correctly generating rolled down classes. model update to follow

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -20,6 +20,7 @@ from linkml_runtime.linkml_model import (
 from pydantic import BaseModel, PrivateAttr
 
 from nwb_linkml.logging import init_logger
+from nwb_linkml.maps.dtype import float_types, integer_types, string_types
 from nwb_schema_language import Attribute, CompoundDtype, Dataset, Group, Schema
 
 if sys.version_info.minor >= 11:
@@ -308,5 +309,48 @@ def has_attrs(cls: Dataset) -> bool:
     return (
         cls.attributes is not None
         and len(cls.attributes) > 0
-        and all([not a.value for a in cls.attributes])
+        and any([not a.value for a in cls.attributes])
     )
+
+
+def defaults(cls: Dataset | Attribute) -> dict:
+    """
+    Handle default values -
+
+    * If ``value`` is present, yield `equals_string` or `equals_number` depending on dtype
+      **as well as** an ``ifabsent`` value - we both constrain the possible values to 1
+      and also supply it as the default
+    * else, if ``default_value`` is present, yield an appropriate ``ifabsent`` value
+    * If neither, yield an empty dict
+
+    Unlike nwb_schema_language, when ``value`` is set, we yield both a ``equals_*`` constraint
+    and an ``ifabsent`` constraint, because an ``equals_*`` can be declared without a default
+    in order to validate that a value is correctly set as the constrained value, and fail
+    if a value isn't provided.
+    """
+    ret = {}
+    if cls.value:
+        if cls.dtype in integer_types:
+            ret["equals_number"] = cls.value
+            ret["ifabsent"] = f"integer({cls.value})"
+        elif cls.dtype in float_types:
+            ret["equals_number"] = cls.value
+            ret["ifabsent"] = f"float({cls.value})"
+        elif cls.dtype in string_types:
+            ret["equals_string"] = cls.value
+            ret["ifabsent"] = f"string({cls.value})"
+        else:
+            ret["equals_string"] = cls.value
+            ret["ifabsent"] = cls.value
+
+    elif cls.default_value:
+        if cls.dtype in string_types:
+            ret["ifabsent"] = f"string({cls.default_value})"
+        elif cls.dtype in integer_types:
+            ret["ifabsent"] = f"int({cls.default_value})"
+        elif cls.dtype in float_types:
+            ret["ifabsent"] = f"float({cls.default_value})"
+        else:
+            ret["ifabsent"] = cls.default_value
+
+    return ret

nwb_linkml/src/nwb_linkml/adapters/attribute.py

@@ -7,26 +7,13 @@ from typing import ClassVar, Optional, Type, TypedDict
 
 from linkml_runtime.linkml_model.meta import SlotDefinition
 
-from nwb_linkml.adapters.adapter import Adapter, BuildResult, is_1d
+from nwb_linkml.adapters.adapter import Adapter, BuildResult, defaults, is_1d
 from nwb_linkml.adapters.array import ArrayAdapter
 from nwb_linkml.maps import Map
 from nwb_linkml.maps.dtype import handle_dtype, inlined
 from nwb_schema_language import Attribute
 
 
-def _make_ifabsent(val: str | int | float | None) -> str | None:
-    if val is None:
-        return None
-    elif isinstance(val, str):
-        return f"string({val})"
-    elif isinstance(val, int):
-        return f"integer({val})"
-    elif isinstance(val, float):
-        return f"float({val})"
-    else:
-        return str(val)
-
-
 class AttrDefaults(TypedDict):
     """Default fields for an attribute"""
 
@@ -38,31 +25,6 @@ class AttrDefaults(TypedDict):
 class AttributeMap(Map):
     """Base class for attribute mapping transformations :)"""
 
-    @classmethod
-    def handle_defaults(cls, attr: Attribute) -> AttrDefaults:
-        """
-        Construct arguments for linkml slot default metaslots from nwb schema lang attribute props
-        """
-        equals_string = None
-        equals_number = None
-        default_value = None
-        if attr.value:
-            if isinstance(attr.value, (int, float)):
-                equals_number = attr.value
-            elif attr.value:
-                equals_string = str(attr.value)
-
-        if equals_number:
-            default_value = _make_ifabsent(equals_number)
-        elif equals_string:
-            default_value = _make_ifabsent(equals_string)
-        elif attr.default_value:
-            default_value = _make_ifabsent(attr.default_value)
-
-        return AttrDefaults(
-            equals_string=equals_string, equals_number=equals_number, ifabsent=default_value
-        )
-
     @classmethod
     @abstractmethod
     def check(cls, attr: Attribute) -> bool:
@@ -105,7 +67,7 @@ class MapScalar(AttributeMap):
             description=attr.doc,
             required=attr.required,
             inlined=inlined(attr.dtype),
-            **cls.handle_defaults(attr),
+            **defaults(attr),
         )
         return BuildResult(slots=[slot])
 
@@ -154,7 +116,7 @@ class MapArray(AttributeMap):
             required=attr.required,
             inlined=inlined(attr.dtype),
             **expressions,
-            **cls.handle_defaults(attr),
+            **defaults(attr),
         )
         return BuildResult(slots=[slot])
 

