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

[Thiago S. <ma...@gm...>]

After downloaded WDK from SVN files=20
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:=20

org.gusdb.wdk.model.WdkModelException:
Failed running query:
"SELECT * FROM ( select usertest.query_result_4.result_index_column, =20
  a.assembly_consistency,          a.contains_mrna,                  =20
   a.number_of_contained_sequences,                       a.sequence =20
             from WDKTestAssembly a, WDKTestTaxonName tn             =20
  , 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-
>=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
> >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 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 data 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.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 m=
uch
> >>>>effort into ensuring the complete functioning of the postgres module.
> >>>>
> >>>>however, a student did successfully use postgres with the wdk.  he ma=
de
> >>>>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 W=
DK 1.5 to
> >>>>>>explore the postgres schema. We noticed that the WDK code is manipu=
lating an
> >>>>>>Oracle database, due to some type columns, sequence using, etc... t=
hat
> >>>>>>generates many errors when running wdk programs (wdkCache, wdkQuery=
,
> >>>>>>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 WD=
K 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
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>
> >>>
> >>>
> >>>
> >
> >
> >
> >
>=20


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