nwb-linkml/nwb_linkml/tests/test_providers/test_provider_schema.py
sneakers-the-rat 5438b2489b Fix relative imports in ectopic models --
Use a MetaPathFinder to allow python to resolve imports from the temporary model directory
Build dependent versions in split builds
Clear package imports when allow_repo=False
2023-10-04 22:06:26 -07:00

97 lines
3 KiB
Python

import pdb
import shutil
import os
import sys
from pathlib import Path
from typing import Optional, Union, List
from ..fixtures import tmp_output_dir, set_config_vars
import pytest
from nwb_linkml.providers.schema import LinkMLProvider, PydanticProvider
import nwb_linkml
from nwb_linkml.maps.naming import version_module_case
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)
# clear any prior output
shutil.rmtree(provider.path, ignore_errors=True)
assert not provider.path.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.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[List[int]],
})
]
)
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()
# 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
assert (tmp_output_dir / 'pydantic' / 'core' / version_module_case(core.version) / 'namespace.py').exists()
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