Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Updating dependencies and simplifying CollectionResponse urls in geneset search #104

Conversation

bergsalex
Copy link
Collaborator

No description provided.

Copy link

github-actions bot commented Dec 10, 2024

Test Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.11.10, pytest-8.3.4, 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-4.7.0
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/3.11.10/x64/lib/python3.11/importlib/resources/_legacy.py:80: 11 warnings
  /opt/hostedtoolcache/Python/3.11.10/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/3.11.10/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 3.11.10-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        47      0   100%
src/geneweaver/api/services/pubmeds.py              0      0   100%
src/geneweaver/api/services/species.py             18      3    83%
-------------------------------------------------------------------
TOTAL                                             947    102    89%
Coverage HTML written to dir htmlcov

Required test coverage of 60% reached. Total coverage: 89.23%
================= 339 passed, 21 skipped, 34 warnings in 5.35s =================

@bergsalex bergsalex temporarily deployed to jax-cluster-dev-10--dev December 10, 2024 14:48 — with GitHub Actions Inactive
@bergsalex bergsalex marked this pull request as ready for review December 10, 2024 14:58
@bergsalex bergsalex merged commit 268bc98 into main Dec 10, 2024
7 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants