nwb-linkml/nwb_linkml/lang_elements.py
sneakers-the-rat 4faaa8efe8 I believe that's a full translation
or at least all the semantics are present. it's not pretty by any stretch of the imagination
2023-08-25 00:22:47 -07:00

94 lines
2.8 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)
Arraylike = ClassDefinition(
name="Arraylike",
description= ("Container for arraylike information held in the dims, shape, and dtype properties."
"this is a special case to be interpreted by downstream i/o. this class has no slots"
"and is abstract by default."
"- Each slot within a subclass indicates a possible dimension."
"- Only dimensions that are present in all the dimension specifiers in the"
" original schema are required."
"- Shape requirements are indicated using max/min cardinalities on the slot."
),
abstract=True
)
AnyType = ClassDefinition(
name="AnyType",
class_uri="linkml:Any",
description="""Needed because some classes in hdmf-common are datasets without dtype"""
)
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=[Arraylike, AnyType],
types=DTypeTypes,
imports=['linkml:types'],
prefixes={'linkml': Prefix('linkml','https://w3id.org/linkml')}
)