🪝 Automatically update

Author: actions-user

docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2025-03-06'
-  revision: 941
+  date: '2025-03-20'
+  revision: 942
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -189,6 +189,9 @@ database:
   - homepage: https://antibodyregistry.org/
     retrieved: '2025-03-05'
     version: '2025-03-05'
+  - homepage: https://antibodyregistry.org/
+    retrieved: '2025-03-20'
+    version: '2025-03-19'
   vtype: date
 - name: Apollo Structured Vocabulary
   prefix: apollosv
@@ -1197,6 +1200,8 @@ database:
     version: '2.234'
   - retrieved: '2025-02-27'
     version: '2.238'
+  - retrieved: '2025-03-20'
+    version: '2.239'
   vtype: date
 - name: Clinical Trials Ontology
   prefix: cto
@@ -2252,7 +2257,7 @@ database:
     version: '2023-09-03'
   vtype: date
 - name: ExPASy
-  prefix: eccode
+  prefix: ec
   releases:
   - retrieved: '2021-01-02'
     version: 02-Dec-2020
@@ -2381,6 +2386,8 @@ database:
     version: '4.192'
   - retrieved: '2025-02-27'
     version: '4.195'
+  - retrieved: '2025-03-20'
+    version: '4.196'
   vtype: date
 - name: Experimental Factor Ontology
   prefix: efo
@@ -2639,6 +2646,8 @@ database:
     version: '2024-12-31'
   - retrieved: '2025-01-28'
     version: '2025-01-14'
+  - retrieved: '2025-03-20'
+    version: '2025-02-28'
   vtype: date
 - name: Flora Phenotype Ontology
   prefix: flopo
@@ -2717,7 +2726,7 @@ database:
   - homepage: http://ftp.flybase.net/releases/FB2025_01/
     retrieved: '2025-02-25'
     version: '2025_01'
-  vtype: date
+  vtype: month
 - name: FlyBase Controlled Vocabulary
   prefix: fbcv
   releases:
@@ -3247,6 +3256,9 @@ database:
   - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2025-02-04.json
     retrieved: '2025-02-12'
     version: '2025-02-04'
+  - homepage: https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2025-03-04.json
+    retrieved: '2025-03-20'
+    version: '2025-03-04'
   vtype: date
 - name: Histopathology Ontology
   prefix: hpath
@@ -3305,6 +3317,8 @@ database:
     version: '2024-06-21'
   - retrieved: '2024-09-01'
     version: '2024-08-19'
+  - retrieved: '2025-03-20'
+    version: '2025-02-24'
   vtype: semver
 - name: Human Cell Atlas Ontology
   prefix: hcao
@@ -3986,6 +4000,8 @@ database:
     version: 4.1.185
   - retrieved: '2025-02-27'
     version: 4.1.190
+  - retrieved: '2025-03-20'
+    version: 4.1.191
   vtype: date
 - name: Mathematical modeling ontology
   prefix: mamo
@@ -4368,6 +4384,10 @@ database:
     homepage: https://github.com/vanallenlab/moalmanac-db/releases/tag/v.2025-02-07
     retrieved: '2025-02-08'
     version: '2025-02-07'
+  - date: '2025-03-06'
+    homepage: https://github.com/vanallenlab/moalmanac-db/releases/tag/v.2025-03-06
+    retrieved: '2025-03-20'
+    version: '2025-03-06'
   vtype: date
 - name: Molecular Process Ontology
   prefix: mop
@@ -4700,6 +4720,9 @@ database:
   - date: '2024-11-25'
     retrieved: '2024-12-12'
     version: 24.11d
+  - date: '2025-03-17'
+    retrieved: '2025-03-20'
+    version: 25.03c
   vtype: other
 - name: NCBI Gene
   prefix: ncbigene
@@ -5483,6 +5506,8 @@ database:
     version: '2025-03-03'
   - retrieved: '2025-03-06'
     version: '2025-03-04'
+  - retrieved: '2025-03-20'
+    version: '2025-03-18'
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -5947,6 +5972,8 @@ database:
     version: 2.0.57
   - retrieved: '2025-02-27'
     version: 2.0.58
+  - retrieved: '2025-03-20'
+    version: 2.0.59
   vtype: semver
 - name: Ontology of units of Measure (OM)
   prefix: om
@@ -6927,6 +6954,8 @@ database:
     version: '2025-02-21'
   - retrieved: '2025-03-04'
     version: '2025-02-28'
+  - retrieved: '2025-03-20'
+    version: '2025-03-14'
   vtype: date
 - name: Rat Strain Ontology
   prefix: rs
@@ -6979,6 +7008,8 @@ database:
     version: '6.239'
   - retrieved: '2025-02-27'
     version: '6.242'
+  - retrieved: '2025-03-20'
+    version: '6.243'
   vtype: date
 - name: Reactome
   prefix: reactome
@@ -8763,6 +8794,8 @@ database:
     version: '2025-03-05'
   - retrieved: '2025-03-06'
     version: '2025-03-06'
+  - retrieved: '2025-03-20'
+    version: '2025-03-20'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -9022,6 +9055,8 @@ database:
     version: '2025-01-07'
   - retrieved: '2025-02-27'
     version: '2025-02-22'
+  - retrieved: '2025-03-20'
+    version: '2025-02-23'
   vtype: semver
 - name: The Virus Infectious Disease Ontology
   prefix: vido
@@ -9345,6 +9380,8 @@ database:
     version: '2024-11-23'
   - retrieved: '2025-01-05'
     version: '2024-12-29'
+  - retrieved: '2025-03-20'
+    version: '2025-02-26'
   vtype: semver
 - name: Variation Ontology
   prefix: vario
@@ -9660,6 +9697,10 @@ database:
     homepage: http://data.wikipathways.org/20250210/
     retrieved: '2025-02-11'
     version: '20250210'
+  - date: '2025-03-10'
+    homepage: http://data.wikipathways.org/20250310/
+    retrieved: '2025-03-20'
+    version: '20250310'
   vtype: date
 - name: Woody Plant Ontology ontology
   prefix: co_357
@@ -11654,6 +11695,8 @@ database:
     version: '2025-03-03'
   - retrieved: '2025-03-06'
     version: '2025-03-04'
+  - retrieved: '2025-03-20'
+    version: '2025-03-19'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

