bioversions 0.6.0__tar.gz → 0.6.2__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-0.6.0 → bioversions-0.6.2}/PKG-INFO +1 -1
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/_data/versions.yml +26 -2
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/failures.md +81 -6
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/img/has_release_url.svg +1 -1
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/img/version_date_types.svg +1 -1
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/img/version_types.svg +1 -1
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/conf.py +1 -1
- {bioversions-0.6.0 → bioversions-0.6.2}/pyproject.toml +2 -2
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/resources/versions.json +44 -2
- bioversions-0.6.2/src/bioversions/sources/hgnc.py +42 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/mesh.py +10 -3
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/version.py +1 -1
- bioversions-0.6.0/src/bioversions/sources/hgnc.py +0 -47
- {bioversions-0.6.0 → bioversions-0.6.2}/.cruft.json +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.github/CODE_OF_CONDUCT.md +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.github/CONTRIBUTING.md +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.github/codecov.yml +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.github/workflows/cruft.yml +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.github/workflows/tests.yml +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.github/workflows/update.yml +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.gitignore +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/.readthedocs.yml +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/LICENSE +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/MANIFEST.in +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/README.md +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/_config.yml +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/_includes/footer.html +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/_includes/head.html +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/download.md +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/index.md +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/cli.rst +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/index.rst +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/installation.rst +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/logo.png +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/source/usage.rst +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/docs/summary.md +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/__init__.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/__main__.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/charts.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/cli.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/py.typed +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/resources/__init__.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/resources/update.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/slack_client.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/__init__.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/antibodyregistry.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/bigg.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/biogrid.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/cellosaurus.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/chebi.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/chembl.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/chemidplus.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/civic.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/complexportal.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/daily.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/depmap.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/dgi.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/disgenet.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/drugbank.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/drugcentral.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/ensembl.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/expasy.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/flybase.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/gtdb.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/guidetopharmacology.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/homologene.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/icd10.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/icd11.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/icf.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/intact.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/interpro.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/itis.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/kegg.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/mgi.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/mirbase.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/moalmanac.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/msigdb.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/ncit.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/npass.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/obo.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/ols.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/omim.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/oncotree.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pathbank.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pathwaycommons.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pfam.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pombase.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pr.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/pubchem.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/reactome.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rfam.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rgd.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rhea.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/rxnorm.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/sgd.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/slm.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/stringdb.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/umls.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/uniprot.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/unversioned.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/wikipathways.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/sources/zfin.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/templates/base.html +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/templates/home.html +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/twitter_client.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/utils.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/src/bioversions/wsgi.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/tests/test_bioversions.py +0 -0
