{"action":"created","issue":{"url":"https://api.github.com/repos/weecology/retriever/issues/551","repository_url":"https://api.github.com/repos/weecology/retriever","labels_url":"https://api.github.com/repos/weecology/retriever/issues/551/labels{/name}","comments_url":"https://api.github.com/repos/weecology/retriever/issues/551/comments","events_url":"https://api.github.com/repos/weecology/retriever/issues/551/events","html_url":"https://github.com/weecology/retriever/issues/551","id":163825969,"number":551,"title":"Current dataset errors","user":{"login":"ethanwhite","id":744427,"avatar_url":"https://avatars.githubusercontent.com/u/744427?v=3","gravatar_id":"","url":"https://api.github.com/users/ethanwhite","html_url":"https://github.com/ethanwhite","followers_url":"https://api.github.com/users/ethanwhite/followers","following_url":"https://api.github.com/users/ethanwhite/following{/other_user}","gists_url":"https://api.github.com/users/ethanwhite/gists{/gist_id}","starred_url":"https://api.github.com/users/ethanwhite/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ethanwhite/subscriptions","organizations_url":"https://api.github.com/users/ethanwhite/orgs","repos_url":"https://api.github.com/users/ethanwhite/repos","events_url":"https://api.github.com/users/ethanwhite/events{/privacy}","received_events_url":"https://api.github.com/users/ethanwhite/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-07-05T11:08:24Z","updated_at":"2016-07-14T07:06:43Z","closed_at":null,"body":"Running `try_install_all.py` on my home machine currently lists these failures (MySQL didn't run for some reason):\r\n\r\n```\r\nEngine, Dataset, Error\r\n('xml', 'EA_Rodriguez-Buritica2013', IndexError('list index out of range',))\r\n('sqlite', 'EA_Rodriguez-Buritica2013', IndexError('list index out of range',))\r\n('postgres', 'EA_Rodriguez-Buritica2013', IndexError('list index out of range',))\r\n('json', 'EA_Rodriguez-Buritica2013', IndexError('list index out of range',))\r\n('csv', 'EA_Rodriguez-Buritica2013', IndexError('list index out of range',))\r\n('xml', 'npn', HTTPError())\r\n('sqlite', 'npn', HTTPError())\r\n('postgres', 'npn', HTTPError())\r\n('json', 'npn', HTTPError())\r\n('download', 'npn', HTTPError())\r\n('csv', 'npn', HTTPError())\r\n('xml', 'EA_Colin2014', IndexError('list index out of range',))\r\n('xml', 'EA_Fray_Jorge2013', IndexError('list index out of range',))\r\n('sqlite', 'EA_Fray_Jorge2013', OperationalError('no such column: ND',))\r\n('postgres', 'EA_Fray_Jorge2013', ProgrammingError('column \"nd\" does not exist\\nLINE 1: ...pling_date, cover) VALUES (\\'ADBE\\', \\'+D+P\\', 3, \\'Jun-97\\', ND);\\n                                                                   ^\\n',))\r\n('postgres', 'bbs50stop', ProgrammingError('relation \"bbs50.species\" does not exist\\nLINE 1: INSERT INTO BBS50.species (species_id, aou, english_common_n...\\n                    ^\\n',))\r\n('xml', 'Dryad_tamburello_etal_2013', IndexError('list index out of range',))\r\n('postgres', 'Dryad_tamburello_etal_2013', ProgrammingError('relation \"homeranges.ranges\" does not exist\\nLINE 1: INSERT INTO HomeRanges.ranges (taxon, common_name, class, or...\\n                    ^\\n',))\r\n('xml', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('sqlite', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('postgres', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('json', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('csv', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('postgres', 'EA_Pelissier2011', ProgrammingError('relation \"treewesternghats.ind_loc_girth\" does not exist\\nLINE 1: INSERT INTO TreeWesternGhats.ind_loc_girth (treeid, spcode, ...\\n                    ^\\n',))\r\n('postgres', 'EA_lynch2013', ProgrammingError('relation \"arcticbreedbird.species\" does not exist\\nLINE 1: INSERT INTO ArcticBreedBird.species (site_id, region, site_n...\\n                    ^\\n',))\r\n('xml', 'leda', IndexError('list index out of range',))\r\n('sqlite', 'leda', IndexError('list index out of range',))\r\n('postgres', 'leda', IndexError('list index out of range',))\r\n('json', 'leda', IndexError('list index out of range',))\r\n('csv', 'leda', IndexError('list index out of range',))\r\n('xml', 'EA_del_moral_2010', IndexError('list index out of range',))\r\n('sqlite', 'EA_del_moral_2010', IndexError('list index out of range',))\r\n('postgres', 'EA_del_moral_2010', IndexError('list index out of range',))\r\n('json', 'EA_del_moral_2010', IndexError('list index out of range',))\r\n('csv', 'EA_del_moral_2010', IndexError('list index out of range',))\r\n('xml', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('sqlite', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('postgres', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('json', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('download', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('csv', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('xml', 