bioversions 0.6.25__tar.gz → 0.6.26__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {bioversions-0.6.25 → bioversions-0.6.26}/PKG-INFO +1 -1
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/_data/versions.yml +9 -2
- bioversions-0.6.26/docs/failures.md +360 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/img/has_release_url.svg +1 -1
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/img/version_date_types.svg +1 -1
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/img/version_types.svg +1 -1
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/source/conf.py +1 -1
- {bioversions-0.6.25 → bioversions-0.6.26}/pyproject.toml +2 -2
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/resources/versions.json +15 -2
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/version.py +1 -1
- bioversions-0.6.25/docs/failures.md +0 -145
- {bioversions-0.6.25 → bioversions-0.6.26}/.cruft.json +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.github/CODE_OF_CONDUCT.md +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.github/CONTRIBUTING.md +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.github/codecov.yml +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.github/workflows/cruft.yml +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.github/workflows/tests.yml +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.github/workflows/update.yml +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.gitignore +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/.readthedocs.yml +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/LICENSE +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/MANIFEST.in +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/README.md +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/_config.yml +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/_includes/footer.html +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/_includes/head.html +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/download.md +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/index.md +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/source/cli.rst +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/source/index.rst +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/source/installation.rst +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/source/logo.png +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/source/usage.rst +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/docs/summary.md +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/__init__.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/__main__.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/charts.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/cli.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/py.typed +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/resources/__init__.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/resources/update.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/slack_client.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/__init__.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/antibodyregistry.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/bigg.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/biogrid.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/cellosaurus.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/chebi.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/chembl.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/chemidplus.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/civic.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/complexportal.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/daily.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/depmap.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/dgi.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/disgenet.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/drugbank.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/drugcentral.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/ensembl.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/expasy.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/flybase.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/gtdb.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/guidetopharmacology.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/hgnc.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/homologene.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/icd10.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/icd11.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/icf.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/intact.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/interpro.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/itis.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/kegg.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/mesh.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/mgi.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/mirbase.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/moalmanac.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/msigdb.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/ncit.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/npass.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/obo.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/ols.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/omim.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/oncotree.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/pathbank.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/pathwaycommons.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/pfam.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/pombase.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/pr.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/pubchem.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/reactome.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/rfam.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/rgd.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/rhea.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/rxnorm.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/sgd.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/slm.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/stringdb.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/umls.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/uniprot.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/unversioned.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/wikipathways.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/sources/zfin.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/templates/base.html +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/templates/home.html +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/twitter_client.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/utils.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/src/bioversions/wsgi.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/tests/test_bioversions.py +0 -0
- {bioversions-0.6.25 → bioversions-0.6.26}/tox.ini +0 -0
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Metadata-Version: 2.4
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Name: bioversions
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Version: 0.6.
