mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-11-10 08:44:30 +00:00
117 lines
4 KiB
Python
117 lines
4 KiB
Python
import pdb
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import numpy as np
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import pytest
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from ..fixtures import nwb_core_fixture
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from linkml_runtime.linkml_model import SchemaDefinition, ClassDefinition, SlotDefinition, TypeDefinition
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from nwb_schema_language import Dataset, Group, Schema, CompoundDtype, Attribute
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from nwb_linkml.adapters import BuildResult
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from ..fixtures import linkml_schema_bare
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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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assert len(list(everything)) == 9959
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@pytest.mark.parametrize(
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['walk_class', 'known_number'],
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[
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(Dataset, 211),
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(Group, 144),
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((Dataset, Group), 355),
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(Schema, 19)
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]
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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(
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schemas=sch,
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classes=cls,
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slots=slot1,
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types=typ
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)
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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(
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'sch_type',
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('schemas', 'classes', 'slots', 'types')
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)
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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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