class_class_uri: ClassVar[URIRef] = TEST.C1 class_class_curie: ClassVar[str] = "test:C1" class_name: ClassVar[str] = "c1" class_model_uri: ClassVar[URIRef] = TEST.C1 s1: Optional[str] = SKOS.label s2: Optional[str] = SKOS.definition def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.s1 is not None and not isinstance(self.s1, str): self.s1 = str(self.s1) if self.s2 is not None and not isinstance(self.s2, str): self.s2 = str(self.s2) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.s1 = Slot(uri=TEST.s1, name="s1", curie=TEST.curie('s1'), model_uri=TEST.s1, domain=None, range=Optional[str]) slots.s2 = Slot(uri=TEST.s2, name="s2", curie=TEST.curie('s2'), model_uri=TEST.s2, domain=None, range=Optional[str])
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.annotations is None: self.annotations = [] if not isinstance(self.annotations, list): self.annotations = [self.annotations] self._normalize_inlined_slot(slot_name="annotations", slot_type=Annotation, key_name="tag", inlined_as_list=True, keyed=False) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.annotations = Slot(uri=LINKML.annotations, name="annotations", curie=LINKML.curie('annotations'), model_uri=LINKML.annotations, domain=None, range=Optional[Union[Union[dict, "Annotation"], List[Union[dict, "Annotation"]]]])
super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.extensions = Slot(uri=LINKML.extensions, name="extensions", curie=LINKML.curie('extensions'), model_uri=LINKML.extensions, domain=None, range=Optional[Union[Union[dict, Extension], List[Union[dict, Extension]]]]) slots.extension_tag = Slot(uri=LINKML.tag, name="extension_tag", curie=LINKML.curie('tag'), model_uri=LINKML.extension_tag, domain=Extension, range=Union[str, URIorCURIE]) slots.extension_value = Slot(uri=LINKML.value, name="extension_value", curie=LINKML.curie('value'), model_uri=LINKML.extension_value,
self.complete = CompleteDirectory(self.complete) super().__post_init__(**kwargs) # Enumerations class CompleteDirectory(EnumDefinitionImpl): COMPLETE = PermissibleValue( text="COMPLETE", description="The Directory contains all of the qualifying entries") PARTIAL = PermissibleValue( text="PARTIAL", description= "The directory contains only a partial listing of the qualifying entries." ) _defn = EnumDefinition(name="CompleteDirectory", ) # Slots class slots: pass slots.directory__complete = Slot(uri=TCCM.complete, name="directory__complete", curie=TCCM.curie('complete'), model_uri=TCCM.directory__complete, domain=None, range=Union[str, "CompleteDirectory"])
def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.id is None: raise ValueError("id must be supplied") if not isinstance(self.id, OntologyClassId): self.id = OntologyClassId(self.id) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=LINKML.id, name="id", curie=LINKML.curie('id'), model_uri=LINKML.id, domain=NamedThing, range=Union[str, NamedThingId]) slots.name = Slot(uri=LINKML.name, name="name", curie=LINKML.curie('name'), model_uri=LINKML.name, domain=NamedThing, range=Optional[Union[str, LabelType]])
self.id = ManagerId(self.id) for k, v in self.has_employees.items(): if not isinstance(v, Employee): self.has_employees[k] = Employee(id=k, **({} if v is None else v)) super().__post_init__(**kwargs) # Slots class slots: pass slots.id = Slot(uri=DEFAULT_.id, name="id", curie=DEFAULT_.curie('id'), model_uri=DEFAULT_.id, domain=None, range=URIRef) slots.name = Slot(uri=DEFAULT_.name, name="name", curie=DEFAULT_.curie('name'), model_uri=DEFAULT_.name, domain=None, range=Optional[str]) slots.aliases = Slot(uri=DEFAULT_.aliases, name="aliases", curie=DEFAULT_.curie('aliases'), model_uri=DEFAULT_.aliases, domain=None,