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Version: 0.6.26
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Summary: Get the current version for biological databases
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Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
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Project-URL: Homepage, https://github.com/biopragmatics/bioversions
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annotations:
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author: runner
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date: '2025-01-
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revision:
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date: '2025-01-03'
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revision: 890
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database:
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- name: A nomenclatural ontology for biological names
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prefix: nomen
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retrieved: '2025-01-01'
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- date: '2025-01-01'
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retrieved: '2025-01-03'
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version: January 1, 2025
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vtype: date
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- name: 'OntoAvida: ontology for Avida digital evolution platform'
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- name: SWO (The Software Ontology)
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- name: Zebrafish Phenotype Ontology
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# Summary of Errors
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- DepMap - failed to resolve DepMap
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- DisGeNet - failed to resolve DisGeNet
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- Antibody Registry - failed to resolve Antibody Registry
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- ChEBI - failed to resolve ChEBI
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- DrugBank - failed to resolve DrugBank
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## DepMap
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Using class: `DepMapGetter`
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```python-traceback
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Traceback (most recent call last):
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 534, in _make_request
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response = conn.getresponse()
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^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 516, in getresponse
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httplib_response = super().getresponse()
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^^^^^^^^^^^^^^^^^^^^^
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File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 1428, in getresponse
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response.begin()
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File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 331, in begin
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version, status, reason = self._read_status()
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^^^^^^^^^^^^^^^^^^^
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File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 292, in _read_status
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line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/socket.py", line 720, in readinto
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return self._sock.recv_into(b)
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^^^^^^^^^^^^^^^^^^^^^^^
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File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1251, in recv_into
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return self.read(nbytes, buffer)
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^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1103, in read
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return self._sslobj.read(len, buffer)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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TimeoutError: The read operation timed out
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The above exception was the direct cause of the following exception:
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Traceback (most recent call last):
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
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resp = conn.urlopen(
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^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 841, in urlopen
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retries = retries.increment(
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^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 474, in increment
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raise reraise(type(error), error, _stacktrace)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 39, in reraise
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raise value
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 787, in urlopen
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response = self._make_request(
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^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 536, in _make_request
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self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 367, in _raise_timeout
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raise ReadTimeoutError(
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urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='depmap.org', port=443): Read timed out. (read timeout=15)
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During handling of the above exception, another exception occurred:
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Traceback (most recent call last):
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File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
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yv = resolve(cls.name)
