classes adapter

docs/index.md

@@ -5,8 +5,10 @@
 :maxdepth: 3
 
 api/index
+todo
 changelog
 
+
 ```
 
 

docs/todo.md

@@ -0,0 +1,8 @@
+# TODO
+
+Important things that are not implemented yet!
+
+- {meth}`nwb_linkml.adapters.classes.ClassAdapter.handle_dtype` does not yet handle compound dtypes,
+  leaving them as `AnyType` instead. This is fine for a first draft since they are used rarely within
+  NWB, but we will need to handle them by making slots for each of the dtypes since they typically
+  represent table-like data.

nwb_linkml/src/nwb_linkml/adapters/classes.py

@@ -10,8 +10,6 @@ from nwb_linkml.maps import QUANTITY_MAP
 from nwb_linkml.maps.naming import camel_to_snake
 
 
-
-
 class ClassAdapter(Adapter):
     """
     Abstract adapter to class-like things in linkml, holds methods common to
@@ -33,10 +31,24 @@ class ClassAdapter(Adapter):
         """
         Build the basic class and attributes before adding any specific
         modifications for groups or datasets.
+
+        The main distinction in behavior for this method is whether this class has a parent class -
+        ie this is one of the anonymous nested child datasets or groups within another group.
+
+        If the class has no parent, then...
+
+        * Its name is inferred from its `neurodata_type_def`,  fixed name, or `neurodata_type_inc` in that order
+        * It is just built as normal class!
+        * It will be indicated as a ``tree_root`` (which will primarily be used to invert the translation for write operations)
+
+        If the class has a parent, then...
+
+        * If it has a `neurodata_type_def` or `inc`,  that will be used as its name, otherwise concatenate `parent__child`,
+          eg. ``TimeSeries__TimeSeriesData``
+        * A slot will also be made and returned with the BuildResult, which the parent will then have as one of its attributes.
         """
 
         # Build this class
-        #name = self._get_full_name()
         kwargs = {}
         if self.parent is not None:
             kwargs['name'] = self._get_full_name()
@@ -105,7 +117,6 @@ class ClassAdapter(Adapter):
         else:
             raise ValueError('Not sure what our name is!')
 
-
         return name
 
     def _get_attr_name(self) -> str:
@@ -113,19 +124,13 @@ class ClassAdapter(Adapter):
         Get the name to use as the attribute name,
         again distinct from the actual name of the instantiated object
         """
-        # return self._get_full_name()
-        name = None
-        if self.cls.neurodata_type_def:
-            # name = camel_to_snake(self.cls.neurodata_type_def)
+        if self.cls.neurodata_type_def is not None:
             name = self.cls.neurodata_type_def
         elif self.cls.name is not None:
-            # we do have a unique name
             name = self.cls.name
-        elif self.cls.neurodata_type_inc:
-            # name = camel_to_snake(self.cls.neurodata_type_inc)
+        elif self.cls.neurodata_type_inc is not None:
             name = self.cls.neurodata_type_inc
-
-        if name is None:
+        else:
             raise ValueError(f'Class has no name!: {self.cls}')
 
         return name
@@ -136,19 +141,13 @@ class ClassAdapter(Adapter):
         used to dodge name overlaps by snake-casing!
         again distinct from the actual name of the instantiated object
         """
-        # return self._get_full_name()
-        name = None
         if self.cls.neurodata_type_def:
             name = camel_to_snake(self.cls.neurodata_type_def)
-            # name = self.cls.neurodata_type_def
         elif self.cls.name is not None:
-            # we do have a unique name
             name = self.cls.name
         elif self.cls.neurodata_type_inc:
             name = camel_to_snake(self.cls.neurodata_type_inc)
-            # name = self.cls.neurodata_type_inc
-
-        if name is None:
+        else:
             raise ValueError(f'Class has no name!: {self.cls}')
 
         return name
@@ -167,7 +166,6 @@ class ClassAdapter(Adapter):
