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Re: [WDKDEV] [GUSDEV] Re: WDK with Postgres?
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From: Michael S. <msa...@pc...> - 2005-08-10 13:19:58
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Thomas, This is very similar to an issue we had with the Oracle OCI drivers, which are much more robust that the thin driver in use around the lab. With our new servers, I'd like websites to begin to use the OCI drivers, so it may b= e 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. >=20 > -thomas >=20 > On Wed, 10 Aug 2005, Steve Fischer wrote: >=20 >> is it possibly caused by my having commented out this line in >> PostegeSQL.java: >>=20 >> // DriverManager.registerDriver(new org.postgresql.Driver(= )); >>=20 >> it didn't seem to make any difference when running outside of tomcat (so >> i took it out). >>=20 >> steve >>=20 >> Thiago Satake wrote: >>=20 >>> We updated WDK release with postgres and WDKToySite Works well. >>>=20 >>>=20 >>>> See bug 114: toySite throws 'No suitable driver' SQLException >>>>=20 >>>>=20 >>> It seems to me that is a tomcat problem,I belive that you must set >>> $CLASSPATH adding jdbc driver for postgres into >>> $CATALINA_HOME/bin/setclass.sh..... >>> as showed bellow: >>>=20 >>>=20 >>>> # Set standard CLASSPATH >>>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.j= ar >>>>=20 >>>>=20 >>>=20 >>>=20 >>> Thanks >>>=20 >>>=20 >>>=20 >>> Thiago Seito Stake >>>=20 >>>=20 >>>=20 >>>=20 >>> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >>>=20 >>>=20 >>>> Another update on the status of release 1.6: >>>>=20 >>>> 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. >>>>=20 >>>> 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' SQLExceptio= n 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. >>>>=20 >>>> I am debugging this and will release after it is fixed. >>>>=20 >>>> -Thomas >>>>=20 >>>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>>>=20 >>>>=20 >>>>=20 >>>>> 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 othe= r >>>>> 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 Record= s. >>>>> this was needed to thoroughly test postgres. >>>>>=20 >>>>> we're working hard to get this release out... >>>>>=20 >>>>> steve >>>>>=20 >>>>> fab...@de... wrote: >>>>>=20 >>>>>=20 >>>>>=20 >>>>>> Thiago, >>>>>>=20 >>>>>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>>>> I'm having this problem too. In wdkSummary it seems that the schema = name >>>>>> is >>>>>> missing before table names in FROM clause. >>>>>>=20 >>>>>> I don't know if this is a Wdk problem or WdkToySite SQL error. >>>>>>=20 >>>>>> Can you help us Steve? >>>>>>=20 >>>>>> Thanks a lot, >>>>>>=20 >>>>>> Fabr=EDcio. >>>>>>=20 >>>>>>=20 >>>>>> Citando Thiago Satake <ma...@gm...>: >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>>> After downloaded WDK from SVN files 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: >>>>>>> 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_= 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...>: >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>> 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 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>=20 >>>>>>>>> Thanks a lot, >>>>>>>>>=20 >>>>>>>>> Can I help you with something ? >>>>>>>>>=20 >>>>>>>>> Thiago Seito Satake >>>>>>>>>=20 >>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provi= ded >>>>>>>>>> by >>>>>>>>>> the student's fixes. i am starting now to look at them and merg= e. >>>>>>>>>>=20 >>>>>>>>>> i have a lot of meetings today, so in a little while i'll need t= o >>>>>>>>>> stop >>>>>>>>>> till tonight >>>>>>>>>>=20 >>>>>>>>>> steve >>>>>>>>>>=20 >>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>> Ok ........ >>>>>>>>>>>=20 >>>>>>>>>>> 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 dat= a >>>>>>>>>>> type >>>>>>>>>>> ( number > numeric ) >>>>>>>>>>> 3- and now we are changing java file to adapt to Postgres ( >>>>>>>>>>> sequence >>>>>>>>>>> manipulation, Postgres.java - jdbc driver and numeric type ) >>>>>>>>>>>=20 >>>>>>>>>>> now we are having problem to use WDKToySite as the log shows: >>>>>>>>>>>=20 >>>>>>>>>>> DEBUG: making a QuestionSetForm >>>>>>>>>>> Aug 4, 2005 11:23:14 AM org.apache.struts.action.RequestProcess= or >>>>>>>>>>> processException >>>>>>>>>>> WARNING: Unhandled Exception thrown: class >>>>>>>>>>> java.lang.ArrayIndexOutOfBoundsException >>>>>>>>>>>=20 >>>>>>>>>>> and other problems ............. >>>>>>>>>>>=20 >>>>>>>>>>> Thanks for the help :-) >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>> 2005/8/4, Steve Fischer <sfi...@pc...>: >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>> Folks- >>>>>>>>>>>>=20 >>>>>>>>>>>> the production uses of wdk so far are in oracle, so we have no= t put >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> much >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> effort into ensuring the complete functioning of the postgres >>>>>>>>>>>> module. >>>>>>>>>>>>=20 >>>>>>>>>>>> however, a student did successfully use postgres with the wdk.= he >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> made >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> improvements in the PostgreSQL.java file, and a small change i= n >>>>>>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>>>>>=20 >>>>>>>>>>>> I will incorporate those changes today and test it. I hope t= o get >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> you >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> a patch by tomorrow. >>>>>>>>>>>>=20 >>>>>>>>>>>> can you describe briefly the problems? >>>>>>>>>>>>=20 >>>>>>>>>>>> steve >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> I am having the same problem......... >>>>>>>>>>>>=20 >>>>>>>>>>>> Does Someone have the wdk working with postgres database ? >>>>>>>>>>>>=20 >>>>>>>>>>>> I would appreciate if someone could help me too !!!!!!!!!!!!!!= !!!!! >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> :-) >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> Thanks ............. >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Seito Satake >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> Hello all, >>>>>>>>>>>>=20 >>>>>>>>>>>> We have a GUS installation running ok and now we're trying to = use >>>>>>>>>>>> WDK >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> 1.5 to >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> manipulating an >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> Oracle database, due to some type columns, sequence using, etc= ... >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> that >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>> wdkQuery, >>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>=20 >>>>>>>>>>>> Because of this, we're having a hard work to debug the code an= d set >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> it to work >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> with the Postgres schema. We would like to know if someone has= a >>>>>>>>>>>> WDK >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> working >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>=20 >>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>=20 >>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>=20 >>>>>>>>>>>> --------------------------------------------------------------= -- >>>>>>>>>>>> This message was sent using IMP, the Internet Messaging Progra= m. >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> WDKDev mailing list >>>>>>>>>>>> WD...@pc... >>>>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>=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 >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>>> ---------------------------------------------------------------- >>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>=20 >>>>>>=20 >>>>>>=20 >>>>> ------------------------------------------------------- >>>>> 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 * Testing= & QA >>>>> Security * Process Improvement & Measurement * http://www.sqe.com/bsc= e5sf >>>>> _______________________________________________ >>>>> Gusdev-gusdev mailing list >>>>> Gus...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>=20 >>>>>=20 >>>>>=20 >>>=20 >>>=20 >>> -- >>> Thiago Seito Satake >>> !! Tenha um bom dia !! >>> Tel: (041) 990-55422 >>>=20 >>>=20 >>>=20 >>>=20 >> _______________________________________________ >> WDKDev mailing list >> WD...@pc... >> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>=20 |
