Merge pull request #14 from p2p-ld/roll-down

roll down parent inheritance recursively

.github/workflows/tests.yml

@@ -46,6 +46,10 @@ jobs:
         run: pytest
         working-directory: nwb_linkml
 
+      - name: Run nwb_schema_language Tests
+        run: pytest
+        working-directory: nwb_schema_language
+
       - name: Coveralls Parallel
         uses: coverallsapp/[email protected]
         if: runner.os != 'macOS'

docs/meta/todo.md

@@ -53,6 +53,9 @@ Loading
 - [ ] Top-level containers are still a little janky, eg. how `ProcessingModule` just accepts 
   extra args rather than properly abstracting `value` as a `__getitem__(self, key) -> T:` 
 
+Changes to linkml
+- [ ] Allow parameterizing "extra" fields, so we don't have to stuff things into `value` dicts
+
 ## Docs TODOs
 
 ```{todolist}

nwb_linkml/pyproject.toml

@@ -12,7 +12,7 @@ dependencies = [
     "nwb-models>=0.2.0",
     "pyyaml>=6.0",
     "linkml-runtime>=1.7.7",
-    "nwb-schema-language>=0.1.3",
+    "nwb-schema-language>=0.2.0",
     "rich>=13.5.2",
     #"linkml>=1.7.10",
     "linkml @ git+https://github.com/sneakers-the-rat/linkml@nwb-linkml",
@@ -22,7 +22,7 @@ dependencies = [
     "pydantic-settings>=2.0.3",
     "tqdm>=4.66.1",
     'typing-extensions>=4.12.2;python_version<"3.11"',
-    "numpydantic>=1.5.0",
+    "numpydantic>=1.6.0",
     "black>=24.4.2",
     "pandas>=2.2.2",
     "networkx>=3.3",

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -17,9 +17,10 @@
     SlotDefinition,
     TypeDefinition,
 )
-from pydantic import BaseModel
+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:
@@ -103,6 +104,7 @@ class Adapter(BaseModel):
 
     _logger: Optional[Logger] = None
     _debug: Optional[bool] = None
+    _nwb_classes: dict[str, Dataset | Group] = PrivateAttr(default_factory=dict)
 
     @property
     def debug(self) -> bool:
@@ -135,7 +137,10 @@ def get(self, name: str) -> Union[Group, Dataset]:
 
         Convenience wrapper around :meth:`.walk_field_values`
         """
-        return next(self.walk_field_values(self, "neurodata_type_def", name))
+        if name not in self._nwb_classes:
+            cls = next(self.walk_field_values(self, "neurodata_type_def", name))
+            self._nwb_classes[name] = cls
+        return self._nwb_classes[name]
 
     def get_model_with_field(self, field: str) -> Generator[Union[Group, Dataset], None, None]:
         """
@@ -170,6 +175,10 @@ def walk(
                 # so skip to avoid combinatoric walking
                 if key == "imports" and type(input).__name__ == "SchemaAdapter":
                     continue
+                # nwb_schema_language objects have a reference to their parent,
+                # which causes cycles
+                if key == "parent":
+                    continue
                 val = getattr(input, key)
                 yield (key, val)
                 if isinstance(val, (BaseModel, dict, list)):
@@ -300,5 +309,85 @@ 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
+
+
+def is_container(group: Group) -> bool:
+    """
+    Check if a group is a container group.
+
+    i.e. a group that...
+    * has no name
+    * multivalued quantity
+    * has a ``neurodata_type_inc``
+    * has no ``neurodata_type_def``
+    * has no sub-groups
+    * has no datasets
+    * has no attributes
+
+    Examples:
+
+        .. code-block:: yaml
+
+            - name: templates
+              groups:
+              - neurodata_type_inc: TimeSeries
+                doc: TimeSeries objects containing template data of presented stimuli.
+                quantity: '*'
+              - neurodata_type_inc: Images
+                doc: Images objects containing images of presented stimuli.
+                quantity: '*'
+    """
+    return (
+        not group.name
+        and group.quantity == "*"
+        and group.neurodata_type_inc
+        and not group.neurodata_type_def
+        and not group.datasets
+        and not group.groups
+        and not group.attributes
     )

nwb_linkml/src/nwb_linkml/adapters/attribute.py

@@ -7,26 +7,13 @@
 
 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 @@ def apply(cls, attr: Attribute, res: Optional[BuildResult] = None) -> BuildResul
             description=attr.doc,
             required=attr.required,
             inlined=inlined(attr.dtype),
-            **cls.handle_defaults(attr),
+            **defaults(attr),
         )
         return BuildResult(slots=[slot])
 
@@ -154,7 +116,7 @@ def apply(cls, attr: Attribute, res: Optional[BuildResult] = None) -> BuildResul
             required=attr.required,
             inlined=inlined(attr.dtype),
             **expressions,
-            **cls.handle_defaults(attr),
+            **defaults(attr),
         )
         return BuildResult(slots=[slot])