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registry data model
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‎src/semsql/builder/registry/registry_schema.py‎

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# Auto generated from registry_schema.yaml by pythongen.py version: 0.9.0
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# Generation date: 2022-09-05T18:53:50
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# Schema: ontology_registry
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#
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# id: https://w3id.org/semsql/registry
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# description: Ontology Registry
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# license: https://creativecommons.org/publicdomain/zero/1.0/
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import dataclasses
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import sys
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import re
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from jsonasobj2 import JsonObj, as_dict
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from typing import Optional, List, Union, Dict, ClassVar, Any
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from dataclasses import dataclass
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from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions
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from linkml_runtime.utils.slot import Slot
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from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode
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from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
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from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
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from linkml_runtime.utils.formatutils import camelcase, underscore, sfx
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from linkml_runtime.utils.enumerations import EnumDefinitionImpl
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from rdflib import Namespace, URIRef
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from linkml_runtime.utils.curienamespace import CurieNamespace
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from linkml_runtime.linkml_model.types import Integer, String
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metamodel_version = "1.7.0"
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version = None
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# Overwrite dataclasses _init_fn to add **kwargs in __init__
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dataclasses._init_fn = dataclasses_init_fn_with_kwargs
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# Namespaces
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LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
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SEMSQL_REGISTRY = CurieNamespace('semsql_registry', 'https://w3id.org/semsql/registry')
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XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#')
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DEFAULT_ = SEMSQL_REGISTRY
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# Types
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class Identifier(String):
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type_class_uri = XSD.string
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type_class_curie = "xsd:string"
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type_name = "identifier"
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type_model_uri = SEMSQL_REGISTRY.Identifier
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class HttpsIdentifier(String):
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type_class_uri = XSD.string
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type_class_curie = "xsd:string"
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type_name = "https identifier"
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type_model_uri = SEMSQL_REGISTRY.HttpsIdentifier
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class HttpIdentifier(String):
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type_class_uri = XSD.string
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type_class_curie = "xsd:string"
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type_name = "http identifier"
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type_model_uri = SEMSQL_REGISTRY.HttpIdentifier
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# Class references
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class OntologyId(extended_str):
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pass
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class PrefixMapPrefix(extended_str):
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pass
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class RegistryId(extended_str):
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pass
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@dataclass
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class Ontology(YAMLRoot):
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_inherited_slots: ClassVar[List[str]] = []
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class_class_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.Ontology
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class_class_curie: ClassVar[str] = "semsql_registry:Ontology"
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class_name: ClassVar[str] = "Ontology"
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class_model_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.Ontology
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id: Union[str, OntologyId] = None
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description: Optional[str] = None
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url: Optional[Union[str, Identifier]] = None
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has_imports: Optional[int] = None
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jsonld_context: Optional[Union[str, HttpsIdentifier]] = None
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prefixmap: Optional[Union[Union[str, PrefixMapPrefix], List[Union[str, PrefixMapPrefix]]]] = empty_list()
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named_prefixmaps: Optional[Union[str, List[str]]] = empty_list()
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format: Optional[str] = None
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compression: Optional[Union[str, "CompressionEnum"]] = None
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def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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if self._is_empty(self.id):
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self.MissingRequiredField("id")
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if not isinstance(self.id, OntologyId):
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self.id = OntologyId(self.id)
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if self.description is not None and not isinstance(self.description, str):
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self.description = str(self.description)
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if self.url is not None and not isinstance(self.url, Identifier):
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self.url = Identifier(self.url)
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if self.has_imports is not None and not isinstance(self.has_imports, int):
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self.has_imports = int(self.has_imports)
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if self.jsonld_context is not None and not isinstance(self.jsonld_context, HttpsIdentifier):
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self.jsonld_context = HttpsIdentifier(self.jsonld_context)
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if not isinstance(self.prefixmap, list):
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self.prefixmap = [self.prefixmap] if self.prefixmap is not None else []
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self.prefixmap = [v if isinstance(v, PrefixMapPrefix) else PrefixMapPrefix(v) for v in self.prefixmap]
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if not isinstance(self.named_prefixmaps, list):
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self.named_prefixmaps = [self.named_prefixmaps] if self.named_prefixmaps is not None else []
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self.named_prefixmaps = [v if isinstance(v, str) else str(v) for v in self.named_prefixmaps]
