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Re: [WDKDEV] [GUSDEV] Re: WDK with Postgres?
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From: Y. T. G. <yon...@pc...> - 2005-08-10 12:56:53
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maybe we need to explicitly register pg drivers. i'll try it. we should=20 not have to add the driver jar to tomcat'S CLASSPATH. -thomas On Wed, 10 Aug 2005, Steve Fischer wrote: > is it possibly caused by my having commented out this line in > PostegeSQL.java: > > // DriverManager.registerDriver(new org.postgresql.Driver()= ); > > it didn't seem to make any difference when running outside of tomcat (so > i took it out). > > steve > > Thiago Satake wrote: > >> We updated WDK release with postgres and WDKToySite Works well. >> >> >>> See bug 114: toySite throws 'No suitable driver' SQLException >>> >>> >> It seems to me that is a tomcat problem,I belive that you must set >> $CLASSPATH adding jdbc driver for postgres into >> $CATALINA_HOME/bin/setclass.sh..... >> as showed bellow: >> >> >>> # Set standard CLASSPATH >>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.= jar >>> >>> >> >> >> Thanks >> >> >> >> Thiago Seito Stake >> >> >> >> >> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >> >> >>> Another update on the status of release 1.6: >>> >>> With tremendous efforts from Steve we were able to get wdkSanityTest >>> (including tests for all Questions/Summaries, Queries, and Records) >>> passing against both oracle and postgres late last night. >>> >>> But we are at the last of the last hurdles: the toySite works fine >>> with Oracle but does not come up with postgres (as Thiago reported >>> earlier). See bug 114: toySite throws 'No suitable driver' SQLException= at >>> start up against postgres (oracle is ok) although sanityTest succeeds >>> (https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D114). >>> The ArrayIndexOutOfBounds exception is a result of this. >>> >>> I am debugging this and will release after it is fixed. >>> >>> -Thomas >>> >>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>> >>> >>> >>>> 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 >>>> features, including an improved Sanity Test. the test will now test a= ll >>>> Questions in the model XML file as well as all Queries and all Records= =2E >>>> 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 n= ame 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, >>>>> >>>>> Fabr=EDcio. >>>>> >>>>> >>>>> Citando Thiago Satake <ma...@gm...>: >>>>> >>>>> >>>>> >>>>> >>>>>> After downloaded WDK from SVN files 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: >>>>>> org.gusdb.wdk.model.WdkModelException: >>>>>> Failed running query: >>>>>> "SELECT * FROM ( select usertest.query_result_4.result_index_column, >>>>>> a.assembly_consistency, a.contains_mrna, >>>>>> a.number_of_contained_sequences, a.sequence >>>>>> from WDKTestAssembly a, WDKTestTaxonName tn , >>>>>> usertest.query_result_4 where a.na_sequence_id =3D >>>>>> usertest.query_result_4.na_sequence_id and a.taxon_i= d >>>>>> =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...>: >>>>>> >>>>>> >>>>>> >>>>>>> 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: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> 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 provid= ed by >>>>>>>>> the student's fixes. i am starting now to look at them and merge= =2E >>>>>>>>> >>>>>>>>> i have a lot of meetings today, so in a little while i'll need to= stop >>>>>>>>> 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 d= river >>>>>>>>>> to postgres. >>>>>>>>>> 2- we had to change testTables files to change the numeric data= type >>>>>>>>>> ( number > numeric ) >>>>>>>>>> 3- and now we are changing java file to adapt to Postgres ( seq= uence >>>>>>>>>> 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.RequestProcesso= r >>>>>>>>>> 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= put >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>> much >>>>>> >>>>>> >>>>>> >>>>>>>>>>> effort into ensuring the complete functioning of the postgres m= odule. >>>>>>>>>>> >>>>>>>>>>> however, a student did successfully use postgres with the wdk. = he >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>> 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= get >>>>>>>>>>> >>>>>>>>>>> >>>>>> 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= use >>>>>>>>>>>>> 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, et= c... >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> that >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>>> wdkQuery, >>>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>> >>>>>>>>>>>>> Because of this, we're having a hard work to debug the code a= nd set >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> it to work >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> with the Postgres schema. We would like to know if someone ha= s a >>>>>>>>>>>>> WDK >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> working >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>> >>>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>> >>>>>>>>>>>>> -------------------------------------------------------------= --- >>>>>>>>>>>>> This message was sent using IMP, the Internet Messaging Progr= am. >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> WDKDev mailing list >>>>>>>>>>>>> WD...@pc... >>>>>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> -- >>>>>> Thiago Seito Satake >>>>>> !! Tenha um bom dia !! >>>>>> Tel: (041) 990-55422 >>>>>> >>>>>> _______________________________________________ >>>>>> WDKDev mailing list >>>>>> WD...@pc... >>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>>> >>>> ------------------------------------------------------- >>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Prac= tices >>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing = & QA >>>> Security * Process Improvement & Measurement * http://www.sqe.com/bsce= 5sf >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >> >> >> -- >> Thiago Seito Satake >> !! Tenha um bom dia !! >> Tel: (041) 990-55422 >> >> >> >> > _______________________________________________ > WDKDev mailing list > WD...@pc... > https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > |
