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Re: [WDKDEV] [GUSDEV] Re: WDK with Postgres?
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From: Steve F. <sfi...@pc...> - 2005-08-10 12:52:03
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is it possibly caused by my having commented out this line in=20
PostegeSQL.java:
=20
// DriverManager.registerDriver(new org.postgresql.Driver(=
));
it didn't seem to make any difference when running outside of tomcat (so=20
i took it out).
steve
Thiago Satake wrote:
>We updated WDK release with postgres and WDKToySite Works well.
> =20
>
>>See bug 114: toySite throws 'No suitable driver' SQLException
>> =20
>>
>It seems to me that is a tomcat problem,I belive that you must set
>$CLASSPATH adding jdbc driver for postgres into
>$CATALINA_HOME/bin/setclass.sh.....
>as showed bellow:
> =20
>
>># Set standard CLASSPATH
>>CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.=
jar
>> =20
>>
>
>
>Thanks
>
>
>
>Thiago Seito Stake
>
>
>
>
>2005/8/10, Y. Thomas Gan <yon...@pc...>:
> =20
>
>>Another update on the status of release 1.6:
>>
>>With tremendous efforts from Steve we were able to get wdkSanityTest
>>(including tests for all Questions/Summaries, Queries, and Records)
>>passing against both oracle and postgres late last night.
>>
>>But we are at the last of the last hurdles: the toySite works fine
>>with Oracle but does not come up with postgres (as Thiago reported
>>earlier). See bug 114: toySite throws 'No suitable driver' SQLException=
at
>>start up against postgres (oracle is ok) although sanityTest succeeds
>>(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:
>>
>> =20
>>
>>>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
>>>features, including an improved Sanity Test. the test will now test a=
ll
>>>Questions in the model XML file as well as all Queries and all Records.
>>>this was needed to thoroughly test postgres.
>>>
>>>we're working hard to get this release out...
>>>
>>>steve
>>>
>>>fab...@de... wrote:
>>>
>>> =20
>>>
>>>>Thiago,
>>>> =20
>>>>
>
>
> =20
>
>>>>I'm having this problem too. In wdkSummary it seems that the schema n=
ame 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,
>>>>
>>>>Fabr=EDcio.
>>>>
>>>>
>>>>Citando Thiago Satake <ma...@gm...>:
>>>>
>>>>
>>>> =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_i=
d
>>>>>=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...>:
>>>>>
>>>>> =20
>>>>>
>>>>>>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:
>>>>>>
>>>>>>
>>>>>> =20
>>>>>>
>>>>>>>Thanks a lot,
>>>>>>>
>>>>>>>Can I help you with something ?
>>>>>>>
>>>>>>>Thiago Seito Satake
>>>>>>>
>>>>>>>2005/8/4, Steve Fischer <sfi...@pc...>:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> =20
>>>>>>>
>>>>>>>>ok, sorry about this. yes, those all of 1,2,3 i think are provid=
ed 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:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> =20
>>>>>>>>
>>>>>>>>>Ok ........
>>>>>>>>>
>>>>>>>>>We can list some problems:
>>>>>>>>>1- we had to change all of perl wdk file ... to set te correct d=
river
>>>>>>>>>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 ( seq=
uence
>>>>>>>>>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.RequestProcesso=
r
>>>>>>>>>processException
>>>>>>>>>WARNING: Unhandled Exception thrown: class
>>>>>>>>>java.lang.ArrayIndexOutOfBoundsException
>>>>>>>>>
>>>>>>>>>and other problems .............
>>>>>>>>>
>>>>>>>>>Thanks for the help :-)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>2005/8/4, Steve Fischer <sfi...@pc...>:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> =20
>>>>>>>>>
>>>>>>>>>>Folks-
>>>>>>>>>>
>>>>>>>>>>the production uses of wdk so far are in oracle, so we have not=
put
>>>>>>>>>>
>>>>>>>>>> =20
>>>>>>>>>>
>>>>>much
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>effort into ensuring the complete functioning of the postgres m=
odule.
>>>>>>>>>>
>>>>>>>>>>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.
>>>>>>>>>>
>>>>>>>>>>I will incorporate those changes today and test it. I hope to=
get
>>>>>>>>>> =20
>>>>>>>>>>
>>>>>you
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>a patch by tomorrow.
>>>>>>>>>>
>>>>>>>>>>can you describe briefly the problems?
>>>>>>>>>>
>>>>>>>>>>steve
>>>>>>>>>>
>>>>>>>>>>Thiago Satake wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> =20
>>>>>>>>>>
>>>>>>>>>>>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
>>>>>>>>>>>
>>>>>:-)
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>Thanks .............
>>>>>>>>>>>
>>>>>>>>>>>Thiago Seito Satake
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>2005/8/4, fab...@de... <fab...@de...>:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> =20
>>>>>>>>>>>
>>>>>>>>>>>>Hello all,
>>>>>>>>>>>>
>>>>>>>>>>>>We have a GUS installation running ok and now we're trying to=
use
>>>>>>>>>>>>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, et=
c...
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>that
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>generates many errors when running wdk programs (wdkCache,
>>>>>>>>>>>>wdkQuery,
>>>>>>>>>>>>wdkRecord,...).
>>>>>>>>>>>>
>>>>>>>>>>>>Because of this, we're having a hard work to debug the code a=
nd set
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>it to work
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>with the Postgres schema. We would like to know if someone ha=
s a
>>>>>>>>>>>>WDK
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>working
>>>>>
>>>>> =20
>>>>>
>>>>>>>>>>>>with GUS Postgres perfectly.
>>>>>>>>>>>>
>>>>>>>>>>>>Thanks a lot,
>>>>>>>>>>>>
>>>>>>>>>>>>Fabr=EDcio.
>>>>>>>>>>>>
>>>>>>>>>>>>-------------------------------------------------------------=
---
>>>>>>>>>>>>This message was sent using IMP, the Internet Messaging Progr=
am.
>>>>>>>>>>>>_______________________________________________
>>>>>>>>>>>>WDKDev mailing list
>>>>>>>>>>>>WD...@pc...
>>>>>>>>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> =20
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> =20
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> =20
>>>>>>>>>
>>>>>>>
>>>>>>> =20
>>>>>>>
>>>>>--
>>>>>Thiago Seito Satake
>>>>>!! Tenha um bom dia !!
>>>>>Tel: (041) 990-55422
>>>>>
>>>>>_______________________________________________
>>>>>WDKDev mailing list
>>>>>WD...@pc...
>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev
>>>>>
>>>>>
>>>>> =20
>>>>>
>>>>
>>>>
>>>>----------------------------------------------------------------
>>>>This message was sent using IMP, the Internet Messaging Program.
>>>>
>>>> =20
>>>>
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>>> =20
>>>
>
>
>--
>Thiago Seito Satake
>!! Tenha um bom dia !!
>Tel: (041) 990-55422
>
>
> =20
>
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