'EA_Wilman_2014', IndexError('list index out of range',))\r\n('postgres', 'EA_Wilman_2014', DataError('value too long for type character varying(55)\\n',))\r\n('xml', 'EA_petraitis2008', IndexError('list index out of range',))\r\n('sqlite', 'EA_petraitis2008', IndexError('list index out of range',))\r\n('postgres', 'EA_petraitis2008', IndexError('list index out of range',))\r\n('json', 'EA_petraitis2008', IndexError('list index out of range',))\r\n('csv', 'EA_petraitis2008', IndexError('list index out of range',))\r\n('xml', 'EA_anderson2011', IndexError('list index out of range',))\r\n('sqlite', 'EA_anderson2011', IndexError('list index out of range',))\r\n('postgres', 'EA_anderson2011', IndexError('list index out of range',))\r\n('json', 'EA_anderson2011', IndexError('list index out of range',))\r\n('csv', 'EA_anderson2011', IndexError('list index out of range',))\r\n('sqlite', 'EA_ramesh2010', OperationalError('no such table: Ramesh2010_macroplots',))\r\n('postgres', 'EA_ramesh2010', ProgrammingError('relation \"ramesh2010.macroplots\" does not exist\\nLINE 1: INSERT INTO Ramesh2010.macroplots (plotid, spcode, tree, Tre...\\n                    ^\\n',))\r\n('postgres', 'EA_Luo', ProgrammingError('relation \"cforbiodata.biomass\" does not exist\\nLINE 1: INSERT INTO CForBioData.biomass (id, province, study_site, l...\\n                    ^\\n',))\r\n('postgres', 'EA_zachmann2010', ProgrammingError('relation \"zachmann2010.monthly_sno\" does not exist\\nLINE 1: INSERT INTO Zachmann2010.monthly_sno (year, january, februar...\\n                    ^\\n',))\r\n('postgres', 'EA_barnes2008', ProgrammingError('relation \"marinesize.main\" does not exist\\nLINE 1: INSERT INTO MarineSize.main (record_number, in_ref_id, indiv...\\n                    ^\\n',))\r\n('postgres', 'EA_strona2013', ProgrammingError('relation \"fishparasitehosts.host_characteristics\" does not exist\\nLINE 1: INSERT INTO FishParasiteHosts.host_characteristics (id, para...\\n                    ^\\n',))\r\n('postgres', 'sev_small_mammals', ProgrammingError('relation \"sevmammals.surveys\" does not exist\\nLINE 1: INSERT INTO SevMammals.surveys (year, location, season, nigh...\\n                    ^\\n',))\r\n('postgres', 'EA_pantheria', ProgrammingError('relation \"pantheria.species\" does not exist\\nLINE 1: INSERT INTO Pantheria.species (msw05_order, msw05_family, ms...\\n                    ^\\n',))\r\n('xml', 'EA_palmer2007', IndexError('list index out of range',))\r\n('postgres', 'EA_palmer2007', ProgrammingError('relation \"palmer2007.pres\" does not exist\\nLINE 1: INSERT INTO Palmer2007.pres (grid, co, rw, code, lev) VALUES...\\n                    ^\\n',))\r\n('xml', 'gentry', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('sqlite', 'gentry', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('postgres', 'gentry', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('json', 'gentry', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('download', 'gentry', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('csv', 'gentry', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('xml', 'EA_woods2009', IndexError('list index out of range',))\r\n('xml', 'gwdd', UnicodeEncodeError('ascii', u'Amorim, L.C. 1991. Varia\\xe7\\xe3o da densidade basica no sentido radial em madeiras tropicais da Amaz\\xf4nia. Relatorio final Periodo abril 90: mar\\xe7o 91. INPA, Manaus, AM 24 pp. In Fearnside, P. M. 1997. Wood density for estimating forest biomass in Brazilian Amazonia. Forest Ecology and Management 90: 59-87.', 24, 26, 'ordinal not in range(128)'))\r\n('sqlite', 'gwdd', UnicodeEncodeError('ascii', u'Amorim, L.C. 1991. Varia\\xe7\\xe3o da densidade basica no sentido radial em madeiras tropicais da Amaz\\xf4nia. Relatorio final Periodo abril 90: mar\\xe7o 91. INPA, Manaus, AM 24 pp. In Fearnside, P. M. 1997. Wood density for estimating forest biomass in Brazilian Amazonia. Forest Ecology and Management 90: 59-87.', 24, 26, 'ordinal not in range(128)'))\r\n('postgres', 'gwdd', UnicodeEncodeError('ascii', u'Amorim, L.C. 1991. Varia\\xe7\\xe3o da densidade basica no sentido radial em madeiras tropicais da Amaz\\xf4nia. Relatorio final Periodo abril 90: mar\\xe7o 91. INPA, Manaus, AM 24 pp. In Fearnside, P. M. 1997. Wood density for estimating forest biomass in Brazilian Amazonia. Forest Ecology and Management 90: 59-87.', 24, 26, 'ordinal not in range(128)'))\r\n('json', 'gwdd', UnicodeEncodeError('ascii', u'Amorim, L.C. 1991. Varia\\xe7\\xe3o da densidade basica no sentido radial em madeiras tropicais da Amaz\\xf4nia. Relatorio final Periodo abril 90: mar\\xe7o 91. INPA, Manaus, AM 24 pp. In Fearnside, P. M. 1997. Wood density for estimating forest biomass in