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

[Y. T. G. <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 more=20
work to do before we release version 1.6 - sorry for the inconvenience.=20
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
>  , 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 an=
d
> 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 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 =
much
>>>>>> effort into ensuring the complete functioning of the postgres module=
=2E
>>>>>>
>>>>>> however, a student did successfully use postgres with the wdk.  he m=
ade
>>>>>> 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 manip=
ulating an
>>>>>>>> Oracle database, due to some type columns, sequence using, etc... =
that
>>>>>>>> generates many errors when running wdk programs (wdkCache, wdkQuer=
y,
>>>>>>>> wdkRecord,...).
>>>>>>>>
>>>>>>>> Because of this, we're having a hard work to debug the code and se=
t it to work
>>>>>>>> with the Postgres schema. We would like to know if someone has a W=
DK 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
> Thiago Seito Satake
> !! Tenha um bom dia !!
> Tel: (041) 990-55422
>
>
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