docs/failures.md

@@ -1,8 +1,8 @@
 # Summary of Errors
 
 - DisGeNet - failed to resolve DisGeNet
+- Pathway Commons - issue parsing Pathway Commons: could not find an element matching args=({'class': 'boost'},) and kwargs={}
 - DrugBank - failed to resolve DrugBank
-- PathBank - failed to resolve PathBank
 
 ## DisGeNet
 
@@ -26,7 +26,7 @@ json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
 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 220, in _iter_versions
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 246, in _iter_versions
     yv = resolve(cls.name)
          ^^^^^^^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 173, in resolve
@@ -44,13 +44,13 @@ Traceback (most recent call last):
   File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 186, in _resolve_helper
     return getter.resolve()
            ^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 224, in resolve
     version=cls.version,
             ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 102, in version
     if isinstance(cls._cache_prop, str):
                   ^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 96, in _cache_prop
     cls._cache = cls().get()
                  ^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/disgenet.py", line 24, in get
@@ -62,13 +62,13 @@ requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
 
 ```
 
-## DrugBank
+## Pathway Commons
 
-Using class: `DrugBankGetter`
+Using class: `PathwayCommonsGetter`
 
 ```python-traceback
 Traceback (most recent call last):
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 220, in _iter_versions
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 246, in _iter_versions
     yv = resolve(cls.name)
          ^^^^^^^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 173, in resolve
@@ -86,81 +86,31 @@ Traceback (most recent call last):
   File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 186, in _resolve_helper
     return getter.resolve()
            ^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 224, in resolve
     version=cls.version,
             ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 102, in version
     if isinstance(cls._cache_prop, str):
                   ^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 96, in _cache_prop
     cls._cache = cls().get()
                  ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
-    res.raise_for_status()
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
-    raise HTTPError(http_error_msg, response=self)
-requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.drugbank.com/releases.json
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/pathwaycommons.py", line 21, in get
+    boost = find(soup, {"class": "boost"})
+            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 71, in find
+    raise ValueError(f"could not find an element matching {args=} and {kwargs=}")
+ValueError: could not find an element matching args=({'class': 'boost'},) and kwargs={}
 
 ```
 
-## PathBank
+## DrugBank
 
-Using class: `PathBankGetter`
+Using class: `DrugBankGetter`
 
 ```python-traceback
 Traceback (most recent call last):
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 534, in _make_request
-    response = conn.getresponse()
-               ^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 516, in getresponse
-    httplib_response = super().getresponse()
-                       ^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/http/client.py", line 1430, in getresponse
-    response.begin()
-  File "/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/http/client.py", line 331, in begin
-    version, status, reason = self._read_status()
-                              ^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.9/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/3.12.9/x64/lib/python3.12/socket.py", line 720, in readinto
-    return self._sock.recv_into(b)
-           ^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/ssl.py", line 1251, in recv_into
-    return self.read(nbytes, buffer)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.9/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 841, 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 787, in urlopen
-    response = self._make_request(
-               ^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 536, 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 367, in _raise_timeout
-    raise ReadTimeoutError(
-urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='pathbank.org', 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 220, in _iter_versions
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 246, in _iter_versions
     yv = resolve(cls.name)
          ^^^^^^^^^^^^^^^^^
   File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 173, in resolve
@@ -178,35 +128,19 @@ Traceback (most recent call last):
   File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 186, in _resolve_helper
     return getter.resolve()
            ^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 216, in resolve
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 224, in resolve
     version=cls.version,
             ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 94, in version
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 102, in version
     if isinstance(cls._cache_prop, str):
                   ^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 96, in _cache_prop
     cls._cache = cls().get()
                  ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/pathbank.py", line 21, 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='pathbank.org', port=443): Read timed out. (read timeout=15)
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
+    res.raise_for_status()
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
+    raise HTTPError(http_error_msg, response=self)
+requests.exceptions.HTTPError: 403 Client Error: Forbidden for url: https://go.drugbank.com/releases.json
 
 ```