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From: <fab...@de...> - 2005-08-04 13:02:55
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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 manipulating= an Oracle database, due to some type columns, sequence using, etc... that 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 WDK work= ing with GUS Postgres perfectly.=20 Thanks a lot, Fabr=EDcio.=20 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
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From: Thiago S. <ma...@gm...> - 2005-08-04 13:18:29
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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 !!!!!!!!!!!!!!!!!!! :-) Thanks ............. Thiago Seito Satake=20 =20 2005/8/4, fab...@de... <fab...@de...>: > Hello all, >=20 > 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 manipulating= an > Oracle database, due to some type columns, sequence using, etc... that > generates many errors when running wdk programs (wdkCache, wdkQuery, > wdkRecord,...). >=20 > 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 WDK work= ing > 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 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
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From: Steve F. <sfi...@pc...> - 2005-08-04 14:16:39
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Folks- the production uses of wdk so far are in oracle, so we have not put much=20 effort into ensuring the complete functioning of the postgres module. however, a student did successfully use postgres with the wdk. he made=20 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 you=20 a patch by tomorrow. can you describe briefly the problems? steve Thiago Satake wrote: >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 !!!!!!!!!!!!!!!!!!! :-) > >Thanks ............. > >Thiago Seito Satake=20 > =20 > >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 1= .5 to >>explore the postgres schema. We noticed that the WDK code is manipulati= ng an >>Oracle database, due to some type columns, sequence using, etc... that >>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 WDK wo= rking >>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 > |
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From: Thiago S. <ma...@gm...> - 2005-08-04 14:35:37
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---------- Forwarded message ---------- From: Thiago Satake <ma...@gm...> Date: 04/08/2005 11:34 Subject: Re: [WDKDEV] WDK with Postgres? To: Steve Fischer <sfi...@pc...> 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. > > however, a student did successfully use postgres with the wdk. he 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 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 manipulati= ng an > >>Oracle database, due to some type columns, sequence using, etc... that > >>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 WDK wo= rking > >>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 > >> > >> > >> > > > > > > > > > -- Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 --=20 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
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From: Y. T. G. <yg...@pc...> - 2005-08-04 15:14:59
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Hi Thiago: For problem 1, we can provide a command line platform switch or somehow config. Problem 2 should not have been a problem as TestDBManager does a platform specific replacement of the testTables files before loading the data (well it is possible that there is a bug though). As for WDKToySite, you should not bother setting it up until all other model problems are addressed. Thomas > -----Original Message----- > From: gus...@li...=20 > [mailto:gus...@li...] On Behalf=20 > Of Thiago Satake > Sent: Thursday, August 04, 2005 9:35 AM > To: gus...@li...; wd...@pc... > Subject: [GUSDEV] Fwd: [WDKDEV] WDK with Postgres? >=20 >=20 > ---------- Forwarded message ---------- > From: Thiago Satake <ma...@gm...> > Date: 04/08/2005 11:34 > Subject: Re: [WDKDEV] WDK with Postgres? > To: Steve Fischer <sfi...@pc...> >=20 >=20 > Ok ........ >=20 > We can list some problems: > 1- we had to change all of perl wdk file ... to set te=20 > correct driver to postgres. > 2- we had to change testTables files to change the numeric=20 > data type ( number > numeric ) > 3- and now we are changing java file to adapt to Postgres (=20 > sequence 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=20 > java.lang.ArrayIndexOutOfBoundsException >=20 > and other problems ............. >=20 > Thanks for the help :-) >=20 >=20 >=20 >=20 > 2005/8/4, Steve Fischer <sfi...@pc...>: > > Folks- > > > > the production uses of wdk so far are in oracle, so we have not put=20 > > much effort into ensuring the complete functioning of the postgres=20 > > module. > > > > however, a student did successfully use postgres with the wdk. he=20 > > made improvements in the PostgreSQL.java file, and a small=20 > change in=20 > > ResultFactory that are not yet in the release. > > > > I will incorporate those changes today and test it. I=20 > 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=20 > !!!!!!!!!!!!!!!!!!!