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.")
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
from dipper.utils.GraphUtils import GraphUtils
# 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.")
