{"action":"opened","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/21","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/21/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/21/events","html_url":"https://github.com/cjfields/redmine-test/issues/21","id":108254535,"number":21,"title":"GO Upload with bp_load_ontology.pl throws errors","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-09-25T03:21:19Z","updated_at":"2015-09-25T03:21:19Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Leighton Pritchard** (Leighton Pritchard)\nOriginal Redmine Issue: 2275, https://redmine.open-bio.org/issues/2275\nOriginal Date: 2007-04-17\nOriginal Assignee: Bioperl Guts\n\n---\n\nI attempted to upload the GO into a clean BioSQL (MySQL, BioSQL 1.4.1)\nschema using the BioPerl bp\\_load\\_ontology.pl script, with the most recent OBOv1.0, OBOv1.2, and flatfiles from\nhttp://www.geneontology.org/GO.downloads.ontology.shtml. None of the\nattempts were been successful. The errors below are from a Linux\ninstallation, but the same errors were also thrown on OS X.\n\nI was using the most recent versions of BioPerl and bioperl-db, installed via CPAN:\n[lpritc@lplinuxdev sequence\\_data]$ perl -MBio::Root::Version -e ‘print\n$Bio::Root::Version::VERSION,“\\\\n”’\n1.005002102\nand bioperl-db 1.5.2.\n\nI currently think that this is an issue with the GO files themselves, due to misformed definition\\_reference fields in the data files, e.g.:\n\nterm: 2,3-dihydroxyindole 2,3-dioxygenase activity\ngoid: GO:0047528\ndefinition: Catalysis of the reaction: 2,3-dihydroxyindole + O2 =\nanthranilate + CO2.\ndefinition\\_reference: :3-DIHYDROXYINDOLE-2\ndefinition\\_reference: :3-DIOXYGENASE-RXN\ndefinition\\_reference: EC:1.13.11.2\ndefinition\\_reference: MetaCyc:2\n\ndef: “Catalysis of the reaction: 2-pyrone-4,6-dicarboxylate + H2O =\n4-carboxy-2-hydroxyhexa-2,4-dienedioate.” [:6-DICARBOXYLATE-LACTONASE-RXN, EC:3.1.1.57, MetaCyc:2-PYRONE-4]\n\nand have reported this on the GO site.\n\nI am submitting this here though, (after some prompting) so that it can be looked over, just in case. There was also some further discussion on the BioSQL and BioPerl mailing lists:\n\nhttp://lists.open-bio.org/pipermail/biosql-l/2007-April/001075.html\n\nhttp://lists.open-bio.org/pipermail/bioperl-l/2007-April/025461.html\n\nTracebacks for my original errors are given below:\n\n[lpritc@lplinuxdev sequence\\_data]$ bp\\_load\\_ontology.pl —host localhost\n—dbname biosql —namespace “Gene Ontology” —dbuser lpritc —dbpass\n\n**** —format obo ~/Downloads/gene\\_ontology\\_edit.obo\nLoading ontology gene\\_ontology:\n … terms\n … relationships\n Done with gene\\_ontology.\nLoading ontology biological\\_process:\n … terms\n\n—————————— WARNING ——————————-\nMSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values\nwere (“”,“”,“0”,“”) FKs ()\nColumn ‘dbname’ cannot be null\n—————————————————————————-\nCould not store term GO:0018901, name ‘2,4-dichlorophenoxyacetic acid\nmetabolic process’:\n\n——————- EXCEPTION: Bio::Root::Exception ——————-\nMSG: create: object (Bio::Annotation::DBLink) failed to insert or to be\nfound by unique key\nSTACK: Error::throw\nSTACK:\nBio::Root::Root::throw /usr/lib/perl5/site\\_perl/5.8.8/Bio/Root/Root.pm:359\nSTACK:\nBio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206\nSTACK:\nBio::DB::BioSQL::TermAdaptor::store\\_children /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/TermAdaptor.pm:293\nSTACK:\nBio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214\nSTACK:\nBio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251\nSTACK:\nBio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271\nSTACK: main::persist\\_term /usr/bin/bp\\_load\\_ontology.pl:805\nSTACK: /usr/bin/bp\\_load\\_ontology.pl:610\n—————————————————————————————-\n\n[lpritc@lplinuxdev sequence\\_data]$ bp\\_load\\_ontology.pl —host localhost\n—dbname biosql —namespace “Gene Ontology” —dbuser lpritc —dbpass\n\n**** —format goflat —fmtargs “-defs,/home/lpritc/Downloads/GO.defs”\n~/Downloads/function.ontology\nLoading ontology Gene Ontology:\n … terms\n\n—————————— WARNING ——————————-\nMSG: insert in Bio::DB::BioSQL::DBLinkAdaptor (driver) failed, values\nwere (“MetaCyc”,“2\\\\,3-DIHYDROXYINDOLE-2\\\\,3-DIOXYGENASE-RXN”,“0”,“”) FKs\n()\nDuplicate entry ‘2\\\\,3-DIHYDROXYINDOLE-2\\\\,3-DIOXYGENASE-RX-MetaCyc-0’ for\nkey 2\n—————————————————————————-\nCould not store term GO:0047528, name ‘2\\\\,3-dihydroxyindole 2\n\\\\,3-dioxygenase activity’:\n\n——————- EXCEPTION: Bio::Root::Exception ——————-\nMSG: create: object (Bio::Annotation::DBLink) failed to insert or to be\nfound by unique key\nSTACK: Error::throw\nSTACK:\nBio::Root::Root::throw /usr/lib/perl5/site\\_perl/5.8.8/Bio/Root/Root.pm:359\nSTACK:\nBio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206\nSTACK:\nBio::DB::BioSQL::TermAdaptor::store\\_children /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/TermAdaptor.pm:293\nSTACK:\nBio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214\nSTACK:\nBio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251\nSTACK:\nBio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site\\_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271\nSTACK: main::persist\\_term /usr/bin/bp\\_load\\_ontology.pl:805\nSTACK: /usr/bin/bp\\_load\\_ontology.pl:610\n—————————————————————————————-\n\nat /usr/bin/bp\\_load\\_ontology.pl line 817\n main::persist\\_term(‘-term’,\n‘Bio::Ontology::GOterm=HASH(0xa6afb9c)’, ‘-db’,\n‘Bio::DB::BioSQL::DBAdaptor=HASH(0x9b5afd0)’, ‘-termfactory’,\n‘Bio::Ontology::TermFactory=HASH(0x9f40d10)’, ‘-throw’,\n‘CODE (0x96f6b68)’, ‘-mergeobs’, …) called\nat /usr/bin/bp\\_load\\_ontology.pl line 610\n\n\n\n\n"}}