=20 > > >:-) > > > > > >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=20 > > >>WDK 1.5 to explore the postgres schema. We noticed that=20 > the WDK code=20 > > >>is manipulating an Oracle database, due to some type columns,=20 > > >>sequence using, etc... that generates many errors when=20 > running wdk=20 > > >>programs (wdkCache, wdkQuery, wdkRecord,...). > > >> > > >>Because of this, we're having a hard work to debug the=20 > code and set=20 > > >>it to work with the Postgres schema. We would like to know if=20 > > >>someone has a WDK working with GUS Postgres perfectly. > > >> > > >>Thanks a lot, > > >> > > >>Fabr=EDcio. > > >> > > >>---------------------------------------------------------------- > > >>This message was sent using IMP, the Internet Messaging Program.=20 > > >>_______________________________________________ > > >>WDKDev mailing list > > >>WD...@pc...=20 > > >>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > > >> > > >> > > >> > > > > > > > > > > > > > > >=20 >=20 > -- > Thiago Seito Satake > !! Tenha um bom dia !! > Tel: (041) 990-55422 >=20 >=20 > --=20 > Thiago Seito Satake > !! Tenha um bom dia !! > Tel: (041) 990-55422 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference &=20 > EXPO September 19-22, 2005 * San Francisco, CA * Development=20 > Lifecycle Practices Agile & Plan-Driven Development *=20 > Managing Projects & Teams * Testing & QA Security * Process=20 > Improvement & Measurement * http://www.sqe.com/bsce5sf=20 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >=20 |
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From: Steve F. <sfi...@pc...> - 2005-08-04 16:15:39
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problem 1: i am going to fix it now. Y. Thomas Gan wrote: >Hi Thiago: >For problem 1, we can provide a command line platform switch or somehow >config. >Problem 2 should not have been a problem as TestDBManager does a >platform specific >replacement of the testTables files before loading the data (well it is >possible >that there is a bug though). > >As for WDKToySite, you should not bother setting it up until all other >model problems are addressed. > >Thomas > > =20 > >>-----Original Message----- >>From: gus...@li...=20 >>[mailto:gus...@li...] On Behalf=20 >>Of Thiago Satake >>Sent: Thursday, August 04, 2005 9:35 AM >>To: gus...@li...; wd...@pc... >>Subject: [GUSDEV] Fwd: [WDKDEV] WDK with Postgres? >> >> >>---------- Forwarded message ---------- >>From: Thiago Satake <ma...@gm...> >>Date: 04/08/2005 11:34 >>Subject: Re: [WDKDEV] WDK with Postgres? >>To: Steve Fischer <sfi...@pc...> >> >> >>Ok ........ >> >>We can list some problems: >>1- we had to change all of perl wdk file ... to set te=20 >>correct driver to postgres. >>2- we had to change testTables files to change the numeric=20 >>data type ( number > numeric ) >>3- and now we are changing java file to adapt to Postgres (=20 >>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=20 >>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 effort into ensuring the complete functioning of the postgres=20 >>>module. >>> >>>however, a student did successfully use postgres with the wdk. he=20 >>>made improvements in the PostgreSQL.java file, and a small=20 >>> =20 >>> >>change in=20 >> =20 >> >>>ResultFactory that are not yet in the release. >>> >>>I will incorporate those changes today and test it. I=20 >>> =20 >>> >>hope to get 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 >>>> >>!!!!!!!!!!!!!!!!!!!=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=20 >>>>>WDK 1.5 to explore the postgres schema. We noticed that=20 >>>>> =20 >>>>> >>the WDK code=20 >> =20 >> >>>>>is manipulating an Oracle database, due to some type columns,=20 >>>>>sequence using, etc... that generates many errors when=20 >>>>> =20 >>>>> >>running wdk=20 >> =20 >> >>>>>programs (wdkCache, wdkQuery, wdkRecord,...). >>>>> >>>>>Because of this, we're having a hard work to debug the=20 >>>>> =20 >>>>> >>code and set=20 >> =20 >> >>>>>it to work with the Postgres schema. We would like to know if=20 >>>>>someone has a WDK working with GUS Postgres perfectly. >>>>> >>>>>Thanks a lot, >>>>> >>>>>Fabr=EDcio. >>>>> >>>>>---------------------------------------------------------------- >>>>>This message was sent using IMP, the Internet Messaging Program.=20 >>>>>_______________________________________________ >>>>>WDKDev mailing list >>>>>WD...@pc...=20 >>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>> >>>>> >>>>> >>>>> =20 >>>>> >>>> >>>> >>>> =20 >>>> >>-- >>Thiago Seito Satake >>!! Tenha um bom dia !! >>Tel: (041) 990-55422 >> >> >>--=20 >>Thiago Seito Satake >>!! Tenha um bom dia !! >>Tel: (041) 990-55422 >> >> >>------------------------------------------------------- >>SF.Net email is Sponsored by the Better Software Conference &=20 >>EXPO September 19-22, 2005 * San Francisco, CA * Development=20 >>Lifecycle Practices Agile & Plan-Driven Development *=20 >>Managing Projects & Teams * Testing & QA Security * Process=20 >>Improvement & Measurement * http://www.sqe.com/bsce5sf=20 >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> =20 >> > > >_______________________________________________ >WDKDev mailing list >WD...@pc... >https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > =20 > |
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From: Steve F. <sfi...@pc...> - 2005-08-05 13:46:21
