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[GUSDEV] Re: [WDKDEV] WDK with Postgres?
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From: Alberto D. <da...@io...> - 2005-08-09 17:54:52
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Great Steve ! I have a question for you, looks like NCBI is (has ?) moving to XML format... since I have been unable to find the standard GenBank format available at NCBI site: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/XML/ncbixml.txt Does GPBarser deal with any of those XML formats from Genbank ? Thanks, Alberto On Tue, 2005-08-09 at 11:37 -0400, Steve Fischer wrote: > just want to give an update on our progress. >=20 > we are planning a release today or tomorrow. >=20 > as well as postgres support (tested) it will include a number of other=20 > features, including an improved Sanity Test. the test will now test all=20 > Questions in the model XML file as well as all Queries and all Records. =20 >=20 > this was needed to thoroughly test postgres. >=20 > we're working hard to get this release out... >=20 > steve >=20 > fab...@de... wrote: >=20 > >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=C3=ADcio. > > > > > >Citando Thiago Satake <ma...@gm...>: > > > > =20 > > > >>After downloaded WDK from SVN files=20 > >>I run: > >>wdkSanityTest -model toyModel > >> > >>and got this > >> > >>***Sanity test summary*** > >>10 queries passed, 4 queries failed > >>1 records passed, 1 records failed > >>Sanity Test FAILED > >> > >> > >>and I run: > >>wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 20 > >>-params NumSeqs 10 ApiTaxon "Neospora caninum" > >> > >>I got:=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" > >> > >> > >>:-( > >> > >> > >>Thanks > >> > >>Thiago Seito Satake > >> > >> > >> > >> > >> > >> > >>2005/8/5, Steve Fischer <sfi...@pc...>: > >> =20 > >> > >>>Folks- > >>> > >>>I have made a lot of progress. > >>> > >>>It is clear that the wdk postgres implementation was never tested. = I > >>>have fixed many, many things. > >>> > >>>Here is where I am at so far. i ran: > >>> % wdkSanityTest -model toyModel > >>> > >>>and got this: > >>> > >>>***Sanity test summary*** > >>>11 queries passed, 1 queries failed > >>>0 records passed, 2 records failed > >>>Sanity Test FAILED > >>> > >>>tomorrow morning i'll look into the remaining problems > >>> > >>>steve > >>> > >>>Thiago Satake wrote: > >>> > >>> =20 > >>> > >>>>Thanks a lot, > >>>> > >>>>Can I help you with something ? > >>>> > >>>>Thiago Seito Satake > >>>> > >>>>2005/8/4, Steve Fischer <sfi...@pc...>: > >>>> > >>>> > >>>> =20 > >>>> > >>>>>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 st= op > >>>>>till tonight > >>>>> > >>>>>steve > >>>>> > >>>>>Thiago Satake wrote: > >>>>> > >>>>> > >>>>> > >>>>> =20 > >>>>> > >>>>>>Ok ........ > >>>>>> > >>>>>>We can list some problems: > >>>>>>1- we had to change all of perl wdk file ... to set te correct driv= er > >>>>>>to postgres. > >>>>>>2- we had to change testTables files to change the numeric data ty= pe > >>>>>>( number > numeric ) > >>>>>>3- and now we are changing java file to adapt to Postgres ( sequen= ce > >>>>>>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...>: > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> =20 > >>>>>> > >>>>>>>Folks- > >>>>>>> > >>>>>>>the production uses of wdk so far are in oracle, so we have not pu= t > >>>>>>> =20 > >>>>>>> > >>much > >> =20 > >> > >>>>>>>effort into ensuring the complete functioning of the postgres modu= le. > >>>>>>> > >>>>>>>however, a student did successfully use postgres with the wdk. he > >>>>>>> =20 > >>>>>>> > >>made > >> =20 > >> > >>>>>>>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 ge= t=20 > >>>>>>> =20 > >>>>>>> > >>you > >> =20 > >> > >>>>>>>a patch by tomorrow. > >>>>>>> > >>>>>>>can you describe briefly the problems? > >>>>>>> > >>>>>>>steve > >>>>>>> > >>>>>>>Thiago Satake wrote: > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> =20 > >>>>>>> > >>>>>>>>I am having the same problem......... > >>>>>>>> > >>>>>>>>Does Someone have the wdk working with postgres database ? > >>>>>>>> > >>>>>>>>I would appreciate if someone could help me too !!!!!!!!!!!!!!!!!= !! > >>>>>>>> =20 > >>>>>>>> > >>:-) > >> =20 > >> > >>>>>>>>Thanks ............. > >>>>>>>> > >>>>>>>>Thiago Seito Satake > >>>>>>>> > >>>>>>>> > >>>>>>>>2005/8/4, fab...@de... <fab...@de...>: > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> =20 > >>>>>>>> > >>>>>>>>>Hello all, > >>>>>>>>> > >>>>>>>>>We have a GUS installation running ok and now we're trying to us= e WDK > >>>>>>>>> =20 > >>>>>>>>> > >>1.5 to > >> =20 > >> > >>>>>>>>>explore the postgres schema. We noticed that the WDK code is > >>>>>>>>> =20 > >>>>>>>>> > >>manipulating an > >> =20 > >> > >>>>>>>>>Oracle database, due to some type columns, sequence using, etc..= . > >>>>>>>>> =20 > >>>>>>>>> > >>that > >> =20 > >> > >>>>>>>>>generates many errors when running wdk programs (wdkCache, wdkQu= ery, > >>>>>>>>>wdkRecord,...). > >>>>>>>>> > >>>>>>>>>Because of this, we're having a hard work to debug the code and = set > >>>>>>>>> =20 > >>>>>>>>> > >>it to work > >> =20 > >> > >>>>>>>>>with the Postgres schema. We would like to know if someone has a= WDK > >>>>>>>>> =20 > >>>>>>>>> > >>working > >> =20 > >> > >>>>>>>>>with GUS Postgres perfectly. > >>>>>>>>> > >>>>>>>>>Thanks a lot, > >>>>>>>>> > >>>>>>>>>Fabr=C3=ADcio. > >>>>>>>>> > >>>>>>>>>---------------------------------------------------------------- > >>>>>>>>>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 > >>>> > >>--=20 > >>Thiago Seito Satake > >>!! Tenha um bom dia !! > >>Tel: (041) 990-55422 > >> |
