mirror of
https://github.com/p2p-ld/nwb-linkml.git
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111 lines
4.2 KiB
Python
111 lines
4.2 KiB
Python
import numpy as np
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import pytest
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from linkml_runtime.linkml_model import (
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ClassDefinition,
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SchemaDefinition,
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SlotDefinition,
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TypeDefinition,
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)
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from nwb_linkml.adapters import BuildResult
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from nwb_schema_language import Attribute, Dataset, Group, Schema
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def test_walk(nwb_core_fixture):
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"""
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Not sure exactly what should be tested here, for now just testing that we get an expected value
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"""
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everything = nwb_core_fixture.walk(nwb_core_fixture)
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# number of items obviously changes based on what version we're talking about
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# this is configured as a test matrix on the nwb_core_fixture, currently only testing the latest version
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if (
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nwb_core_fixture.versions["core"] == "2.6.0-alpha"
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and nwb_core_fixture.versions["hdmf-common"] == "1.5.0"
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):
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assert len(list(everything)) == 9908
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@pytest.mark.parametrize(
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["walk_class", "known_number"],
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[(Dataset, 212), (Group, 146), ((Dataset, Group), 358), (Schema, 19)],
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)
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def test_walk_types(nwb_core_fixture, walk_class, known_number):
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classes = nwb_core_fixture.walk_types(nwb_core_fixture, walk_class)
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class_list = list(classes)
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assert len(class_list) == known_number
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def test_walk_fields(nwb_core_fixture):
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# should get same number of dtype fields as there are datasets and attributes + compound dtypes
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dtype = list(nwb_core_fixture.walk_fields(nwb_core_fixture, "dtype"))
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dtype_havers = list(nwb_core_fixture.walk_types(nwb_core_fixture, (Dataset, Attribute)))
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compound_dtypes = [len(d.dtype) for d in dtype_havers if isinstance(d.dtype, list)]
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expected_dtypes = np.sum(compound_dtypes) + len(dtype_havers)
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assert expected_dtypes == len(dtype)
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def test_walk_field_values(nwb_core_fixture):
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dtype_models = list(nwb_core_fixture.walk_field_values(nwb_core_fixture, "dtype", value=None))
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assert all([hasattr(d, "dtype") for d in dtype_models])
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text_models = list(nwb_core_fixture.walk_field_values(nwb_core_fixture, "dtype", value="text"))
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assert all([d.dtype == "text" for d in text_models])
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# 135 known value from regex search
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assert len(text_models) == len([d for d in dtype_models if d.dtype == "text"]) == 135
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def test_build_result(linkml_schema_bare):
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"""
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build results can hold lists of class, slot, and type definitions
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"""
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schema = linkml_schema_bare
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sch = schema.core
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cls = sch.classes["MainTopLevel"]
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slot1 = cls.attributes["name"]
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typ = sch.types["numeric"]
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# Build result should hold the results and coerce to list type
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res = BuildResult(schemas=sch, classes=cls, slots=slot1, types=typ)
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for field in ("schemas", "classes", "slots", "types"):
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assert isinstance(getattr(res, field), list)
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assert len(getattr(res, field)) == 1
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@pytest.mark.parametrize("sch_type", ("schemas", "classes", "slots", "types"))
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def test_build_result_add(linkml_schema_bare, sch_type):
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"""
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Build results can be added together without duplicating
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"""
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schema = linkml_schema_bare
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if sch_type == "schemas":
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obj = schema.core
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other_obj = SchemaDefinition(name="othername", id="othername", version="1.0.1")
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elif sch_type == "classes":
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obj = schema.core.classes["MainTopLevel"]
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other_obj = ClassDefinition(name="othername")
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elif sch_type == "slots":
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obj = schema.core.classes["MainTopLevel"].attributes["name"]
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other_obj = SlotDefinition(name="othername", range="string")
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elif sch_type == "types":
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obj = schema.core.types["numeric"]
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other_obj = TypeDefinition(name="othername", typeof="float")
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else:
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raise ValueError(f"Dont know how to test type {sch_type}")
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res1 = BuildResult(**{sch_type: [obj]})
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res2 = BuildResult(**{sch_type: [obj]})
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assert len(getattr(res1, sch_type)) == 1
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assert len(getattr(res2, sch_type)) == 1
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assert len(getattr(res1 + res2, sch_type)) == 1
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assert len(getattr(res2 + res1, sch_type)) == 1
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# and then addition works as normal for not same named items
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res3 = BuildResult(**{sch_type: [other_obj]})
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assert len(getattr(res1 + res3, sch_type)) == 2
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assert len(getattr(res2 + res3, sch_type)) == 2
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res_combined_2 = res1 + res3
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assert getattr(res_combined_2, sch_type)[-1] is other_obj
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