def test_ncname(self):
self.assertEqual('A123', NCName('A123'))
x = NCName('A1.B_C-')
self.assertEqual('A1.B_C-', x)
self.assertIsInstance(x, str)
self.assertIsInstance(x, NCName)
self.assertEqual(x, NCName(x))
x = str(x)
self.assertIsInstance(x, str)
self.assertFalse(isinstance(x, NCName))
with self.assertRaises(ValueError):
NCName('1')
with self.assertRaises(ValueError):
NCName('A12!')
def _fix_elements(self):
super()._fix_elements()
self.id_prefixes = [
v if isinstance(v, NCName) else NCName(v) for v in self.id_prefixes
]
if not isinstance(self.name, ElementName):
self.name = ElementName(self.name)
for k, v in self.local_names.items():
if not isinstance(v, LocalName):
self.local_names[k] = LocalName(k, v)
self.mappings = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.mappings
]
for k, v in self.alt_descriptions.items():
if not isinstance(v, AltDescription):
self.alt_descriptions[k] = AltDescription(k, v)
self.examples = [
v if isinstance(v, Example) else Example(**v)
for v in self.examples
]
self.in_subset = [
v
if isinstance(v, SubsetDefinitionName) else SubsetDefinitionName(v)
for v in self.in_subset
]
if self.from_schema is not None and not isinstance(
self.from_schema, URI):
self.from_schema = URI(self.from_schema)
self.see_also = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.see_also
]
def __setitem__(self, key, value):
k = NCName(key)
v = Namespace(str(value))
if k in self:
if self[k] != v:
raise ValueError(f"Namespace {k} is already mapped to {self[k]}")
else:
super().__setitem__(k, v)
def __post_init__(self, **kwargs: Dict[str, Any]):
self.id_prefixes = [
v if isinstance(v, NCName) else NCName(v) for v in self.id_prefixes
]
if self.name is None:
raise ValueError(f"name must be supplied")
if not isinstance(self.name, ElementName):
self.name = ElementName(self.name)
if self.definition_uri is not None and not isinstance(
self.definition_uri, URIorCURIE):
self.definition_uri = URIorCURIE(self.definition_uri)
for k, v in self.local_names.items():
if not isinstance(v, LocalName):
self.local_names[k] = LocalName(k, v)
self.mappings = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.mappings
]
for k, v in self.alt_descriptions.items():
if not isinstance(v, AltDescription):
self.alt_descriptions[k] = AltDescription(k, v)
self.examples = [
v if isinstance(v, Example) else Example(**v)
for v in self.examples
]
self.in_subset = [
v
if isinstance(v, SubsetDefinitionName) else SubsetDefinitionName(v)
for v in self.in_subset
]
if self.from_schema is not None and not isinstance(
self.from_schema, URI):
self.from_schema = URI(self.from_schema)
self.see_also = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.see_also
]
self.exact_mappings = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.exact_mappings
]
self.close_mappings = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.close_mappings
]
self.related_mappings = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.related_mappings
]
if self.deprecated_element_has_exact_replacement is not None and not isinstance(
self.deprecated_element_has_exact_replacement, URIorCURIE):
self.deprecated_element_has_exact_replacement = URIorCURIE(
self.deprecated_element_has_exact_replacement)
if self.deprecated_element_has_possible_replacement is not None and not isinstance(
self.deprecated_element_has_possible_replacement, URIorCURIE):
self.deprecated_element_has_possible_replacement = URIorCURIE(
self.deprecated_element_has_possible_replacement)
super().__post_init__(**kwargs)
def __post_init__(self, **kwargs: Dict[str, Any]):
if self.id is None:
raise ValueError(f"id must be supplied")
if not isinstance(self.id, C1Id):
self.id = C1Id(self.id)
if self.hasCurie is not None and not isinstance(self.hasCurie, Curie):
self.hasCurie = Curie(self.hasCurie)
if self.hasURI is not None and not isinstance(self.hasURI, URI):
self.hasURI = URI(self.hasURI)
if self.hasNcName is not None and not isinstance(
self.hasNcName, NCName):
self.hasNcName = NCName(self.hasNcName)
if self.id2 is not None and not isinstance(self.id2, NodeIdentifier):
self.id2 = NodeIdentifier(self.id2)
super().__post_init__(**kwargs)
def __post_init__(self, **kwargs: Dict[str, Any]):
if self.default_prefix is None:
self.default_prefix = sfx(str(self.id))
if self.name is None:
