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‎linkml_model/__init__.py

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from linkml_model.types import String, Integer, Boolean, Float, Double, Decimal, Time, Date, Datetime, Uriorcurie, Uri, \
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Ncname, Objectidentifier, Nodeidentifier
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from linkml_model.extensions import Extension, Extensible
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from linkml_model.annotations import Annotation, Annotatable
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from linkml_model.meta import ElementName, SchemaDefinitionName, TypeDefinitionName, SubsetDefinitionName, DefinitionName, \
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EnumDefinitionName, SlotDefinitionName, ClassDefinitionName, PrefixPrefixPrefix, LocalNameLocalNameSource, \
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AltDescriptionSource, PermissibleValueText, Element, SchemaDefinition, TypeDefinition, SubsetDefinition, \
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Definition, EnumDefinition, SlotDefinition, ClassDefinition, Prefix, LocalName, Example, AltDescription, \
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PermissibleValue, PvFormulaOptions
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‎linkml_model/annotations.py

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# Auto generated from annotations.yaml by pythongen.py version: 0.9.0
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# Generation date: 2021-03-25 11:34
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# Schema: annotations
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#
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# id: https://w3id.org/linkml/annotations
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# description: Annotations mixin
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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 typing import Optional, List, Union, Dict, ClassVar, Any
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from dataclasses import dataclass
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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.utils.metamodelcore import URIorCURIE
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from linkml_model.extensions import Extension
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from linkml_model.types import String, Uriorcurie
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metamodel_version = "1.7.0"
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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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DEFAULT_ = LINKML
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# Types
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# Class references
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@dataclass
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class Annotatable(YAMLRoot):
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"""
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mixin for classes that support annotations
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"""
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_inherited_slots: ClassVar[List[str]] = []
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class_class_uri: ClassVar[URIRef] = LINKML.Annotatable
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class_class_curie: ClassVar[str] = "linkml:Annotatable"
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class_name: ClassVar[str] = "annotatable"
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class_model_uri: ClassVar[URIRef] = LINKML.Annotatable
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annotations: Optional[Union[Union[dict, "Annotation"], List[Union[dict, "Annotation"]]]] = empty_list()
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def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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if self.annotations is None:
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self.annotations = []
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if not isinstance(self.annotations, list):
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self.annotations = [self.annotations]
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self._normalize_inlined_slot(slot_name="annotations", slot_type=Annotation, key_name="tag", inlined_as_list=True, keyed=False)
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super().__post_init__(**kwargs)
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@dataclass
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class Annotation(Extension):
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"""
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a tag/value pair with the semantics of OWL Annotation
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"""
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_inherited_slots: ClassVar[List[str]] = []
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class_class_uri: ClassVar[URIRef] = LINKML.Annotation
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class_class_curie: ClassVar[str] = "linkml:Annotation"
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class_name: ClassVar[str] = "annotation"
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class_model_uri: ClassVar[URIRef] = LINKML.Annotation
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tag: Union[str, URIorCURIE] = None
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value: str = None
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annotations: Optional[Union[Union[dict, "Annotation"], List[Union[dict, "Annotation"]]]] = empty_list()
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def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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if self.annotations is None:
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self.annotations = []
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if not isinstance(self.annotations, list):
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self.annotations = [self.annotations]
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self._normalize_inlined_slot(slot_name="annotations", slot_type=Annotation, key_name="tag", inlined_as_list=True, keyed=False)
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super().__post_init__(**kwargs)
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# Enumerations
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# Slots
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‎linkml_model/extensions.py

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# Auto generated from extensions.yaml by pythongen.py version: 0.9.0
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# Generation date: 2021-03-25 11:34
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# Schema: extensions
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#
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# id: https://w3id.org/linkml/extensions
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# description: Extension mixin
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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 typing import Optional, List, Union, Dict, ClassVar, Any
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from dataclasses import dataclass
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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.utils.metamodelcore import URIorCURIE
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from linkml_model.types import String, Uriorcurie
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metamodel_version = "1.7.0"
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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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DEFAULT_ = LINKML
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# Types
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# Class references
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@dataclass
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class Extension(YAMLRoot):
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"""
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a tag/value pair used to add non-model information to an entry
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"""
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_inherited_slots: ClassVar[List[str]] = []
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class_class_uri: ClassVar[URIRef] = LINKML.Extension
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class_class_curie: ClassVar[str] = "linkml:Extension"
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class_name: ClassVar[str] = "extension"
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class_model_uri: ClassVar[URIRef] = LINKML.Extension
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tag: Union[str, URIorCURIE] = None
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value: str = None
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extensions: Optional[Union[Union[dict, "Extension"], List[Union[dict, "Extension"]]]] = empty_list()
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def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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if self.tag is None:
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raise ValueError("tag must be supplied")
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if not isinstance(self.tag, URIorCURIE):
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self.tag = URIorCURIE(self.tag)
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if self.value is None:
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raise ValueError("value must be supplied")
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if not isinstance(self.value, str):
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self.value = str(self.value)
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if self.extensions is None:
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self.extensions = []
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if not isinstance(self.extensions, list):
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self.extensions = [self.extensions]
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self._normalize_inlined_slot(slot_name="extensions", slot_type=Extension, key_name="tag", inlined_as_list=True, keyed=False)
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super().__post_init__(**kwargs)
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@dataclass
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class Extensible(YAMLRoot):
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"""
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mixin for classes that support extension
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"""
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_inherited_slots: ClassVar[List[str]] = []
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class_class_uri: ClassVar[URIRef] = LINKML.Extensible
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class_class_curie: ClassVar[str] = "linkml:Extensible"
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class_name: ClassVar[str] = "extensible"
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class_model_uri: ClassVar[URIRef] = LINKML.Extensible
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extensions: Optional[Union[Union[dict, Extension], List[Union[dict, Extension]]]] = empty_list()
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def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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if self.extensions is None:
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self.extensions = []
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if not isinstance(self.extensions, list):
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self.extensions = [self.extensions]
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self._normalize_inlined_slot(slot_name="extensions", slot_type=Extension, key_name="tag", inlined_as_list=True, keyed=False)
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super().__post_init__(**kwargs)
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# Enumerations
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# Slots
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‎linkml_model/linkml_files.py

