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)
class OboDocumentBuilder:
def __init__(self):
self.document = OboDocument()
self.scope = self.document.header
self.qualifiers = {}
self.xrefs = []
def term(self):
self.scope = self.document.add_term()
def add_xref(self, xref, description):
self.xrefs.append(OboXref(xref, description))
def def_tag_value(self, value):
definition = OboDef(value, self.xrefs)
self.xrefs = []
self.scope.def_ = definition
self._process_qualifiers("def_")
def typedef(self):
self.scope = self.document.add_typedef()
def xref_tag(self):
if len(self.xrefs) != 1:
raise OboDocumentBuildingError.expected_only_one_xref(self.xrefs)
self.scope.xref = self.xrefs.pop()
self._process_qualifiers("xref")
def tag_value_pair(self, tag, value):
attribute = OboDocumentBuilder._extract_attribute(tag)
self._ensure_attribute_is_defined(attribute)
self._set_attribute_value(tag, attribute, value)
self._process_qualifiers(attribute)
def _process_qualifiers(self, attribute):
if len(self.qualifiers) > 0:
self.scope.add_qualifiers(attribute, self.qualifiers)
self.qualifiers = {}
def boolean_tag_value_pair(self, tag, boolean_value):
attribute = OboDocumentBuilder._extract_attribute(tag)
self._set_boolean_attribute_value(tag, attribute, boolean_value)
self._process_qualifiers(attribute)
def qualifier(self, id, value):
self.qualifiers[id] = value
def _set_attribute_value(self, tag, attribute, value):
current_value = self.scope.__dict__.get(attribute)
if current_value is None:
self.scope.__dict__[attribute] = value
return
if type(current_value) == list:
current_value.append(value)
return
if current_value != value:
raise OboDocumentBuildingError.invalid_tag_pair_merge(
tag, current_value, value)
def _set_boolean_attribute_value(self, tag, attribute, value):
current_value = self.scope.__dict__.get(attribute)
if current_value is None:
self.scope.__dict__[attribute] = value
return
if type(current_value) == list:
raise OboDocumentBuildingError.unexpected_boolean_value(
tag, current_value, value)
if current_value != value:
raise OboDocumentBuildingError.invalid_tag_pair_merge(
tag, current_value, value)
def _ensure_attribute_is_defined(self, attribute):
if attribute not in self.scope.__dict__:
self.scope.__dict__[attribute] = []
@staticmethod
def _extract_attribute(tag):
attribute = tag.replace("-", "_")
if attribute == "version":
return "data_version"
if attribute == "import":
return "import_"
if attribute == "def":
return "def_"
return attribute
