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[GUSDEV] Re: [WDKDEV] WDK with Postgres?
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From: Steve F. <sfi...@pc...> - 2005-08-09 22:13:00
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just want to give an update on our progress. we are planning a release today or tomorrow. 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 this was needed to thoroughly test postgres. we're working hard to get this release out... steve fab...@de... wrote: >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...>: > > =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=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 >>>> >>--=20 >>Thiago Seito Satake >>!! Tenha um bom dia !! >>Tel: (041) 990-55422 >> >>_______________________________________________ >>WDKDev mailing list >>WD...@pc... >>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >> >> =20 >> > > > > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > =20 > |