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import os
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from enum import Enum, auto
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from typing import Optional, Union
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import requests
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from rdflib import Namespace
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LINKML_URL_BASE = "https://w3id.org/linkml/"
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LINKML_NAMESPACE = Namespace(LINKML_URL_BASE)
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GITHUB_IO_BASE = "https://linkml.github.io/linkml-model/"
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GITHUB_BASE = "https://raw.githubusercontent.com/linkml/linkml-model/"
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LOCAL_BASE = os.path.abspath(os.path.dirname(__file__))
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GITHUB_API_BASE = "https://api.github.com/repos/linkml/linkml-model/"
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GITHUB_RELEASES = GITHUB_BASE + "releases"
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GITHUB_TAGS = GITHUB_BASE + "tags"
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class _AutoName(Enum):
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@staticmethod
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def _generate_next_value_(name, start, count, last_values):
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return name.lower()
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class Source(_AutoName):
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""" LinkML package source name """
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META = auto()
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TYPES = auto()
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MAPPINGS = auto()
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ANNOTATIONS = auto()
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EXTENSIONS = auto()
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class Format(Enum):
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""" LinkML package formats """
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GRAPHQL = "graphql"
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HTML = ""
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JSON = "json"
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JSONLD = "context.jsonld"
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JSON_SCHEMA = "schema.json"
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NATIVE_JSONLD = "model.context.jsonld"
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NATIVE_RDF = "model.ttl"
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NATIVE_SHEXC = "model.shex"
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NATIVE_SHEXJ = "model.shexj"
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OWL = "owl.ttl"
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PYTHON = "py"
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RDF = "ttl"
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SHEXC = "shex"
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SHEXJ = "shexj"
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YAML = "yaml"
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class _Path(Enum):
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""" LinkML Relative paths"""
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GRAPHQL = "graphql"
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HTML = "docs"
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JSON = "json"
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JSONLD = "jsonld"
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JSON_SCHEMA = "jsonschema"
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NATIVE_JSONLD = "jsonld"
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NATIVE_RDF = "ttl"
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NATIVE_SHEXC = "shex"
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NATIVE_SHEXJ = "shex"
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OWL = "owl"
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PYTHON = "linkml_model"
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RDF = "rdf"
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SHEXC = "shex"
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SHEXJ = "shex"
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YAML = "model/schema"
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class ReleaseTag(_AutoName):
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""" Release tags
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LATEST - the absolute latest in the supplied branch
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CURRENT - the latest _released_ version in the supplied branch """
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LATEST = auto()
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CURRENT = auto()
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def _build_path(source: Source, fmt: Format) -> str:
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""" Create the relative path for source and fmt """
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return f"{_Path[fmt.name].value}/{source.value}.{fmt.value}"
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def _build_loc(base: str, source: Source, fmt: Format) -> str:
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return f"{base}{_build_path(source, fmt)}"
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def URL_FOR(source: Source, fmt: Format) -> str:
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""" Return the URL to retrieve source in format """
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return f"{LINKML_URL_BASE}{source.value}.{fmt.value}"
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def LOCAL_PATH_FOR(source: Source, fmt: Format) -> str:
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return os.path.join(LOCAL_BASE, _build_path(source, fmt))
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def GITHUB_IO_PATH_FOR(source: Source, fmt: Format) -> str:
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return _build_loc(GITHUB_IO_BASE, source, fmt)
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def GITHUB_PATH_FOR(source: Source,
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fmt: Format,
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release: Optional[Union[ReleaseTag, str]] = ReleaseTag.CURRENT,
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branch: Optional[str] = "main") -> str:
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def do_request(url) -> object:
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resp = requests.get(url)
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if resp.ok:
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return resp.json()
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raise requests.HTTPError(f"{resp.status_code} - {resp.reason}: {url}")
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def tag_to_commit(tag: str) -> str:
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tags = do_request(f"{GITHUB_API_BASE}tags")
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for tagent in tags:
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if tagent['name'] == tag:
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return _build_loc(f"{GITHUB_BASE}blob/{tagent['commit']['sha']}/", source, fmt)
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raise ValueError(f"Tag: {tag} not found!")
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if release is not ReleaseTag.CURRENT and branch != "main":
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raise ValueError("Cannot specify both a release and a branch")
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# Return the absolute latest entry for branch
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if release is ReleaseTag.LATEST or (release is ReleaseTag.CURRENT and branch != "main"):
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return f"{GITHUB_BASE}{branch}/{_build_path(source, fmt)}"
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# Return the latest published version
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elif release is ReleaseTag.CURRENT:
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release = do_request(f"{GITHUB_API_BASE}releases/latest")
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return tag_to_commit(release['tag_name'])
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# Return a specific tag
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else:
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return tag_to_commit(release)
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