             # so we'll... uh... treat them as slots.
              # TODO
             return 'AnyType'
-            #raise NotImplementedError('got distracted, need to implement')
 
         else:
             # flat dtype

nwb_linkml/tests/test_adapters/test_adapter_classes.py

@@ -4,11 +4,190 @@ import pytest
 
 from ..fixtures import linkml_schema_bare, linkml_schema, nwb_schema
 
-from nwb_linkml.adapters import DatasetAdapter, ClassAdapter
+from linkml_runtime.linkml_model import SlotDefinition
+from nwb_linkml.adapters import DatasetAdapter, ClassAdapter, GroupAdapter
+from nwb_schema_language import Group, Dataset, ReferenceDtype, CompoundDtype
 
 def test_build_base(nwb_schema):
-    # simplest case, nothing special here
+    # simplest case, nothing special here. Should be same behavior between dataset and group
     dset = DatasetAdapter(cls=nwb_schema.datasets['image'])
+    base = dset.build_base()
+    assert len(base.slots) == 0
+    assert len(base.classes) == 1
+    img = base.classes[0]
+    assert img.name == "Image"
+    # no parent class, tree_root shoudl be true
+    assert img.tree_root
+    assert len(img.attributes) == 3
+
+    # now with parent class
+    groups = GroupAdapter(cls=nwb_schema.groups['images'])
+    dset.parent = groups
+    base = dset.build_base()
+    # we made a self-slot (will be tested elsewhere)
+    assert len(base.slots) == 1
+    assert len(base.classes) == 1
+    img = base.classes[0]
+    assert not img.tree_root
+    assert len(img.attributes) == 3
+
+    # now try adding an extra attribute
+    slot = SlotDefinition(name="newslot", range="string")
+    # should coerce single slot to a list within the method
+    base = dset.build_base(extra_attrs=slot)
+    assert len(base.slots) == 1
+    assert len(base.classes) == 1
+    img = base.classes[0]
+    assert len(img.attributes) == 4
+    assert img.attributes['newslot'] is slot
+
+def test_get_attr_name():
+    """Name method used by parentless classes"""
+    cls = Dataset(neurodata_type_def='MyClass', doc='a class')
+    adapter = DatasetAdapter(cls=cls)
+    # type_defs get their original name
+    assert adapter._get_attr_name() == 'MyClass'
+
+    # explicit names get that name, but only if there is no type_def
+    adapter.cls.name = 'MyClassName'
+    assert adapter._get_attr_name() == 'MyClass'
+    adapter.cls.neurodata_type_def = None
+    assert adapter._get_attr_name() == 'MyClassName'
+
+    # if neither, use the type inc
+    adapter.cls.neurodata_type_inc = 'MyThirdName'
+    assert adapter._get_attr_name() == 'MyClassName'
+    adapter.cls.name = None
+    assert adapter._get_attr_name() == 'MyThirdName'
+
+    # if none are present, raise a value error
+    adapter.cls.neurodata_type_inc = None
+    with pytest.raises(ValueError):
+        adapter._get_attr_name()
+
+def test_get_full_name():
+    """Name used by child classes"""
+    cls = Dataset(neurodata_type_def='Child', doc='a class')
+    parent = GroupAdapter(cls=Group(neurodata_type_def='Parent', doc='a class'))
+    adapter = DatasetAdapter(cls=cls, parent=parent)
+
+    # if child has its own type_def, use that
+    assert adapter._get_full_name() == 'Child'
+
+    # same thing with type_inc
+    adapter.cls.neurodata_type_def = None
+    adapter.cls.neurodata_type_inc = 'ChildInc'
+    assert adapter._get_full_name() == 'ChildInc'
+
+    # if it just has a name, it gets concatenated with its parents
+    adapter.cls.neurodata_type_inc = None
+    adapter.cls.name = 'ChildName'
+    assert adapter._get_full_name() == 'Parent__ChildName'
+
+    # this should work at any depth of nesting if the parent is not an independently defined class
+    grandparent = GroupAdapter(cls=Group(neurodata_type_def='Grandparent', doc='a class'))
+    parent.cls.neurodata_type_def = None
+    parent.cls.name = 'ParentName'
+    parent.parent = grandparent
+    assert adapter._get_full_name() == 'Grandparent__ParentName__ChildName'
+
+    # if it has none, raise value error
+    adapter.cls.name = None
+    with pytest.raises(ValueError):
+        adapter._get_full_name()
+
+def test_self_slot():
+    """
+    Slot that represents ourselves to our parent
+
+    Quantity map is tested elsewhere
+    """
+    cls = Dataset(neurodata_type_def='ChildClass', doc='a class', quantity='?')