- {bioversions-0.6.0 → bioversions-0.6.2}/tox.ini +0 -0
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Metadata-Version: 2.3
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Name: bioversions
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Version: 0.6.
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Version: 0.6.2
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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: '2024-12-
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revision:
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date: '2024-12-10'
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revision: 866
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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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- Antibody Registry - failed to resolve Antibody Registry
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## DisGeNet
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```python-traceback
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Traceback (most recent call last):
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The above exception was the direct cause of the following exception:
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File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 538, in _make_request
|
196
|
+
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 369, in _raise_timeout
|
198
|
+
raise ReadTimeoutError(
|
199
|
+
urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='bidd.group', port=443): Read timed out. (read timeout=15)
|
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|
+
|
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|
+
During handling of the above exception, another exception occurred:
|
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|
+
|
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|
Traceback (most recent call last):
|
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204
|
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
|
154
205
|
yv = resolve(cls.name)
|
@@ -177,9 +228,33 @@ Traceback (most recent call last):
|
|
177
228
|
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
|
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229
|
cls._cache = cls().get()
|
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|
^^^^^^^^^^^
|
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|
-
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/
|
181
|
-
|
182
|
-
|
231
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/npass.py", line 21, in get
|
232
|
+
soup = get_soup(URL)
|
233
|
+
^^^^^^^^^^^^^
|
234
|
+
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 62, in get_soup
|
235
|
+
res = requests.get(url, verify=verify, timeout=timeout or 15, headers=headers)
|
236
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
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|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
|
238
|
+
return request("get", url, params=params, **kwargs)
|
239
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
240
|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
|
241
|
+
return session.request(method=method, url=url, **kwargs)
|
242
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
243
|
+
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)
|
245
|
+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
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|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 724, in send
|
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|
+
history = [resp for resp in gen]
|
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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 265, in resolve_redirects
|
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|
+
resp = self.send(
|
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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 703, in send
|
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|
+
r = adapter.send(request, **kwargs)
|
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+
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
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|
+
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
|
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|
+
raise ReadTimeout(e, request=request)
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+
requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='bidd.group', port=443): Read timed out. (read timeout=15)
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|
```
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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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<cc:Work>
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<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
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-
<dc:date>2024-12-
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+
<dc:date>2024-12-10T01:08:18.087409</dc:date>
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<dc:format>image/svg+xml</dc:format>
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<dc:creator>
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<cc:Agent>
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@@ -6,7 +6,7 @@
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6
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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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<cc:Work>
