bioversions 0.6.6__tar.gz → 0.6.8__tar.gz

{bioversions-0.6.6 → bioversions-0.6.8}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: bioversions
-Version: 0.6.6
+Version: 0.6.8
 Summary: Get the current version for biological databases
 Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
 Project-URL: Homepage, https://github.com/biopragmatics/bioversions
@@ -29,6 +29,7 @@ License: MIT License
         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
+License-File: LICENSE
 Keywords: biological databases,biomedical databases,cookiecutter,databases,snekpack
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console

{bioversions-0.6.6 → bioversions-0.6.8}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-12-14'
-  revision: 870
+  date: '2024-12-16'
+  revision: 872
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -1062,6 +1062,8 @@ database:
     version: '2.229'
   - retrieved: '2024-12-08'
     version: '2.230'
+  - retrieved: '2024-12-15'
+    version: '2.231'
   vtype: date
 - name: Clinical Trials Ontology
   prefix: cto
@@ -1673,6 +1675,8 @@ database:
     version: '2024-08-07'
   - retrieved: '2024-10-27'
     version: '2024-10-17'
+  - retrieved: '2024-12-15'
+    version: '2024-12-04'
   vtype: date
 - name: Drosophila gross anatomy
   prefix: fbbt
@@ -1713,6 +1717,8 @@ database:
     version: '2024-08-08'
   - retrieved: '2024-10-27'
     version: '2024-10-17'
+  - retrieved: '2024-12-15'
+    version: '2024-12-05'
   vtype: date
 - name: Drosophila Phenotype Ontology
   prefix: dpo
@@ -1761,6 +1767,8 @@ database:
     version: '2024-08-08'
   - retrieved: '2024-10-27'
     version: '2024-10-17'
+  - retrieved: '2024-12-15'
+    version: '2024-12-05'
   vtype: date
 - name: Drosophila Phenotype Ontology (DPO)
   prefix: dpo
@@ -2190,6 +2198,8 @@ database:
     version: '4.187'
   - retrieved: '2024-12-08'
     version: '4.188'
+  - retrieved: '2024-12-15'
+    version: '4.189'
   vtype: date
 - name: Experimental Factor Ontology
   prefix: efo
@@ -2436,6 +2446,8 @@ database:
     version: '2024-11-12'
   - retrieved: '2024-12-08'
     version: '2024-11-28'
+  - retrieved: '2024-12-15'
+    version: '2024-12-05'
   vtype: date
 - name: Flora Phenotype Ontology
   prefix: flopo
@@ -2557,6 +2569,8 @@ database:
     version: '2024-08-08'
   - retrieved: '2024-10-27'
     version: '2024-10-17'
+  - retrieved: '2024-12-15'
+    version: '2024-12-05'
   vtype: date
 - name: FlyBase Controlled Vocabulary (FBcv)
   prefix: fbcv
@@ -3200,6 +3214,8 @@ database:
     version: '2024-07-01'
   - retrieved: '2024-08-17'
     version: '2024-08-13'
+  - retrieved: '2024-12-15'
+    version: '2024-12-12'
   vtype: date
 - name: Human Reference Atlas Common Coordinate Framework Ontology
   prefix: ccf
@@ -3596,6 +3612,8 @@ database:
     version: '2.14'
   - retrieved: '2021-10-15'
     version: '2.30'
+  - retrieved: '2024-12-15'
+    version: '2.34'
   vtype: semver
 - name: KiSAO
   prefix: biomodels.kisao
@@ -3798,6 +3816,8 @@ database:
     version: '2.143'
   - retrieved: '2024-12-08'
     version: '2.144'
+  - retrieved: '2024-12-15'
+    version: '2.145'
   vtype: date
 - name: Medaka Developmental Stages
   prefix: olatdv
@@ -4192,6 +4212,8 @@ database:
     version: '2024-10-01'
   - retrieved: '2024-11-10'
     version: '2024-11-05'
+  - retrieved: '2024-12-15'
+    version: '2024-12-03'
   vtype: date
 - name: MOP
   prefix: mop
@@ -5098,6 +5120,9 @@ database:
   - date: '2024-12-12'
     retrieved: '2024-12-14'
     version: December 12, 2024
+  - date: '2024-12-13'
+    retrieved: '2024-12-15'
+    version: December 13, 2024
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -5612,6 +5637,8 @@ database:
     version: '4.4'
   - retrieved: '2024-08-11'
     version: '4.5'
+  - retrieved: '2024-12-15'
+    version: '4.6'
   vtype: semver
 - name: Orthology Ontology
   prefix: orth
@@ -6521,6 +6548,8 @@ database:
     version: '6.235'
   - retrieved: '2024-11-17'
     version: '6.236'
+  - retrieved: '2024-12-15'
+    version: '6.238'
   vtype: date
 - name: Reactome
   prefix: reactome
@@ -8140,6 +8169,10 @@ database:
     version: '2024-12-13'
   - retrieved: '2024-12-14'
     version: '2024-12-14'
+  - retrieved: '2024-12-15'
+    version: '2024-12-15'
+  - retrieved: '2024-12-16'
+    version: '2024-12-16'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -8192,6 +8225,8 @@ database:
   releases:
   - retrieved: '2021-02-02'
     version: '2016-04-15'
+  - retrieved: '2024-12-15'
+    version: '2024-11-28'
   vtype: date
 - name: Taxonomy
   prefix: ncbitaxon
@@ -8788,6 +8823,8 @@ database:
     version: '2024-11-05'
   - retrieved: '2024-12-08'
     version: '2024-11-22'
+  - retrieved: '2024-12-15'
+    version: '2024-11-26'
   vtype: date
 - name: VEuPathDB Ontology
   prefix: eupath
@@ -10861,6 +10898,8 @@ database:
     version: '2024-12-11'
   - retrieved: '2024-12-14'
     version: '2024-12-12'
+  - retrieved: '2024-12-16'
+    version: '2024-12-14'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