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if self.format is not None and not isinstance(self.format, str):
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self.format = str(self.format)
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if self.compression is not None and not isinstance(self.compression, CompressionEnum):
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self.compression = CompressionEnum(self.compression)
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super().__post_init__(**kwargs)
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@dataclass
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class PrefixMap(YAMLRoot):
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_inherited_slots: ClassVar[List[str]] = []
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class_class_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.PrefixMap
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class_class_curie: ClassVar[str] = "semsql_registry:PrefixMap"
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class_name: ClassVar[str] = "PrefixMap"
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class_model_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.PrefixMap
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prefix: Union[str, PrefixMapPrefix] = None
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prefix_value: Optional[Union[str, HttpIdentifier]] = None
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def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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if self._is_empty(self.prefix):
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self.MissingRequiredField("prefix")
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if not isinstance(self.prefix, PrefixMapPrefix):
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self.prefix = PrefixMapPrefix(self.prefix)
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if self.prefix_value is not None and not isinstance(self.prefix_value, HttpIdentifier):
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self.prefix_value = HttpIdentifier(self.prefix_value)
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super().__post_init__(**kwargs)
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@dataclass
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class Registry(YAMLRoot):
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_inherited_slots: ClassVar[List[str]] = []
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class_class_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.Registry
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class_class_curie: ClassVar[str] = "semsql_registry:Registry"
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class_name: ClassVar[str] = "Registry"
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class_model_uri: ClassVar[URIRef] = SEMSQL_REGISTRY.Registry
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id: Union[str, RegistryId] = None
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description: Optional[str] = None
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license: Optional[str] = None
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ontologies: Optional[Union[Dict[Union[str, OntologyId], Union[dict, Ontology]], List[Union[dict, Ontology]]]] = empty_dict()
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def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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if self._is_empty(self.id):
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self.MissingRequiredField("id")
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if not isinstance(self.id, RegistryId):
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self.id = RegistryId(self.id)
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if self.description is not None and not isinstance(self.description, str):
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self.description = str(self.description)
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if self.license is not None and not isinstance(self.license, str):
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self.license = str(self.license)
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self._normalize_inlined_as_dict(slot_name="ontologies", slot_type=Ontology, key_name="id", keyed=True)
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super().__post_init__(**kwargs)
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# Enumerations
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class FormatEnum(EnumDefinitionImpl):
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n3 = PermissibleValue(text="n3",
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description="n3")
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_defn = EnumDefinition(
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name="FormatEnum",
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)
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class CompressionEnum(EnumDefinitionImpl):
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gzip = PermissibleValue(text="gzip",
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description="gzip")
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_defn = EnumDefinition(
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name="CompressionEnum",
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)
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# Slots
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class slots:
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pass
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slots.description = Slot(uri=SEMSQL_REGISTRY.description, name="description", curie=SEMSQL_REGISTRY.curie('description'),
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model_uri=SEMSQL_REGISTRY.description, domain=None, range=Optional[str])
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slots.url = Slot(uri=SEMSQL_REGISTRY.url, name="url", curie=SEMSQL_REGISTRY.curie('url'),
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model_uri=SEMSQL_REGISTRY.url, domain=None, range=Optional[Union[str, Identifier]])
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slots.id = Slot(uri=SEMSQL_REGISTRY.id, name="id", curie=SEMSQL_REGISTRY.curie('id'),
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model_uri=SEMSQL_REGISTRY.id, domain=None, range=URIRef)
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slots.has_imports = Slot(uri=SEMSQL_REGISTRY.has_imports, name="has_imports", curie=SEMSQL_REGISTRY.curie('has_imports'),
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model_uri=SEMSQL_REGISTRY.has_imports, domain=None, range=Optional[int])
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slots.jsonld_context = Slot(uri=SEMSQL_REGISTRY.jsonld_context, name="jsonld_context", curie=SEMSQL_REGISTRY.curie('jsonld_context'),
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model_uri=SEMSQL_REGISTRY.jsonld_context, domain=None, range=Optional[Union[str, HttpsIdentifier]])
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slots.prefixmap = Slot(uri=SEMSQL_REGISTRY.prefixmap, name="prefixmap", curie=SEMSQL_REGISTRY.curie('prefixmap'),
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model_uri=SEMSQL_REGISTRY.prefixmap, domain=None, range=Optional[Union[Union[str, PrefixMapPrefix], List[Union[str, PrefixMapPrefix]]]])
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slots.named_prefixmaps = Slot(uri=SEMSQL_REGISTRY.named_prefixmaps, name="named_prefixmaps", curie=SEMSQL_REGISTRY.curie('named_prefixmaps'),
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model_uri=SEMSQL_REGISTRY.named_prefixmaps, domain=None, range=Optional[Union[str, List[str]]])
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slots.format = Slot(uri=SEMSQL_REGISTRY.format, name="format", curie=SEMSQL_REGISTRY.curie('format'),
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model_uri=SEMSQL_REGISTRY.format, domain=None, range=Optional[str])
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slots.compression = Slot(uri=SEMSQL_REGISTRY.compression, name="compression", curie=SEMSQL_REGISTRY.curie('compression'),
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model_uri=SEMSQL_REGISTRY.compression, domain=None, range=Optional[Union[str, "CompressionEnum"]])
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slots.prefix = Slot(uri=SEMSQL_REGISTRY.prefix, name="prefix", curie=SEMSQL_REGISTRY.curie('prefix'),
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model_uri=SEMSQL_REGISTRY.prefix, domain=None, range=URIRef)
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slots.prefix_value = Slot(uri=SEMSQL_REGISTRY.prefix_value, name="prefix_value", curie=SEMSQL_REGISTRY.curie('prefix_value'),
