nwb-linkml/nwb_linkml/tests/test_adapters/test_adapter_namespaces.py

import pytest
from pathlib import Path
from nwb_linkml.adapters import NamespacesAdapter, SchemaAdapter
from nwb_schema_language import Attribute, Group, Namespace, Dataset, Namespaces, Schema, FlatDtype


@pytest.mark.parametrize(
    ["class_name", "schema_file", "namespace_name"],
    [
        ("DynamicTable", "table.yaml", "hdmf-common"),
        ("Container", "base.yaml", "hdmf-common"),
        ("TimeSeries", "nwb.base.yaml", "core"),
        ("ImageSeries", "nwb.image.yaml", "core"),
    ],
)
def test_find_type_source(nwb_core_fixture, class_name, schema_file, namespace_name):
    defining_sch = nwb_core_fixture.find_type_source(class_name)
    assert defining_sch.path.name == schema_file
    assert namespace_name == defining_sch.namespace


def test_populate_imports(nwb_core_fixture):
    nwb_core_fixture.populate_imports()
    schema: SchemaAdapter
    assert len(nwb_core_fixture.schemas) > 0
    for schema in nwb_core_fixture.schemas:
        need_imports = [
            nwb_core_fixture.find_type_source(cls.neurodata_type_def).namespace
            for cls in schema.created_classes
            if cls.neurodata_type_inc is not None
        ]
        need_imports = [i for i in need_imports if i != schema.namespace]
        for i in need_imports:
            assert i in schema.imports


def test_build(nwb_core_fixture):
    pass


def test_skip_imports(nwb_core_fixture):
    """
    We can build just the namespace in question without also building the other namespaces that it imports
    """
    res = nwb_core_fixture.build(skip_imports=True)

    # we shouldn't have any of the hdmf-common schema in with us
    namespaces = [sch.annotations["namespace"].value for sch in res.schemas]
    assert all([ns == "core" for ns in namespaces])


def test_roll_down_inheritance():
    """
    Classes should receive and override the properties of their parents
    when they have neurodata_type_inc
    Args:
        nwb_core_fixture:

    Returns:

    """
    parent_cls = Group(
        neurodata_type_def="Parent",
        doc="parent",
        attributes=[
            Attribute(name="a", dims=["a", "b"], shape=[1, 2], doc="a", value="a"),
            Attribute(name="b", dims=["c", "d"], shape=[3, 4], doc="b", value="b"),
        ],
        datasets=[
            Dataset(
                name="data",
                dims=["a", "b"],
                shape=[1, 2],
                doc="data",
                attributes=[
                    Attribute(name="c", dtype=FlatDtype.int32, doc="c"),
                    Attribute(name="d", dtype=FlatDtype.int32, doc="d"),
                ],
            )
        ],
    )
    parent_sch = Schema(source="parent.yaml")
    parent_ns = Namespaces(
        namespaces=[
            Namespace(
                author="hey",
                contact="sup",
                name="parent",
                doc="a parent",
                version="1",
                schema=[parent_sch],
            )
        ]
    )

    child_cls = Group(
        neurodata_type_def="Child",
        neurodata_type_inc="Parent",
        doc="child",
        attributes=[Attribute(name="a", doc="a")],
        datasets=[
            Dataset(
                name="data",
                doc="data again",
                attributes=[Attribute(name="a", doc="c", value="z"), Attribute(name="c", doc="c")],
            )
        ],
    )
    child_sch = Schema(source="child.yaml")
    child_ns = Namespaces(
        namespaces=[
            Namespace(
                author="hey",
                contact="sup",
                name="child",
                doc="a child",
                version="1",
                schema=[child_sch, Schema(namespace="parent")],
            )
        ]
    )

    parent_schema_adapter = SchemaAdapter(path=Path("parent.yaml"), groups=[parent_cls])
    parent_ns_adapter = NamespacesAdapter(namespaces=parent_ns, schemas=[parent_schema_adapter])
    child_schema_adapter = SchemaAdapter(path=Path("child.yaml"), groups=[child_cls])
    child_ns_adapter = NamespacesAdapter(
        namespaces=child_ns, schemas=[child_schema_adapter], imported=[parent_ns_adapter]
    )

    child_ns_adapter.complete_namespaces()

    child = child_ns_adapter.get("Child")