{bioversions-0.6.6 → bioversions-0.6.8}/docs/failures.md

@@ -3,6 +3,7 @@
 - DisGeNet - failed to resolve DisGeNet
 - Antibody Registry - failed to resolve Antibody Registry
 - DrugBank - failed to resolve DrugBank
+- National Cancer Institute Thesaurus - failed to resolve National Cancer Institute Thesaurus
 
 ## DisGeNet
 
@@ -143,3 +144,111 @@ requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.d
 
 ```
 
+## National Cancer Institute Thesaurus
+
+Using class: `NCItGetter`
+
+```python-traceback
+Traceback (most recent call last):
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 536, in _make_request
+    response = conn.getresponse()
+               ^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 507, in getresponse
+    httplib_response = super().getresponse()
+                       ^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 1428, in getresponse
+    response.begin()
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 331, in begin
+    version, status, reason = self._read_status()
+                              ^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/http/client.py", line 292, in _read_status
+    line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
+               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/socket.py", line 720, in readinto
+    return self._sock.recv_into(b)
+           ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1251, in recv_into
+    return self.read(nbytes, buffer)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1103, in read
+    return self._sslobj.read(len, buffer)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+TimeoutError: The read operation timed out
+
+The above exception was the direct cause of the following exception:
+
+Traceback (most recent call last):
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 667, in send
+    resp = conn.urlopen(
+           ^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 843, in urlopen
+    retries = retries.increment(
+              ^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/retry.py", line 474, in increment
+    raise reraise(type(error), error, _stacktrace)
+          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/util.py", line 39, in reraise
+    raise value
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 789, in urlopen
+    response = self._make_request(
+               ^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 538, in _make_request
+    self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 369, in _raise_timeout
+    raise ReadTimeoutError(
+urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='ncithesaurus.nci.nih.gov', port=443): Read timed out. (read timeout=15)
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 216, in _iter_versions
+    yv = resolve(cls.name)
+         ^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 169, in resolve
+    return _resolve_helper_cached(name)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
+    return _calc_entry(core, key, func, args, kwds)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
+    func_res = func(*args, **kwds)
+               ^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 176, in _resolve_helper_cached
+    return _resolve_helper(name)
+           ^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 182, in _resolve_helper
+    return getter.resolve()
+           ^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
+    version=cls.version,
+            ^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
+    if isinstance(cls._cache_prop, str):
+                  ^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
+    cls._cache = cls().get()
+                 ^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/ncit.py", line 27, in get
+    soup = get_soup(URL)
+           ^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 62, in get_soup
+    res = requests.get(url, verify=verify, timeout=timeout or 15, headers=headers)
+          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 73, in get
+    return request("get", url, params=params, **kwargs)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/api.py", line 59, in request
+    return session.request(method=method, url=url, **kwargs)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
+    resp = self.send(prep, **send_kwargs)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
+    r = adapter.send(request, **kwargs)
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 713, in send
+    raise ReadTimeout(e, request=request)
+requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='ncithesaurus.nci.nih.gov', port=443): Read timed out. (read timeout=15)
+
+```
+

{bioversions-0.6.6 → bioversions-0.6.8}/docs/img/has_release_url.svg

@@ -6,11 +6,11 @@
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    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-12-14T01:05:35.316393</dc:date>
+    <dc:date>2024-12-16T01:10:38.044862</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>
-      <dc:title>Matplotlib v3.9.4, https://matplotlib.org/</dc:title>
+      <dc:title>Matplotlib v3.10.0, https://matplotlib.org/</dc:title>
      </cc:Agent>
     </dc:creator>
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{bioversions-0.6.6 → bioversions-0.6.8}/docs/img/version_date_types.svg

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