mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-09-19 23:44:28 +00:00
120 lines
3.8 KiB
Python
120 lines
3.8 KiB
Python
import pdb
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import shutil
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import os
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import sys
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import warnings
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from pathlib import Path
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import yaml
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from pprint import pformat
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from typing import Optional, Union, List
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from ..fixtures import tmp_output_dir
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import pytest
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from nwb_linkml.providers.schema import LinkMLProvider, PydanticProvider
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import nwb_linkml
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from nwb_linkml.maps.naming import version_module_case
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from nwb_linkml.providers.git import DEFAULT_REPOS
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from nwb_linkml.adapters import NamespacesAdapter
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from nwb_linkml.types.ndarray import NDArray
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from nptyping import Shape, UByte
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CORE_MODULES = (
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"core.nwb.base",
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"core.nwb.device",
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"core.nwb.epoch",
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"core.nwb.image",
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"core.nwb.file",
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"core.nwb.misc",
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"core.nwb.behavior",
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"core.nwb.ecephys",
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"core.nwb.icephys",
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"core.nwb.ogen",
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"core.nwb.ophys",
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"core.nwb.retinotopy",
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"core.nwb.language"
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)
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@pytest.mark.parametrize(
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["repo_version", "schema_version", "schema_dir"],
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[
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('2.6.0', '2.6.0-alpha', 'v2_6_0_alpha')
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]
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)
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def test_linkml_provider(tmp_output_dir, repo_version, schema_version, schema_dir):
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provider = LinkMLProvider(path=tmp_output_dir, allow_repo=False)
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# clear any prior output
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shutil.rmtree(provider.path)
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assert not provider.path.exists()
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assert not (provider.namespace_path('core', repo_version) / 'namespace.yaml').exists()
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# end to end, check that we can get the 'core' repo at the latest version
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# in the gitrepo
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core = provider.get('core', version=repo_version)
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assert core.schema.version == schema_version
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assert all([mod in core.schema.imports for mod in CORE_MODULES])
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assert schema_dir in [path.name for path in (provider.path / 'core').iterdir()]
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@pytest.mark.skip()
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def test_linkml_build_from_yaml(tmp_output_dir):
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core = DEFAULT_REPOS['core']
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git_dir = nwb_linkml.Config().git_dir / 'core'
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if git_dir.exists():
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shutil.rmtree(str(git_dir))
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ns_file = core.provide_from_git('2.6.0')
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assert git_dir.exists()
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assert ns_file.exists()
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provider = LinkMLProvider(path=tmp_output_dir, allow_repo=False)
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res = provider.build_from_yaml(ns_file)
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@pytest.mark.depends(on=['test_linkml_provider'])
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@pytest.mark.parametrize(
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['class_name', 'test_fields'],
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[
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('TimeSeries', {
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'name':str,
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'description': Optional[str],
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'comments': Optional[str],
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'data': 'TimeSeriesData',
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'timestamps': 'Optional', # __name__ just gets the first part of Optional[TimeSeriesTimestamps]
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'control': Optional[NDArray[Shape['* num_times'], UByte]],
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})
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]
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)
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def test_pydantic_provider_core(tmp_output_dir, class_name, test_fields):
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provider = PydanticProvider(path=tmp_output_dir)
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# clear any prior output
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assert provider.path.parent == tmp_output_dir
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shutil.rmtree(provider.path, ignore_errors=True)
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assert not provider.path.exists()
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# first, we should not build if we're allowed to get core from repo
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core = provider.get('core', allow_repo=True)
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assert Path(nwb_linkml.__file__).parent in Path(core.__file__).parents
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assert not (provider.path / 'core').exists()
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# then, if we're not allowed to get repo versions, we build!
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del sys.modules[core.__name__]
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core = provider.get('core', allow_repo=False)
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# ensure we didn't get the builtin one
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assert Path(nwb_linkml.__file__).parent not in Path(core.__file__).parents
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namespace_path = (tmp_output_dir / 'pydantic' / 'core' / version_module_case(core.version) / 'namespace.py')
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assert namespace_path.exists()
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assert Path(core.__file__) == namespace_path
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test_class = getattr(core, class_name)
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assert test_class == provider.get_class('core', class_name)
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for k, v in test_fields.items():
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if isinstance(v, str):
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assert test_class.model_fields[k].annotation.__name__ == v
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else:
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assert test_class.model_fields[k].annotation == v
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