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

[Y. T. G. <yon...@pc...>]

Another update on the status of release 1.6:

With tremendous efforts from Steve we were able to get wdkSanityTest=20
(including tests for all Questions/Summaries, Queries, and Records)=20
passing against both oracle and postgres late last night.

But we are at the last of the last hurdles: the toySite works fine=20
with Oracle but does not come up with postgres (as Thiago reported=20
earlier). See bug 114: toySite throws 'No suitable driver' SQLException at=
=20
start up against postgres  (oracle is ok) although sanityTest succeeds=20
(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=20
> features, including an improved Sanity Test.  the test will now test all=
=20
> Questions in the model XML file as well as all Queries and all Records.=
=20
> this was needed to thoroughly test postgres.
>
> we're working hard to get this release out...
>
> steve
>
> fab...@de... wrote:
>
>> Thiago,
>>=20
>> I'm having this problem too. In wdkSummary it seems that the schema 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
>>> 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:=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"
>>>=20
>>>=20
>>> :-(
>>>=20
>>>=20
>>> Thanks
>>>=20
>>> Thiago Seito Satake
>>>=20
>>>=20
>>>=20
>>>=20
>>>=20
>>>=20
>>> 2005/8/5, Steve Fischer <sfi...@pc...>:
>>>=20
>>>> 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
>>>>=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
>>>>>> 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.
>>>>>>=20
>>>>>> i have a lot of meetings today, so in a little while i'll need to st=
op
>>>>>> till tonight
>>>>>>=20
>>>>>> steve
>>>>>>=20
>>>>>> Thiago Satake wrote:
>>>>>>=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 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 )
>>>>>>>=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.RequestProcessor
>>>>>>> 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
>>>>>>>> Folks-
>>>>>>>>=20
>>>>>>>> the production uses of wdk so far are in oracle, so we have not pu=
t
>>>>>>>>=20
>>> much
>>>=20
>>>>>>>> effort into ensuring the complete functioning of the postgres modu=
le.
>>>>>>>>=20
>>>>>>>> however, a student did successfully use postgres with the wdk.  he
>>>>>>>>=20
>>> made
>>>=20
>>>>>>>> improvements in the PostgreSQL.java file, and a small change in
>>>>>>>> ResultFactory that are not yet in the release.
>>>>>>>>=20
>>>>>>>> I will incorporate those changes today and test it.   I hope to ge=
t=20
>>> you
>>>=20
>>>>>>>> a patch by tomorrow.
>>>>>>>>=20
>>>>>>>> can you describe briefly the problems?
>>>>>>>>=20
>>>>>>>> steve
>>>>>>>>=20
>>>>>>>> Thiago Satake wrote:
>>>>>>>>=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
>>>>>>>>> Thanks .............
>>>>>>>>>=20
>>>>>>>>> Thiago Seito Satake
>>>>>>>>>=20
>>>>>>>>>=20
>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>:
>>>>>>>>>=20
>>>>>>>>>=20
>>>>>>>>>=20
>>>>>>>>>=20
>>>>>>>>>=20
>>>>>>>>>=20
>>>>>>>>>=20
>>>>>>>>>> Hello all,
>>>>>>>>>>=20
>>>>>>>>>> We have a GUS installation running ok and now we're trying to us=
e=20
>>>>>>>>>> WDK
>>>>>>>>>>=20
>>> 1.5 to
>>>=20
>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is
>>>>>>>>>>=20
>>> manipulating an
>>>=20
>>>>>>>>>> Oracle database, due to some type columns, sequence using, etc..=
=2E
>>>>>>>>>>=20
>>> that
>>>=20
>>>>>>>>>> generates many errors when running wdk programs (wdkCache,=20
>>>>>>>>>> wdkQuery,
>>>>>>>>>> wdkRecord,...).
>>>>>>>>>>=20
>>>>>>>>>> Because of this, we're having a hard work to debug the code and =
set
>>>>>>>>>>=20
>>> it to work
>>>=20
>>>>>>>>>> with the Postgres schema. We would like to know if someone has a=
=20
>>>>>>>>>> WDK
>>>>>>>>>>=20
>>> working
>>>=20
>>>>>>>>>> with GUS Postgres perfectly.
>>>>>>>>>>=20
>>>>>>>>>> Thanks a lot,
>>>>>>>>>>=20
>>>>>>>>>> Fabr=EDcio.
>>>>>>>>>>=20
>>>>>>>>>> ----------------------------------------------------------------
>>>>>>>>>> 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
>>>>>>>>>>=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
>
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