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<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
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-
<dc:date>2024-12-
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+
<dc:date>2024-12-10T01:08:18.035245</dc:date>
|
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<dc:format>image/svg+xml</dc:format>
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<dc:creator>
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<cc:Agent>
|
@@ -6,7 +6,7 @@
|
|
6
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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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<cc:Work>
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<dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
|
9
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-
<dc:date>2024-12-
|
9
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+
<dc:date>2024-12-10T01:08:17.897990</dc:date>
|
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<dc:format>image/svg+xml</dc:format>
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<dc:creator>
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|
<cc:Agent>
|
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
|
|
4
4
|
|
5
5
|
[project]
|
6
6
|
name = "bioversions"
|
7
|
-
version = "0.6.
|
7
|
+
version = "0.6.2"
|
8
8
|
description = "Get the current version for biological databases"
|
9
9
|
readme = "README.md"
|
10
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|
authors = [
|
@@ -222,7 +222,7 @@ known-first-party = [
|
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|
docstring-code-format = true
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|
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|
[tool.bumpversion]
|
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-
current_version = "0.6.
|
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|
+
current_version = "0.6.2"
|
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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}",
|
@@ -1,7 +1,7 @@
|
|
1
1
|
{
|
2
2
|
"annotations": {
|
3
|
-
"revision":
|
4
|
-
"date": "2024-12-
|
3
|
+
"revision": 866,
|
4
|
+
"date": "2024-12-10",
|
5
5
|
"author": "runner"
|
6
6
|
},
|
7
7
|
"database": [
|
@@ -2184,6 +2184,12 @@
|
|
2184
2184
|
"version": "2024-09-08",
|
2185
2185
|
"homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-09-08/",
|
2186
2186
|
"date": "2024-09-08"
|
2187
|
+
},
|
2188
|
+
{
|
2189
|
+
"retrieved": "2024-12-10",
|
2190
|
+
"version": "2024-11-29",
|
2191
|
+
"homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-11-29/",
|
2192
|
+
"date": "2024-11-29"
|
2187
2193
|
}
|
2188
2194
|
],
|
2189
2195
|
"vtype": "date"
|
@@ -5491,6 +5497,11 @@
|
|
5491
5497
|
"retrieved": "2024-12-03",
|
5492
5498
|
"version": "2024-11-01",
|
5493
5499
|
"homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-11-01.json"
|
5500
|
+
},
|
5501
|
+
{
|
5502
|
+
"retrieved": "2024-12-09",
|
5503
|
+
"version": "2024-12-03",
|
5504
|
+
"homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-12-03.json"
|
5494
5505
|
}
|
5495
5506
|
],
|
5496
5507
|
"name": "HGNC",
|
@@ -6044,6 +6055,12 @@
|
|
6044
6055
|
"version": "2024-09-08",
|
6045
6056
|
"homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-09-08/",
|
6046
6057
|
"date": "2024-09-08"
|
6058
|
+
},
|
6059
|
+
{
|
6060
|
+
"retrieved": "2024-12-10",
|
6061
|
+
"version": "2024-11-29",
|
6062
|
+
"homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-11-29/",
|
6063
|
+
"date": "2024-11-29"
|
6047
6064
|
}
|
6048
6065
|
],
|
6049
6066
|
"vtype": "date"
|
@@ -7047,6 +7064,11 @@
|
|
7047
7064
|
"retrieved": "2023-12-01",
|
7048
7065
|
"version": "2024",
|
7049
7066
|
"homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2024"
|
7067
|
+
},
|
7068
|
+
{
|
7069
|
+
"retrieved": "2024-12-09",
|
7070
|
+
"version": "2025",
|
7071
|
+
"homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2025"
|
7050
7072
|
}
|
7051
7073
|
],
|
7052
7074
|
"name": "MeSH",
|
@@ -11645,6 +11667,10 @@
|
|
11645
11667
|
{
|
11646
11668
|
"retrieved": "2024-12-03",
|
11647
11669
|
"version": "2024-11-29"
|
11670
|
+
},
|
11671
|
+
{
|
11672
|
+
"retrieved": "2024-12-10",
|
11673
|
+
"version": "2024-12-06"
|
11648
11674
|
}
|
11649
11675
|
],
|
11650
11676
|
"name": "Rat Genome Database",
|
@@ -11813,6 +11839,10 @@
|
|
11813
11839
|
{
|
11814
11840
|
"retrieved": "2024-10-03",
|
11815
11841
|
"version": "90"
|
11842
|
+
},
|
11843
|
+
{
|
11844
|
+
"retrieved": "2024-12-10",
|
11845
|
+
"version": "91"
|
11816
11846
|
}
|
11817
11847
|
],
|
11818
11848
|
"vtype": "sequential"
|
@@ -14854,6 +14884,14 @@
|
|
14854
14884
|
{
|
14855
14885
|
"retrieved": "2024-12-08",
|
14856
14886
|
"version": "2024-12-08"
|
14887
|
+
},
|
14888
|
+
{
|
14889
|
+
"retrieved": "2024-12-09",
|
14890
|
+
"version": "2024-12-09"
|
14891
|
+
},
|
14892
|
+
{
|
14893
|
+
"retrieved": "2024-12-10",
|
14894
|
+
"version": "2024-12-10"
|
14857
14895
|
}
|
14858
14896
|
],
|
14859
14897
|
"name": "SwissLipids",
|
@@ -19816,6 +19854,10 @@
|
|
19816
19854
|
{
|
19817
19855
|
"retrieved": "2024-12-08",
|
19818
19856
|
"version": "2024-12-07"
|
19857
|
+
},
|
19858
|
+
{
|
19859
|
+
"retrieved": "2024-12-10",
|
19860
|
+
"version": "2024-12-08"
|
19819
19861
|
}
|
19820
19862
|
],
|
19821
19863
|
"name": "Zebrafish Information Network",
|
@@ -0,0 +1,42 @@
|
|
1
|
+
"""A getter for HGNC."""
|
2
|
+
|
3
|
+
import logging
|
4
|
+
|
5
|
+
import requests
|
6
|
+
|
7
|
+
from bioversions.utils import Getter, VersionType
|
8
|
+
|
9
|
+
__all__ = [
|
10
|
+
"HGNCGetter",
|
11
|
+
]
|
12
|
+
|
13
|
+
logger = logging.getLogger(__name__)
|
14
|
+
|
15
|
+
PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
|
16
|
+
URL = "https://storage.googleapis.com/storage/v1/b/public-download-files/o?prefix=hgnc/archive/archive/monthly"
|
17
|
+
PREFIX = "hgnc/archive/archive/monthly/json/hgnc_complete_set_"
|
18
|
+
SUFFIX = ".json"
|
19
|
+
|
20
|
+
|
21
|
+
class HGNCGetter(Getter):
|
22
|
+
"""A getter for HGNC."""
|
23
|
+
|
24
|
+
bioregistry_id = "hgnc"
|
25
|
+
name = "HGNC"
|
26
|
+
homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
|
27
|
+
|
28
|
+
version_type = VersionType.date
|
29
|
+
|
30
|
+
def get(self) -> str:
|
31
|
+
"""Get the latest monthly HGNC version number."""
