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fixing tests by using temp directory and changing random prior commit hash from nwb core schema

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sneakers-the-rat 2023-09-11 19:55:45 -07:00
parent c69cbdfb38
commit 095d0bc6a9
5 changed files with 17 additions and 6 deletions
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1
nwb_linkml/src/nwb_linkml/config.py
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@ -37,6 +37,7 @@ class Config(BaseSettings):
@field_validator('cache_dir', mode='before') @field_validator('cache_dir', mode='before')
@classmethod @classmethod
def folder_exists(cls, v: Path, info: FieldValidationInfo) -> Path: def folder_exists(cls, v: Path, info: FieldValidationInfo) -> Path:
v = Path(v)
v.mkdir(exist_ok=True) v.mkdir(exist_ok=True)
assert v.exists() assert v.exists()
return v return v

7
nwb_linkml/tests/fixtures.py
View file

@ -1,4 +1,5 @@
import pytest import pytest
import os
from nwb_linkml.io import schema as io from nwb_linkml.io import schema as io
from nwb_linkml.adapters.namespaces import NamespacesAdapter from nwb_linkml.adapters.namespaces import NamespacesAdapter
@ -14,9 +15,15 @@ def tmp_output_dir() -> Path:
return path return path
@pytest.fixture(autouse=True, scope='session')
def set_config_vars(tmp_output_dir):
os.environ['NWB_LINKML_CACHE_DIR'] = str(tmp_output_dir)
@pytest.fixture(scope="session") @pytest.fixture(scope="session")
def nwb_core_fixture() -> NamespacesAdapter: def nwb_core_fixture() -> NamespacesAdapter:
nwb_core = io.load_nwb_core() nwb_core = io.load_nwb_core()
nwb_core.populate_imports() nwb_core.populate_imports()
return nwb_core return nwb_core

2
nwb_linkml/tests/test_io/test_io_hdf5.py
View file

@ -2,7 +2,7 @@ import pytest
from pathlib import Path from pathlib import Path
from nwb_linkml.io.hdf5 import HDF5IO from nwb_linkml.io.hdf5 import HDF5IO
@pytest.mark.skip()
def test_hdf_read(): def test_hdf_read():
NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb') NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
if not NWBFILE.exists(): if not NWBFILE.exists():

2
nwb_linkml/tests/test_providers/test_provider_git.py
View file

@ -8,7 +8,7 @@ from nwb_schema_language import Namespaces
@pytest.mark.parametrize( @pytest.mark.parametrize(
['source', 'commit'], ['source', 'commit'],
[ [
(NWB_CORE_REPO, 'b4f8838cbfbb7f8a117bd7e0aad19133d26868b4'), (NWB_CORE_REPO, '761a0d7838304864643f8bc3ab88c93bfd437f2a'),
(HDMF_COMMON_REPO, '660b6ac0780dd9d2cb1e56fea8b62c671ca5e2c8') (HDMF_COMMON_REPO, '660b6ac0780dd9d2cb1e56fea8b62c671ca5e2c8')
] ]
) )

9
nwb_linkml/tests/test_providers/test_provider_schema.py
View file

@ -1,8 +1,9 @@
import pdb import pdb
import shutil import shutil
import os
from typing import Optional, Union, List from typing import Optional, Union, List
from ..fixtures import tmp_output_dir from ..fixtures import tmp_output_dir, set_config_vars
import pytest import pytest
@ -63,6 +64,10 @@ def test_linkml_provider(tmp_output_dir, repo_version, schema_version, schema_di
) )
def test_pydantic_provider(tmp_output_dir, class_name, test_fields): def test_pydantic_provider(tmp_output_dir, class_name, test_fields):
provider = PydanticProvider(path=tmp_output_dir) 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()
core = provider.get('core') core = provider.get('core')
@ -76,5 +81,3 @@ def test_pydantic_provider(tmp_output_dir, class_name, test_fields):
assert test_class.model_fields[k].annotation == v assert test_class.model_fields[k].annotation == v
pdb.set_trace()