Thread: [GUSDEV] Question regarding GUS3.0

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Hi,
  I have GUS3.0 installed and pointed to dev database.Now I want to use
the same GUS installation to point to different database 'Test' which
parameter do I need to change.
I have already copied all the GUS database objects from Dev to Test
database.

Thanks
Sanjeev=20

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Today's Topics:

   1. Re: [WDKDEV] WDK with Postgres? (Thiago Satake)
   2. Re: [WDKDEV] WDK with Postgres? (fab...@de...)
   3. Re: Re: [WDKDEV] WDK with Postgres? (Y. Thomas Gan)
   4. Re: Re: [WDKDEV] WDK with Postgres? (Thiago Satake)

--__--__--

Message: 1
Date: Mon, 8 Aug 2005 11:54:18 -0300
From: Thiago Satake <ma...@gm...>
To: Steve Fischer <sfi...@pc...>,
gus...@li...,=20
	wd...@pc...
Subject: [GUSDEV] Re: [WDKDEV] WDK with Postgres?

After downloaded WDK from SVN files=3D20
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:=3D20

org.gusdb.wdk.model.WdkModelException:
Failed running query:
"SELECT * FROM ( select usertest.query_result_4.result_index_column, =
=3D20
  a.assembly_consistency,          a.contains_mrna,                  =
=3D20
   a.number_of_contained_sequences,                       a.sequence =
=3D20
             from WDKTestAssembly a, WDKTestTaxonName tn             =
=3D20
  , usertest.query_result_4 where a.na_sequence_id =3D3D
usertest.query_result_4.na_sequence_id                 and a.taxon_id
=3D3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D3D =
1
and usertest.query_result_4.result_index_column <=3D3D 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-
>=3D20
> I have made a lot of progress.
>=3D20
> It is clear that the wdk postgres implementation was never tested.
I
> have fixed many, many things.
>=3D20
> Here is where I am at so far.  i ran:
>   % wdkSanityTest -model toyModel
>=3D20
> and got this:
>=3D20
> ***Sanity test summary***
> 11 queries passed, 1 queries failed
> 0 records passed, 2 records failed
> Sanity Test FAILED
>=3D20
> tomorrow morning i'll look into the remaining problems =3D20  steve =
=3D20

>Thiago Satake wrote:
>=3D20
> >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=20
> >>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=20
> >>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=20
> >>>driver to postgres.
> >>>2- we had to change  testTables files to change the numeric data=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=20
> >>>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=20
> >>>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=20
> >>>>put m=3D
uch
> >>>>effort into ensuring the complete functioning of the postgres
module.
> >>>>
> >>>>however, a student did successfully use postgres with the wdk.  he

> >>>>ma=3D
de
> >>>>improvements in the PostgreSQL.java file, and a small change in=20
> >>>>ResultFactory that are not yet in the release.
> >>>>
> >>>>I will incorporate those changes today and test it.   I hope to
get  =3D
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=20
> >>>>>!!!!!!!!!!!!!!!!!!! =3D
:-)
> >>>>>
> >>>>>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=20
> >>>>>>use W=3D
DK 1.5 to
> >>>>>>explore the postgres schema. We noticed that the WDK code is=20
> >>>>>>manipu=3D
lating an
> >>>>>>Oracle database, due to some type columns, sequence using,=20
> >>>>>>etc... t=3D
hat
> >>>>>>generates many errors when running wdk programs (wdkCache,=20
> >>>>>>wdkQuery=3D
,
> >>>>>>wdkRecord,...).
> >>>>>>
> >>>>>>Because of this, we're having a hard work to debug the code and=20
> >>>>>>set=3D
 it to work
> >>>>>>with the Postgres schema. We would like to know if someone has a

> >>>>>>WD=3D
K working
> >>>>>>with GUS Postgres perfectly.
> >>>>>>
> >>>>>>Thanks a lot,
> >>>>>>
> >>>>>>Fabr=3DEDcio.
> >>>>>>
> >>>>>>----------------------------------------------------------------
> >>>>>>This message was sent using IMP, the Internet Messaging Program.
> >>>>>>_______________________________________________
> >>>>>>WDKDev mailing list
> >>>>>>WD...@pc...
> >>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>
> >>>
> >>>
> >>>
> >
> >
> >
> >
>=3D20

--=3D20
Thiago Seito Satake
!! Tenha um bom dia !!
Tel: (041) 990-55422

--__--__--

Message: 2
Date: Mon, 08 Aug 2005 12:02:39 -0300
From: fab...@de...
To: Thiago Satake <ma...@gm...>
Cc: gus...@li..., wd...@pc...,
	Steve Fischer <sfi...@pc...>
Subject: [GUSDEV] Re: [WDKDEV] WDK with Postgres?

