from dataclasses import dataclass, field from pathlib import Path from types import ModuleType from typing import Dict, Optional import pytest from linkml_runtime.dumpers import yaml_dumper from linkml_runtime.linkml_model.meta import ( ArrayExpression, ClassDefinition, DimensionExpression, Prefix, SchemaDefinition, SlotDefinition, TypeDefinition, ) from nwb_linkml.adapters import NamespacesAdapter from nwb_linkml.io import schema as io from nwb_linkml.providers import LinkMLProvider, PydanticProvider from nwb_linkml.providers.linkml import LinkMLSchemaBuild from nwb_schema_language import Attribute, Dataset, Group @pytest.fixture(scope="session", params=[{"core_version": "2.7.0", "hdmf_version": "1.8.0"}]) def nwb_core_fixture(request) -> NamespacesAdapter: nwb_core = io.load_nwb_core(**request.param) assert ( request.param["core_version"] in nwb_core.versions["core"] ) # 2.6.0 is actually 2.6.0-alpha assert nwb_core.versions["hdmf-common"] == request.param["hdmf_version"] return nwb_core @pytest.fixture(scope="session") def nwb_core_linkml(nwb_core_fixture, tmp_output_dir) -> LinkMLSchemaBuild: provider = LinkMLProvider(tmp_output_dir, allow_repo=False, verbose=False) result = provider.build(ns_adapter=nwb_core_fixture, force=True) return result["core"] @pytest.fixture(scope="session") def nwb_core_module(nwb_core_linkml: LinkMLSchemaBuild, tmp_output_dir) -> ModuleType: """ Generated pydantic namespace from nwb core """ provider = PydanticProvider(tmp_output_dir, verbose=False) result = provider.build(nwb_core_linkml.namespace, force=True) mod = provider.get("core", version=nwb_core_linkml.version, allow_repo=False) return mod @dataclass class TestSchemas: __test__ = False core: SchemaDefinition imported: SchemaDefinition namespace: SchemaDefinition core_path: Optional[Path] = None imported_path: Optional[Path] = None namespace_path: Optional[Path] = None @pytest.fixture(scope="module") def linkml_schema_bare() -> TestSchemas: schema = TestSchemas( core=SchemaDefinition( name="core", id="core", version="1.0.1", imports=["imported", "linkml:types"], default_prefix="core", prefixes={"linkml": Prefix("linkml", "https://w3id.org/linkml")}, description="Test core schema", classes=[ ClassDefinition( name="MainTopLevel", description="The main class we are testing!", is_a="MainThing", tree_root=True, attributes=[ SlotDefinition( name="name", description="A fixed property that should use Literal and be frozen", range="string", required=True, ifabsent="string(toplevel)", equals_string="toplevel", identifier=True, ), SlotDefinition( name="inline_dict", description=( "This should be inlined as a dictionary despite this class having" " an identifier" ), multivalued=True, inlined=True, inlined_as_list=False, any_of=[{"range": "OtherClass"}, {"range": "StillAnotherClass"}], ), SlotDefinition( name="value", description="Main class's array", range="numeric", any_of=[ { "array": ArrayExpression( dimensions=[ DimensionExpression(alias="x"), DimensionExpression(alias="y"), ] ) }, { "array": ArrayExpression( dimensions=[ DimensionExpression(alias="x"), DimensionExpression(alias="y"), DimensionExpression(alias="z", exact_cardinality=3), ] ) }, { "array": ArrayExpression( dimensions=[ DimensionExpression(alias="x"), DimensionExpression(alias="y"), DimensionExpression(alias="z", exact_cardinality=3), DimensionExpression(alias="a", exact_cardinality=4), ] ) }, ], ), ], ), ClassDefinition( name="OtherClass", description="Another class yno!", attributes=[ SlotDefinition(name="name", range="string", required=True, identifier=True) ], ), ClassDefinition( name="StillAnotherClass", description="And yet another!", attributes=[ SlotDefinition(name="name", range="string", required=True, identifier=True) ], ), ], types=[TypeDefinition(name="numeric", typeof="float")], ), imported=SchemaDefinition( name="imported", id="imported", version="1.4.5", default_prefix="core", imports=["linkml:types"], prefixes={"linkml": Prefix("linkml", "https://w3id.org/linkml")}, classes=[ ClassDefinition( name="MainThing", description="Class imported by our main thing class!", attributes=[SlotDefinition(name="meta_slot", range="string")], ), ClassDefinition(name="Arraylike", abstract=True), ], ), namespace=SchemaDefinition( name="namespace", id="namespace", version="1.1.1", default_prefix="namespace", annotations=[ {"tag": "is_namespace", "value": "True"}, {"tag": "namespace", "value": "core"}, ], description="A namespace package that should import all other classes", imports=["core", "imported"], ), ) return schema @pytest.fixture(scope="module") def linkml_schema(tmp_output_dir_mod, linkml_schema_bare) -> TestSchemas: """ A test schema that includes - Two schemas, one importing from the other - Arraylike - Required/static "name" field - linkml metadata like tree_root - skipping classes """ schema = linkml_schema_bare test_schema_path = tmp_output_dir_mod / "test_schema" test_schema_path.mkdir() core_path = test_schema_path / "core.yaml" imported_path = test_schema_path / "imported.yaml" namespace_path = test_schema_path / "namespace.yaml" schema.core_path = core_path schema.imported_path = imported_path schema.namespace_path = namespace_path yaml_dumper.dump(schema.core, schema.core_path) yaml_dumper.dump(schema.imported, schema.imported_path) yaml_dumper.dump(schema.namespace, schema.namespace_path) return schema @dataclass class NWBSchemaTest: datasets: Dict[str, Dataset] = field(default_factory=dict) groups: Dict[str, Group] = field(default_factory=dict) @pytest.fixture() def nwb_schema() -> NWBSchemaTest: """Minimal NWB schema for testing""" image = Dataset( neurodata_type_def="Image", dtype="numeric", neurodata_type_inc="NWBData", dims=[["x", "y"], ["x", "y", "r, g, b"], ["x", "y", "r, g, b, a"]], shape=[[None, None], [None, None, 3], [None, None, 4]], doc="An image!", attributes=[ Attribute(dtype="float32", name="resolution", doc="resolution!"), Attribute(dtype="text", name="description", doc="Description!"), ], ) images = Group( neurodata_type_def="Images", neurodata_type_inc="NWBDataInterface", default_name="Images", doc="Images!", attributes=[Attribute(dtype="text", name="description", doc="description!")], datasets=[ Dataset(neurodata_type_inc="Image", quantity="+", doc="images!"), Dataset( neurodata_type_inc="ImageReferences", name="order_of_images", doc="Image references!", quantity="?", ), ], ) return NWBSchemaTest(datasets={"image": image}, groups={"images": images})