bioversions 0.6.31__tar.gz → 0.6.32__tar.gz

{bioversions-0.6.31 → bioversions-0.6.32}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bioversions
-Version: 0.6.31
+Version: 0.6.32
 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-0.6.31 → bioversions-0.6.32}/docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: runner
-  date: '2025-01-08'
-  revision: 895
+  date: '2025-01-09'
+  revision: 896
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -5187,6 +5187,9 @@ database:
   - date: '2025-01-03'
     retrieved: '2025-01-05'
     version: January 3, 2025
+  - date: '2025-01-07'
+    retrieved: '2025-01-09'
+    version: January 7, 2025
   vtype: date
 - name: 'OntoAvida: ontology for Avida digital evolution platform'
   prefix: ontoavida
@@ -8301,6 +8304,8 @@ database:
     version: '2025-01-07'
   - retrieved: '2025-01-08'
     version: '2025-01-08'
+  - retrieved: '2025-01-09'
+    version: '2025-01-09'
   vtype: date
 - name: SWO (The Software Ontology)
   prefix: swo
@@ -11076,6 +11081,8 @@ database:
     version: '2025-01-05'
   - retrieved: '2025-01-08'
     version: '2025-01-06'
+  - retrieved: '2025-01-09'
+    version: '2025-01-07'
   vtype: date
 - name: Zebrafish Phenotype Ontology
   prefix: zp

bioversions-0.6.32/docs/failures.md

@@ -0,0 +1,371 @@
+# Summary of Errors
+
+- DisGeNet - failed to resolve DisGeNet
+- Antibody Registry - failed to resolve Antibody Registry
+- DrugBank - failed to resolve DrugBank
+- Protein Ontology - failed to resolve Protein Ontology
+- Protein Ontology - failed to resolve Protein Ontology
+
+## DisGeNet
+
+Using class: `DisGeNetGetter`
+
+```python-traceback
+Traceback (most recent call last):
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 974, in json
+    return complexjson.loads(self.text, **kwargs)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/__init__.py", line 346, in loads
+    return _default_decoder.decode(s)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 338, in decode
+    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
+               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
+    raise JSONDecodeError("Expecting value", s, err.value) from None
+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 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/disgenet.py", line 24, in get
+    res_json = res.json()
+               ^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
+    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
+requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
+
+```
+
+## Antibody Registry
+
+Using class: `AntibodyRegistryGetter`
+
+```python-traceback
+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/antibodyregistry.py", line 21, in get
+    return soup.find(**{"class": "footer"}).find("a").text.lstrip("v")
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+AttributeError: 'NoneType' object has no attribute 'find'
+
+```
+
+## DrugBank
+
+Using class: `DrugBankGetter`
+
+```python-traceback
+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/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
+
+```
+
+## Protein Ontology
+
+Using class: `PRGetter`
+
+```python-traceback
+Traceback (most recent call last):
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 464, in _make_request
+    self._validate_conn(conn)
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1093, in _validate_conn
+    conn.connect()
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 741, in connect
+    sock_and_verified = _ssl_wrap_socket_and_match_hostname(
+                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 920, in _ssl_wrap_socket_and_match_hostname
+    ssl_sock = ssl_wrap_socket(
+               ^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 460, in ssl_wrap_socket
+    ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
+               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/ssl_.py", line 504, in _ssl_wrap_socket_impl
+    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 455, in wrap_socket
+    return self.sslsocket_class._create(
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1041, in _create
+    self.do_handshake()
+  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/ssl.py", line 1319, in do_handshake
+    self._sslobj.do_handshake()
+TimeoutError: _ssl.c:983: The handshake 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 488, in _make_request
+    raise new_e
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 466, in _make_request
+    self._raise_timeout(err=e, url=url, timeout_value=conn.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='proconsortium.org', port=443): Read timed out. (read timeout=60)
+
+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/utils.py", line 282, in get
+    return self.process(get_obo_version(url))
+                        ^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 255, in get_obo_version
+    with requests.get(url, stream=True, timeout=60) as res:
+         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  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 724, in send
+    history = [resp for resp in gen]
+                                ^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 265, in resolve_redirects
+    resp = self.send(
+           ^^^^^^^^^^
+  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='proconsortium.org', port=443): Read timed out. (read timeout=60)
+
+```
+
+## Protein Ontology
+
+Using class: `PrGetter`
+
+```python-traceback
+Traceback (most recent call last):
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 198, in _new_conn
+    sock = connection.create_connection(
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/connection.py", line 85, in create_connection
+    raise err
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/util/connection.py", line 73, in create_connection
+    sock.connect(sa)
+TimeoutError: 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/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 488, in _make_request
+    raise new_e
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 464, in _make_request
+    self._validate_conn(conn)
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connectionpool.py", line 1093, in _validate_conn
+    conn.connect()
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 704, in connect
+    self.sock = sock = self._new_conn()
+                       ^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 207, in _new_conn
+    raise ConnectTimeoutError(
+urllib3.exceptions.ConnectTimeoutError: (<urllib3.connection.HTTPSConnection object at 0x7f1139ac8f80>, 'Connection to proconsortium.org timed out. (connect timeout=60)')
+
+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 519, in increment
+    raise MaxRetryError(_pool, url, reason) from reason  # type: ignore[arg-type]
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='proconsortium.org', port=443): Max retries exceeded with url: /download/current/pro_reasoned.obo (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x7f1139ac8f80>, 'Connection to proconsortium.org timed out. (connect timeout=60)'))
+
+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/utils.py", line 282, in get
+    return self.process(get_obo_version(url))
+                        ^^^^^^^^^^^^^^^^^^^^
+  File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 255, in get_obo_version
+    with requests.get(url, stream=True, timeout=60) as res:
+         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  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 724, in send
+    history = [resp for resp in gen]
+                                ^^^
+  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/sessions.py", line 265, in resolve_redirects
+    resp = self.send(
+           ^^^^^^^^^^
+  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 688, in send
+    raise ConnectTimeout(e, request=request)
+requests.exceptions.ConnectTimeout: HTTPSConnectionPool(host='proconsortium.org', port=443): Max retries exceeded with url: /download/current/pro_reasoned.obo (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x7f1139ac8f80>, 'Connection to proconsortium.org timed out. (connect timeout=60)'))
+
+```
+