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^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
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return _resolve_helper_cached(name)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
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return _calc_entry(core, key, func, args, kwds)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
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func_res = func(*args, **kwds)
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^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
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^^^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
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return getter.resolve()
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^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
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version=cls.version,
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^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
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if isinstance(cls._cache_prop, str):
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^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
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cls._cache = cls().get()
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^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/depmap.py", line 22, in get
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res = requests.get(URL, timeout=15)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
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return request("get", url, params=params, **kwargs)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
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return session.request(method=method, url=url, **kwargs)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
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resp = self.send(prep, **send_kwargs)
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
105
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+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
|
106
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r = adapter.send(request, **kwargs)
|
107
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+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
108
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+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
|
109
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+
raise ReadTimeout(e, request=request)
|
110
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+
requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='depmap.org', port=443): Read timed out. (read timeout=15)
|
111
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+
|
112
|
+
```
|
113
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+
|
114
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+
## DisGeNet
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115
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+
|
116
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Using class: `DisGeNetGetter`
|
117
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+
|
118
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+
```python-traceback
|
119
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+
Traceback (most recent call last):
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120
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+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 974, in json
|
121
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+
return complexjson.loads(self.text, **kwargs)
|
122
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+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
123
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+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/__init__.py", line 346, in loads
|
124
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+
return _default_decoder.decode(s)
|
125
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+
^^^^^^^^^^^^^^^^^^^^^^^^^^
|
126
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+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 338, in decode
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127
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+
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
|
128
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+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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129
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+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
|
130
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raise JSONDecodeError("Expecting value", s, err.value) from None
|
131
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+
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
132
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+
|
133
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+
During handling of the above exception, another exception occurred:
|
134
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+
|
135
|
+
Traceback (most recent call last):
|
136
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+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
137
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+
yv = resolve(cls.name)
|
138
|
+
^^^^^^^^^^^^^^^^^
|
139
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+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
140
|
+
return _resolve_helper_cached(name)
|
141
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
142
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
143
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+
return _calc_entry(core, key, func, args, kwds)
|
144
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
145
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
146
|
+
func_res = func(*args, **kwds)
|
147
|
+
^^^^^^^^^^^^^^^^^^^
|
148
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
149
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+
return _resolve_helper(name)
|
150
|
+
^^^^^^^^^^^^^^^^^^^^^
|
151
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
152
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+
return getter.resolve()
|
153
|
+
^^^^^^^^^^^^^^^^
|
154
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
155
