Summary of Errors
Summary of Errors
- SILVA ribosomal RNA database
[silva.taxon] issue parsing: 'date' - KEGG
[KEGG] failed to resolve: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
SILVA ribosomal RNA database
Using class: SILVAGetter
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 267, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 189, in resolve
return _resolve_helper_cached(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 393, in func_wrapper
return _call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 332, in _call
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 66, in _calc_entry
func_res = func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 199, in _resolve_helper_cached
return getter.resolve()
^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 219, in resolve
date=cls.date,
^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 110, in date
date = cls._cache_prop["date"]
~~~~~~~~~~~~~~~^^^^^^^^
KeyError: 'date'
KEGG
Using class: KEGGGetter
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 534, in _make_request
response = conn.getresponse()
^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 571, in getresponse
httplib_response = super().getresponse()
^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/http/client.py", line 1430, in getresponse
response.begin()
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/http/client.py", line 331, in begin
version, status, reason = self._read_status()
^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/http/client.py", line 300, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/requests/adapters.py", line 644, 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 38, in reraise
raise value.with_traceback(tb)
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 534, in _make_request
response = conn.getresponse()
^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/urllib3/connection.py", line 571, in getresponse
httplib_response = super().getresponse()
^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/http/client.py", line 1430, in getresponse
response.begin()
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/http/client.py", line 331, in begin
version, status, reason = self._read_status()
^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/http/client.py", line 300, in _read_status
raise RemoteDisconnected("Remote end closed connection without"
urllib3.exceptions.ProtocolError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))
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 267, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 189, in resolve
return _resolve_helper_cached(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 393, in func_wrapper
return _call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/cachier/core.py", line 332, in _call
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 66, in _calc_entry
func_res = func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 199, in _resolve_helper_cached
return getter.resolve()
^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 215, in resolve
version=cls.version,
^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 93, in version
if isinstance(cls._cache_prop, str):
^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/utils.py", line 87, in _cache_prop
cls._cache = cls().get()
^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/kegg.py", line 27, in get
soup = get_soup(URL)
^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/pystow/utils.py", line 1441, 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 659, in send
raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))