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

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:-)

Ok ..... I am waiting for new  release version !!!

Thiago Seito Satake

2005/8/8, Y. Thomas Gan <yon...@pc...>:
> Hi Thiago,
> Usually you should get stable released versions from the download
> site. Steve and I have beening working on the svn trunk and we have more
> work to do before we release version 1.6 - sorry for the inconvenience.
> Please look out for release announcement soon.
>=20
> -Thomas
>=20
>=20
>=20
> On Mon, 8 Aug 2005, Thiago Satake wrote:
>=20
> > 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_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 provided =
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 st=
op
> >>>> 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 driv=
er
> >>>>> to postgres.
> >>>>> 2- we had to change  testTables files to change the numeric data ty=
pe
> >>>>> ( number > numeric )
> >>>>> 3- and now we are changing  java file to adapt to Postgres ( sequen=
ce
> >>>>> 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 pu=
t much
> >>>>>> effort into ensuring the complete functioning of the postgres modu=
le.
> >>>>>>
> >>>>>> 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 ge=
t  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 us=
e WDK 1.5 to
> >>>>>>>> explore the postgres schema. We noticed that the WDK code is man=
ipulating an
> >>>>>>>> Oracle database, due to some type columns, sequence using, etc..=
. that
> >>>>>>>> generates many errors when running wdk programs (wdkCache, wdkQu=
ery,
> >>>>>>>> wdkRecord,...).
> >>>>>>>>
> >>>>>>>> Because of this, we're having a hard work to debug the code and =
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 Program.
> >>>>>>>> _______________________________________________
> >>>>>>>> WDKDev mailing list
> >>>>>>>> WD...@pc...
> >>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>
> >>>
> >>>
> >>>
> >>
> >
> >
> > --
> > Thiago Seito Satake
> > !! Tenha um bom dia !!
> > Tel: (041) 990-55422
> >
> >
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> >
>=20

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