Thiago,

I'm having this problem too. In wdkSummary it seems that the schema name
=3D 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,
=3D20
Fabr=3DEDcio.

Citando Thiago Satake <ma...@gm...>:

> After downloaded WDK from SVN files=3D20  I run:
> wdkSanityTest -model toyModel
>=3D20
> and got this
>=3D20
> ***Sanity test summary***
> 10 queries passed, 4 queries failed
> 1 records passed, 1 records failed
> Sanity Test FAILED
>=3D20
>=3D20
> and I run:
> wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 20

>-params NumSeqs 10 ApiTaxon "Neospora caninum"
>=3D20
> I got:=3D20
>=3D20
> org.gusdb.wdk.model.WdkModelException:
> Failed running query:
> "SELECT * FROM ( select usertest.query_result_4.result_index_column,
=3D20
>   a.assembly_consistency,          a.contains_mrna,
=3D20
>    a.number_of_contained_sequences,                       a.sequence
=3D20
>              from WDKTestAssembly a, WDKTestTaxonName tn
=3D20
>   , usertest.query_result_4 where a.na_sequence_id =3D3D
> usertest.query_result_4.na_sequence_id                 and a.taxon_id
> =3D3D tn.taxon_id and usertest.query_result_4.result_index_column =
>=3D3D 1

>=3D
and
> usertest.query_result_4.result_index_column <=3D3D 20 order by =20
>usertest.query_result_4.result_index_column ) ORDER BY =20
>result_index_column"
>=3D20
>=3D20
> :-(
>=3D20
>=3D20
> Thanks
>=3D20
> Thiago Seito Satake
>=3D20
>=3D20
>=3D20
>=3D20
>=3D20
>=3D20
> 2005/8/5, Steve Fischer <sfi...@pc...>:
> > Folks-
> >=3D20
> > I have made a lot of progress.
> >=3D20
> > It is clear that the wdk postgres implementation was never tested.
=3D
 I
> > have fixed many, many things.
> >=3D20
> > Here is where I am at so far.  i ran:
> >   % wdkSanityTest -model toyModel
> >=3D20
> > and got this:
> >=3D20
> > ***Sanity test summary***
> > 11 queries passed, 1 queries failed
> > 0 records passed, 2 records failed
> > Sanity Test FAILED
> >=3D20
> > tomorrow morning i'll look into the remaining problems =3D20  steve=20
> >=3D20  Thiago Satake wrote:
> >=3D20
> > >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=20
> > >>provided=3D
 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=20
> > >>s=3D
top
> > >>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=20
> > >>>dri=3D
ver
> > >>>to postgres.
> > >>>2- we had to change  testTables files to change the numeric data=20
> > >>>t=3D
ype
> > >>>( number > numeric )
> > >>>3- and now we are changing  java file to adapt to Postgres (=20
> > >>>seque=3D
nce
> > >>>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=20
> > >>>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=20
> > >>>>p=3D
ut
> much
> > >>>>effort into ensuring the complete functioning of the postgres=20
> > >>>>mod=3D
ule.
> > >>>>
> > >>>>however, a student did successfully use postgres with the wdk. =20
> > >>>>h=3D
e
> made
> > >>>>improvements in the PostgreSQL.java file, and a small change in=20
> > >>>>ResultFactory that are not yet in the release.
> > >>>>
> > >>>>I will incorporate those changes today and test it.   I hope to
g=3D
et=3D20
> 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=20
> > >>>>>!!!!!!!!!!!!!!!!=3D
!!!
> :-)
> > >>>>>
> > >>>>>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=20
> > >>>>>>u=3D
se 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,=20
> > >>>>>>etc.=3D
..
> that
> > >>>>>>generates many errors when running wdk programs (wdkCache,=20
> > >>>>>>wdkQ=3D
uery,
> > >>>>>>wdkRecord,...).
> > >>>>>>
> > >>>>>>Because of this, we're having a hard work to debug the code=20
> > >>>>>>and=3D
 set
> it to work
> > >>>>>>with the Postgres schema. We would like to know if someone has