self.object = ObjectRange1Id(self.object) if self.sex_qualifier is not None and not isinstance(self.sex_qualifier, NamedThingId): self.sex_qualifier = NamedThingId(self.sex_qualifier) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=DEFAULT_.id, name="id", curie=DEFAULT_.curie('id'), model_uri=DEFAULT_.id, domain=NamedThing, range=Union[str, NamedThingId]) slots.name = Slot(uri=DEFAULT_.name, name="name", curie=DEFAULT_.curie('name'), model_uri=DEFAULT_.name, domain=NamedThing, range=str) slots.subject = Slot(uri=DEFAULT_.subject, name="subject", curie=DEFAULT_.curie('subject'), model_uri=DEFAULT_.subject, domain=None, range=Union[str, NamedThingId]) slots.object = Slot(uri=DEFAULT_.object, name="object", curie=DEFAULT_.curie('object'), model_uri=DEFAULT_.object, domain=None, range=Union[str, NamedThingId]) slots.sex_qualifier = Slot(uri=DEFAULT_.sex_qualifier, name="sex qualifier", curie=DEFAULT_.curie('sex_qualifier'), model_uri=DEFAULT_.sex_qualifier, domain=None, range=Optional[Union[str, NamedThingId]]) slots.mixin_owner_subject = Slot(uri=DEFAULT_.subject, name="mixin_owner_subject", curie=DEFAULT_.curie('subject'), model_uri=DEFAULT_.mixin_owner_subject, domain=MixinOwner, range=Union[str, SubjectRange1Id])
self.dfltns = str(self.dfltns) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.s1 = Slot(uri=TEST.s1, name="s1", curie=TEST.curie('s1'), model_uri=TEST.s1, domain=None, range=Optional[str]) slots.s1p = Slot(uri=TEST.s1p, name="s1p", curie=TEST.curie('s1p'), model_uri=TEST.s1p, domain=None, range=Optional[str]) slots.s2 = Slot(uri=TEST.s2, name="s2", curie=TEST.curie('s2'), model_uri=TEST.s2, domain=None,
self.id = TestClass3Id(self.id) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=DEFAULT_.id, name="id", curie=DEFAULT_.curie('id'), model_uri=DEFAULT_.id, domain=None, range=URIRef) slots.optional_mixin_slot = Slot(uri=DEFAULT_.optional_mixin_slot, name="optional_mixin_slot", curie=DEFAULT_.curie('optional_mixin_slot'), model_uri=DEFAULT_.optional_mixin_slot, domain=None, range=Optional[str]) slots.required_mixin_slot = Slot(uri=DEFAULT_.required_mixin_slot, name="required_mixin_slot", curie=DEFAULT_.curie('required_mixin_slot'), model_uri=DEFAULT_.required_mixin_slot, domain=None,
self.k = GeographicLocationAtTimeK(self.k) if self.timepoint is not None and not isinstance( self.timepoint, TimeType): self.timepoint = TimeType(self.timepoint) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.k = Slot(uri=DEFAULT_.k, name="k", curie=DEFAULT_.curie('k'), model_uri=DEFAULT_.k, domain=GeographicLocation, range=Union[str, GeographicLocationK]) slots.timepoint = Slot(uri=DEFAULT_.timepoint, name="timepoint", curie=DEFAULT_.curie('timepoint'), model_uri=DEFAULT_.timepoint, domain=GeographicLocationAtTime, range=Optional[Union[str, TimeType]])
class_class_uri: ClassVar[URIRef] = URIRef( "https://microbiomedata/schema/SampleClass") class_class_curie: ClassVar[str] = None class_name: ClassVar[str] = "SampleClass" class_model_uri: ClassVar[URIRef] = URIRef( "https://microbiomedata/schema/SampleClass") slot_1: Optional[Union[str, "SampleEnum"]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.slot_1 is not None and not isinstance(self.slot_1, SampleEnum): self.slot_1 = SampleEnum(self.slot_1) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.slot_1 = Slot(uri=DEFAULT_.slot_1, name="slot_1", curie=DEFAULT_.curie('slot_1'), model_uri=DEFAULT_.slot_1, domain=None, range=Optional[Union[str, "SampleEnum"]])
self.id = EId(self.id) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=DEFAULT_.id, name="id", curie=DEFAULT_.curie('id'), model_uri=DEFAULT_.id, domain=None, range=URIRef) slots.has_a = Slot(uri=DEFAULT_.has_a, name="has a", curie=DEFAULT_.curie('has_a'), model_uri=DEFAULT_.has_a, domain=None, range=Optional[Union[str, AId]]) slots.has_b = Slot(uri=DEFAULT_.has_b, name="has b", curie=DEFAULT_.curie('has_b'), model_uri=DEFAULT_.has_b, domain=None,
self.id2 = NodeIdentifier(self.id2) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=M.id, name="id", curie=M.curie('id'), model_uri=M.id, domain=None, range=URIRef) slots.hasCurie = Slot(uri=M.hasCurie, name="hasCurie", curie=M.curie('hasCurie'), model_uri=M.hasCurie, domain=None, range=Optional[Union[str, Curie]]) slots.hasURI = Slot(uri=M.hasURI, name="hasURI", curie=M.curie('hasURI'), model_uri=M.hasURI, domain=None,
