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[GUSDEV] Re: [WDKDEV] WDK with Postgres?
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From: <fab...@de...> - 2005-08-08 15:02:59
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Thiago, I'm having this problem too. In wdkSummary it seems that the schema name = is missing before table names in FROM clause. I don't know if this is a Wdk problem or WdkToySite SQL error. Can you help us Steve? Thanks a lot, =20 Fabr=EDcio. Citando Thiago Satake <ma...@gm...>: > After downloaded WDK from SVN files=20 > I run: > wdkSanityTest -model toyModel >=20 > and got this >=20 > ***Sanity test summary*** > 10 queries passed, 4 queries failed > 1 records passed, 1 records failed > Sanity Test FAILED >=20 >=20 > and I run: > wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 20 > -params NumSeqs 10 ApiTaxon "Neospora caninum" >=20 > I got:=20 >=20 > org.gusdb.wdk.model.WdkModelException: > Failed running query: > "SELECT * FROM ( select usertest.query_result_4.result_index_column, =20 > a.assembly_consistency, a.contains_mrna, =20 > a.number_of_contained_sequences, a.sequence =20 > from WDKTestAssembly a, WDKTestTaxonName tn =20 > , usertest.query_result_4 where a.na_sequence_id =3D > usertest.query_result_4.na_sequence_id and a.taxon_id > =3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D 1 = and > usertest.query_result_4.result_index_column <=3D 20 order by > usertest.query_result_4.result_index_column ) ORDER BY > result_index_column" >=20 >=20 > :-( >=20 >=20 > Thanks >=20 > Thiago Seito Satake >=20 >=20 >=20 >=20 >=20 >=20 > 2005/8/5, Steve Fischer <sfi...@pc...>: > > Folks- > >=20 > > I have made a lot of progress. > >=20 > > It is clear that the wdk postgres implementation was never tested. = I > > have fixed many, many things. > >=20 > > Here is where I am at so far. i ran: > > % wdkSanityTest -model toyModel > >=20 > > and got this: > >=20 > > ***Sanity test summary*** > > 11 queries passed, 1 queries failed > > 0 records passed, 2 records failed > > Sanity Test FAILED > >=20 > > tomorrow morning i'll look into the remaining problems > >=20 > > steve > >=20 > > Thiago Satake wrote: > >=20 > > >Thanks a lot, > > > > > >Can I help you with something ? > > > > > >Thiago Seito Satake > > > > > >2005/8/4, Steve Fischer <sfi...@pc...>: > > > > > > > > >>ok, sorry about this. yes, those all of 1,2,3 i think are provided= by > > >>the student's fixes. i am starting now to look at them and merge. > > >> > > >>i have a lot of meetings today, so in a little while i'll need to s= top > > >>till tonight > > >> > > >>steve > > >> > > >>Thiago Satake wrote: > > >> > > >> > > >> > > >>>Ok ........ > > >>> > > >>>We can list some problems: > > >>>1- we had to change all of perl wdk file ... to set te correct dri= ver > > >>>to postgres. > > >>>2- we had to change testTables files to change the numeric data t= ype > > >>>( number > numeric ) > > >>>3- and now we are changing java file to adapt to Postgres ( seque= nce > > >>>manipulation, Postgres.java - jdbc driver and numeric type ) > > >>> > > >>>now we are having problem to use WDKToySite as the log shows: > > >>> > > >>>DEBUG: making a QuestionSetForm > > >>>Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcessor > > >>>processException > > >>>WARNING: Unhandled Exception thrown: class > > >>>java.lang.ArrayIndexOutOfBoundsException > > >>> > > >>>and other problems ............. > > >>> > > >>>Thanks for the help :-) > > >>> > > >>> > > >>> > > >>> > > >>>2005/8/4, Steve Fischer <sfi...@pc...>: > > >>> > > >>> > > >>> > > >>> > > >>>>Folks- > > >>>> > > >>>>the production uses of wdk so far are in oracle, so we have not p= ut > much > > >>>>effort into ensuring the complete functioning of the postgres mod= ule. > > >>>> > > >>>>however, a student did successfully use postgres with the wdk. h= e > made > > >>>>improvements in the PostgreSQL.java file, and a small change in > > >>>>ResultFactory that are not yet in the release. > > >>>> > > >>>>I will incorporate those changes today and test it. I hope to g= et=20 > you > > >>>>a patch by tomorrow. > > >>>> > > >>>>can you describe briefly the problems? > > >>>> > > >>>>steve > > >>>> > > >>>>Thiago Satake wrote: > > >>>> > > >>>> > > >>>> > > >>>> > > >>>> > > >>>>>I am having the same problem......... > > >>>>> > > >>>>>Does Someone have the wdk working with postgres database ? > > >>>>> > > >>>>>I would appreciate if someone could help me too !!!!!!!!!!!!!!!!= !!! > :-) > > >>>>> > > >>>>>Thanks ............. > > >>>>> > > >>>>>Thiago Seito Satake > > >>>>> > > >>>>> > > >>>>>2005/8/4, fab...@de... <fab...@de...>: > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>>>Hello all, > > >>>>>> > > >>>>>>We have a GUS installation running ok and now we're trying to u= se WDK > 1.5 to > > >>>>>>explore the postgres schema. We noticed that the WDK code is > manipulating an > > >>>>>>Oracle database, due to some type columns, sequence using, etc.= .. > that > > >>>>>>generates many errors when running wdk programs (wdkCache, wdkQ= uery, > > >>>>>>wdkRecord,...). > > >>>>>> > > >>>>>>Because of this, we're having a hard work to debug the code and= set > it to work > > >>>>>>with the Postgres schema. We would like to know if someone has = a WDK > working > > >>>>>>with GUS Postgres perfectly. > > >>>>>> > > >>>>>>Thanks a lot, > > >>>>>> > > >>>>>>Fabr=EDcio. > > >>>>>> > > >>>>>>---------------------------------------------------------------= - > > >>>>>>This message was sent using IMP, the Internet Messaging Program= . > > >>>>>>_______________________________________________ > > >>>>>>WDKDev mailing list > > >>>>>>WD...@pc... > > >>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>> > > >>> > > >>> > > >>> > > > > > > > > > > > > > >=20 >=20 >=20 > --=20 > Thiago Seito Satake > !! Tenha um bom dia !! > Tel: (041) 990-55422 >=20 > _______________________________________________ > WDKDev mailing list > WD...@pc... > https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >=20 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
