bioversions 0.5.565__tar.gz → 0.5.566__tar.gz

{bioversions-0.5.565 → bioversions-0.5.566}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioversions
-Version: 0.5.565
+Version: 0.5.566
 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

{bioversions-0.5.565 → bioversions-0.5.566}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2024-12-06'
-  revision: 861
+  date: '2024-12-07'
+  revision: 862
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -5046,6 +5046,9 @@ database:
   - date: '2024-12-04'
     retrieved: '2024-12-06'
     version: December 4, 2024
+  - date: '2024-12-05'
+    retrieved: '2024-12-07'
+    version: December 5, 2024
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -8061,6 +8064,8 @@ database:
     version: '2024-12-05'
   - retrieved: '2024-12-06'
     version: '2024-12-06'
+  - retrieved: '2024-12-07'
+    version: '2024-12-07'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -10756,6 +10761,8 @@ database:
     version: '2024-12-03'
   - retrieved: '2024-12-06'
     version: '2024-12-04'
+  - retrieved: '2024-12-07'
+    version: '2024-12-05'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

{bioversions-0.5.565 → bioversions-0.5.566}/docs/failures.md

@@ -4,6 +4,7 @@
 - Antibody Registry - failed to resolve Antibody Registry
 - DrugBank - failed to resolve DrugBank
 - MeSH - issue parsing MeSH: 
+- National Cancer Institute Thesaurus - failed to resolve National Cancer Institute Thesaurus
 
 ## DisGeNet
 
@@ -183,3 +184,111 @@ ValueError
 
 ```
 
+## 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/3.12.7/x64/lib/python3.12/http/client.py", line 1428, in getresponse
+    response.begin()
+  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/http/client.py", line 331, in begin
+    version, status, reason = self._read_status()
+                              ^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.7/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/3.12.7/x64/lib/python3.12/socket.py", line 720, in readinto
+    return self._sock.recv_into(b)
+           ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/ssl.py", line 1251, in recv_into
+    return self.read(nbytes, buffer)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.7/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-0.5.565 → bioversions-0.5.566}/docs/img/has_release_url.svg

@@ -6,7 +6,7 @@
   <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#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-12-06T01:06:29.541904</dc:date>
+    <dc:date>2024-12-07T01:06:13.217366</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.565 → bioversions-0.5.566}/docs/img/version_date_types.svg

@@ -6,7 +6,7 @@
   <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#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-12-06T01:06:29.430511</dc:date>
+    <dc:date>2024-12-07T01:06:13.110942</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.565 → bioversions-0.5.566}/docs/img/version_types.svg

@@ -6,7 +6,7 @@
   <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#">
    <cc:Work>
     <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
-    <dc:date>2024-12-06T01:06:29.346280</dc:date>
+    <dc:date>2024-12-07T01:06:13.027243</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.5.565 → bioversions-0.5.566}/docs/source/conf.py

@@ -26,7 +26,7 @@ copyright = f"{date.today().year}, Charles Tapley Hoyt"
 author = "Charles Tapley Hoyt"
 
 # The full version, including alpha/beta/rc tags.
-release = "0.5.565"
+release = "0.5.566"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.5.565 → bioversions-0.5.566}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.5.565"
+version = "0.5.566"
 description = "Get the current version for biological databases"
 readme = "README.md"
 authors = [
@@ -223,7 +223,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.5.565"
+current_version = "0.5.566"
 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-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{bioversions-0.5.565 → bioversions-0.5.566}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 861,
-    "date": "2024-12-06",
+    "revision": 862,
+    "date": "2024-12-07",
     "author": "runner"
   },
   "database": [
@@ -9110,6 +9110,11 @@
           "retrieved": "2024-12-06",
           "version": "December 4, 2024",
           "date": "2024-12-04"
+        },
+        {
+          "retrieved": "2024-12-07",
+          "version": "December 5, 2024",
+          "date": "2024-12-05"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -14808,6 +14813,10 @@
         {
           "retrieved": "2024-12-06",
           "version": "2024-12-06"
+        },
+        {
+          "retrieved": "2024-12-07",
+          "version": "2024-12-07"
         }
       ],
       "name": "SwissLipids",
@@ -19746,6 +19755,10 @@
         {
           "retrieved": "2024-12-06",
           "version": "2024-12-04"
+        },
+        {
+          "retrieved": "2024-12-07",
+          "version": "2024-12-05"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.5.565 → bioversions-0.5.566}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.565"
+VERSION = "0.5.566"
 
 
 def get_git_hash() -> str: