class CTDTestCase(SourceTestCase):
def setUp(self):
self.source = CTD()
self.source.settestonly(True)
self.source.setnobnodes(True)
self._setDirToSource()
return
def tearDown(self):
self.source = None
return
def test_therapeutic_relationship(self):
from dipper.utils.TestUtils import TestUtils
from dipper.utils.GraphUtils import GraphUtils
from dipper import curie_map
# Make testutils object and load ttl
test_query = TestUtils(self.source.graph)
test_query.load_testgraph_from_turtle(self.source)
# Expected structure
# TODO can this be unified OBAN and the Annot models to be automatically generated?
sparql_query = """
SELECT ?assoc ?pubmed ?disease ?chemical
WHERE {
?assoc a Annotation: ;
dc:evidence OBO:ECO_0000033 ;
dc:source ?pubmed ;
:hasObject ?disease ;
:hasPredicate OBO:RO_0002606 ;
:hasSubject ?chemical .}
"""
# SPARQL variables to check
gu = GraphUtils(curie_map.get())
chem_id = 'MESH:D009538'
chem_uri = gu.getNode(chem_id)
disease_id = 'OMIM:188890'
disease_uri = gu.getNode(disease_id)
eco = 'ECO:0000033'
rel_id = gu.object_properties['substance_that_treats']
pubmed_id = 'PMID:16785264'
pubmed_uri = gu.getNode(pubmed_id)
# consider replacing with make_ctd_chem_disease_assoc_id()
assoc_id = self.source.make_association_id('ctd', chem_id, rel_id, disease_id, eco, pubmed_id)
assoc_uri = gu.getNode(assoc_id)
# One of the expected outputs from query
expected_output = [assoc_uri, pubmed_uri, disease_uri, chem_uri]
# Query graph
sparql_output = test_query.query_graph(sparql_query)
self.assertTrue(expected_output in sparql_output, "did not find expected association: " + assoc_id +
" found: " + pprint.pformat(sparql_output))
logger.info("Test query data finished.")
def setUp(self):
self.test_util = TestUtils()
self.source = CTD('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_row = [
'Nicotine', 'D009538', '', 'TOBACCO ADDICTION, SUSCEPTIBILITY TO',
'OMIM:188890', 'therapeutic', '', '', '', '12345|56789'
]
return
class CTDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.source = CTD('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_row = [
'Nicotine',
'D009538',
'',
'TOBACCO ADDICTION, SUSCEPTIBILITY TO',
'OMIM:188890',
'therapeutic',
'',
'',
'',
'12345|56789'
]
return
def tearDown(self):
self.source = None
return
def test_therapeutic_relationship(self):
# test that graph is empty
self.assertTrue(len(list(self.source.graph)) == 0)
self.source._process_interactions(self.test_row)
triples = """
:MONARCH_b6c289df47cb72653f79 a OBAN:association ;
RO:0002558 ECO:0000033 ;
dcterms:source PMID:12345, PMID:56789 ;
OBAN:association_has_object OMIM:188890 ;
OBAN:association_has_predicate RO:0002606 ;
OBAN:association_has_subject MESH:D009538 .
MESH:D009538 a owl:Class ;
rdfs:label "Nicotine" ;
biolink:category biolink:ChemicalSubstance ;
RO:0002606 OMIM:188890 .
PMID:12345 a IAO:0000013 .
PMID:56789 a IAO:0000013 .
OMIM:188890 a owl:Class ;
biolink:category biolink:DiseaseOrPhenotypicFeature .
