nwb-linkml/nwb_linkml/lang_elements.py

"""
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, flat_to_python


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,
        base=flat_to_python[nwbtype]
    )
    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'),
        'nwb.language': f'https://example.com/nwb.language/'},
    default_prefix='nwb.language',

)