G3 122 gene id mapping

[francastell]

No description provided.

[github-actions]

Test Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.11.7, pytest-7.4.4, pluggy-1.4.0
rootdir: /home/runner/work/geneweaver-api/geneweaver-api
plugins: asyncio-0.21.1, anyio-4.2.0, cov-4.1.0
asyncio: mode=Mode.STRICT
collected 37 items

tests/controllers/test_genes.py .....                                    [ 13%]
tests/controllers/test_genesets.py .......                               [ 32%]
tests/services/test_gene.py ....                                         [ 43%]
tests/services/test_genset.py ......                                     [ 59%]
tests/services/io/test_read_file_contents.py ...............             [100%]

=============================== warnings summary ===============================
tests/data/__init__.py:8
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:8: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    geneset_response_json = importlib.resources.read_text(

../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/importlib/resources/_legacy.py:80
  /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/importlib/resources/_legacy.py:80: DeprecationWarning: open_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    with open_text(package, resource, encoding, errors) as fp:

tests/data/__init__.py:11
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:11: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    geneset_w_gene_id_type_json = importlib.resources.read_text(

tests/data/__init__.py:15
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:15: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    gene_homologus_ids_json = importlib.resources.read_text(

tests/controllers/test_genes.py::test_gene_id_mapping_response_post_req
tests/controllers/test_genes.py::test_gene_id_mapping_invalid_url
tests/controllers/test_genes.py::test_gene_id_mapping_invalid_post_data_
tests/controllers/test_genes.py::test_gene_id_mapping_missing_target_gene_identifier
tests/controllers/test_genes.py::test_gene_id_mapping_missing_gene_list
  /opt/hostedtoolcache/Python/3.11.7/x64/lib/python3.11/site-packages/httpx/_content.py:204: DeprecationWarning: Use 'content=<...>' to upload raw bytes/text content.
    warnings.warn(message, DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

---------- coverage: platform linux, python 3.11.7-final-0 -----------
Name                                            Stmts   Miss  Cover
-------------------------------------------------------------------
src/geneweaver/api/__init__.py                      0      0   100%
src/geneweaver/api/controller/__init__.py           0      0   100%
src/geneweaver/api/controller/api.py               10      0   100%
src/geneweaver/api/controller/batch.py             12      3    75%
src/geneweaver/api/controller/genes.py             12      0   100%
src/geneweaver/api/controller/genesets.py          61      8    87%
src/geneweaver/api/controller/message.py            3      0   100%
src/geneweaver/api/controller/search.py             0      0   100%
src/geneweaver/api/core/__init__.py                 0      0   100%
src/geneweaver/api/core/config.py                   2      0   100%
src/geneweaver/api/core/config_class.py            27      1    96%
src/geneweaver/api/core/db.py                       0      0   100%
src/geneweaver/api/core/deps.py                     3      0   100%
src/geneweaver/api/core/exceptions.py              10      3    70%
src/geneweaver/api/core/security.py               118     76    36%
src/geneweaver/api/dependencies.py                 32     14    56%
src/geneweaver/api/main.py                          1      0   100%
src/geneweaver/api/schemas/__init__.py              0      0   100%
src/geneweaver/api/schemas/apimodels.py            14      0   100%
src/geneweaver/api/schemas/auth.py                 19      0   100%
src/geneweaver/api/schemas/batch.py                 6      0   100%
src/geneweaver/api/schemas/messages.py             18      0   100%
src/geneweaver/api/schemas/score.py                13     13     0%
src/geneweaver/api/services/__init__.py             0      0   100%
src/geneweaver/api/services/batch.py               13     13     0%
src/geneweaver/api/services/genes.py               13      3    77%
src/geneweaver/api/services/geneset.py             36      3    92%
src/geneweaver/api/services/io.py                   4      0   100%
src/geneweaver/api/services/parse/__init__.py       0      0   100%
src/geneweaver/api/services/parse/batch.py         11      5    55%
src/geneweaver/api/services/pubmeds.py              0      0   100%
-------------------------------------------------------------------
TOTAL                                             438    142    68%
Coverage HTML written to dir htmlcov

Required test coverage of 60% reached. Total coverage: 67.58%
======================= 37 passed, 11 warnings in 2.32s ========================