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foks- i have upgraded the wdk code base (and the SVN repostitory) to properly=20 work with postgres. we'll get a release out today. steve Y. Thomas Gan wrote: >Hi Thiago: >For problem 1, we can provide a command line platform switch or somehow >config. >Problem 2 should not have been a problem as TestDBManager does a >platform specific >replacement of the testTables files before loading the data (well it is >possible >that there is a bug though). > >As for WDKToySite, you should not bother setting it up until all other >model problems are addressed. > >Thomas > > =20 > >>-----Original Message----- >>From: gus...@li...=20 >>[mailto:gus...@li...] On Behalf=20 >>Of Thiago Satake >>Sent: Thursday, August 04, 2005 9:35 AM >>To: gus...@li...; wd...@pc... >>Subject: [GUSDEV] Fwd: [WDKDEV] WDK with Postgres? >> >> >>---------- Forwarded message ---------- >>From: Thiago Satake <ma...@gm...> >>Date: 04/08/2005 11:34 >>Subject: Re: [WDKDEV] WDK with Postgres? >>To: Steve Fischer <sfi...@pc...> >> >> >>Ok ........ >> >>We can list some problems: >>1- we had to change all of perl wdk file ... to set te=20 >>correct driver to postgres. >>2- we had to change testTables files to change the numeric=20 >>data type ( number > numeric ) >>3- and now we are changing java file to adapt to Postgres (=20 >>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=20 >>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 effort into ensuring the complete functioning of the postgres=20 >>>module. >>> >>>however, a student did successfully use postgres with the wdk. he=20 >>>made improvements in the PostgreSQL.java file, and a small=20 >>> =20 >>> >>change in=20 >> =20 >> >>>ResultFactory that are not yet in the release. >>> >>>I will incorporate those changes today and test it. I=20 >>> =20 >>> >>hope to get 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 >>>> >>!!!!!!!!!!!!!!!!!!!=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=20 >>>>>WDK 1.5 to explore the postgres schema. We noticed that=20 >>>>> =20 >>>>> >>the WDK code=20 >> =20 >> >>>>>is manipulating an Oracle database, due to some type columns,=20 >>>>>sequence using, etc... that generates many errors when=20 >>>>> =20 >>>>> >>running wdk=20 >> =20 >> >>>>>programs (wdkCache, wdkQuery, wdkRecord,...). >>>>> >>>>>Because of this, we're having a hard work to debug the=20 >>>>> =20 >>>>> >>code and set=20 >> =20 >> >>>>>it to work with the Postgres schema. We would like to know if=20 >>>>>someone has a WDK working with GUS Postgres perfectly. >>>>> >>>>>Thanks a lot, >>>>> >>>>>Fabr=EDcio. >>>>> >>>>>---------------------------------------------------------------- >>>>>This message was sent using IMP, the Internet Messaging Program.=20 >>>>>_______________________________________________ >>>>>WDKDev mailing list >>>>>WD...@pc...=20 >>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>> >>>>> >>>>> >>>>> =20 >>>>> >>>> >>>> >>>> =20 >>>> >>-- >>Thiago Seito Satake >>!! Tenha um bom dia !! >>Tel: (041) 990-55422 >> >> >>--=20 >>Thiago Seito Satake >>!! Tenha um bom dia !! >>Tel: (041) 990-55422 >> >> >>------------------------------------------------------- >>SF.Net email is Sponsored by the Better Software Conference &=20 >>EXPO September 19-22, 2005 * San Francisco, CA * Development=20 >>Lifecycle Practices Agile & Plan-Driven Development *=20 >>Managing Projects & Teams * Testing & QA Security * Process=20 >>Improvement & Measurement * http://www.sqe.com/bsce5sf=20 >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> =20 >> > > >_______________________________________________ >WDKDev mailing list >WD...@pc... >https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > =20 > |
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From: Thiago S. <ma...@gm...> - 2005-08-08 14:54:39
|
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
|
|
From: <fab...@de...> - 2005-08-08 15:02:59
|
Thiago, I'm having this problem too. In wdkSummary it seems that the schema name = 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, =20 Fabr=EDcio. Citando Thiago Satake <ma...@gm...>: > After downloaded WDK from SVN files=20 > 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 >=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...>: > > 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 s= 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 dri= ver > > >>>to postgres. > > >>>2- we had to change testTables files to change the numeric data t= ype > > >>>( number > numeric ) > > >>>3- and now we are changing java file to adapt to Postgres ( seque= 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 > > >>>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 p= ut > much > > >>>>effort into ensuring the complete functioning of the postgres mod= ule. > > >>>> > > >>>>however, a student did successfully use postgres with the wdk. h= e > 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 g= et=20 > 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 u= 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, etc.= .. > that > > >>>>>>generates many errors when running wdk programs (wdkCache, wdkQ= uery, > > >>>>>>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 WDK > 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 >=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 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