Brazilian Amazonia. Forest Ecology and Management 90: 59-87.', 24, 26, 'ordinal not in range(128)'))\r\n('download', 'gwdd', UnicodeEncodeError('ascii', u'Amorim, L.C. 1991. Varia\\xe7\\xe3o da densidade basica no sentido radial em madeiras tropicais da Amaz\\xf4nia. Relatorio final Periodo abril 90: mar\\xe7o 91. INPA, Manaus, AM 24 pp. In Fearnside, P. M. 1997. Wood density for estimating forest biomass in Brazilian Amazonia. Forest Ecology and Management 90: 59-87.', 24, 26, 'ordinal not in range(128)'))\r\n('csv', 'gwdd', UnicodeEncodeError('ascii', u'Amorim, L.C. 1991. Varia\\xe7\\xe3o da densidade basica no sentido radial em madeiras tropicais da Amaz\\xf4nia. Relatorio final Periodo abril 90: mar\\xe7o 91. INPA, Manaus, AM 24 pp. In Fearnside, P. M. 1997. Wood density for estimating forest biomass in Brazilian Amazonia. Forest Ecology and Management 90: 59-87.', 24, 26, 'ordinal not in range(128)'))\r\n('xml', 'EA_Matter_2014', IndexError('list index out of range',))\r\n('sqlite', 'EA_Matter_2014', IndexError('list index out of range',))\r\n('postgres', 'EA_Matter_2014', IndexError('list index out of range',))\r\n('json', 'EA_Matter_2014', IndexError('list index out of range',))\r\n('csv', 'EA_Matter_2014', IndexError('list index out of range',))\r\n('postgres', 'bbs', DataError('value too long for type character varying(50)\\n',))\r\n('xml', 'EA_Turcotte', IndexError('list index out of range',))\r\n('postgres', 'EA_Turcotte', ProgrammingError('relation \"leaf_herbivory.leaf_herbivory\" does not exist\\nLINE 1: INSERT INTO leaf_herbivory.Leaf_herbivory (record_id_number,...\\n                    ^\\n',))\r\n('xml', 'USDA_plants', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('sqlite', 'USDA_plants', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('postgres', 'USDA_plants', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('json', 'USDA_plants', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('download', 'USDA_plants', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n('csv', 'USDA_plants', AttributeError(\"'_fileobject' object has no attribute 'readinto'\",))\r\n```"},"comment":{"url":"https://api.github.com/repos/weecology/retriever/issues/comments/232578212","html_url":"https://github.com/weecology/retriever/issues/551#issuecomment-232578212","issue_url":"https://api.github.com/repos/weecology/retriever/issues/551","id":232578212,"user":{"login":"henrykironde","id":5192965,"avatar_url":"https://avatars.githubusercontent.com/u/5192965?v=3","gravatar_id":"","url":"https://api.github.com/users/henrykironde","html_url":"https://github.com/henrykironde","followers_url":"https://api.github.com/users/henrykironde/followers","following_url":"https://api.github.com/users/henrykironde/following{/other_user}","gists_url":"https://api.github.com/users/henrykironde/gists{/gist_id}","starred_url":"https://api.github.com/users/henrykironde/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/henrykironde/subscriptions","organizations_url":"https://api.github.com/users/henrykironde/orgs","repos_url":"https://api.github.com/users/henrykironde/repos","events_url":"https://api.github.com/users/henrykironde/events{/privacy}","received_events_url":"https://api.github.com/users/henrykironde/received_events","type":"User","site_admin":false},"created_at":"2016-07-14T07:06:43Z","updated_at":"2016-07-14T07:06:43Z","body":"most of the errors are from Unicode\r\n\r\nwe shall have to include these scripts in the INGORE list\r\n\r\n\r\n```\r\n('xml', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('sqlite', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('postgres', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('json', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('mysql', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n('csv', 'MammalSuperTree', Exception(\"This dataset contains only non-tabular data files, and can only be used with the 'download only' engine.\\nTry 'retriever download datasetname instead.\",))\r\n\r\n('xml', 'npn', HTTPError())\r\n('sqlite', 'npn', HTTPError())\r\n('postgres', 'npn', HTTPError())\r\n('json', 'npn', HTTPError())\r\n('mysql', 'npn', HTTPError())\r\n('download', 'npn', HTTPError())\r\n('csv', 'npn', HTTPError())\r\n\r\n('xml', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('csv', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('sqlite', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('postgres', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('json', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('mysql', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n('download', 'eBird_observation', URLError(error(110, 'Connection timed out'),))\r\n```\r\n\r\nThe xml files fail because of some formatting issue. I will look through that.\r\n"}}
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