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Re: [GUSDEV] bug in GUS schema, evidentiated by InsertSequenceFeatures
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From: Michael S. <m...@sa...> - 2006-10-07 23:39:22
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Antonio is correct here-- it looks like the postgres triggers aren't being correctly generated for this table. I had thought I had fixed this, but I guess not. These are in the db writer for postgres within the db admin package. Search for 'ON INSERT TO'. Antonio-- it may help if you forward along your install logs (that include all SQL used in generating the instance). Steve's also correct-- bug 177 appears to track a different issue. --Mike ----- Original Message ----- From: "Chris Stoeckert" <sto...@pc...> To: "Steve Fischer" <sfi...@pc...> Cc: <gus...@li...> Sent: Saturday, October 07, 2006 2:39 PM Subject: Re: [GUSDEV] bug in GUS schema,evidentiated by InsertSequenceFeatures > John Iodice in our group is working on a postgres instance of GUS so > will ask him to help but if anyone else out there has some ideas that > would be great to hear. > Chris > > On Oct 7, 2006, at 10:08 AM, Steve Fischer wrote: > >> Antonio- >> >> i don't think this is the same problem as bug 177. in that bug, >> there >> was a uniqueness constraint violation, not a non-null constraint >> violation. >> >> we don't have much postgres expertise in-house. i'll see if >> anybody can >> help on this. >> >> otherwise, you might need to propose a solution yourself. >> >> steve >> >> an...@ne... wrote: >>> Hello all, >>> using ISF I've found a bug of the schema very similar to the one >>> signalled >>> here: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=177 >>> >>> When using ISF like this: >>> >>> ga GUS::Supported::Plugin::InsertSequenceFeatures \ >>> --mapFile $GUS_HOME/config/genbank2gus.xml \ >>> --inputFileOrDir CHR_I/NC_003279.gbk --fileFormat Genbank \ >>> --extDbName "NCBI Genome data" --extDbRlsVer 2006.02.16 \ >>> --veryVerbose --sqlVerbose --commit >>> >>> the procedure does complete the insert of all relevant data, but >>> this single >>> SQL instruction fails: >>> >>> sqlExec: >>> INSERT INTO DoTSVer.SourceVer select v.*,215,now(),30 from >>> DoTS.Source v >>> where v.na_feature_id = ? >>> bindValues (5) >>> >>> DBD::Pg::st execute failed: ERROR: null value in column >>> "na_feature_id" >>> violates not-null constraint at >>> /hardmnt/mpa/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >>> line 147, >>> <GEN39> line 368238. >>> >>> The SQL instruction is indeed incorrect: trying it manually in >>> PostgreSQL >>> >>> dbgus=# INSERT INTO DoTSVer.SourceVer >>> select v.*,215,now(),30 from DoTS.Source v where v.na_feature_id >>> = 5 >>> ; >>> >>> gives the very same error. >>> >>> The problem lies in the INSERT trigger for the view >>> DoTSVer.SourceVer, which >>> PostgreSQL spells out as follows: >>> >>> ON INSERT TO dotsver.sourcever DO INSTEAD >>> INSERT INTO dotsver.nafeatureimpver ( >>> modification_date, user_read, user_write, group_read, >>> group_write, >>> other_read, other_write, row_user_id, row_group_id, >>> row_project_id, >>> row_alg_invocation_id, version_alg_invocation_id, version_date, >>> version_transaction_id >>> ) VALUES ( >>> new.modification_date, new.user_read, new.user_write, >>> new.group_read, >>> new.group_write, new.other_read, new.other_write, >>> new.row_user_id, >>> new.row_group_id, new.row_project_id, new.row_alg_invocation_id, >>> new.version_alg_invocation_id, new.version_date, >>> new.version_transaction_id >>> ) >>> >>> Now, the description for underlying table DoTS.NAFeatureimpVer >>> starts with >>> >>> dbgus=# \d dotsver.nafeatureimpver >>> Table "dotsver.nafeatureimpver" >>> Column | Type | >>> Modifiers >>> ------------------------------+----------------------------- >>> +----------- >>> na_feature_id | numeric(10,0) | not >>> null >>> >>> Clearly the DoTSVer.SourceVer trigger for INSERTs is wrong, since >>> it misses >>> to set the (provided) value to na_feature_id column. >>> >>> Bug #177 signalled in you Bugzilla is generated by the very same >>> problem, but >>> on view DoTSVer.TranslatedAAFeatureVer (and using Oracle), so >>> quite likely >>> this might a more general issue related to how DoTSVer views are >>> created. >>> >>> Let me know if you need more information for tackling the problem, >>> >>> Antonio Galea >>> >>> >>> >>> ---------------------------------------------------------------- >>> Net Wise webmail system - http://www.netwise.it >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >>> --------------------------------------------------------------------- >>> ---- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys -- and earn >>> cash >>> http://www.techsay.com/default.php? >>> page=join.php&p=sourceforge&CID=DEVDEV >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> >> ---------------------------------------------------------------------- >> --- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys -- and earn >> cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
