Summary of Errors
Summary of Errors
- PathBank
[pathbank] failed to resolve
PathBank
Using class: PathBankGetter
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 565, in getresponse
httplib_response = super().getresponse()
^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.10/x64/lib/python3.12/http/client.py", line 1430, in getresponse
response.begin()
File "/opt/hostedtoolcache/Python/3.12.10/x64/lib/python3.12/http/client.py", line 331, in begin
version, status, reason = self._read_status()
^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.10/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/3.12.10/x64/lib/python3.12/socket.py", line 720, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.10/x64/lib/python3.12/ssl.py", line 1251, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.10/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 259, in iter_versions
yv = resolve(cls.name)
^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 180, 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 187, in _resolve_helper_cached
return _resolve_helper(name)
^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 198, in _resolve_helper
return getter.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 102, in version
if isinstance(cls._cache_prop, str):
^^^^^^^^^^^^^^^
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)