def test_add_term(self):
actual = OboDocument()
term = actual.add_term()
term.id = TestDocument.A_TERM_ID
expected = OboDocument()
expected_term = OboTerm()
expected_term.id = TestDocument.A_TERM_ID
expected.terms = [expected_term]
self.assertDocumentEquals(actual, expected)
def test_term_initialization(self):
term = OboTerm()
self.assertIsNone(term.id)
self.assertIsNone(term.is_anonymous)
self.assertIsNone(term.name)
self.assertIsNone(term.namespace)
self.assertIsNone(term.def_)
self.assertIsNone(term.comment)
self.assertIsNone(term.builtin)
self.assertIsNone(term.is_obsolete)
self.assertIsNone(term.created_by)
self.assertIsNone(term.creation_date)
self.assertEquals(term.alt_id, [])
self.assertEquals(term.subset, [])
self.assertEquals(term.synonym, [])
self.assertEquals(term.xref, [])
self.assertEquals(term.property_value, [])
self.assertEquals(term.is_a, [])
self.assertEquals(term.intersection_of, [])
self.assertEquals(term.union_of, [])
self.assertEquals(term.equivalent_to, [])
self.assertEquals(term.disjoint_from, [])
self.assertEquals(term.relationship, [])
self.assertEquals(term.replaced_by, [])
self.assertEquals(term.consider, [])
def test_should_read_lines(self):
actual = read((line for line in [
"format-version: 1.2\n",
"another-format-version: 1.3\n",
"[Term]\n",
"id: GO:0015137\n",
"name: citrate transmembrane transporter activity\n",
"namespace: molecular_function\n",
'''def: "Enables the transfer of citrate from one side of a membrane to the other." [GOC:ai]\n''',
"""synonym: "tricarboxylate transport protein" RELATED [] {comment="WIkipedia:Mitochondrial_carrier"}\n""",
'xref: reactome:R-HSA-433104 "NACT co-transports trivalent citrate and a sodium ion"\n',
"is_a: GO:0015142 ! tricarboxylic acid transmembrane transporter activity\n",
"is_a: GO:0042895 ! antibiotic transmembrane transporter activity\n",
"relationship: part_of GO:0015746 ! citrate transport\n",
"is_obsolete: true ! this is just to test a boolean\n",
"[Typedef]\n",
"id: ends_during\n",
"name: ends_during\n",
"namespace: external\n",
"xref: RO:0002093\n",
]))
expected = OboDocument()
expected.header.format_version = "1.2"
expected.header.another_format_version = ["1.3"]
term = OboTerm()
term.id = "GO:0015137"
term.name = "citrate transmembrane transporter activity"
term.namespace = "molecular_function"
term.def_ = OboDef(
'''Enables the transfer of citrate from one side of a membrane to the other.''',
[OboXref("GOC:ai", None)])
term.synonym = ['"tricarboxylate transport protein" RELATED []']
term.xref = OboXref(
'reactome:R-HSA-433104',
"NACT co-transports trivalent citrate and a sodium ion")
term.is_a = ["GO:0015142", "GO:0042895"]
term.relationship = ["part_of GO:0015746"]
term.is_obsolete = True
term._qualifiers["synonym"] = {
"comment": "WIkipedia:Mitochondrial_carrier"
}
typedef = OboTypedef()
typedef.id = "ends_during"
typedef.name = "ends_during"
typedef.namespace = "external"
typedef.xref = OboXref("RO:0002093", None)
expected.terms = [term]
expected.typedefs = [typedef]
self.assertDocumentEquals(actual, expected)
def expected_terms():
return [OboTerm()]
def expected_terms():
term = OboTerm()
term.is_obsolete = True
return [term]
def expected_terms():
term = OboTerm()
term.data_version = ["world"]
term.data_version2 = ["world2"]
term._qualifiers["data_version"] = {"q1": "v1"}
return [term]
def expected_terms():
term = OboTerm()
term.xref = OboXref('HELLO', 'WORLD')
return [term]
def expected_terms():
term = OboTerm()
term.def_ = OboDef("some value", [OboXref('GOC:ai', None), OboXref('HELLO', 'WORLD')])
return [term]