G3 304 publication service fix

[francastell]

No description provided.

[github-actions]

Test Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.11.12, pytest-8.3.5, pluggy-1.5.0
rootdir: /home/runner/work/geneweaver-api/geneweaver-api
configfile: pyproject.toml
plugins: asyncio-0.21.2, cov-4.1.0, anyio-4.9.0
asyncio: mode=Mode.STRICT
collected 360 items

tests/controllers/test_api_standards.py ................................ [  8%]
........................................................................ [ 28%]
.sssssssssssssssssssss                                                   [ 35%]
tests/controllers/test_genes.py .............                            [ 38%]
tests/controllers/test_genesets.py ..................................... [ 48%]
......................                                                   [ 55%]
tests/controllers/test_monitor.py .                                      [ 55%]
tests/controllers/test_publications.py ........                          [ 57%]
tests/controllers/test_return_schemas.py .                               [ 57%]
tests/controllers/test_search.py ..                                      [ 58%]
tests/controllers/test_species.py ....                                   [ 59%]
tests/core/test_security.py ..........                                   [ 62%]
tests/services/io/test_read_file_contents.py ...............             [ 66%]
tests/services/test_gene.py ..............                               [ 70%]
tests/services/test_genset.py .......................................... [ 81%]
.............................................                            [ 94%]
tests/services/test_monitors.py ..                                       [ 95%]
tests/services/test_ontology.py ....                                     [ 96%]
tests/services/test_publications.py .......                              [ 98%]
tests/services/test_species.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/3.11.12/x64/lib/python3.11/importlib/resources/_legacy.py:80: 11 warnings
  /opt/hostedtoolcache/Python/3.11.12/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.
    geneset_list_response_json = importlib.resources.read_text("tests.data", "geneset.json")

tests/data/__init__.py:19
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:19: 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: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.
    gene_id_mapping_json = importlib.resources.read_text("tests.data", "gene_maping.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.
    publications_json = importlib.resources.read_text("tests.data", "publications.json")

tests/data/__init__.py:27
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:27: 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: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.
    species_json = importlib.resources.read_text("tests.data", "species.json")

tests/data/__init__.py:33
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:33: 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/data/__init__.py:35
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:35: 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.
    monitors_json = importlib.resources.read_text("tests.data", "monitors.json")

tests/data/__init__.py:37
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:37: 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.
    ontology_json = importlib.resources.read_text("tests.data", "ontology.json")

tests/controllers/test_genes.py: 10 warnings
tests/controllers/test_genesets.py: 2 warnings
  /opt/hostedtoolcache/Python/3.11.12/x64/lib/python3.11/site-packages/httpx/_models.py:408: DeprecationWarning: Use 'content=<...>' to upload raw bytes/text content.
    headers, stream = encode_request(

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

---------- coverage: platform linux, python 3.11.12-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               14      0   100%
src/geneweaver/api/controller/genes.py             39      0   100%
src/geneweaver/api/controller/genesets.py          98      4    96%
src/geneweaver/api/controller/message.py           27      0   100%
src/geneweaver/api/controller/monitors.py          16      0   100%
src/geneweaver/api/controller/publications.py      35      0   100%
src/geneweaver/api/controller/search.py            21      0   100%
src/geneweaver/api/controller/species.py           17      0   100%
src/geneweaver/api/controller/utilities.py          9      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            31      0   100%
src/geneweaver/api/core/exceptions.py              13      1    92%
src/geneweaver/api/core/security.py               121     20    83%
src/geneweaver/api/dependencies.py                 61     30    51%
src/geneweaver/api/main.py                          1      0   100%
src/geneweaver/api/schemas/__init__.py              0      0   100%
src/geneweaver/api/schemas/apimodels.py            61      6    90%
src/geneweaver/api/schemas/auth.py                 18      0   100%
src/geneweaver/api/schemas/messages.py             18     18     0%
src/geneweaver/api/schemas/score.py                13     13     0%
src/geneweaver/api/schemas/search.py               19      0   100%
src/geneweaver/api/services/__init__.py             0      0   100%
src/geneweaver/api/services/genes.py               45      0   100%
src/geneweaver/api/services/geneset.py            184      5    97%
src/geneweaver/api/services/io.py                   4      0   100%
src/geneweaver/api/services/monitors.py            10      0   100%
src/geneweaver/api/services/parse/__init__.py       0      0   100%
src/geneweaver/api/services/publications.py        48      0   100%
src/geneweaver/api/services/pubmeds.py              0      0   100%
src/geneweaver/api/services/species.py             18      3    83%
-------------------------------------------------------------------
TOTAL                                             948    102    89%
Coverage HTML written to dir htmlcov

Required test coverage of 60% reached. Total coverage: 89.24%
================= 339 passed, 21 skipped, 34 warnings in 5.12s =================