nwb-linkml/nwb_linkml/tests/test_providers/test_provider_schema.py

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