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.")