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+
version=cls.version,
|
156
|
+
^^^^^^^^^^^
|
157
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
158
|
+
if isinstance(cls._cache_prop, str):
|
159
|
+
^^^^^^^^^^^^^^^
|
160
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
161
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+
cls._cache = cls().get()
|
162
|
+
^^^^^^^^^^^
|
163
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/disgenet.py", line 24, in get
|
164
|
+
res_json = res.json()
|
165
|
+
^^^^^^^^^^
|
166
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
|
167
|
+
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
|
168
|
+
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
169
|
+
|
170
|
+
```
|
171
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+
|
172
|
+
## Antibody Registry
|
173
|
+
|
174
|
+
Using class: `AntibodyRegistryGetter`
|
175
|
+
|
176
|
+
```python-traceback
|
177
|
+
Traceback (most recent call last):
|
178
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
179
|
+
yv = resolve(cls.name)
|
180
|
+
^^^^^^^^^^^^^^^^^
|
181
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
182
|
+
return _resolve_helper_cached(name)
|
183
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
184
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
185
|
+
return _calc_entry(core, key, func, args, kwds)
|
186
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
187
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
188
|
+
func_res = func(*args, **kwds)
|
189
|
+
^^^^^^^^^^^^^^^^^^^
|
190
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
191
|
+
return _resolve_helper(name)
|
192
|
+
^^^^^^^^^^^^^^^^^^^^^
|
193
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
194
|
+
return getter.resolve()
|
195
|
+
^^^^^^^^^^^^^^^^
|
196
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
197
|
+
version=cls.version,
|
198
|
+
^^^^^^^^^^^
|
199
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
200
|
+
if isinstance(cls._cache_prop, str):
|
201
|
+
^^^^^^^^^^^^^^^
|
202
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
203
|
+
cls._cache = cls().get()
|
204
|
+
^^^^^^^^^^^
|
205
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/antibodyregistry.py", line 21, in get
|
206
|
+
return soup.find(**{"class": "footer"}).find("a").text.lstrip("v")
|
207
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
208
|
+
AttributeError: 'NoneType' object has no attribute 'find'
|
209
|
+
|
210
|
+
```
|
211
|
+
|
212
|
+
## ChEBI
|
213
|
+
|
214
|
+
Using class: `ChEBIGetter`
|
215
|
+
|
216
|
+
```python-traceback
|
217
|
+
Traceback (most recent call last):
|
218
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 534, in _make_request
|
219
|
+
response = conn.getresponse()
|
220
|
+
^^^^^^^^^^^^^^^^^^
|
221
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 516, in getresponse
|
222
|
+
httplib_response = super().getresponse()
|
223
|
+
^^^^^^^^^^^^^^^^^^^^^
|
224
|
+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 1428, in getresponse
|
225
|
+
response.begin()
|
226
|
+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 331, in begin
|
227
|
+
version, status, reason = self._read_status()
|
228
|
+
^^^^^^^^^^^^^^^^^^^
|
229
|
+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 292, in _read_status
|
230
|
+
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
|
231
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
232
|
+
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/socket.py", line 720, in readinto
|
233
|
+
return self._sock.recv_into(b)
|
234
|
+
^^^^^^^^^^^^^^^^^^^^^^^
|
235
|
+
TimeoutError: timed out
|
236
|
+
|
237
|
+
The above exception was the direct cause of the following exception:
|
238
|
+
|
239
|
+
Traceback (most recent call last):
|
240
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
|
241
|
+
resp = conn.urlopen(
|
242
|
+
^^^^^^^^^^^^^
|
243
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 841, in urlopen
|
244
|
+
retries = retries.increment(
|
245
|
+
^^^^^^^^^^^^^^^^^^
|
246
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 474, in increment
|
247
|
+
raise reraise(type(error), error, _stacktrace)
|
248
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
249
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 39, in reraise
|
250
|
+
raise value
|
251
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 787, in urlopen
|
252
|
+
response = self._make_request(
|
253
|
+
^^^^^^^^^^^^^^^^^^^
|
254
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 536, in _make_request
|
255
|
+
self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
|
256
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 367, in _raise_timeout
|
257
|
+
raise ReadTimeoutError(
|
258
|
+
urllib3.exceptions.ReadTimeoutError: HTTPConnectionPool(host='ftp.ebi.ac.uk', port=80): Read timed out. (read timeout=60)
|
259
|
+
|
260
|
+
During handling of the above exception, another exception occurred:
|
261
|
+
|
262
|
+
Traceback (most recent call last):
|
263
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
264
|
+
yv = resolve(cls.name)
|
265
|
+
^^^^^^^^^^^^^^^^^
|
266
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
267
|
+
return _resolve_helper_cached(name)
|
268
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
269
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
270
|
+
return _calc_entry(core, key, func, args, kwds)
|
271
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
272
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
273
|
+
func_res = func(*args, **kwds)
|
274
|
+
^^^^^^^^^^^^^^^^^^^
|
275
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
276
|
+
return _resolve_helper(name)
|
277
|
+
^^^^^^^^^^^^^^^^^^^^^
|
278
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
279
|
+
return getter.resolve()
|
280
|
+
^^^^^^^^^^^^^^^^
|
281
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
282
|
+
version=cls.version,
|
283
|
+
^^^^^^^^^^^
|
284
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
285
|
+
if isinstance(cls._cache_prop, str):
|
286
|
+
^^^^^^^^^^^^^^^
|
287
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
288
|
+
cls._cache = cls().get()
|
289
|
+
^^^^^^^^^^^
|
290
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 282, in get
|
291
|
+
return self.process(get_obo_version(url))
|
292
|
+
^^^^^^^^^^^^^^^^^^^^
|
293
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 255, in get_obo_version
|
294
|
+
with requests.get(url, stream=True, timeout=60) as res:
