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Re: [WDKDEV] [GUSDEV] Re: WDK with Postgres?
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From: Y. T. G. <yon...@pc...> - 2005-08-10 13:25:29
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Yeah, I remember working with you trying to switch to it but was not able= =20 to get it to work. I can give it another shot soon. -Thomas On Wed, 10 Aug 2005, Michael Saffitz wrote: > > Thomas, > > This is very similar to an issue we had with the Oracle OCI drivers, whic= h > are much more robust that the thin driver in use around the lab. With ou= r > new servers, I'd like websites to begin to use the OCI drivers, so it may= be > worth our while to test with those as well. > > --Mike > > > > On 8/10/05 8:56 AM, "Y. Thomas Gan" <yon...@pc...> wrote: > >> maybe we need to explicitly register pg drivers. i'll try it. we should >> 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 (s= o >>> 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.jdbc= 3.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' SQLExcepti= on at >>>>> start up against postgres (oracle is ok) although sanityTest succeed= s >>>>> (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 oth= er >>>>>> features, including an improved Sanity Test. the test will now test= all >>>>>> Questions in the model XML file as well as all Queries and all Recor= ds. >>>>>> 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, >>>>>>> >>>>>>> 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_colum= n, >>>>>>>> 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= _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...>: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Folks- >>>>>>>>> >>>>>>>>> I have made a lot of progress. >>>>>>>>> >>>>>>>>> It is clear that the wdk postgres implementation was never tested= =2E 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 prov= ided >>>>>>>>>>> by >>>>>>>>>>> the student's fixes. i am starting now to look at them and mer= ge. >>>>>>>>>>> >>>>>>>>>>> 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 >>>>>>>>>>>> driver >>>>>>>>>>>> to postgres. >>>>>>>>>>>> 2- we had to change testTables files to change the numeric da= ta >>>>>>>>>>>> type >>>>>>>>>>>> ( number > numeric ) >>>>>>>>>>>> 3- and now we are changing java file to adapt to Postgres ( >>>>>>>>>>>> sequence >>>>>>>>>>>> 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.RequestProces= sor >>>>>>>>>>>> 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 n= ot put >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> much >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> effort into ensuring the complete functioning of the postgres >>>>>>>>>>>>> module. >>>>>>>>>>>>> >>>>>>>>>>>>> however, a student did successfully use postgres with the wdk= =2E 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 >>>>>> Practices >>>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testin= g & QA >>>>>> Security * Process Improvement & Measurement * http://www.sqe.com/bs= ce5sf >>>>>> _______________________________________________ >>>>>> 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 >>> > > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