@dataclass class Course(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = SAMP.Course class_class_curie: ClassVar[str] = "samp:Course" class_name: ClassVar[str] = "course" class_model_uri: ClassVar[URIRef] = SAMP.Course name: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.name is not None and not isinstance(self.name, str): self.name = str(self.name) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.name = Slot(uri=SAMP.name, name="name", curie=SAMP.curie('name'), model_uri=SAMP.name, domain=None, range=Optional[str]) slots.courses = Slot(uri=SAMP.courses, name="courses", curie=SAMP.curie('courses'), model_uri=SAMP.courses, domain=None, range=Optional[Union[dict, Course]])
# Enumerations # Slots class slots: pass slots.container__entry = Slot(uri=SCT.entry, name="container__entry", curie=SCT.curie('entry'), model_uri=SCT.container__entry, domain=None, range=Optional[Union[Dict[Union[str, ContaineeId], Union[dict, Containee]], List[Union[dict, Containee]]]]) slots.containee__id = Slot(uri=SCT.id, name="containee__id", curie=SCT.curie('id'), model_uri=SCT.containee__id, domain=None, range=URIRef) slots.containee__value = Slot(uri=SCT.value, name="containee__value",
class NamedThing(YAMLRoot): _inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = URIRef("https://example.com/test44/NamedThing") class_class_curie: ClassVar[str] = None class_name: ClassVar[str] = "named thing" class_model_uri: ClassVar[URIRef] = URIRef("https://example.com/test44/NamedThing") category: Union[Union[str, IriType], List[Union[str, IriType]]] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.category is None: raise ValueError("category must be supplied") elif not isinstance(self.category, list): self.category = [self.category] elif len(self.category) == 0: raise ValueError(f"category must be a non-empty list") self.category = [v if isinstance(v, IriType) else IriType(v) for v in self.category] super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.category = Slot(uri=RDFS.subClassOf, name="category", curie=RDFS.curie('subClassOf'), model_uri=DEFAULT_.category, domain=NamedThing, range=Union[Union[str, IriType], List[Union[str, IriType]]])
class_class_uri: ClassVar[URIRef] = URIRef( "http://example.org/tests/issue_260a/C260a") class_class_curie: ClassVar[str] = None class_name: ClassVar[str] = "C260a" class_model_uri: ClassVar[URIRef] = URIRef( "http://example.org/tests/issue_260a/C260a") id: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.id is not None and not isinstance(self.id, str): self.id = str(self.id) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=DEFAULT_.id, name="id", curie=DEFAULT_.curie('id'), model_uri=DEFAULT_.id, domain=None, range=Optional[str])
keyed=True) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.code = Slot(uri=SKOS.notation, name="code", curie=SKOS.curie('notation'), model_uri=TERMCI.code, domain=None, range=str) slots.designation = Slot(uri=SKOS.prefLabel, name="designation", curie=SKOS.curie('prefLabel'), model_uri=TERMCI.designation, domain=None, range=Optional[str]) slots.definition = Slot(uri=SKOS.definition, name="definition", curie=SKOS.curie('definition'), model_uri=TERMCI.definition, domain=None,
self.text = str(self.text) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.identifier__value = Slot(uri=TYPES.value, name="identifier__value", curie=TYPES.curie('value'), model_uri=TYPES.identifier__value, domain=None, range=Optional[str]) slots.identifier__system = Slot(uri=TYPES.system, name="identifier__system", curie=TYPES.curie('system'), model_uri=TYPES.identifier__system, domain=None, range=Optional[str]) slots.identifier__type = Slot(uri=TYPES.type, name="identifier__type", curie=TYPES.curie('type'), model_uri=TYPES.identifier__type, domain=None,