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -7,7 +7,7 @@ from typing import ClassVar, Optional, Type
 
 from linkml_runtime.linkml_model.meta import ArrayExpression, SlotDefinition
 
-from nwb_linkml.adapters.adapter import BuildResult, has_attrs, is_1d, is_compound
+from nwb_linkml.adapters.adapter import BuildResult, defaults, has_attrs, is_1d, is_compound
 from nwb_linkml.adapters.array import ArrayAdapter
 from nwb_linkml.adapters.classes import ClassAdapter
 from nwb_linkml.maps import QUANTITY_MAP, Map
@@ -108,6 +108,7 @@ class MapScalar(DatasetMap):
             description=cls.doc,
             range=handle_dtype(cls.dtype),
             **QUANTITY_MAP[cls.quantity],
+            **defaults(cls),
         )
         res = BuildResult(slots=[this_slot])
         return res
@@ -208,7 +209,19 @@ class MapScalarAttributes(DatasetMap):
         """
         Map to a scalar attribute with an adjoining "value" slot
         """
-        value_slot = SlotDefinition(name="value", range=handle_dtype(cls.dtype), required=True)
+        # the *value slot* within the generated class is always required,
+        # but the slot in the parent class referring to this one will indicate whether the whole
+        # thing is optional or not. You can't provide the attributes of the optional dataset
+        # without providing its value
+        quantity = QUANTITY_MAP[cls.quantity].copy()
+        quantity["required"] = True
+
+        value_slot = SlotDefinition(
+            name="value",
+            range=handle_dtype(cls.dtype),
+            **quantity,
+            **defaults(cls),
+        )
         res.classes[0].attributes["value"] = value_slot
         return res
 

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -266,11 +266,7 @@ class NamespacesAdapter(Adapter):
             in_schema = False
             if isinstance(cls, str) and cls in [
                 c.neurodata_type_def for c in schema.created_classes
-            ]:
+            ] or isinstance(cls, Dataset) and cls in schema.datasets or isinstance(cls, Group) and cls in schema.groups:
-                in_schema = True
-            elif isinstance(cls, Dataset) and cls in schema.datasets:
-                in_schema = True
-            elif isinstance(cls, Group) and cls in schema.groups:
                 in_schema = True
 
             if in_schema:
@@ -397,16 +393,16 @@ def roll_down_nwb_class(
     Merge an ancestor (via ``neurodata_type_inc`` ) source class with a
     child ``target`` class.
 
-    On the first recurive pass, only those values that are set on the target are copied from the
+    On the first recursive pass, only those values that are set on the target are copied from the
     source class - this isn't a true merging, what we are after is to recursively merge all the
     values that are modified in the child class with those of the parent class below the top level,
     the top-level attributes will be carried through via normal inheritance.
 
     Rather than re-instantiating the child class, we return the dictionary so that this
     function can be used in series to merge a whole ancestry chain within
-    :class:`.NamespacesAdapter` , but this isn't exposed in the function since
+    :class:`.NamespacesAdapter` , but merging isn't exposed in the function since
-    class definitions can be spread out over many schemas, and we need the orchestration
+    ancestor class definitions can be spread out over many schemas,
-    of the adapter to have them in all cases we'd be using this.
+    and we need the orchestration of the adapter to have them in all cases we'd be using this.
 
     Args:
         source (dict): source dictionary
@@ -420,9 +416,9 @@ def roll_down_nwb_class(
 
     """
     if isinstance(source, (Group, Dataset)):
-        source = source.model_dump(exclude_unset=True, exclude_none=True)
+        source = source.model_dump(exclude_none=True)
     if isinstance(target, (Group, Dataset)):
-        target = target.model_dump(exclude_unset=True, exclude_none=True)
+        target = target.model_dump(exclude_none=True)
 
     exclude = ("neurodata_type_def",)
 

nwb_linkml/src/nwb_linkml/maps/dtype.py

@@ -66,6 +66,26 @@ flat_to_np = {
     "isodatetime": np.datetime64,
 }
 
+integer_types = {
+    "long",
+    "int64",
+    "int",
+    "int32",
+    "int16",
+    "short",
+    "int8",
+    "uint",
+    "uint32",
+    "uint16",
+    "uint8",
+    "uint64",
+}
+
+float_types = {"float", "float32", "double", "float64", "numeric"}
+
+string_types = {"text", "utf", "utf8", "utf_8", "ascii"}
+
+
 np_to_python = {
     Any: Any,
     np.number: float,

nwb_linkml/src/nwb_linkml/maps/quantity.py

@@ -9,10 +9,16 @@ We will handle cardinality of array dimensions elsewhere
 """
 
 QUANTITY_MAP = {
-    "*": {"required": False, "multivalued": True},
+    "*": {"required": None, "multivalued": True},
     "+": {"required": True, "multivalued": True},
-    "?": {"required": False, "multivalued": False},
+    "?": {"required": None, "multivalued": None},
-    1: {"required": True, "multivalued": False},
+    1: {"required": True, "multivalued": None},
     # include the NoneType for indexing
     None: {"required": None, "multivalued": None},
 }
+"""
+Map between NWB quantity values and linkml quantity metaslot values. 
+
+Use ``None`` for defaults (required: False, multivalued: False) rather than ``False``
+to avoid adding unnecessary attributes
+"""