G3 226 add publication endpoint #62

francastell · 2024-05-01T20:15:51Z

No description provided.

github-actions · 2024-05-01T20:16:58Z

Test Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.11.9, pytest-8.2.0, pluggy-1.5.0
rootdir: /home/runner/work/geneweaver-api/geneweaver-api
configfile: pyproject.toml
plugins: asyncio-0.21.2, anyio-4.3.0, cov-4.1.0
asyncio: mode=Mode.STRICT
collected 195 items

tests/controllers/test_api_standards.py ................................ [ 16%]
......................................ssssssssssssss                     [ 43%]
tests/controllers/test_genes.py .............                            [ 49%]
tests/controllers/test_genesets.py ................                      [ 57%]
tests/controllers/test_publications.py .......                           [ 61%]
tests/controllers/test_species.py ....                                   [ 63%]
tests/core/test_security.py ..........                                   [ 68%]
tests/services/io/test_read_file_contents.py ...............             [ 76%]
tests/services/test_gene.py ..............                               [ 83%]
tests/services/test_genset.py ....................                       [ 93%]
tests/services/test_publications.py .....                                [ 96%]
tests/services/test_species.py .......                                   [100%]

=============================== warnings summary ===============================
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/httpx/_client.py:680: 1 warning
tests/controllers/test_genes.py: 13 warnings
tests/controllers/test_genesets.py: 16 warnings
tests/controllers/test_publications.py: 7 warnings
tests/controllers/test_species.py: 4 warnings
  /opt/hostedtoolcache/Python/3.11.9/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/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/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80
  /opt/hostedtoolcache/Python/3.11.9/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/controllers/test_genes.py: 10 warnings
  /opt/hostedtoolcache/Python/3.11.9/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 3.11.9-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             38      0   100%
src/geneweaver/api/controller/genesets.py          87      3    97%
src/geneweaver/api/controller/message.py           19      0   100%
src/geneweaver/api/controller/publications.py      30      0   100%
src/geneweaver/api/controller/search.py             0      0   100%
src/geneweaver/api/controller/species.py           17      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                 56     30    46%
src/geneweaver/api/main.py                          1      0   100%
src/geneweaver/api/schemas/__init__.py              0      0   100%
src/geneweaver/api/schemas/apimodels.py            44      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               45      0   100%
src/geneweaver/api/services/geneset.py             90      2    98%
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        39      0   100%
src/geneweaver/api/services/pubmeds.py              0      0   100%
src/geneweaver/api/services/species.py             18      3    83%
-------------------------------------------------------------------
TOTAL                                             712     94    87%
Coverage HTML written to dir htmlcov

Required test coverage of 60% reached. Total coverage: 86.80%
================= 181 passed, 14 skipped, 69 warnings in 3.18s =================

bergsalex

Looks good, just one minor change.

bergsalex · 2024-05-01T20:42:44Z

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-api"
-version = "0.4.0"
+version = "0.4.1.a01"


This will be version 0.5.0a0.

bergsalex · 2024-05-01T20:42:53Z

pyproject.toml

@@ -21,7 +21,7 @@ python = "^3.9"
 geneweaver-core = "^0.9.1"
 fastapi = {extras = ["all"], version = "^0.99.1"}
 uvicorn = {extras = ["standard"], version = "^0.24.0"}
-geneweaver-db = "^0.3.0"
+geneweaver-db = "^0.3.3"


bergsalex · 2024-05-01T20:45:00Z

src/geneweaver/api/services/publications.py

+        # check publication is not already in the DB
+        pub = db_publication.by_pubmed_id(cursor, pubmed_id)
+        if pub:
+            return {"error": True, "message": message.RECORD_EXISTS}


If the publication exists, you can just return it. That would make the endpoint idempotent, which is desirable.

francastell added 3 commits May 1, 2024 16:01

G3-226 add publication endpoint

ac32358

G3-226 add publication return model

97db411

G3-226 add publication return model

a48b463

francastell temporarily deployed to jax-cluster-dev-10--dev May 1, 2024 20:19 — with GitHub Actions Inactive

francastell requested review from obwalton, gerring, bergsalex, rjbluis, desais-jax and C-1337ka May 1, 2024 20:23

bergsalex requested changes May 1, 2024

View reviewed changes

G3-226 change to make endpoint idempotent

500e5ba

francastell had a problem deploying to jax-cluster-dev-10--dev May 2, 2024 14:49 — with GitHub Actions Failure

G3-226 change to make endpoint idempotent

0259568

francastell temporarily deployed to jax-cluster-dev-10--dev May 2, 2024 14:52 — with GitHub Actions Inactive

bergsalex self-requested a review May 2, 2024 15:50

bergsalex approved these changes May 2, 2024

View reviewed changes

francastell merged commit d1dcc2c into main May 2, 2024
7 checks passed

bergsalex deleted the G3-226-add-publication-endpoint branch May 29, 2024 20:50

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G3 226 add publication endpoint #62

G3 226 add publication endpoint #62

francastell commented May 1, 2024

github-actions bot commented May 1, 2024 •

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bergsalex May 1, 2024

bergsalex May 1, 2024

G3 226 add publication endpoint #62

G3 226 add publication endpoint #62

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francastell commented May 1, 2024

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