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https://github.com/p2p-ld/nwb-linkml.git
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76 lines
2 KiB
Python
76 lines
2 KiB
Python
"""
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Language elements in nwb schema language that have a fixed, alternative representation
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in LinkML. These are exported as an nwb.language.yml file along with every generated namespace
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"""
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from nwb_schema_language.datamodel.nwb_schema_pydantic import FlatDtype as FlatDtype_source
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from linkml_runtime.linkml_model import \
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ClassDefinition, \
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EnumDefinition, \
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SchemaDefinition, \
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SlotDefinition, \
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TypeDefinition,\
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Prefix,\
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PermissibleValue
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from nwb_linkml.maps.dtype import flat_to_linkml
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FlatDType = EnumDefinition(
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name="FlatDType",
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permissible_values=[PermissibleValue(p) for p in FlatDtype_source.__members__.keys()],
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)
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DimNameSlot = SlotDefinition(
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name="dim_name",
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range="string",
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description="The name of a dimension"
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)
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DimShapeSlot = SlotDefinition(
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name="dim_shape",
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range="integer",
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required=False
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)
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DimClass = ClassDefinition(
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name="Dimension",
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slots=[DimNameSlot.name, DimShapeSlot.name],
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description="A single dimension within a shape"
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)
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DimSlot = SlotDefinition(
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name="dim",
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range=DimClass.name,
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multivalued=True,
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description="Slot representing the dimensions that a Shape can have"
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)
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# ShapeClass = ClassDefinition(
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# name="Shape",
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# description="A possible shape for an array-like dataset",
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# slots=[DimSlot.name]
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# )
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DTypeTypes = []
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for nwbtype, linkmltype in flat_to_linkml.items():
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amin = None
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if nwbtype.startswith('uint'):
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amin = 0
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atype = TypeDefinition(
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name=nwbtype,
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minimum_value=amin,
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typeof=linkmltype
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)
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DTypeTypes.append(atype)
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NwbLangSchema = SchemaDefinition(
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name="nwb.language",
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id='nwb.language',
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description="Adapter objects to mimic the behavior of elements in the nwb-schema-language",
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enums=[FlatDType],
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slots=[DimNameSlot, DimShapeSlot, DimSlot],
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classes=[DimClass],
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types=DTypeTypes,
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imports=['linkml:types'],
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prefixes={'linkml': Prefix('linkml','https://w3id.org/linkml')}
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)
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