Summary of Errors
Summary of Errors
- DisGeNet - failed to resolve DisGeNet
- Antibody Registry - failed to resolve Antibody Registry
- DrugBank - failed to resolve DrugBank
- MeSH - issue parsing MeSH:
- OncoTree - failed to resolve OncoTree
DisGeNet
Using class: DisGeNetGetter
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/3.12.7/x64/lib/python3.12/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/json/decoder.py", line 355, 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
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
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
MeSH
Using class: MeshGetter
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/mesh.py", line 28, in get
raise ValueError
ValueError
OncoTree
Using class: OncoTreeGetter
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)
^^^^^^^^^^^^^^^^^^^^^^^
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/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: HTTPConnectionPool(host='oncotree.mskcc.org', port=80): Read timed out. (read timeout=5)
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/oncotree.py", line 23, in get
res = requests.get(
^^^^^^^^^^^^^
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: HTTPConnectionPool(host='oncotree.mskcc.org', port=80): Read timed out. (read timeout=5)