[GUSDEV] Re: [WDKDEV] WDK with Postgres?

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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 a=
t
> 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 al=
l
> > Questions in the model XML file as well as all Queries and all Records.
> > 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 na=
me 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 2=
0
> >>> -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_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.  =
  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 provide=
d 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 =
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 dr=
iver
> >>>>>>> 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 ( sequ=
ence
> >>>>>>> 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...>:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>> 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 mo=
dule.
> >>>>>>>>
> >>>>>>>> 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, etc=
...
> >>>>>>>>>>
> >>> that
> >>>
> >>>>>>>>>> generates many errors when running wdk programs (wdkCache,
> >>>>>>>>>> wdkQuery,
> >>>>>>>>>> wdkRecord,...).
> >>>>>>>>>>
> >>>>>>>>>> Because of this, we're having a hard work to debug the code an=
d set
> >>>>>>>>>>
> >>> it to work
> >>>
> >>>>>>>>>> with the Postgres schema. We would like to know if someone has=
 a
> >>>>>>>>>> WDK
> >>>>>>>>>>
> >>> working
> >>>
> >>>>>>>>>> with GUS Postgres perfectly.
> >>>>>>>>>>
> >>>>>>>>>> Thanks a lot,
> >>>>>>>>>>
> >>>>>>>>>> Fabr=EDcio.
> >>>>>>>>>>
> >>>>>>>>>> --------------------------------------------------------------=
--
> >>>>>>>>>> This message was sent using IMP, the Internet Messaging Progra=
m.
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> 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
> >>>
> >>>
> >>
> >>
> >>
> >>
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> >>
> >
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--
Thiago Seito Satake
!! Tenha um bom dia !!
Tel: (041) 990-55422


--=20
Thiago Seito Satake
!! Tenha um bom dia !!
Tel: (041) 990-55422