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https://github.com/p2p-ld/nwb-linkml.git
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99 lines
3 KiB
Python
99 lines
3 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, flat_to_python
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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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base=flat_to_python[nwbtype]
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)
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DTypeTypes.append(atype)
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Arraylike = ClassDefinition(
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name="Arraylike",
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description= ("Container for arraylike information held in the dims, shape, and dtype properties."
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"this is a special case to be interpreted by downstream i/o. this class has no slots"
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"and is abstract by default."
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"- Each slot within a subclass indicates a possible dimension."
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"- Only dimensions that are present in all the dimension specifiers in the"
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" original schema are required."
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"- Shape requirements are indicated using max/min cardinalities on the slot."
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),
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abstract=True
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)
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AnyType = ClassDefinition(
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name="AnyType",
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class_uri="linkml:Any",
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description="""Needed because some classes in hdmf-common are datasets without dtype"""
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)
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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=[Arraylike, AnyType],
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types=DTypeTypes,
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imports=['linkml:types'],
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prefixes={
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'linkml': Prefix('linkml','https://w3id.org/linkml'),
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'nwb.language': f'https://example.com/nwb.language/'},
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default_prefix='nwb.language',
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)
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