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model_uri=SEMSQL_REGISTRY.prefix_value, domain=None, range=Optional[Union[str, HttpIdentifier]])
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slots.license = Slot(uri=SEMSQL_REGISTRY.license, name="license", curie=SEMSQL_REGISTRY.curie('license'),
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model_uri=SEMSQL_REGISTRY.license, domain=None, range=Optional[str])
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slots.ontologies = Slot(uri=SEMSQL_REGISTRY.ontologies, name="ontologies", curie=SEMSQL_REGISTRY.curie('ontologies'),
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model_uri=SEMSQL_REGISTRY.ontologies, domain=None, range=Optional[Union[Dict[Union[str, OntologyId], Union[dict, Ontology]], List[Union[dict, Ontology]]]])

‎src/semsql/builder/registry/registry_schema.yaml‎

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id: https://w3id.org/semsql/registry
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name: ontology_registry
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description: Ontology Registry
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imports:
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- linkml:types
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prefixes:
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linkml: https://w3id.org/linkml/
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semsql_registry: https://w3id.org/semsql/registry
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default_prefix: semsql_registry
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types:
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identifier:
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typeof: string
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https identifier:
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typeof: string
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http identifier:
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typeof: string
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enums:
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format_enum:
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permissible_values:
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n3:
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description: n3
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compression_enum:
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permissible_values:
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gzip:
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description: gzip
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slots:
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description:
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examples:
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- value: Monarch Phenomics Integrated Ontology
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range: string
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url:
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examples:
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- value: https://lov.linkeddata.es/lov.n3.gz
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range: identifier
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id:
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examples:
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- value: lov
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identifier: true
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range: string
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has_imports:
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examples:
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- value: 'True'
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range: integer
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jsonld_context:
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examples:
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- value: https://biolink.github.io/biolink-model/context.jsonld
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range: https identifier
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prefixmap:
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examples:
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- value: '[''$ref:Prefixmap'', ''$ref:Prefixmap'']'
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multivalued: true
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range: PrefixMap
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named_prefixmaps:
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examples:
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- value: '[''sweet'', ''prefixcc'']'
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multivalued: true
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range: string
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format:
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examples:
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- value: n3
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#range: format_enum
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compression:
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examples:
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- value: gzip
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range: compression_enum
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prefix:
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examples:
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- value: fix
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identifier: true
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range: string
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prefix_value:
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examples:
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- value: http://purl.org/obo/owl/FIX#
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range: http identifier
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license:
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examples:
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- value: CC0
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range: string
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ontologies:
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examples:
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- value: '[''$ref:Ontology'', ''$ref:Ontology'', ''$ref:Ontology'', ''$ref:Ontology'',
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''$ref:Ontology'', ''$ref:Ontology'', ''$ref:Ontology'', ''$ref:Ontology'',
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''$ref:Ontology'', ''$ref:Ontology'', ''$ref:Ontology'', ''$ref:Ontology'',
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''$ref:Ontology'']'
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multivalued: true
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inlined: true
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inlined_as_list: false
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range: Ontology
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suppress:
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range: boolean
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classes:
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Ontology:
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slots:
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- description
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- url
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- id
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- has_imports
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- jsonld_context
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- prefixmap
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- named_prefixmaps
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- format
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- compression
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- suppress
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PrefixMap:
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slots:
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- prefix
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- prefix_value
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Registry:
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slots:
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- id
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- description
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- license
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- ontologies
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tree_root: true
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