{bioversions-0.6.31 → bioversions-0.6.32}/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>2025-01-08T01:02:07.874002</dc:date>
+    <dc:date>2025-01-09T01:03:42.395761</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.31 → bioversions-0.6.32}/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>2025-01-08T01:02:07.828933</dc:date>
+    <dc:date>2025-01-09T01:03:42.283087</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.31 → bioversions-0.6.32}/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>2025-01-08T01:02:07.691954</dc:date>
+    <dc:date>2025-01-09T01:03:42.206399</dc:date>
     <dc:format>image/svg+xml</dc:format>
     <dc:creator>
      <cc:Agent>

{bioversions-0.6.31 → bioversions-0.6.32}/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 = "0.6.31"
+release = "0.6.32"
 
 # The short X.Y version.
 parsed_version = re.match(

{bioversions-0.6.31 → bioversions-0.6.32}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "bioversions"
-version = "0.6.31"
+version = "0.6.32"
 description = "Get the current version for biological databases"
 readme = "README.md"
 authors = [
@@ -222,7 +222,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.6.31"
+current_version = "0.6.32"
 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-0.6.31 → bioversions-0.6.32}/src/bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 895,
-    "date": "2025-01-08",
+    "revision": 896,
+    "date": "2025-01-09",
     "author": "runner"
   },
   "database": [
@@ -9359,6 +9359,11 @@
           "retrieved": "2025-01-05",
           "version": "January 3, 2025",
           "date": "2025-01-03"
+        },
+        {
+          "retrieved": "2025-01-09",
+          "version": "January 7, 2025",
+          "date": "2025-01-07"
         }
       ],
       "name": "Online Mendelian Inheritance in Man",
@@ -15250,6 +15255,10 @@
         {
           "retrieved": "2025-01-08",
           "version": "2025-01-08"
+        },
+        {
+          "retrieved": "2025-01-09",
+          "version": "2025-01-09"
         }
       ],
       "name": "SwissLipids",
@@ -20346,6 +20355,10 @@
         {
           "retrieved": "2025-01-08",
           "version": "2025-01-06"
+        },
+        {
+          "retrieved": "2025-01-09",
+          "version": "2025-01-07"
         }
       ],
       "name": "Zebrafish Information Network",

{bioversions-0.6.31 → bioversions-0.6.32}/src/bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.6.31"
+VERSION = "0.6.32"
 
 
 def get_git_hash() -> str:

bioversions-0.6.31/docs/failures.md

@@ -1,145 +0,0 @@
-# Summary of Errors
-
-- DisGeNet - failed to resolve DisGeNet
-- Antibody Registry - failed to resolve Antibody Registry
-- DrugBank - failed to resolve DrugBank
-
-## DisGeNet
-
-Using class: `DisGeNetGetter`
-
-```python-traceback
-Traceback (most recent call last):
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 974, in json
-    return complexjson.loads(self.text, **kwargs)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/__init__.py", line 346, in loads
-    return _default_decoder.decode(s)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 338, in decode
-    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
-               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
-    raise JSONDecodeError("Expecting value", s, err.value) from None
-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 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/disgenet.py", line 24, in get
-    res_json = res.json()
-               ^^^^^^^^^^
-  File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/models.py", line 978, in json
-    raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
-requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
-
-```
-
-## Antibody Registry
-
-Using class: `AntibodyRegistryGetter`
-
-```python-traceback
-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/antibodyregistry.py", line 21, in get
-    return soup.find(**{"class": "footer"}).find("a").text.lstrip("v")
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-AttributeError: 'NoneType' object has no attribute 'find'
-
-```
-
-## DrugBank
-
-Using class: `DrugBankGetter`
-
-```python-traceback
-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/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
-
-```
-