class_class_uri: ClassVar[URIRef] = URIRef( "http://example.org/tests/namespace/C1") class_class_curie: ClassVar[str] = None class_name: ClassVar[str] = "c1" class_model_uri: ClassVar[URIRef] = URIRef( "http://example.org/tests/namespace/C1") s1: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.s1 is not None and not isinstance(self.s1, str): self.s1 = str(self.s1) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.s1 = Slot(uri=DEFAULT_.s1, name="s1", curie=DEFAULT_.curie('s1'), model_uri=DEFAULT_.s1, domain=None, range=Optional[str])
# Types # Class references # Enumerations # Slots class slots: pass slots.mappings = Slot(uri=SKOS.mappingRelation, name="mappings", curie=SKOS.curie('mappingRelation'), model_uri=LINKML.mappings, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]]) slots.exact_mappings = Slot(uri=SKOS.exactMatch, name="exact mappings", curie=SKOS.curie('exactMatch'), model_uri=LINKML.exact_mappings, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]]) slots.close_mappings = Slot(uri=SKOS.closeMatch, name="close mappings", curie=SKOS.curie('closeMatch'), model_uri=LINKML.close_mappings, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]]) slots.related_mappings = Slot(uri=SKOS.relatedMatch, name="related mappings", curie=SKOS.curie('relatedMatch'), model_uri=LINKML.related_mappings, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]]) slots.narrow_mappings = Slot(uri=SKOS.narrowMatch, name="narrow mappings", curie=SKOS.curie('narrowMatch'), model_uri=LINKML.narrow_mappings, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]]) slots.broad_mappings = Slot(uri=SKOS.broadMatch, name="broad mappings", curie=SKOS.curie('broadMatch'), model_uri=LINKML.broad_mappings, domain=None, range=Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]])
id: Union[str, C3Id] = None s2: Optional[str] = None def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.id is None: raise ValueError("id must be supplied") if not isinstance(self.id, C3Id): self.id = C3Id(self.id) if self.s2 is not None and not isinstance(self.s2, str): self.s2 = str(self.s2) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=DEFAULT_.id, name="id", curie=DEFAULT_.curie('id'), model_uri=DEFAULT_.id, domain=None, range=URIRef) slots.s1 = Slot(uri=DEFAULT_.s1, name="s1", curie=DEFAULT_.curie('s1'), model_uri=DEFAULT_.s1, domain=C1, range=Optional[str]) slots.s2 = Slot(uri=DEFAULT_.s2, name="s2", curie=DEFAULT_.curie('s2'), model_uri=DEFAULT_.s2, domain=C1, range=Optional[str])
self.test_attribute_2 = str(self.test_attribute_2) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.attribute = Slot(uri=DEFAULT_.attribute, name="attribute", curie=DEFAULT_.curie('attribute'), model_uri=DEFAULT_.attribute, domain=NamedThing, range=Optional[str]) slots.test_attribute_1 = Slot(uri=DEFAULT_.test_attribute_1, name="test attribute 1", curie=DEFAULT_.curie('test_attribute_1'), model_uri=DEFAULT_.test_attribute_1, domain=NamedThing, range=Optional[str]) slots.test_attribute_2 = Slot(uri=DEFAULT_.test_attribute_2, name="test attribute 2", curie=DEFAULT_.curie('test_attribute_2'), model_uri=DEFAULT_.test_attribute_2, domain=None,
print(str(x)) x.as_str = "s:James t:17" print(str(x)) x = C(as_str="s:ess t:tee") print(str(x)) x.as_str = "a b c " # Slots class slots: pass slots.s = Slot(uri=DEFAULT_.s, name="s", curie=DEFAULT_.curie('s'), model_uri=DEFAULT_.s, domain=None, range=Optional[str]) slots.t = Slot(uri=DEFAULT_.t, name="t", curie=DEFAULT_.curie('t'), model_uri=DEFAULT_.t, domain=None, range=Optional[str]) slots.as_str = Slot(uri=DEFAULT_.as_str, name="as_str", curie=DEFAULT_.curie('as_str'), model_uri=DEFAULT_.as_str, domain=None,
