Summary of Errors
Summary of Errors
- SILVA ribosomal RNA database
[silva.taxon] issue parsing: 'date' - Ensembl
[ensembl] failed to resolve: HTTPSConnectionPool(host='www.ensembl.org', port=443): Read timed out. (read timeout=15) - Research Organization Registry `[ror] issue parsing: Could not look up zenodo/api_token and no default given.
This can be solved with one of the following:
- Set the ZENODO_API_TOKEN environment variable
- Windows, via GUI: https://www.computerhope.com/issues/ch000549.htm
- Windows, via CLI: https://learn.microsoft.com/en-us/windows-server/administration/windows-commands/set_1
- Mac OS: https://apple.stackexchange.com/questions/106778/how-do-i-set-environment-variables-on-os-x
- Linux: https://www.freecodecamp.org/news/how-to-set-an-environment-variable-in-linux/
-
Use the PyStow CLI from the command line to set the configuration like so:
$ pystow set zenodo api_token
This creates an INI file in /home/runner/.config/zenodo.ini with the configuration in the right place.
-
Create/edit an INI file in /home/runner/.config/zenodo.ini and manually fill it in by 1) creating a section inside it called [zenodo] and 2) setting a value for api_token =
that looks like: /home/runner/.config/zenodo.ini
[zenodo] api_token =
See https://github.com/cthoyt/pystow#%EF%B8%8F%EF%B8%8F-configuration for more information. `
SILVA ribosomal RNA database
Using class: SILVAGetter
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 271, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 193, 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 203, 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'
Ensembl
Using class: EnsemblGetter
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 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 292, in _read_status
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/socket.py", line 720, in readinto
return self._sock.recv_into(b)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.12/x64/lib/python3.12/ssl.py", line 1251, in recv_into
return self.read(nbytes, buffer)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.12/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 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 490, 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='www.ensembl.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 271, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 193, 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 203, 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/ensembl.py", line 23, in get
soup = get_soup(URL)
^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/pystow/utils/__init__.py", line 861, 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 690, in send
raise ReadTimeout(e, request=request)
requests.exceptions.ReadTimeout: HTTPSConnectionPool(host='www.ensembl.org', port=443): Read timed out. (read timeout=15)
Research Organization Registry
Using class: RORGetter
Traceback (most recent call last):
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 271, in iter_versions
yv = resolve(cls)
^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/src/bioversions/sources/__init__.py", line 193, 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 203, 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/ror.py", line 22, in get
version_info = ror_downloader.get_version_info(download=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/ror_downloader/api.py", line 227, in get_version_info
client = zenodo_client.Zenodo()
^^^^^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/zenodo_client/api.py", line 117, in __init__
self.access_token = pystow.get_config(
^^^^^^^^^^^^^^^^^^
File "/home/runner/work/bioversions/bioversions/.tox/update/lib/python3.12/site-packages/pystow/config_api.py", line 161, in get_config
raise ConfigError(module=module, key=key)
pystow.config_api.ConfigError: Could not look up zenodo/api_token and no default given.
This can be solved with one of the following:
1. Set the ZENODO_API_TOKEN environment variable
- Windows, via GUI: https://www.computerhope.com/issues/ch000549.htm
- Windows, via CLI: https://learn.microsoft.com/en-us/windows-server/administration/windows-commands/set_1
- Mac OS: https://apple.stackexchange.com/questions/106778/how-do-i-set-environment-variables-on-os-x
- Linux: https://www.freecodecamp.org/news/how-to-set-an-environment-variable-in-linux/
2. Use the PyStow CLI from the command line to
set the configuration like so:
$ pystow set zenodo api_token <value>
This creates an INI file in /home/runner/.config/zenodo.ini
with the configuration in the right place.
3. Create/edit an INI file in /home/runner/.config/zenodo.ini and manually
fill it in by 1) creating a section inside it called [zenodo]
and 2) setting a value for api_token = <value> that looks like:
# /home/runner/.config/zenodo.ini
[zenodo]
api_token = <value>
See https://github.com/cthoyt/pystow#%EF%B8%8F%EF%B8%8F-configuration for more information.