|
295
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
296
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
|
297
|
+
return request("get", url, params=params, **kwargs)
|
298
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
299
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
|
300
|
+
return session.request(method=method, url=url, **kwargs)
|
301
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
302
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
|
303
|
+
resp = self.send(prep, **send_kwargs)
|
304
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
305
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 724, in send
|
306
|
+
history = [resp for resp in gen]
|
307
|
+
^^^
|
308
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 265, in resolve_redirects
|
309
|
+
resp = self.send(
|
310
|
+
^^^^^^^^^^
|
311
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
|
312
|
+
r = adapter.send(request, **kwargs)
|
313
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
314
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
|
315
|
+
raise ReadTimeout(e, request=request)
|
316
|
+
requests.exceptions.ReadTimeout: HTTPConnectionPool(host='ftp.ebi.ac.uk', port=80): Read timed out. (read timeout=60)
|
317
|
+
|
318
|
+
```
|
319
|
+
|
320
|
+
## DrugBank
|
321
|
+
|
322
|
+
Using class: `DrugBankGetter`
|
323
|
+
|
324
|
+
```python-traceback
|
325
|
+
Traceback (most recent call last):
|
326
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
327
|
+
yv = resolve(cls.name)
|
328
|
+
^^^^^^^^^^^^^^^^^
|
329
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
330
|
+
return _resolve_helper_cached(name)
|
331
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
332
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
333
|
+
return _calc_entry(core, key, func, args, kwds)
|
334
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
335
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
336
|
+
func_res = func(*args, **kwds)
|
337
|
+
^^^^^^^^^^^^^^^^^^^
|
338
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
339
|
+
return _resolve_helper(name)
|
340
|
+
^^^^^^^^^^^^^^^^^^^^^
|
341
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
342
|
+
return getter.resolve()
|
343
|
+
^^^^^^^^^^^^^^^^
|
344
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
345
|
+
version=cls.version,
|
346
|
+
^^^^^^^^^^^
|
347
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
348
|
+
if isinstance(cls._cache_prop, str):
|
349
|
+
^^^^^^^^^^^^^^^
|
350
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
351
|
+
cls._cache = cls().get()
|
352
|
+
^^^^^^^^^^^
|
353
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
|
354
|
+
res.raise_for_status()
|
355
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
|
356
|
+
raise HTTPError(http_error_msg, response=self)
|
357
|
+
requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.drugbank.com/releases.json
|
358
|
+
|
359
|
+
```
|
360
|
+
|
@@ -6,7 +6,7 @@
|
|
6
6
|
<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
|
7
7
|
<cc:Work>
|
8
8
|
<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
9
|
-
<dc:date>2025-01-
|
9
|
+
<dc:date>2025-01-03T01:02:50.333861</dc:date>
|
10
10
|
<dc:format>image/svg+xml</dc:format>
|
11
11
|
<dc:creator>
|
12
12
|
<cc:Agent>
|
@@ -6,7 +6,7 @@
|
|
6
6
|
<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
|
7
7
|
<cc:Work>
|
8
8
|
<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
9
|
-
<dc:date>2025-01-
|
9
|
+
<dc:date>2025-01-03T01:02:50.289129</dc:date>
|
10
10
|
<dc:format>image/svg+xml</dc:format>
|
11
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@@ -6,7 +6,7 @@
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<rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<dc:date>2025-01-
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<dc:date>2025-01-03T01:02:50.144967</dc:date>
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[project]
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name = "bioversions"
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version = "0.6.
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version = "0.6.26"
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description = "Get the current version for biological databases"
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readme = "README.md"
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authors = [
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docstring-code-format = true
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[tool.bumpversion]
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current_version = "0.6.
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current_version = "0.6.26"
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parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
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serialize = [
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"{major}.{minor}.{patch}-{release}+{build}",
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{
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"annotations": {
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"revision":
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"date": "2025-01-
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"revision": 890,
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"date": "2025-01-03",
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"author": "runner"
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},
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"database": [
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"retrieved": "2025-01-01",
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"version": "December 30, 2024",
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},
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{
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"retrieved": "2025-01-03",
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"version": "January 1, 2025",
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"date": "2025-01-01"
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{
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},
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{
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"version": "2025-01-03"
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{
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"retrieved": "2025-01-02",
