def test_init(self):
with self.assertRaises(ValueError):
pronto.Xref("PMC SOMETHING")
if __debug__:
with self.assertRaises(TypeError):
pronto.Xref(1)
with self.assertRaises(TypeError):
pronto.Xref("PMC:5392374", 1)
def test_term_definition_as_axiom(self):
ont = self.get_ontology("""
<owl:Ontology/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TST_001">
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a term</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TST:001</oboInOwl:id>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TST_001"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a term</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ISBN:1234</oboInOwl:hasDbXref>
</owl:Axiom>
""")
self.assertIn("TST:001", ont)
self.assertEqual(ont["TST:001"].definition, "a term")
self.assertEqual(
list(ont["TST:001"].definition.xrefs)[0], pronto.Xref("ISBN:1234"))
def test_term_synonym_as_axiom(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore", pronto.warnings.SyntaxWarning)
ont = self.get_ontology("""
<owl:Ontology/>
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TST_001">
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">stuff</oboInOwl:hasExactSynonym>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">TST:001</oboInOwl:id>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TST_001"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">stuff</owl:annotatedTarget>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ISBN:1234</oboInOwl:hasDbXref>
</owl:Axiom>
""")
self.assertIn("TST:001", ont)
self.assertEqual(len(ont["TST:001"].synonyms), 1)
syn = next(iter(ont["TST:001"].synonyms))
self.assertEqual(syn.description, "stuff")
self.assertEqual(syn.scope, "EXACT")
self.assertEqual(syn.xrefs, {pronto.Xref("ISBN:1234")})
def test_repr(self):
x1 = pronto.Xref("PMC:5392374")
self.assertEqual(repr(x1), "Xref('PMC:5392374')")
def setUp(self):
self.x1 = pronto.Xref("PMC:5392374")
self.x2 = pronto.Xref("PMC:5392374")
self.x3 = pronto.Xref("PMC:5706746")
def test_repr(self):
d1 = pronto.Definition("something")
self.assertEqual(repr(d1), "Definition('something')")
d2 = pronto.Definition("something", xrefs={pronto.Xref("Bgee:fbb")})
self.assertEqual(repr(d2), "Definition('something', xrefs={Xref('Bgee:fbb')})")