|
32
|
+
res = requests.get(URL, timeout=5)
|
33
|
+
items = res.json()["items"]
|
34
|
+
return max(
|
35
|
+
item["name"].removeprefix(PREFIX).removesuffix(SUFFIX)
|
36
|
+
for item in items
|
37
|
+
if (name := item["name"]).startswith(PREFIX) and name.endswith(SUFFIX)
|
38
|
+
)
|
39
|
+
|
40
|
+
|
41
|
+
if __name__ == "__main__":
|
42
|
+
HGNCGetter.print()
|
@@ -8,6 +8,10 @@ __all__ = [
|
|
8
8
|
"MeshGetter",
|
9
9
|
]
|
10
10
|
|
11
|
+
#: In 2024 and before, these were .gz, but after
|
12
|
+
#: became .xml files
|
13
|
+
SUFFIXES = [".xml", ".xml.gz", ".gz"]
|
14
|
+
|
11
15
|
|
12
16
|
class MeshGetter(Getter):
|
13
17
|
"""A getter for MeSH."""
|
@@ -22,9 +26,12 @@ class MeshGetter(Getter):
|
|
22
26
|
with ftplib.FTP("nlmpubs.nlm.nih.gov") as ftp:
|
23
27
|
ftp.login()
|
24
28
|
ftp.cwd("/online/mesh/MESH_FILES/xmlmesh/")
|
25
|
-
for name, _ in ftp.mlsd()
|
26
|
-
|
27
|
-
|
29
|
+
names = [name for name, _ in ftp.mlsd()]
|
30
|
+
|
31
|
+
for name in names:
|
32
|
+
for suffix in SUFFIXES:
|
33
|
+
if name.startswith("desc") and name.endswith(suffix):
|
34
|
+
return name[len("desc") : -len(suffix)]
|
28
35
|
raise ValueError
|
29
36
|
|
30
37
|
|
@@ -1,47 +0,0 @@
|
|
1
|
-
"""A getter for HGNC."""
|
2
|
-
|
3
|
-
import datetime
|
4
|
-
import logging
|
5
|
-
|
6
|
-
import requests
|
7
|
-
|
8
|
-
from bioversions.utils import Getter, VersionType
|
9
|
-
|
10
|
-
__all__ = [
|
11
|
-
"HGNCGetter",
|
12
|
-
]
|
13
|
-
|
14
|
-
logger = logging.getLogger(__name__)
|
15
|
-
|
16
|
-
PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
|
17
|
-
PREFIX = "hgnc_complete_set_"
|
18
|
-
SUFFIX = ".json"
|
19
|
-
|
20
|
-
|
21
|
-
class HGNCGetter(Getter):
|
22
|
-
"""A getter for HGNC."""
|
23
|
-
|
24
|
-
bioregistry_id = "hgnc"
|
25
|
-
name = "HGNC"
|
26
|
-
homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
|
27
|
-
|
28
|
-
version_type = VersionType.date
|
29
|
-
|
30
|
-
def get(self) -> str:
|
31
|
-
"""Get the latest HGNC version number."""
|
32
|
-
today = datetime.date.today()
|
33
|
-
this_year = int(today.strftime("%Y"))
|
34
|
-
this_month = int(today.strftime("%m"))
|
35
|
-
maybe = today.strftime("%Y-%m-01")
|
36
|
-
res = requests.head(self.homepage_fmt.format(version=maybe), timeout=15)
|
37
|
-
if res.status_code == 200:
|
38
|
-
return maybe
|
39
|
-
if this_month == 1:
|
40
|
-
maybe_last_month = f"{this_year - 1}-12-01"
|
41
|
-
else:
|
42
|
-
maybe_last_month = f"{this_year}-{this_month - 1}-01"
|
43
|
-
return maybe_last_month
|
44
|
-
|
45
|
-
|
46
|
-
if __name__ == "__main__":
|
47
|
-
HGNCGetter.print()
|
File without changes
|
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|
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|
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|
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|
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|
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|
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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File without changes
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