{"action":"closed","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/819","repository_url":"https://api.github.com/repos/biopython/biopython","labels_url":"https://api.github.com/repos/biopython/biopython/issues/819/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/819/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/819/events","html_url":"https://github.com/biopython/biopython/issues/819","id":154230405,"number":819,"title":"New BioSQL test_taxon_left_right_values test requires internet","user":{"login":"peterjc","id":63959,"avatar_url":"https://avatars.githubusercontent.com/u/63959?v=3","gravatar_id":"","url":"https://api.github.com/users/peterjc","html_url":"https://github.com/peterjc","followers_url":"https://api.github.com/users/peterjc/followers","following_url":"https://api.github.com/users/peterjc/following{/other_user}","gists_url":"https://api.github.com/users/peterjc/gists{/gist_id}","starred_url":"https://api.github.com/users/peterjc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/peterjc/subscriptions","organizations_url":"https://api.github.com/users/peterjc/orgs","repos_url":"https://api.github.com/users/peterjc/repos","events_url":"https://api.github.com/users/peterjc/events{/privacy}","received_events_url":"https://api.github.com/users/peterjc/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-05-11T12:23:40Z","updated_at":"2016-06-09T16:37:59Z","closed_at":"2016-06-09T16:37:59Z","body":"See #809 and https://github.com/biopython/biopython/commit/6348a037dce08e6f64de3fa4b3e2ee99eb1edacc which can give a failure in ``test_taxon_left_right_values`` as follows:\r\n\r\n```\r\n======================================================================\r\nERROR: test_taxon_left_right_values (common_BioSQL.TaxonomyTest)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/Tests/common_BioSQL.py\", line 621, in test_taxon_left_right_values\r\n    self.db.load(self.iterator, True)\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/BioSQL/BioSeqDatabase.py\", line 807, in load\r\n    db_loader.load_seqrecord(cur_record)\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/BioSQL/Loader.py\", line 57, in load_seqrecord\r\n    bioentry_id = self._load_bioentry_table(record)\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/BioSQL/Loader.py\", line 595, in _load_bioentry_table\r\n    taxon_id = self._get_taxon_id(record)\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/BioSQL/Loader.py\", line 195, in _get_taxon_id\r\n    common_name)\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/BioSQL/Loader.py\", line 425, in _get_taxon_id_from_ncbi_taxon_id\r\n    db=\"taxonomy\", id=ncbi_taxon_id, retmode=\"XML\")\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/Bio/Entrez/__init__.py\", line 180, in efetch\r\n    return _open(cgi, variables, post=post)\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/Bio/Entrez/__init__.py\", line 556, in _open\r\n    raise exception\r\n  File \"/home_local/buildslave/BuildBot_Biopython/lin3464/build/build/lib.linux-x86_64-3.4/Bio/Entrez/__init__.py\", line 554, in _open\r\n    handle = _urlopen(cgi)\r\n  File \"/home_local/buildslave/lib/python3.4/urllib/request.py\", line 153, in urlopen\r\n    return opener.open(url, data, timeout)\r\n  File \"/home_local/buildslave/lib/python3.4/urllib/request.py\", line 461, in open\r\n    response = meth(req, response)\r\n  File \"/home_local/buildslave/lib/python3.4/urllib/request.py\", line 574, in http_response\r\n    'http', request, response, code, msg, hdrs)\r\n  File \"/home_local/buildslave/lib/python3.4/urllib/request.py\", line 499, in error\r\n    return self._call_chain(*args)\r\n  File \"/home_local/buildslave/lib/python3.4/urllib/request.py\", line 433, in _call_chain\r\n    result = func(*args)\r\n  File \"/home_local/buildslave/lib/python3.4/urllib/request.py\", line 582, in http_error_default\r\n    raise HTTPError(req.full_url, code, msg, hdrs, fp)\r\nurllib.error.HTTPError: HTTP Error 503: Service Temporarily Unavailable\r\n\r\n----------------------------------------------------------------------\r\n```\r\n\r\nNormally we'd just need to move this into a separate like ``test_BioSQL_online.py`` file which declares it requires the internet, but here it probably means another triple set for the different database backends?\r\n\r\n@ctSkennerton Am I right in thinking this test does require the internet in order to fetch NCBI taxonomy information via Entrez?"}}
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