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},
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{
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"retrieved": "2025-01-03",
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|
@@ -1,145 +0,0 @@
|
|
1
|
-
# Summary of Errors
|
2
|
-
|
3
|
-
- DisGeNet - failed to resolve DisGeNet
|
4
|
-
- Antibody Registry - failed to resolve Antibody Registry
|
5
|
-
- DrugBank - failed to resolve DrugBank
|
6
|
-
|
7
|
-
## DisGeNet
|
8
|
-
|
9
|
-
Using class: `DisGeNetGetter`
|
10
|
-
|
11
|
-
```python-traceback
|
12
|
-
Traceback (most recent call last):
|
13
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 974, in json
|
14
|
-
return complexjson.loads(self.text, **kwargs)
|
15
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
16
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/__init__.py", line 346, in loads
|
17
|
-
return _default_decoder.decode(s)
|
18
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^
|
19
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 338, in decode
|
20
|
-
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
|
21
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
22
|
-
File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
|
23
|
-
raise JSONDecodeError("Expecting value", s, err.value) from None
|
24
|
-
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
25
|
-
|
26
|
-
During handling of the above exception, another exception occurred:
|
27
|
-
|
28
|
-
Traceback (most recent call last):
|
29
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
30
|
-
yv = resolve(cls.name)
|
31
|
-
^^^^^^^^^^^^^^^^^
|
32
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
33
|
-
return _resolve_helper_cached(name)
|
34
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
35
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
36
|
-
return _calc_entry(core, key, func, args, kwds)
|
37
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
38
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
39
|
-
func_res = func(*args, **kwds)
|
40
|
-
^^^^^^^^^^^^^^^^^^^
|
41
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
42
|
-
return _resolve_helper(name)
|
43
|
-
^^^^^^^^^^^^^^^^^^^^^
|
44
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
45
|
-
return getter.resolve()
|
46
|
-
^^^^^^^^^^^^^^^^
|
47
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
48
|
-
version=cls.version,
|
49
|
-
^^^^^^^^^^^
|
50
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
51
|
-
if isinstance(cls._cache_prop, str):
|
52
|
-
^^^^^^^^^^^^^^^
|
53
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
54
|
-
cls._cache = cls().get()
|
55
|
-
^^^^^^^^^^^
|
56
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/disgenet.py", line 24, in get
|
57
|
-
res_json = res.json()
|
58
|
-
^^^^^^^^^^
|
59
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
|
60
|
-
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
|
61
|
-
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
|
62
|
-
|
63
|
-
```
|
64
|
-
|
65
|
-
## Antibody Registry
|
66
|
-
|
67
|
-
Using class: `AntibodyRegistryGetter`
|
68
|
-
|
69
|
-
```python-traceback
|
70
|
-
Traceback (most recent call last):
|
71
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
72
|
-
yv = resolve(cls.name)
|
73
|
-
^^^^^^^^^^^^^^^^^
|
74
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
75
|
-
return _resolve_helper_cached(name)
|
76
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
77
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
78
|
-
return _calc_entry(core, key, func, args, kwds)
|
79
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
80
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
81
|
-
func_res = func(*args, **kwds)
|
82
|
-
^^^^^^^^^^^^^^^^^^^
|
83
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
84
|
-
return _resolve_helper(name)
|
85
|
-
^^^^^^^^^^^^^^^^^^^^^
|
86
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
87
|
-
return getter.resolve()
|
88
|
-
^^^^^^^^^^^^^^^^
|
89
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
90
|
-
version=cls.version,
|
91
|
-
^^^^^^^^^^^
|
92
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
93
|
-
if isinstance(cls._cache_prop, str):
|
94
|
-
^^^^^^^^^^^^^^^
|
95
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
96
|
-
cls._cache = cls().get()
|
97
|
-
^^^^^^^^^^^
|
98
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/antibodyregistry.py", line 21, in get
|
99
|
-
return soup.find(**{"class": "footer"}).find("a").text.lstrip("v")
|
100
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
101
|
-
AttributeError: 'NoneType' object has no attribute 'find'
|
102
|
-
|
103
|
-
```
|
104
|
-
|
105
|
-
## DrugBank
|
106
|
-
|
107
|
-
Using class: `DrugBankGetter`
|
108
|
-
|
109
|
-
```python-traceback
|
110
|
-
Traceback (most recent call last):
|
111
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
112
|
-
yv = resolve(cls.name)
|
113
|
-
^^^^^^^^^^^^^^^^^
|
114
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
|
115
|
-
return _resolve_helper_cached(name)
|
116
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
117
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
|
118
|
-
return _calc_entry(core, key, func, args, kwds)
|
119
|
-
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
120
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
|
121
|
-
func_res = func(*args, **kwds)
|
122
|
-
^^^^^^^^^^^^^^^^^^^
|
123
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
|
124
|
-
return _resolve_helper(name)
|
125
|
-
^^^^^^^^^^^^^^^^^^^^^
|
126
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
|
127
|
-
return getter.resolve()
|
128
|
-
^^^^^^^^^^^^^^^^
|
129
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
|
130
|
-
version=cls.version,
|
131
|
-
^^^^^^^^^^^
|
132
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
|
133
|
-
if isinstance(cls._cache_prop, str):
|
134
|
-
^^^^^^^^^^^^^^^
|
135
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
136
|
-
cls._cache = cls().get()
|
137
|
-
^^^^^^^^^^^
|
138
|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
|
139
|
-
res.raise_for_status()
|
140
|
-
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
|
141
|
-
raise HTTPError(http_error_msg, response=self)
|
142
|
-
requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.drugbank.com/releases.json
|
143
|
-
|
144
|
-
```
|
145
|
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