mirror of
https://github.com/p2p-ld/nwb-linkml.git
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188 lines
6.6 KiB
Python
188 lines
6.6 KiB
Python
import pytest
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from linkml_runtime.linkml_model import SlotDefinition
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from nwb_linkml.adapters import DatasetAdapter, GroupAdapter
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from nwb_linkml.maps.dtype import handle_dtype
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from nwb_schema_language import CompoundDtype, Dataset, Group, ReferenceDtype
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@pytest.mark.xfail()
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def test_build_base(nwb_schema):
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# simplest case, nothing special here. Should be same behavior between dataset and group
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dset = DatasetAdapter(cls=nwb_schema.datasets["image"])
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base = dset.build_base()
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assert len(base.slots) == 0
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assert len(base.classes) == 1
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img = base.classes[0]
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assert img.name == "Image"
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# no parent class, tree_root should be true
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assert img.tree_root
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assert len(img.attributes) == 3
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# now with parent class
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groups = GroupAdapter(cls=nwb_schema.groups["images"])
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dset.parent = groups
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base = dset.build_base()
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# we made a self-slot (will be tested elsewhere)
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assert len(base.slots) == 1
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assert len(base.classes) == 1
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img = base.classes[0]
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assert not img.tree_root
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assert len(img.attributes) == 3
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# now try adding an extra attribute
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slot = SlotDefinition(name="newslot", range="string")
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# should coerce single slot to a list within the method
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base = dset.build_base(extra_attrs=slot)
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assert len(base.slots) == 1
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assert len(base.classes) == 1
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img = base.classes[0]
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assert len(img.attributes) == 4
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assert img.attributes["newslot"] == slot
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def test_get_attr_name():
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"""Name method used by parentless classes"""
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cls = Dataset(neurodata_type_def="MyClass", doc="a class")
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adapter = DatasetAdapter(cls=cls)
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# type_defs get their original name
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assert adapter._get_attr_name() == "MyClass"
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# explicit names get that name, but only if there is no type_def
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adapter.cls.name = "MyClassName"
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assert adapter._get_attr_name() == "MyClass"
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adapter.cls.neurodata_type_def = None
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assert adapter._get_attr_name() == "MyClassName"
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# if neither, use the type inc
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adapter.cls.neurodata_type_inc = "MyThirdName"
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assert adapter._get_attr_name() == "MyClassName"
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adapter.cls.name = None
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assert adapter._get_attr_name() == "MyThirdName"
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# if none are present, raise a value error
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adapter.cls.neurodata_type_inc = None
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with pytest.raises(ValueError):
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adapter._get_attr_name()
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def test_get_full_name():
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"""Name used by child classes"""
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cls = Dataset(neurodata_type_def="Child", doc="a class")
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parent = GroupAdapter(cls=Group(neurodata_type_def="Parent", doc="a class"))
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adapter = DatasetAdapter(cls=cls, parent=parent)
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# if child has its own type_def, use that
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assert adapter._get_full_name() == "Child"
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# same thing with type_inc
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adapter.cls.neurodata_type_def = None
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adapter.cls.neurodata_type_inc = "ChildInc"
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assert adapter._get_full_name() == "ChildInc"
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# if it just has a name, it gets concatenated with its parents
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adapter.cls.neurodata_type_inc = None
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adapter.cls.name = "ChildName"
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assert adapter._get_full_name() == "Parent__ChildName"
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# this should work at any depth of nesting if the parent is not an independently defined class
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grandparent = GroupAdapter(cls=Group(neurodata_type_def="Grandparent", doc="a class"))
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parent.cls.neurodata_type_def = None
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parent.cls.name = "ParentName"
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parent.parent = grandparent
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assert adapter._get_full_name() == "ParentName__ChildName"
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# if it has none, raise value error
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adapter.cls.name = None
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with pytest.raises(ValueError):
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adapter._get_full_name()
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def test_self_slot():
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"""
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Slot that represents ourselves to our parent
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Quantity map is tested elsewhere
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"""
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cls = Dataset(neurodata_type_def="ChildClass", doc="a class", quantity="?")
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parent = GroupAdapter(cls=Group(neurodata_type_def="Parent", doc="a class"))
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adapter = DatasetAdapter(cls=cls, parent=parent)
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# base case - snake case a type def
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slot = adapter.build_self_slot()
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assert slot.name == "child_class"
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assert slot.range == "ChildClass" == adapter._get_full_name()
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# this should be the slot that gets build with the build_base method
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base = adapter.build_base()
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assert len(base.slots) == 1
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assert base.slots[0] == slot
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# if class has a unique name, use that without changing, but only if no type_def
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adapter.cls.name = "FixedName"
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slot = adapter.build_self_slot()
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assert slot.name == "child_class"
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adapter.cls.neurodata_type_def = None
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slot = adapter.build_self_slot()
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assert slot.name == "FixedName"
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assert slot.range == adapter._get_full_name()
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# type_inc works the same as type_def, but only if name and type_def are None
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adapter.cls.neurodata_type_inc = "IncName"
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slot = adapter.build_self_slot()
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assert slot.name == "FixedName"
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adapter.cls.name = None
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slot = adapter.build_self_slot()
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assert slot.name == "inc_name"
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assert slot.range == adapter._get_full_name()
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# if we have nothing, raise value error
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adapter.cls.neurodata_type_inc = None
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with pytest.raises(ValueError):
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adapter.build_self_slot()
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def test_name_slot():
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"""Classes with a fixed name should name slot with a fixed value"""
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# no name
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cls = DatasetAdapter(cls=Dataset(neurodata_type_def="MyClass", doc="a class"))
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slot = cls.build_name_slot()
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assert slot.name == "name"
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assert slot.required
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assert slot.range == "string"
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assert slot.identifier is None
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assert slot.ifabsent is None
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assert slot.equals_string is None
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cls.cls.name = "FixedName"
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slot = cls.build_name_slot()
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assert slot.name == "name"
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assert slot.required
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assert slot.range == "string"
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assert slot.identifier is None
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assert slot.ifabsent == "string(FixedName)"
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assert slot.equals_string == "FixedName"
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def test_handle_dtype(nwb_schema):
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"""
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Dtypes should be translated from nwb schema language to linkml
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Dtypes are validated by the nwb_schema_language classes, so we don't do that here
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"""
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cls = DatasetAdapter(cls=Dataset(neurodata_type_def="MyClass", doc="a class"))
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reftype = ReferenceDtype(target_type="TargetClass", reftype="reference")
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compoundtype = [
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CompoundDtype(name="field_a", doc="field a!", dtype="int32"),
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CompoundDtype(name="field_b", doc="field b!", dtype="text"),
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CompoundDtype(name="reference", doc="reference!", dtype=reftype),
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]
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assert handle_dtype(reftype) == "TargetClass"
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assert handle_dtype(None) == "AnyType"
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assert handle_dtype([]) == "AnyType"
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# handling compound types is currently TODO
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assert handle_dtype(compoundtype) == "AnyType"
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assert handle_dtype("int32") == "int32"
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