mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-10 00:34:29 +00:00
77 lines
2 KiB
Python
77 lines
2 KiB
Python
|
"""
|
||
|
|
Language elements in nwb schema language that have a fixed, alternative representation
|
||
|
|
in LinkML. These are exported as an nwb.language.yml file along with every generated namespace
|
||
|
|
"""
|
||
|
|
|
||
|
|
from nwb_schema_language.datamodel.nwb_schema_pydantic import FlatDtype as FlatDtype_source
|
||
|
|
from linkml_runtime.linkml_model import \
|
||
|
|
ClassDefinition, \
|
||
|
|
EnumDefinition, \
|
||
|
|
SchemaDefinition, \
|
||
|
|
SlotDefinition, \
|
||
|
|
TypeDefinition,\
|
||
|
|
Prefix,\
|
||
|
|
PermissibleValue
|
||
|
|
from nwb_linkml.maps.dtype import flat_to_linkml
|
||
|
|
|
||
|
|
|
||
|
|
FlatDType = EnumDefinition(
|
||
|
|
name="FlatDType",
|
||
|
|
permissible_values=[PermissibleValue(p) for p in FlatDtype_source.__members__.keys()],
|
||
|
|
)
|
||
|
|
|
||
|
|
DimNameSlot = SlotDefinition(
|
||
|
|
name="dim_name",
|
||
|
|
range="string",
|
||
|
|
description="The name of a dimension"
|
||
|
|
)
|
||
|
|
DimShapeSlot = SlotDefinition(
|
||
|
|
name="dim_shape",
|
||
|
|
range="integer",
|
||
|
|
required=False
|
||
|
|
)
|
||
|
|
DimClass = ClassDefinition(
|
||
|
|
name="Dimension",
|
||
|
|
slots=[DimNameSlot.name, DimShapeSlot.name],
|
||
|
|
description="A single dimension within a shape"
|
||
|
|
)
|
||
|
|
DimSlot = SlotDefinition(
|
||
|
|
name="dim",
|
||
|
|
range=DimClass.name,
|
||
|
|
multivalued=True,
|
||
|
|
description="Slot representing the dimensions that a Shape can have"
|
||
|
|
)
|
||
|
|
|
||
|
|
# ShapeClass = ClassDefinition(
|
||
|
|
# name="Shape",
|
||
|
|
# description="A possible shape for an array-like dataset",
|
||
|
|
# slots=[DimSlot.name]
|
||
|
|
# )
|
||
|
|
|
||
|
|
DTypeTypes = []
|
||
|
|
for nwbtype, linkmltype in flat_to_linkml.items():
|
||
|
|
amin = None
|
||
|
|
if nwbtype.startswith('uint'):
|
||
|
|
amin = 0
|
||
|
|
|
||
|
|
atype = TypeDefinition(
|
||
|
|
name=nwbtype,
|
||
|
|
minimum_value=amin,
|
||
|
|
typeof=linkmltype
|
||
|
|
)
|
||
|
|
DTypeTypes.append(atype)
|
||
|
|
|
||
|
|
|
||
|
|
NwbLangSchema = SchemaDefinition(
|
||
|
|
name="nwb.language",
|
||
|
|
id='nwb.language',
|
||
|
|
description="Adapter objects to mimic the behavior of elements in the nwb-schema-language",
|
||
|
|
enums=[FlatDType],
|
||
|
|
slots=[DimNameSlot, DimShapeSlot, DimSlot],
|
||
|
|
classes=[DimClass],
|
||
|
|
types=DTypeTypes,
|
||
|
|
imports=['linkml:types'],
|
||
|
|
prefixes={'linkml': Prefix('linkml','https://w3id.org/linkml')}
|
||
|
|
)
|
||
|
|
|