"""
# test exact contents of graph
self.assertTrue(self.test_util.test_graph_equality(
triples, self.source.graph))
class CTDTestCase(unittest.TestCase):
def setUp(self):
self.test_util = TestUtils()
self.source = CTD('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_row = [
'Nicotine',
'D009538',
'',
'TOBACCO ADDICTION, SUSCEPTIBILITY TO',
'OMIM:188890',
'therapeutic',
'',
'',
'',
'12345|56789'
]
return
def tearDown(self):
self.source = None
return
def test_therapeutic_relationship(self):
# test that graph is empty
self.assertTrue(len(list(self.source.graph)) == 0)
self.source._process_interactions(self.test_row)
triples = """
:MONARCH_b6c289df47cb72653f79 a OBAN:association ;
RO:0002558 ECO:0000033 ;
dc:source PMID:12345, PMID:56789 ;
OBAN:association_has_object OMIM:188890 ;
OBAN:association_has_predicate RO:0002606 ;
OBAN:association_has_subject MESH:D009538 .
MESH:D009538 a owl:Class ;
rdfs:label "Nicotine" ;
RO:0002606 OMIM:188890 .
PMID:12345 a IAO:0000013 .
PMID:56789 a IAO:0000013 .
OMIM:188890 a owl:Class .
"""
# test exact contents of graph
self.assertTrue(self.test_util.test_graph_equality(
triples, self.source.graph))
def setUp(self):
self.graph = Graph()
self.curie_map = curie_map.get()
self.ctd = CTD('rdf_graph', True)
self.ctd.g = self.ctd.graph
row1 = [
'06-Paris-LA-66 protocol', 'C046983', 'foo',
'Precursor Cell Lymphoblastic Leukemia-Lymphoma', 'MESH:D054198',
'therapeutic', 'bar', 'baz', 'foo', '4519131'
]
row2 = [
'10,10-bis(4-pyridinylmethyl)-9(10H)-anthracenone', 'C112297',
'foo', 'Hyperkinesis', 'MESH:D006948', 'marker/mechanism', 'bar',
'baz', 'foo', '19098162'
]
self.ctd._process_interactions(row1)
self.ctd._process_interactions(row2)
def setUp(self):
self.graph = Graph()
self.curie_map = curie_map.get()
self.ctd = CTD()
self.ctd.graph = Graph()
self.ctd.g = self.ctd.graph
row1 = ['06-Paris-LA-66 protocol', 'C046983', 'foo',
'Precursor Cell Lymphoblastic Leukemia-Lymphoma',
'MESH:D054198', 'therapeutic', 'bar', 'baz', 'foo', '4519131']
row2 = ['10,10-bis(4-pyridinylmethyl)-9(10H)-anthracenone',
'C112297', 'foo', 'Hyperkinesis', 'MESH:D006948',
'marker/mechanism', 'bar', 'baz', 'foo', '19098162']
self.ctd._process_interactions(row1)
self.ctd._process_interactions(row2)
def setUp(self):
self.test_util = TestUtils()
self.source = CTD('rdf_graph', True)
self.source.graph = RDFGraph(True)
self.test_row = [
'Nicotine',
'D009538',
'',
'TOBACCO ADDICTION, SUSCEPTIBILITY TO',
'OMIM:188890',
'therapeutic',
'',
'',
'',
'12345|56789'
]
return
class InteractionsTestCase(unittest.TestCase):
def setUp(self):
self.graph = Graph()
self.curie_map = curie_map.get()
self.ctd = CTD()
self.ctd.graph = Graph()
self.ctd.g = self.ctd.graph
row1 = ['06-Paris-LA-66 protocol', 'C046983', 'foo',
'Precursor Cell Lymphoblastic Leukemia-Lymphoma',
'MESH:D054198', 'therapeutic', 'bar', 'baz', 'foo', '4519131']
row2 = ['10,10-bis(4-pyridinylmethyl)-9(10H)-anthracenone',
'C112297', 'foo', 'Hyperkinesis', 'MESH:D006948',
'marker/mechanism', 'bar', 'baz', 'foo', '19098162']
self.ctd._process_interactions(row1)
self.ctd._process_interactions(row2)