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From: Steve F. <sfi...@pc...> - 2005-08-09 22:13:00
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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, > >I'm having this problem too. In wdkSummary it seems that the schema name= 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, >=20 >Fabr=EDcio. > > >Citando Thiago Satake <ma...@gm...>: > > =20 > >>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...>: >> =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 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 st= op >>>>>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 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 ) >>>>>> >>>>>>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...>: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> =20 >>>>>> >>>>>>>Folks- >>>>>>> >>>>>>>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. >>>>>>> >>>>>>>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 ge= t=20 >>>>>>> =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 us= e 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... >>>>>>>>> =20 >>>>>>>>> >>that >> =20 >> >>>>>>>>>generates many errors when running wdk programs (wdkCache, wdkQu= ery, >>>>>>>>>wdkRecord,...). >>>>>>>>> >>>>>>>>>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= WDK >>>>>>>>> =20 >>>>>>>>> >>working >> =20 >> >>>>>>>>>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 >>>>>>>> >>>>>> >>>>>> >>>>>> =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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From: Alberto D. <da...@io...> - 2005-08-09 17:54:52
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Great Steve ! I have a question for you, looks like NCBI is (has ?) moving to XML format... since I have been unable to find the standard GenBank format available at NCBI site: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/XML/ncbixml.txt Does GPBarser deal with any of those XML formats from Genbank ? Thanks, Alberto On Tue, 2005-08-09 at 11:37 -0400, Steve Fischer wrote: > just want to give an update on our progress. >=20 > we are planning a release today or tomorrow. >=20 > 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 >=20 > this was needed to thoroughly test postgres. >=20 > we're working hard to get this release out... >=20 > steve >=20 > fab...@de... wrote: >=20 > >Thiago, > > > >I'm having this problem too. In wdkSummary it seems that the schema name= 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, > >=20 > >Fabr=C3=ADcio. > > > > > >Citando Thiago Satake <ma...@gm...>: > > > > =20 > > > >>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...>: > >> =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 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 st= op > >>>>>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 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 ) > >>>>>> > >>>>>>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...>: > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> =20 > >>>>>> > >>>>>>>Folks- > >>>>>>> > >>>>>>>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. > >>>>>>> > >>>>>>>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 ge= t=20 > >>>>>>> =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 us= e 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..= . > >>>>>>>>> =20 > >>>>>>>>> > >>that > >> =20 > >> > >>>>>>>>>generates many errors when running wdk programs (wdkCache, wdkQu= ery, > >>>>>>>>>wdkRecord,...). > >>>>>>>>> > >>>>>>>>>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= WDK > >>>>>>>>> =20 > >>>>>>>>> > >>working > >> =20 > >> > >>>>>>>>>with GUS Postgres perfectly. > >>>>>>>>> > >>>>>>>>>Thanks a lot, > >>>>>>>>> > >>>>>>>>>Fabr=C3=ADcio. > >>>>>>>>> > >>>>>>>>>---------------------------------------------------------------- > >>>>>>>>>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 > >>Thiago Seito Satake > >>!! Tenha um bom dia !! > >>Tel: (041) 990-55422 > >> |
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From: Y. T. G. <yon...@pc...> - 2005-08-10 11:52:57
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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 > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Thiago S. <ma...@gm...> - 2005-08-10 12:39:12
|
We updated WDK release with postgres and WDKToySite Works well. >See bug 114: toySite throws 'No suitable driver' SQLException It seems to me that is a tomcat problem,I belive that you must set $CLASSPATH adding jdbc driver for postgres into $CATALINA_HOME/bin/setclass.sh..... as showed bellow: ># Set standard CLASSPATH >CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.jar Thanks Thiago Seito Stake 2005/8/10, Y. Thomas Gan <yon...@pc...>: > 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 a= t > 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: > > > 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 al= l > > 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: > > > >> Thiago, > >> > >> I'm having this problem too. In wdkSummary it seems that the schema na= me 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...