raise ValueError(f"name must be supplied")
if not isinstance(self.name, SchemaDefinitionName):
self.name = SchemaDefinitionName(self.name)
if self.id is None:
raise ValueError(f"id must be supplied")
if not isinstance(self.id, URI):
self.id = URI(self.id)
self.imports = [
v if isinstance(v, URIorCURIE) else URIorCURIE(v)
for v in self.imports
]
for k, v in self.prefixes.items():
if not isinstance(v, Prefix):
self.prefixes[k] = Prefix(k, v)
self.emit_prefixes = [
v if isinstance(v, NCName) else NCName(v)
for v in self.emit_prefixes
]
if self.default_range is not None and not isinstance(
self.default_range, TypeDefinitionName):
self.default_range = TypeDefinitionName(self.default_range)
for k, v in self.subsets.items():
if not isinstance(v, SubsetDefinition):
self.subsets[k] = SubsetDefinition(name=k,
**({} if v is None else v))
for k, v in self.types.items():
if not isinstance(v, TypeDefinition):
self.types[k] = TypeDefinition(name=k,
**({} if v is None else v))
for k, v in self.slots.items():
if not isinstance(v, SlotDefinition):
self.slots[k] = SlotDefinition(name=k,
**({} if v is None else v))
for k, v in self.classes.items():
if not isinstance(v, ClassDefinition):
self.classes[k] = ClassDefinition(name=k,
**({} if v is None else v))
if self.source_file_date is not None and not isinstance(
self.source_file_date, XSDDateTime):
self.source_file_date = XSDDateTime(self.source_file_date)
if self.generation_date is not None and not isinstance(
self.generation_date, XSDDateTime):
self.generation_date = XSDDateTime(self.generation_date)
super().__post_init__(**kwargs)
def add_prefixmap(self, map_name: str, include_defaults: bool= True) -> None:
"""
Add a prefixcommons map. Only prefixes that have not been previously defined are added.
:param map_name: prefixcommons map name
:param include_defaults: if True, take defaults from the map.
:return:
"""
for k, v in curie_util.read_biocontext(map_name).items():
if not k:
if include_defaults and not self._default:
self._default = v
elif k not in self:
if NCName.is_valid(k):
self[k] = v
else:
print(f"Warning: biocontext map {map_name} has illegal prefix: {k}", file=sys.stderr)
def _fix_elements(self):
super()._fix_elements()
if self.name is not None and not isinstance(self.name,
SchemaDefinitionName):
self.name = SchemaDefinitionName(self.name)
if self.id is not None and not isinstance(self.id, URI):
self.id = URI(self.id)
self.imports = [
v if isinstance(v, URI) else URI(v) for v in self.imports
]
for k, v in self.prefixes.items():
if not isinstance(v, Prefix):
self.prefixes[k] = Prefix(k, v)
self.emit_prefixes = [
v if isinstance(v, NCName) else NCName(v)
for v in self.emit_prefixes
]
if self.default_range is not None and not isinstance(
self.default_range, DefinitionName):
self.default_range = DefinitionName(self.default_range)
for k, v in self.subsets.items():
if not isinstance(v, SubsetDefinition):
self.subsets[k] = SubsetDefinition(name=k,
**({} if v is None else v))
for k, v in self.types.items():
if not isinstance(v, TypeDefinition):
self.types[k] = TypeDefinition(name=k,
**({} if v is None else v))
for k, v in self.slots.items():
if not isinstance(v, SlotDefinition):
self.slots[k] = SlotDefinition(name=k,
**({} if v is None else v))
for k, v in self.classes.items():
if not isinstance(v, ClassDefinition):
self.classes[k] = ClassDefinition(name=k,
**({} if v is None else v))
if self.source_file_date is not None and not isinstance(
self.source_file_date, XSDDate):
self.source_file_date = XSDDate(self.source_file_date)
if self.generation_date is not None and not isinstance(
self.generation_date, XSDDate):
self.generation_date = XSDDate(self.generation_date)
def uri_for(self, uri_or_curie: Any) -> URIRef:
"""
Map a curie or URI into a full URIRef.
:param uri_or_curie: "NCNAME ':' suffix" or plain URI
:return: Corresponding URI
"""
uri_or_curie = str(uri_or_curie)
if '://' in uri_or_curie:
return URIRef(uri_or_curie)
if ':' in uri_or_curie:
prefix, local = str(uri_or_curie).split(':', 1)
if not prefix:
prefix = self._default_key
elif not NCName.is_valid(prefix):
raise ValueError(f"Not a valid CURIE: {uri_or_curie}")
else:
prefix, local = self._base_key, uri_or_curie
if prefix not in self:
raise ValueError(f"Unknown CURIE prefix: {prefix}")
return URIRef(self.join(self[prefix], local))