def tearDown(self):
self.ctd.graph = None
self.ctd = None
def test_therapeutic_relationship(self):
from dipper.utils.TestUtils import TestUtils
from dipper.utils.GraphUtils import GraphUtils
# Make testutils object and load bindings
test_query = TestUtils(self.ctd.graph)
self.ctd.load_bindings()
# Expected structure
sparql_query = """
SELECT ?assoc ?pubmed ?disease ?chemical
WHERE {
?assoc a Annotation: ;
dc:evidence OBO:ECO_0000033 ;
dc:source ?pubmed ;
:hasObject ?disease ;
:hasPredicate OBO:RO_0002606 ;
:hasSubject ?chemical .}
"""
# SPARQL variables to check
gu = GraphUtils(curie_map.get())
chem_id = 'MESH:D009538'
chem_uri = gu.getNode(chem_id)
disease_id = 'OMIM:188890'
disease_uri = gu.getNode(disease_id)
pubmed_id = 'PMID:16785264'
pubmed_uri = gu.getNode(pubmed_id)
rel_id = gu.object_properties['substance_that_treats']
eco = 'ECO:0000033'
assoc_id = self.ctd.make_association_id('ctd', chem_id, rel_id, disease_id, eco, pubmed_id)
assoc_uri = gu.getNode(assoc_id)
# Expected output from query
expected_output = [assoc_uri, pubmed_uri, disease_uri, chem_uri]
# Query graph
sparql_output = test_query.query_graph(sparql_query)
self.assertTrue(expected_output in sparql_output)
logger.info("Test finished.")
class InteractionsTestCase(unittest.TestCase):
def setUp(self):
self.graph = Graph()
self.curie_map = curie_map.get()
self.ctd = CTD('rdf_graph', True)
self.ctd.g = self.ctd.graph
row1 = [
'06-Paris-LA-66 protocol', 'C046983', 'foo',
'Precursor Cell Lymphoblastic Leukemia-Lymphoma', 'MESH:D054198',
'therapeutic', 'bar', 'baz', 'foo', '4519131'
]
row2 = [
'10,10-bis(4-pyridinylmethyl)-9(10H)-anthracenone', 'C112297',
'foo', 'Hyperkinesis', 'MESH:D006948', 'marker/mechanism', 'bar',
'baz', 'foo', '19098162'
]
self.ctd._process_interactions(row1)
self.ctd._process_interactions(row2)
def tearDown(self):
self.ctd.graph = None
self.ctd = None
def test_therapeutic_relationship(self):
from dipper.utils.TestUtils import TestUtils
# Make testutils object and load bindings
test_query = TestUtils(self.ctd.graph)
# Expected structure
sparql_query = """
SELECT ?assoc ?pubmed ?disease ?chemical
WHERE {
?assoc a Annotation: ;
dc:evidence OBO:ECO_0000033 ;
dc:source ?pubmed ;
:hasObject ?disease ;
:hasPredicate OBO:RO_0002606 ;
:hasSubject ?chemical .}
"""
# SPARQL variables to check
chem_id = 'MESH:D009538'
chem_uri = self.graph._getNode(chem_id)
disease_id = 'OMIM:188890'
disease_uri = self.graph._getNode(disease_id)
pubmed_id = 'PMID:16785264'
pubmed_uri = self.graph._getNode(pubmed_id)
rel_id = self.model.object_properties['substance_that_treats']
eco = 'ECO:0000033'
# TODO PYLINT make_association_id() does not exist in CTD
# there is "_make_association()" with a different sig
assoc_id = self.ctd.make_association_id('ctd', chem_id, rel_id,
disease_id, eco, pubmed_id)
assoc_uri = self.graph._getNode(assoc_id)
# Expected output from query
expected_output = [assoc_uri, pubmed_uri, disease_uri, chem_uri]
# Query graph
sparql_output = test_query.query_graph(sparql_query)
self.assertTrue(expected_output in sparql_output)
logger.info("Test finished.")