>: > >> > >> > >>> 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 2= 0 > >>> -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 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- > >>>> > >>>> 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 provide= d 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 dr= iver > >>>>>>> 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 ( sequ= ence > >>>>>>> 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 mo= dule. > >>>>>>>> > >>>>>>>> however, a student did successfully use postgres with the wdk. = he > >>>>>>>> > >>> 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 = 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 > >>>>>>>>>> > >>> manipulating an > >>> > >>>>>>>>>> Oracle database, due to some type columns, sequence using, etc= ... > >>>>>>>>>> > >>> that > >>> > >>>>>>>>>> generates many errors when running wdk programs (wdkCache, > >>>>>>>>>> wdkQuery, > >>>>>>>>>> wdkRecord,...). > >>>>>>>>>> > >>>>>>>>>> Because of this, we're having a hard work to debug the code an= d set > >>>>>>>>>> > >>> it to work > >>> > >>>>>>>>>> with the Postgres schema. We would like to know if someone has= a > >>>>>>>>>> WDK > >>>>>>>>>> > >>> working > >>> > >>>>>>>>>> with GUS Postgres perfectly. > >>>>>>>>>> > >>>>>>>>>> Thanks a lot, > >>>>>>>>>> > >>>>>>>>>> Fabr=EDcio. > >>>>>>>>>> > >>>>>>>>>> --------------------------------------------------------------= -- > >>>>>>>>>> This message was sent using IMP, the Internet Messaging Progra= m. > >>>>>>>>>> _______________________________________________ > >>>>>>>>>> WDKDev mailing list > >>>>>>>>>> WD...@pc... > >>>>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>> > >>>>> > >>>>> > >>> -- > >>> Thiago Seito Satake > >>> !! Tenha um bom dia !! > >>> Tel: (041) 990-55422 > >>> > >>> _______________________________________________ > >>> WDKDev mailing list > >>> WD...@pc... > >>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > >>> > >>> > >> > >> > >> > >> > >> ---------------------------------------------------------------- > >> This message was sent using IMP, the Internet Messaging Program. > >> > > > > > > ------------------------------------------------------- > > SF.Net email is Sponsored by the Better Software Conference & EXPO > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract= ices > > Agile & Plan-Driven Development * Managing Projects & Teams * Testing &= QA > > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5= sf > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 --=20 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
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From: Y. T. G. <yon...@pc...> - 2005-08-08 15:03:00
|
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 > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Thiago S. <ma...@gm...> - 2005-08-08 15:14:32
|
:-) 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 > site. Steve and I have beening working on the svn trunk and we have more > work to do before we release version 1.6 - sorry for the inconvenience. > Please look out for release announcement soon. >=20 > -Thomas >=20 >=20 >=20 > On Mon, 8 Aug 2005, Thiago Satake wrote: >=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_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- > >> > >> 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 st= 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 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 ) > >>>>> > >>>>> 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 pu= t much > >>>>>> effort into ensuring the complete functioning of the postgres modu= le. > >>>>>> > >>>>>> however, a student did successfully use postgres with the wdk. he= 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= 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 !!!!!!!!!!!!!!!!!= !! :-) > >>>>>>> > >>>>>>> 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= e WDK 1.5 to > >>>>>>>> explore the postgres schema. We noticed that the WDK code is man= ipulating an > >>>>>>>> Oracle database, due to some type columns, sequence using, etc..= . that > >>>>>>>> generates many errors when running wdk programs (wdkCache, wdkQu= ery, > >>>>>>>> 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= WDK 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 > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>> > >>> > >>> > >>> > >> > > > > > > -- > > Thiago Seito Satake > > !! Tenha um bom dia !! > > Tel: (041) 990-55422 > > > > > > ------------------------------------------------------- > > SF.Net email is Sponsored by the Better Software Conference & EXPO > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract= ices > > Agile & Plan-Driven Development * Managing Projects & Teams * Testing &= QA > > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5= sf > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > >=20 --=20 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
|
From: Steve F. <sfi...@pc...> - 2005-08-10 12:52:03
|
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
>>>>
>>>-------------------------------------------------------
>>>SF.Net email is Sponsored by the Better Software Conference & EXPO
>>>September 19-22, 2005 * San Francisco, CA * Development Lifecycle Prac=
tices
>>>Agile & Plan-Driven Development * Managing Projects & Teams * Testing =
& QA
>>>Security * Process Improvement & Measurement * http://www.sqe.com/bsce=
5sf
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>> =20
>>>
>
>
>--
>Thiago Seito Satake
>!! Tenha um bom dia !!