+    parent = GroupAdapter(cls=Group(neurodata_type_def='Parent', doc='a class'))
+    adapter = DatasetAdapter(cls=cls, parent=parent)
+
+    # base case - snake case a type def
+    slot = adapter.build_self_slot()
+    assert slot.name == 'child_class'
+    assert slot.range == 'ChildClass' == adapter._get_full_name()
+
+    # this should be the slot that gets build with the build_base method
+    base = adapter.build_base()
+    assert len(base.slots) == 1
+    assert base.slots[0] == slot
+
+    # if class has a unique name, use that without changing, but only if no type_def
+
+    adapter.cls.name = "FixedName"
+    slot = adapter.build_self_slot()
+    assert slot.name == 'child_class'
+    adapter.cls.neurodata_type_def = None
+    slot = adapter.build_self_slot()
+    assert slot.name == 'FixedName'
+    assert slot.range == adapter._get_full_name()
+
+    # type_inc works the same as type_def, but only if name and type_def are None
+    adapter.cls.neurodata_type_inc = 'IncName'
+    slot = adapter.build_self_slot()
+    assert slot.name == 'FixedName'
+    adapter.cls.name = None
+    slot = adapter.build_self_slot()
+    assert slot.name == 'inc_name'
+    assert slot.range == adapter._get_full_name()
+
+    # if we have nothing, raise value error
+    adapter.cls.neurodata_type_inc = None
+    with pytest.raises(ValueError):
+        adapter.build_self_slot()
+
+
+def test_name_slot():
+    """Classes with a fixed name should name slot with a fixed value"""
+    # no name
+    cls = DatasetAdapter(cls=Dataset(neurodata_type_def='MyClass', doc='a class'))
+    slot = cls.build_name_slot()
+    assert slot.name == 'name'
+    assert slot.required
+    assert slot.range == 'string'
+    assert slot.identifier
+    assert slot.ifabsent is None
+    assert slot.equals_string is None
+
+    cls.cls.name = 'FixedName'
+    slot = cls.build_name_slot()
+    assert slot.name == 'name'
+    assert slot.required
+    assert slot.range == 'string'
+    assert slot.identifier
+    assert slot.ifabsent == 'string(FixedName)'
+    assert slot.equals_string == 'FixedName'
+
+
+def test_handle_dtype(nwb_schema):
+    """
+    Dtypes should be translated from nwb schema language to linkml
+
+    Dtypes are validated by the nwb_schema_language classes, so we don't do that here
+    """
+    cls = DatasetAdapter(cls=Dataset(neurodata_type_def='MyClass', doc='a class'))
+
+    reftype = ReferenceDtype(target_type='TargetClass', reftype='reference')
+    compoundtype = [
+        CompoundDtype(name='field_a', doc='field a!', dtype='int32'),
+        CompoundDtype(name='field_b', doc='field b!', dtype='text'),
+        CompoundDtype(name="reference", doc="reference!", dtype=reftype)
+    ]
+
+
+    assert cls.handle_dtype(reftype) == 'TargetClass'
+    assert cls.handle_dtype(None) == 'AnyType'
+    assert cls.handle_dtype([]) == 'AnyType'
+    # handling compound types is currently TODO
+    assert cls.handle_dtype(compoundtype) == 'AnyType'
+    assert cls.handle_dtype('int32') == 'int32'
+
+
+
+
+
 
-    #pdb.set_trace()
-    pass