> > >>>>>>=3D
a WDK
> working
> > >>>>>>with GUS Postgres perfectly.
> > >>>>>>
> > >>>>>>Thanks a lot,
> > >>>>>>
> > >>>>>>Fabr=3DEDcio.
> > >>>>>>
> > >>>>>>--------------------------------------------------------------
> > >>>>>>-=3D
-
> > >>>>>>This message was sent using IMP, the Internet Messaging=20
> > >>>>>>Program=3D
.
> > >>>>>>_______________________________________________
> > >>>>>>WDKDev mailing list
> > >>>>>>WD...@pc...
> > >>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >
> > >
> > >
> > >
> >=3D20
>=3D20
>=3D20
> --=3D20
> Thiago Seito Satake
> !! Tenha um bom dia !!
> Tel: (041) 990-55422
>=3D20
> _______________________________________________
> WDKDev mailing list
> WD...@pc...
> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>=3D20

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

--__--__--

Message: 3
Date: Mon, 8 Aug 2005 11:02:52 -0400 (EDT)
From: "Y. Thomas Gan" <yon...@pc...>
To: Thiago Satake <ma...@gm...>
cc: Steve Fischer <sfi...@pc...>,
        gus...@li..., wd...@pc...
Subject: Re: [GUSDEV] Re: [WDKDEV] WDK with Postgres?

  This message is in MIME format.  The first part should be readable
text,
  while the remaining parts are likely unreadable without MIME-aware
tools.

--2074436185-2060476898-1123513372=3D:14783
Content-Type: TEXT/PLAIN; charset=3DISO-8859-1; format=3Dflowed
Content-Transfer-Encoding: QUOTED-PRINTABLE

Hi Thiago,
Usually you should get stable released versions from the download=3D20
site. Steve and I have beening working on the svn trunk and we have
more=3D20 work to do before we release version 1.6 - sorry for the
inconvenience.=3D20 Please look out for release announcement soon.

-Thomas

On Mon, 8 Aug 2005, Thiago Satake wrote:

> 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  ,=20
> usertest.query_result_4 where a.na_sequence_id =3D3D
> usertest.query_result_4.na_sequence_id                 and a.taxon_id
> =3D3D tn.taxon_id and usertest.query_result_4.result_index_column =
>=3D3D 1

> an=3D
d
> usertest.query_result_4.result_index_column <=3D3D 20 order by=20
> usertest.query_result_4.result_index_column ) ORDER BY=20
> 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=20
>>>> 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=20
>>>>> driver to postgres.
>>>>> 2- we had to change  testTables files to change the numeric data=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=20
>>>>> 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=20
>>>>> 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=20
>>>>>> put =3D
much
>>>>>> effort into ensuring the complete functioning of the postgres=20
>>>>>> module=3D
=3D2E
>>>>>>
>>>>>> however, a student did successfully use postgres with the wdk. =20
>>>>>> he m=3D
ade
>>>>>> improvements in the PostgreSQL.java file, and a small change in=20
>>>>>> ResultFactory that are not yet in the release.
>>>>>>
>>>>>> I will incorporate those changes today and test it.   I hope to
get =3D
 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=20
>>>>>>> !!!!!!!!!!!!!!!!!!!=3D
 :-)
>>>>>>>
>>>>>>> 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=20
>>>>>>>> use =3D
WDK 1.5 to
>>>>>>>> explore the postgres schema. We noticed that the WDK code is=20
>>>>>>>> manip=3D
ulating an
>>>>>>>> Oracle database, due to some type columns, sequence using,=20
>>>>>>>> etc... =3D
that
>>>>>>>> generates many errors when running wdk programs (wdkCache,=20
>>>>>>>> wdkQuer=3D
y,
>>>>>>>> wdkRecord,...).
>>>>>>>>
>>>>>>>> Because of this, we're having a hard work to debug the code and

