname(__file__), './resources/test_terms.yaml'))
self.orphanet.rawdir = os.path.join(
os.path.dirname(__file__), 'resources/orphanet')
def tearDown(self):
self.orphanet = None
return
def test_germline_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8")
)
expected_triples = """
MONARCH:b40e89f44906ccededb6 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/bc50c3aece4f4f161d4d> .
ENSEMBL:ENSG00000166813 a owl:Class .
HGNC:30497 a owl:Class .
HGNC:30497 a owl:Class ;
rdfs:label "KS1" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf OBO:SO_0001217 ;
owl:equivalentClass ENSEMBL:ENSG00000166813,
ORPHA:268061 .
<https://monarchinitiative.org/.well-known/genid/bc50c3aece4f4f161d4d> a GENO:0000002 ;
rdfs:label "germline variant of KS1" ;
GENO:0000418 HGNC:30497;
RO:0003303 ORPHA:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(self.test_util.test_graph_equality(
expected_triples, self.orphanet.graph))
return
def test_germline_lof_variant_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-germline-lof.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.warning(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle").decode("utf-8")
)
expected_triples = """
MONARCH:b40e89f44906ccededb6 OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0003303 ;
OBAN:association_has_subject <https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> .
HGNC:30497 a owl:Class ;
rdfs:label "KS1" ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
<https://monarchinitiative.org/.well-known/genid/ba0884fb61004110> a GENO:0000002 ;
rdfs:label "germline loss of function variant of KS1" ;
GENO:0000418 HGNC:30497 ;
RO:0003303 ORPHA:938475 ;
:MONARCH_anonymous true ;
:has_cell_origin GENO:0000900 ;
:has_functional_consequence SO:0002054 .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(
self.test_util.test_graph_equality(expected_triples, self.orphanet.graph))
return
def test_gene_to_disease(self):
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-variant.xml'
self.orphanet._process_diseasegene(limit=None)
LOG.debug(
"Reference graph: %s",
self.orphanet.graph.serialize(format="turtle") .decode("utf-8")
)
expected_triples = """
MONARCH:bd8eebdc522f33aca860 a OBAN:association ;
RO:0002558 ECO:0000322 ;
OBAN:association_has_object ORPHA:938475 ;
OBAN:association_has_predicate RO:0003304 ;
OBAN:association_has_subject HGNC:30497 .
HGNC:30497 a owl:Class ;
rdfs:label "KS1" ;
RO:0003304 ORPHA:938475 ;
oboInOwl:hasExactSynonym "KAS1" ;
rdfs:subClassOf SO:0001217 .
ORPHA:938475 a owl:Class ;
rdfs:label "too much unit testing disorder" .
"""
self.assertTrue(self.test_util.test_graph_equality(
expected_triples, self.orphanet.graph))
return
def test_unmapped_disease_assoc_type(self):
"""
Test that a gene disease type that we have
not mapped in translationtable/orphanet.yaml
raises a ValueError
"""
self.orphanet.graph = RDFGraph() # Reset graph
self.orphanet.files['disease-gene']['file'] = 'orph-no-mapping.xml'
self.assertRaises(
ValueError, lambda: self.orphanet._process_diseasegene(limit=None))
return