code: str def __post_init__(self) -> None: self.code = str(self.code) if self.code not in MappedEvidence.defn.permissible_values: raise ValueError(f"Unknown MappedEvidence value: {self.code}") # Slots class slots: pass slots.allEnums__entry_name = Slot(uri=EVIDENCE.entry_name, name="allEnums__entry_name", curie=EVIDENCE.curie('entry_name'), model_uri=EVIDENCE.allEnums__entry_name, domain=None, range=URIRef) slots.allEnums__code_1 = Slot(uri=EVIDENCE.code_1, name="allEnums__code_1", curie=EVIDENCE.curie('code_1'), model_uri=EVIDENCE.allEnums__code_1, domain=None, range=Union[Union[str, "OpenEnum"], List[Union[str, "OpenEnum"]]]) slots.allEnums__code_2 = Slot(uri=EVIDENCE.code_2, name="allEnums__code_2", curie=EVIDENCE.curie('code_2'), model_uri=EVIDENCE.allEnums__code_2,
self.id = OntologyClassId(self.id) if self.name is not None and not isinstance(self.name, str): self.name = str(self.name) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=NMDC.id, name="id", curie=NMDC.curie('id'), model_uri=NMDC.id, domain=None, range=URIRef) slots.name = Slot(uri=NMDC.name, name="name", curie=NMDC.curie('name'), model_uri=NMDC.name, domain=None, range=Optional[str]) slots.description = Slot(uri=DCTERMS.description, name="description", curie=DCTERMS.curie('description'), model_uri=NMDC.description, domain=None, range=Optional[str]) slots.has_characteristic = Slot(uri=NMDC.has_characteristic, name="has characteristic", curie=NMDC.curie('has_characteristic'), model_uri=NMDC.has_characteristic, domain=Annotation, range=Optional[Union[ElementIdentifier, CharacteristicId]]) slots.instance_of = Slot(uri=NMDC.instance_of, name="instance of", curie=NMDC.curie('instance_of'), model_uri=NMDC.instance_of, domain=None, range=Optional[Union[ElementIdentifier, OntologyClassId]]) slots.has_raw_value = Slot(uri=NMDC.has_raw_value, name="has raw value", curie=NMDC.curie('has_raw_value'), model_uri=NMDC.has_raw_value, domain=Annotation, range=str)
self.id = BaseId(self.id) if self.value is None: raise ValueError("value must be supplied") if not isinstance(self.value, str): self.value = str(self.value) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=EX.id, name="id", curie=EX.curie('id'), model_uri=EX.id, domain=None, range=URIRef) slots.value = Slot(uri=EX.value, name="value", curie=EX.curie('value'), model_uri=EX.value, domain=None, range=str)
_inherited_slots: ClassVar[List[str]] = [] class_class_uri: ClassVar[URIRef] = URIRef( "https://microbiomedata/schema/mixs/ImportedClass") class_class_curie: ClassVar[str] = None class_name: ClassVar[str] = "imported class" class_model_uri: ClassVar[URIRef] = URIRef( "https://microbiomedata/schema/ImportedClass") # Enumerations # Slots class slots: pass slots.depth = Slot(uri=DEFAULT_['mixs/depth'], name="depth", curie=DEFAULT_.curie('mixs/depth'), model_uri=DEFAULT_.depth, domain=None, range=Optional[str]) slots.biosample_depth = Slot(uri=DEFAULT_.depth, name="biosample_depth", curie=DEFAULT_.curie('depth'), model_uri=DEFAULT_.biosample_depth, domain=Biosample, range=Optional[str])
if self.id is None: raise ValueError("id must be supplied") if not isinstance(self.id, PersonId): self.id = PersonId(self.id) if self.name is None: raise ValueError("name must be supplied") if not isinstance(self.name, str): self.name = str(self.name) if self.age is not None and not isinstance(self.age, int): self.age = int(self.age) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=BIOLINK.id, name="id", curie=BIOLINK.curie('id'), model_uri=BIOLINK.id, domain=None, range=URIRef) slots.name = Slot(uri=BIOLINK.name, name="name", curie=BIOLINK.curie('name'), model_uri=BIOLINK.name, domain=None, range=str) slots.age = Slot(uri=BIOLINK.age, name="age", curie=BIOLINK.curie('age'), model_uri=BIOLINK.age, domain=None, range=Optional[int])
self.text = str(self.text) super().__post_init__(**kwargs) # Enumerations # Slots class slots: pass slots.id = Slot(uri=CCDH.id, name="id", curie=CCDH.curie('id'), model_uri=CCDH.id, domain=None, range=URIRef) slots.specimen__identifier = Slot( uri=CCDH.identifier, name="specimen__identifier", curie=CCDH.curie('identifier'), model_uri=CCDH.specimen__identifier, domain=None, range=Optional[Union[Union[dict, Identifier], List[Union[dict, Identifier]]]]) slots.specimen__associated_project = Slot( uri=CCDH.associated_project, name="specimen__associated_project",