Task/fix release gates - pt 2

[bergsalex]

No description provided.

[github-actions]

Test Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.11.8, pytest-7.4.4, pluggy-1.4.0
rootdir: /home/runner/work/geneweaver-api/geneweaver-api
plugins: anyio-4.3.0, asyncio-0.21.1, cov-4.1.0
asyncio: mode=Mode.STRICT
collected 83 items

tests/controllers/test_genes.py ............                             [ 14%]
tests/controllers/test_genesets.py ...........                           [ 27%]
tests/controllers/test_publications.py .....                             [ 33%]
tests/controllers/test_species.py ...                                    [ 37%]
tests/core/test_security.py ..........                                   [ 49%]
tests/services/test_gene.py ............                                 [ 63%]
tests/services/test_genset.py ........                                   [ 73%]
tests/services/test_publications.py ..                                   [ 75%]
tests/services/test_species.py .....                                     [ 81%]
tests/services/io/test_read_file_contents.py ...............             [100%]

=============================== warnings summary ===============================
tests/data/__init__.py:10
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:10: 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/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/importlib/resources/_legacy.py:80
  /opt/hostedtoolcache/Python/3.11.8/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:13
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:13: 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:17
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:17: 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/data/__init__.py:21
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:21: 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_id_mapping_json = importlib.resources.read_text("tests.data", "gene_maping.json")

tests/data/__init__.py:23
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:23: 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.
    publications_json = importlib.resources.read_text("tests.data", "publications.json")

tests/data/__init__.py:25
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:25: 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.
    jwt_test_keys_json = importlib.resources.read_text(

tests/data/__init__.py:29
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:29: 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.
    species_json = importlib.resources.read_text("tests.data", "species.json")

tests/data/__init__.py:31
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:31: 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.
    genes_json = importlib.resources.read_text("tests.data", "genes.json")

tests/controllers/test_genes.py: 12 warnings
tests/controllers/test_genesets.py: 11 warnings
tests/controllers/test_publications.py: 5 warnings
tests/controllers/test_species.py: 3 warnings
  /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/httpx/_client.py:680: DeprecationWarning: The 'app' shortcut is now deprecated. Use the explicit style 'transport=WSGITransport(app=...)' instead.
    warnings.warn(message, DeprecationWarning)

tests/controllers/test_genes.py: 10 warnings
  /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/httpx/_content.py:202: 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 3.11.8-final-0 -----------
Name                                            Stmts   Miss  Cover
-------------------------------------------------------------------
src/geneweaver/api/__init__.py                      5      2    60%
src/geneweaver/api/controller/__init__.py           0      0   100%
src/geneweaver/api/controller/api.py               12      0   100%
src/geneweaver/api/controller/genes.py             33      0   100%
src/geneweaver/api/controller/genesets.py          73     14    81%
src/geneweaver/api/controller/message.py            8      0   100%
src/geneweaver/api/controller/publications.py      19      0   100%
src/geneweaver/api/controller/search.py             0      0   100%
src/geneweaver/api/controller/species.py           11      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/exceptions.py              10      1    90%
src/geneweaver/api/core/security.py               118     21    82%
src/geneweaver/api/dependencies.py                 50     26    48%
src/geneweaver/api/main.py                          1      0   100%
src/geneweaver/api/schemas/__init__.py              0      0   100%
src/geneweaver/api/schemas/apimodels.py            18      0   100%
src/geneweaver/api/schemas/auth.py                 19      0   100%
src/geneweaver/api/schemas/messages.py             18     18     0%
src/geneweaver/api/schemas/score.py                13     13     0%
src/geneweaver/api/services/__init__.py             0      0   100%
src/geneweaver/api/services/genes.py               38      3    92%
src/geneweaver/api/services/geneset.py             70     24    66%
src/geneweaver/api/services/io.py                   4      0   100%
src/geneweaver/api/services/parse/__init__.py       0      0   100%
src/geneweaver/api/services/publications.py        17      6    65%
src/geneweaver/api/services/pubmeds.py              0      0   100%
src/geneweaver/api/services/species.py             16      3    81%
-------------------------------------------------------------------
TOTAL                                             582    132    77%
Coverage HTML written to dir htmlcov

Required test coverage of 60% reached. Total coverage: 77.32%
======================= 83 passed, 57 warnings in 2.73s ========================