>>>>>>>> se=3D
t it to work
>>>>>>>> with the Postgres schema. We would like to know if someone has=20
>>>>>>>> a W=3D
DK working
>>>>>>>> with GUS Postgres perfectly.
>>>>>>>>
>>>>>>>> Thanks a lot,
>>>>>>>>
>>>>>>>> Fabr=3DEDcio.
>>>>>>>>
>>>>>>>> ---------------------------------------------------------------
>>>>>>>> - This message was sent using IMP, the Internet Messaging=20
>>>>>>>> Program.
>>>>>>>> _______________________________________________
>>>>>>>> WDKDev mailing list
>>>>>>>> WD...@pc...
>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>>>
>>
>
>
> --=3D20
> Thiago Seito Satake
> !! Tenha um bom dia !!
> Tel: (041) 990-55422
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO=20
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20
> Practic=3D
es
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing=20
> & Q=3D
A
> Security * Process Improvement & Measurement *=20
> http://www.sqe.com/bsce5sf=20
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
--2074436185-2060476898-1123513372=3D:14783--

--__--__--

Message: 4
Date: Mon, 8 Aug 2005 12:14:24 -0300
From: Thiago Satake <ma...@gm...>
To: "Y. Thomas Gan" <yon...@pc...>
Subject: Re: [GUSDEV] Re: [WDKDEV] WDK with Postgres?
Cc: Steve Fischer <sfi...@pc...>,
gus...@li...,=20
	wd...@pc...

:-)

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 =20
>site. Steve and I have beening working on the svn trunk and we have=20
>more  work to do before we release version 1.6 - sorry for the
inconvenience.
> Please look out for release announcement soon.
>=3D20
> -Thomas
>=3D20
>=3D20
>=3D20
> On Mon, 8 Aug 2005, Thiago Satake wrote:
>=3D20
> > 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
> > 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  ,=20
> > usertest.query_result_4 where a.na_sequence_id =3D3D
> > usertest.query_result_4.na_sequence_id                 and
a.taxon_id
> > =3D3D tn.taxon_id and usertest.query_result_4.result_index_column =
>=3D3D

> > 1 =3D
and
> > usertest.query_result_4.result_index_column <=3D3D 20 order by=20
> > usertest.query_result_4.result_index_column ) ORDER BY=20
> > 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.
=3D
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=20
> >> 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=20
> >>>> provided =3D
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=3D
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=20
> >>>>> driv=3D
er
> >>>>> to postgres.
> >>>>> 2- we had to change  testTables files to change the numeric data

> >>>>> ty=3D
pe
> >>>>> ( number > numeric )
> >>>>> 3- and now we are changing  java file to adapt to Postgres (=20
> >>>>> sequen=3D
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=20
> >>>>> org.apache.struts.action.RequestProcessor
> >>>>> processException
> >>>>> WARNING: Unhandled Exception thrown: class=20
> >>>>> 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=3D
t much
> >>>>>> effort into ensuring the complete functioning of the postgres=20
> >>>>>> modu=3D
le.
> >>>>>>
> >>>>>> however, a student did successfully use postgres with the wdk.

> >>>>>> he=3D
 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=3D
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=20
> >>>>>>> !!!!!!!!!!!!!!!!!=3D
!! :-)
> >>>>>>>
> >>>>>>> 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=3D
e WDK 1.5 to
> >>>>>>>> explore the postgres schema. We noticed that the WDK code is=20
> >>>>>>>> man=3D
ipulating an
> >>>>>>>> Oracle database, due to some type columns, sequence using,=20
> >>>>>>>> etc..=3D
. that
> >>>>>>>> generates many errors when running wdk programs (wdkCache,=20
> >>>>>>>> wdkQu=3D
ery,
> >>>>>>>> wdkRecord,...).
> >>>>>>>>
> >>>>>>>> Because of this, we're having a hard work to debug the code=20
> >>>>>>>> and =3D
set it to work
> >>>>>>>> with the Postgres schema. We would like to know if someone=20
> >>>>>>>> has a=3D
 WDK working
> >>>>>>>> with GUS Postgres perfectly.
> >>>>>>>>
> >>>>>>>> Thanks a lot,
> >>>>>>>>
> >>>>>>>> Fabr=3DEDcio.
> >>>>>>>>
> >>>>>>>> -------------------------------------------------------------
> >>>>>>>> --- This message was sent using IMP, the Internet Messaging=20
> >>>>>>>> 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
> >
> >
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference & EXPO=20
> > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20
> > Pract=3D
ices
> > Agile & Plan-Driven Development * Managing Projects & Teams *=20
> > Testing &=3D
 QA
> > Security * Process Improvement & Measurement *=20
> > http://www.sqe.com/bsce5=3D
sf
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>=3D20

--=3D20
Thiago Seito Satake
!! Tenha um bom dia !!
Tel: (041) 990-55422

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