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Re: [WDKDEV] [GUSDEV] Re: WDK with Postgres?
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From: Y. T. G. <yon...@pc...> - 2005-08-10 13:03:18
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yes indeed. we need to explicitly register pg drivers (but not oracle=20 drivers). cheers, thomas On Wed, 10 Aug 2005, Y. Thomas Gan wrote: > maybe we need to explicitly register pg drivers. i'll try it. we should n= ot=20 > 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: >>=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= =2Ejar >>>>=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=20 >>>> 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= =20 >>>>>> 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.= =20 >>>>>>>> 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=20 >>>>>>>>>> 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=20 >>>>>>>>>> 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= =20 >>>>>>>>>>> driver >>>>>>>>>>> to postgres. >>>>>>>>>>> 2- we had to change testTables files to change the numeric dat= a=20 >>>>>>>>>>> type >>>>>>>>>>> ( number > numeric ) >>>>>>>>>>> 3- and now we are changing java file to adapt to Postgres (=20 >>>>>>>>>>> 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=20 >>>>>>>>>>>> put >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> much >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> effort into ensuring the complete functioning of the postgres= =20 >>>>>>>>>>>> module. >>>>>>>>>>>>=20 >>>>>>>>>>>> however, a student did successfully use postgres with the wdk.= =20 >>>>>>>>>>>> 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=20 >>>>>>>>>>>> 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 >>>>>>>=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 t= o=20 >>>>>>>>>>>>>> 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,= =20 >>>>>>>>>>>>>> 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 = and=20 >>>>>>>>>>>>>> set >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> it to work >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> with the Postgres schema. We would like to know if someone h= as=20 >>>>>>>>>>>>>> a >>>>>>>>>>>>>> WDK >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> working >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> ------------------------------------------------------------= ---- >>>>>>>>>>>>>> This message was sent using IMP, the Internet Messaging=20 >>>>>>>>>>>>>> Program. >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> 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=20 >>>>> Practices >>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing= &=20 >>>>> QA >>>>> Security * Process Improvement & Measurement *=20 >>>>> http://www.sqe.com/bsce5sf >>>>> _______________________________________________ >>>>> 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 > |
