def test_supports_multiple_treat_xrefs_as_genus_differentia_but_does_not_validate_content(self):
actual = read((line for line in
["treat-xrefs-as-genus-differentia: an invalid treat-xrefs-as-genus-differentia\n",
"treat-xrefs-as-genus-differentia: ID \"value\"\n"]))
expected = OboDocument()
expected.header.treat_xrefs_as_genus_differentia = ["an invalid treat-xrefs-as-genus-differentia", 'ID "value"']
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_owl_axioms(self):
actual = read(
(line for line in
["owl-axioms: an axiom\n", "owl-axioms: another axiom\n"]))
expected = OboDocument()
expected.header.owl_axioms = ["an axiom", "another axiom"]
self.assertDocumentEquals(actual, expected)
def test_supports_single_relax_unique_identifier_assumption_for_namespace_but_does_not_validate_content(self):
actual = read((line for line in [
"relax-unique-identifier-assumption-for-namespace: an invalid relax-unique-identifier-assumption-for-namespace"]))
expected = OboDocument()
expected.header.relax_unique_identifier_assumption_for_namespace = [
"an invalid relax-unique-identifier-assumption-for-namespace"]
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_remarks(self):
actual = read(
(line for line in
["remark: some comment\n", "remark: some other comment\n"]))
expected = OboDocument()
expected.header.remark = ["some comment", "some other comment"]
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_relax_unique_label_assumption_for_namespace_but_does_not_validate_content(self):
actual = read((line for line in [
"relax-unique-label-assumption-for-namespace: an invalid relax-unique-label-assumption-for-namespace\n",
"relax-unique-label-assumption-for-namespace: ID \"value\"\n"]))
expected = OboDocument()
expected.header.relax_unique_label_assumption_for_namespace = [
"an invalid relax-unique-label-assumption-for-namespace", 'ID "value"']
self.assertDocumentEquals(actual, expected)
def test_supports_single_treat_xrefs_as_reverse_genus_differentia_but_does_not_validate_content(self):
actual = read(
(line for line in
["treat-xrefs-as-reverse-genus-differentia: an invalid treat-xrefs-as-reverse-genus-differentia"]))
expected = OboDocument()
expected.header.treat_xrefs_as_reverse_genus_differentia = [
"an invalid treat-xrefs-as-reverse-genus-differentia"]
self.assertDocumentEquals(actual, expected)
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 test_supports_single_remark(self):
actual = read((line for line in ["remark: some comment"]))
expected = OboDocument()
expected.header.remark = ["some comment"]
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_treat_xrefs_as_equivalent_but_does_not_validate_content(self):
actual = read((line for line in ["treat-xrefs-as-equivalent: an invalid treat-xrefs-as-equivalent\n",
"treat-xrefs-as-equivalent: ID\n"]))
expected = OboDocument()
expected.header.treat_xrefs_as_equivalent = ["an invalid treat-xrefs-as-equivalent", 'ID']
self.assertDocumentEquals(actual, expected)
def test_supports_default_namespace(self):
actual = read((line for line in ["default-namespace: hello"]))
expected = OboDocument()
expected.header.default_namespace = "hello"
self.assertDocumentEquals(actual, expected)
def test_supports_auto_generated_by(self):
actual = read((line for line in ["auto-generated-by: myself"]))
expected = OboDocument()
expected.header.auto_generated_by = "myself"
self.assertDocumentEquals(actual, expected)
def test_supports_date(self):
actual = read((line for line in ["date: 22:05:1987 10:54"]))
expected = OboDocument()
expected.header.date = "22:05:1987 10:54"
self.assertDocumentEquals(actual, expected)
def test_supports_ontology(self):
actual = read((line for line in ["ontology: hello"]))
expected = OboDocument()
expected.header.ontology = "hello"
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_idspace_but_does_not_validate_content(self):
actual = read((line for line in ["idspace: an invalid idspace\n", "idspace: ID \"value\"\n"]))
expected = OboDocument()
expected.header.idspace = ["an invalid idspace", 'ID "value"']
self.assertDocumentEquals(actual, expected)
def test_supports_single_treat_xrefs_as_is_a_but_does_not_validate_content(self):
actual = read((line for line in ["treat-xrefs-as-is_a: an invalid treat-xrefs-as-is_a"]))
expected = OboDocument()
expected.header.treat_xrefs_as_is_a = ["an invalid treat-xrefs-as-is_a"]
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_treat_xrefs_as_relationship_but_does_not_validate_content(self):
actual = read((line for line in ["treat-xrefs-as-relationship: an invalid treat-xrefs-as-relationship\n",
"treat-xrefs-as-relationship: ID \"value\"\n"]))
expected = OboDocument()
expected.header.treat_xrefs_as_relationship = ["an invalid treat-xrefs-as-relationship", 'ID "value"']
self.assertDocumentEquals(actual, expected)
def test_supports_single_property_value_but_does_not_validate_content(self):
actual = read((line for line in ["property_value: an invalid property_value"]))
expected = OboDocument()
expected.header.property_value = ["an invalid property_value"]
self.assertDocumentEquals(actual, expected)
def test_supports_format_version(self):
actual = read((line for line in ["format-version: 1.2"]))
expected = OboDocument()
expected.header.format_version = "1.2"
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_synonymtypedef_but_does_not_validate_content(self):
actual = read(
(line for line in ["synonymtypedef: an invalid synonymtypedef\n", "synonymtypedef: ID \"value\"\n"]))
expected = OboDocument()
expected.header.synonymtypedef = ["an invalid synonymtypedef", 'ID "value"']
self.assertDocumentEquals(actual, expected)
def test_supports_single_synonymtypedef_but_does_not_validate_content(self):
actual = read((line for line in ["synonymtypedef: an invalid synonymtypedef"]))
expected = OboDocument()
expected.header.synonymtypedef = ["an invalid synonymtypedef"]
self.assertDocumentEquals(actual, expected)
def test_supports_multiple_imports_but_does_not_validate_url(self):
actual = read((line for line in ["import: an invalid import\n", "import: http://someurl/\n"]))
expected = OboDocument()
expected.header.import_ = ["an invalid import", "http://someurl/"]
self.assertDocumentEquals(actual, expected)
def test_supports_single_import_but_does_not_validate_url(self):
actual = read((line for line in ["import: an invalid import"]))
expected = OboDocument()
expected.header.import_ = ["an invalid import"]
self.assertDocumentEquals(actual, expected)
def test_supports_single_owl_axiom(self):
actual = read((line for line in ["owl-axioms: an axiom"]))
expected = OboDocument()
expected.header.owl_axioms = ["an axiom"]
self.assertDocumentEquals(actual, expected)
def test_supports_invalid_date(self):
"""This test should not pass, the date should be validated"""
actual = read((line for line in ["date: some invalid date"]))
expected = OboDocument()
expected.header.date = "some invalid date"
self.assertDocumentEquals(actual, expected)
def test_supports_default_relationship_id_prefix(self):
actual = read(
(line for line in ["default-relationship-id-prefix: prefix"]))
expected = OboDocument()
expected.header.default_relationship_id_prefix = "prefix"
self.assertDocumentEquals(actual, expected)
def test_supports_single_idspace_but_does_not_validate_content(self):
actual = read((line for line in ["idspace: an invalid idspace"]))
expected = OboDocument()
expected.header.idspace = ["an invalid idspace"]
self.assertDocumentEquals(actual, expected)
