import pytest from linkml_runtime.linkml_model import SlotDefinition from nwb_linkml.adapters import DatasetAdapter, GroupAdapter from nwb_schema_language import CompoundDtype, Dataset, Group, ReferenceDtype @pytest.mark.xfail() def test_build_base(nwb_schema): # 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 should 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"] == 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"