def setUp(self):
self.source = CTD()
self.source.settestonly(True)
self.source.setnobnodes(True)
self._setDirToSource()
return
def setUp(self):
self.source = CTD('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
class CTDTestCase(SourceTestCase):
def setUp(self):
self.source = CTD('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
def tearDown(self):
self.source = None
return
def test_therapeutic_relationship(self):
from dipper.utils.TestUtils import TestUtils
from dipper.models.Model import Model
# Make testutils object and load ttl
test_query = TestUtils(self.source.graph)
test_query.load_testgraph_from_turtle(self.source)
graph = self.source.graph
model = Model(graph)
# Expected structure
# TODO can this be unified OBAN and the Annot models
# to be automatically generated?
sparql_query = """
SELECT ?assoc ?disease ?rel ?chemical
WHERE {
?assoc a OBAN:association ;
OBAN:association_has_object ?disease ;
OBAN:association_has_predicate ?rel ;
OBAN:association_has_subject ?chemical .}
"""
# SPARQL variables to check
chem_id = 'MESH:D009538'
chem_uri = graph._getNode(chem_id)
disease_id = 'OMIM:188890'
disease_uri = graph._getNode(disease_id)
rel_id = model.object_properties['substance_that_treats']
rel_uri = graph._getNode(rel_id)
# TODO unused
# pubmed_id = 'PMID:16785264'
# pubmed_uri = gu.getNode(pubmed_id)
# eco = 'ECO:0000033'
assoc = G2PAssoc(graph, self.source.name, chem_id, disease_id, rel_id)
assoc_id = assoc.make_g2p_id()
assoc_uri = self.source.graph._getNode(assoc_id)
# One of the expected outputs from query
expected_output = [assoc_uri, disease_uri, rel_uri, chem_uri]
# Query graph
sparql_output = test_query.query_graph(sparql_query)
self.assertTrue(
expected_output in sparql_output,
"did not find expected association: " + str(expected_output) +
" found " +
str(len(sparql_output)) + " others:\n" + str(sparql_output))
logger.info("Test query data finished.")
def setUp(self):
self.source = CTD('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
class CTDTestCase(SourceTestCase):
def setUp(self):
self.source = CTD('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
def tearDown(self):
self.source = None
return
def test_therapeutic_relationship(self):
from dipper.utils.TestUtils import TestUtils
from dipper.models.Model import Model
# Make testutils object and load ttl
test_query = TestUtils(self.source.graph)
test_query.load_testgraph_from_turtle(self.source)
graph = self.source.graph
model = Model(graph)
# Expected structure
# TODO can this be unified OBAN and the Annot models
# to be automatically generated?
sparql_query = """
SELECT ?assoc ?disease ?rel ?chemical
WHERE {
?assoc a OBAN:association ;
OBAN:association_has_object ?disease ;
OBAN:association_has_predicate ?rel ;
OBAN:association_has_subject ?chemical .}
"""
# SPARQL variables to check
chem_id = 'MESH:D009538'
chem_uri = graph._getNode(chem_id)
disease_id = 'OMIM:188890'
disease_uri = graph._getNode(disease_id)
rel_id = model.object_properties['substance_that_treats']
rel_uri = graph._getNode(rel_id)
# TODO unused
# pubmed_id = 'PMID:16785264'
# pubmed_uri = gu.getNode(pubmed_id)
# eco = 'ECO:0000033'
assoc = G2PAssoc(graph, self.source.name, chem_id, disease_id, rel_id)
assoc_id = assoc.make_g2p_id()
assoc_uri = self.source.graph._getNode(assoc_id)
# One of the expected outputs from query
expected_output = [assoc_uri, disease_uri, rel_uri, chem_uri]
# Query graph
sparql_output = test_query.query_graph(sparql_query)
self.assertTrue(
expected_output in sparql_output,
"did not find expected association: " + str(expected_output) +
" found " + str(len(sparql_output)) + " others:\n" +
str(sparql_output))
logger.info("Test query data finished.")