>Tel: (041) 990-55422
>
>
> =20
>
|
|
From: Y. T. G. <yon...@pc...> - 2005-08-10 12:56:53
|
maybe we need to explicitly register pg drivers. i'll try it. we should=20 not have to add the driver jar to tomcat'S CLASSPATH. -thomas On Wed, 10 Aug 2005, Steve Fischer wrote: > is it possibly caused by my having commented out this line in > PostegeSQL.java: > > // DriverManager.registerDriver(new org.postgresql.Driver()= ); > > it didn't seem to make any difference when running outside of tomcat (so > i took it out). > > steve > > Thiago Satake wrote: > >> We updated WDK release with postgres and WDKToySite Works well. >> >> >>> See bug 114: toySite throws 'No suitable driver' SQLException >>> >>> >> It seems to me that is a tomcat problem,I belive that you must set >> $CLASSPATH adding jdbc driver for postgres into >> $CATALINA_HOME/bin/setclass.sh..... >> as showed bellow: >> >> >>> # Set standard CLASSPATH >>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.= jar >>> >>> >> >> >> Thanks >> >> >> >> Thiago Seito Stake >> >> >> >> >> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >> >> >>> 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: >>> >>> >>> >>>> 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= =2E >>>> this was needed to thoroughly test postgres. >>>> >>>> we're working hard to get this release out... >>>> >>>> steve >>>> >>>> fab...@de... wrote: >>>> >>>> >>>> >>>>> Thiago, >>>>> >>>>> >> >> >> >> >>>>> 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...>: >>>>> >>>>> >>>>> >>>>> >>>>>> 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...>: >>>>>> >>>>>> >>>>>> >>>>>>> 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 provid= ed by >>>>>>>>> the student's fixes. i am starting now to look at them and merge= =2E >>>>>>>>> >>>>>>>>> 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 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...>: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> 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 m= odule. >>>>>>>>>>> >>>>>>>>>>> however, a student did successfully use postgres with the wdk. = he >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>> 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= 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 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> manipulating an >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> Oracle database, due to some type columns, sequence using, et= c... >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> that >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> 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 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> it to work >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> with the Postgres schema. We would like to know if someone ha= s a >>>>>>>>>>>>> WDK >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>> working >>>>>> >>>>>> >>>>>> >>>>>>>>>>>>> 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 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> -- >>>>>> Thiago Seito Satake >>>>>> !! Tenha um bom dia !! >>>>>> Tel: (041) 990-55422 >>>>>> >>>>>> _______________________________________________ >>>>>> WDKDev mailing list >>>>>> WD...@pc... >>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> ---------------------------------------------------------------- >>>>> This message was sent using IMP, the Internet Messaging Program. >>>>> >>>>> >>>>> >>>> ------------------------------------------------------- >>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Prac= tices >>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing = & QA >>>> Security * Process Improvement & Measurement * http://www.sqe.com/bsce= 5sf >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >> >> >> -- >> Thiago Seito Satake >> !! Tenha um bom dia !! >> Tel: (041) 990-55422 >> >> >> >> > _______________________________________________ > WDKDev mailing list > WD...@pc... > https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > |
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From: Y. T. G. <yon...@pc...> - 2005-08-10 13:03:18
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yes indeed. we need to explicitly register pg drivers (but not oracle=20 drivers). cheers, thomas On Wed, 10 Aug 2005, Y. Thomas Gan wrote: > maybe we need to explicitly register pg drivers. i'll try it. we should n= ot=20 > have to add the driver jar to tomcat'S CLASSPATH. > > -thomas > > On Wed, 10 Aug 2005, Steve Fischer wrote: > >> is it possibly caused by my having commented out this line in >> PostegeSQL.java: >>=20 >> // DriverManager.registerDriver(new org.postgresql.Driver(= )); >>=20 >> it didn't seem to make any difference when running outside of tomcat (so >> i took it out). >>=20 >> steve >>=20 >> Thiago Satake wrote: >>=20 >>> We updated WDK release with postgres and WDKToySite Works well. >>>=20 >>>=20 >>>> See bug 114: toySite throws 'No suitable driver' SQLException >>>>=20 >>>>=20 >>> It seems to me that is a tomcat problem,I belive that you must set >>> $CLASSPATH adding jdbc driver for postgres into >>> $CATALINA_HOME/bin/setclass.sh..... >>> as showed bellow: >>>=20 >>>=20 >>>> # Set standard CLASSPATH >>>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3= =2Ejar >>>>=20 >>>>=20 >>>=20 >>>=20 >>> Thanks >>>=20 >>>=20 >>>=20 >>> Thiago Seito Stake >>>=20 >>>=20 >>>=20 >>>=20 >>> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >>>=20 >>>=20 >>>> Another update on the status of release 1.6: >>>>=20 >>>> 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. >>>>=20 >>>> 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' SQLExceptio= n=20 >>>> 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. >>>>=20 >>>> I am debugging this and will release after it is fixed. >>>>=20 >>>> -Thomas >>>>=20 >>>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>>>=20 >>>>=20 >>>>=20 >>>>> just want to give an update on our progress. >>>>>=20 >>>>> we are planning a release today or tomorrow. >>>>>=20 >>>>> as well as postgres support (tested) it will include a number of othe= r >>>>> features, including an improved Sanity Test. the test will now test = all >>>>> Questions in the model XML file as well as all Queries and all Record= s. >>>>> this was needed to thoroughly test postgres. >>>>>=20 >>>>> we're working hard to get this release out... >>>>>=20 >>>>> steve >>>>>=20 >>>>> fab...@de... wrote: >>>>>=20 >>>>>=20 >>>>>=20 >>>>>> Thiago, >>>>>>=20 >>>>>>=20 >>>=20 >>>=20 >>>=20 >>>=20 >>>>>> I'm having this problem too. In wdkSummary it seems that the schema= =20 >>>>>> 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 >>>>>>=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: >>>>>>> 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 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 >>>>>>>=20 >>>>>>>=20 >>>>>>>> Folks- >>>>>>>>=20 >>>>>>>> I have made a lot of progress. >>>>>>>>=20 >>>>>>>> It is clear that the wdk postgres implementation was never tested.= =20 >>>>>>>> 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 >>>>>>>>=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 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provi= ded=20 >>>>>>>>>> by >>>>>>>>>> the student's fixes. i am starting now to look at them and merg= e. >>>>>>>>>>=20 >>>>>>>>>> i have a lot of meetings today, so in a little while i'll need t= o=20 >>>>>>>>>> stop >>>>>>>>>> till tonight >>>>>>>>>>=20 >>>>>>>>>> steve >>>>>>>>>>=20 >>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=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= =20 >>>>>>>>>>> driver >>>>>>>>>>> to postgres. >>>>>>>>>>> 2- we had to change testTables files to change the numeric dat= a=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 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.RequestProcess= or >>>>>>>>>>> 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 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>> Folks- >>>>>>>>>>>>=20 >>>>>>>>>>>> the production uses of wdk so far are in oracle, so we have no= t=20 >>>>>>>>>>>> put >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> much >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> effort into ensuring the complete functioning of the postgres= =20 >>>>>>>>>>>> module. >>>>>>>>>>>>=20 >>>>>>>>>>>> however, a student did successfully use postgres with the wdk.= =20 >>>>>>>>>>>> he >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> made >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> improvements in the PostgreSQL.java file, and a small change i= n >>>>>>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>>>>>=20 >>>>>>>>>>>> I will incorporate those changes today and test it. I hope t= o=20 >>>>>>>>>>>> get >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> you >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> a patch by tomorrow. >>>>>>>>>>>>=20 >>>>>>>>>>>> can you describe briefly the problems? >>>>>>>>>>>>=20 >>>>>>>>>>>> steve >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=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 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>> :-) >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>> Thanks ............. >>>>>>>>>>>>>=20 >>>>>>>>>>>>> Thiago Seito Satake >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Hello all, >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> We have a GUS installation running ok and now we're trying t= o=20 >>>>>>>>>>>>>> use >>>>>>>>>>>>>> WDK >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> 1.5 to >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> manipulating an >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> Oracle database, due to some type columns, sequence using,= =20 >>>>>>>>>>>>>> etc... >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> that >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>>>> wdkQuery, >>>>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Because of this, we're having a hard work to debug the code = and=20 >>>>>>>>>>>>>> set >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> it to work >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> with the Postgres schema. We would like to know if someone h= as=20 >>>>>>>>>>>>>> a >>>>>>>>>>>>>> WDK >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>> working >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>>=20 >>>>>>>>>>>>>> ------------------------------------------------------------= ---- >>>>>>>>>>>>>> This message was sent using IMP, the Internet Messaging=20 >>>>>>>>>>>>>> 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 >>>>>>>>>=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 >>>>>>=20 >>>>>>=20 >>>>> ------------------------------------------------------- >>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 >>>>> Practices >>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing= &=20 >>>>> QA >>>>> Security * Process Improvement & Measurement *=20 >>>>> http://www.sqe.com/bsce5sf >>>>> _______________________________________________ >>>>> Gusdev-gusdev mailing list >>>>> Gus...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>=20 >>>>>=20 >>>>>=20 >>>=20 >>>=20 >>> -- >>> Thiago Seito Satake >>> !! Tenha um bom dia !! >>> Tel: (041) 990-55422 >>>=20 >>>=20 >>>=20 >>>=20 >> _______________________________________________ >> WDKDev mailing list >> WD...@pc... >> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > |
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From: Michael S. <msa...@pc...> - 2005-08-10 13:19:58
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Thomas, This is very similar to an issue we had with the Oracle OCI drivers, which are much more robust that the thin driver in use around the lab. With our new servers, I'd like websites to begin to use the OCI drivers, so it may b= e worth our while to test with those as well. --Mike On 8/10/05 8:56 AM, "Y. Thomas Gan" <yon...@pc...> wrote: > maybe we need to explicitly register pg drivers. i'll try it. we should > not have to add the driver jar to tomcat'S CLASSPATH. >=20 > -thomas >=20 > On Wed, 10 Aug 2005, Steve Fischer wrote: >=20 >> is it possibly caused by my having commented out this line in >> PostegeSQL.java: >>=20 >> // DriverManager.registerDriver(new org.postgresql.Driver(= )); >>=20 >> it didn't seem to make any difference when running outside of tomcat (so >> i took it out). >>=20 >> steve >>=20 >> Thiago Satake wrote: >>=20 >>> We updated WDK release with postgres and WDKToySite Works well. >>>=20 >>>=20 >>>> See bug 114: toySite throws 'No suitable driver' SQLException >>>>=20 >>>>=20 >>> It seems to me that is a tomcat problem,I belive that you must set >>> $CLASSPATH adding jdbc driver for postgres into >>> $CATALINA_HOME/bin/setclass.sh..... >>> as showed bellow: >>>=20 >>>=20 >>>> # Set standard CLASSPATH >>>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc3.j= ar >>>>=20 >>>>=20 >>>=20 >>>=20 >>> Thanks >>>=20 >>>=20 >>>=20 >>> Thiago Seito Stake >>>=20 >>>=20 >>>=20 >>>=20 >>> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >>>=20 >>>=20 >>>> Another update on the status of release 1.6: >>>>=20 >>>> 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. >>>>=20 >>>> 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' SQLExceptio= n 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. >>>>=20 >>>> I am debugging this and will release after it is fixed. >>>>=20 >>>> -Thomas >>>>=20 >>>> On Tue, 9 Aug 2005, Steve Fischer wrote: >>>>=20 >>>>=20 >>>>=20 >>>>> just want to give an update on our progress. >>>>>=20 >>>>> we are planning a release today or tomorrow. >>>>>=20 >>>>> as well as postgres support (tested) it will include a number of othe= r >>>>> features, including an improved Sanity Test. the test will now test = all >>>>> Questions in the model XML file as well as all Queries and all Record= s. >>>>> this was needed to thoroughly test postgres. >>>>>=20 >>>>> we're working hard to get this release out... >>>>>=20 >>>>> steve >>>>>=20 >>>>> fab...@de... wrote: >>>>>=20 >>>>>=20 >>>>>=20 >>>>>> Thiago, >>>>>>=20 >>>>>>=20 >>>=20 >>>=20 >>>=20 >>>=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 >>>>>>=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: >>>>>>> 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 = 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 >>>>>>>=20 >>>>>>>=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 >>>>>>>>=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 >>>>>>>>>=20 >>>>>>>>>=20 >>>>>>>>>> ok, sorry about this. yes, those all of 1,2,3 i think are provi= ded >>>>>>>>>> by >>>>>>>>>> the student's fixes. i am starting now to look at them and merg= e. >>>>>>>>>>=20 >>>>>>>>>> i have a lot of meetings today, so in a little while i'll need t= o >>>>>>>>>> stop >>>>>>>>>> till tonight >>>>>>>>>>=20 >>>>>>>>>> steve >>>>>>>>>>=20 >>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>=20 >>>>>>>>>>=20 >>>>>>>>>>=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 >>>>>>>>>>> driver >>>>>>>>>>> to postgres. >>>>>>>>>>> 2- we had to change testTables files to change the numeric dat= a >>>>>>>>>>> type >>>>>>>>>>> ( number > numeric ) >>>>>>>>>>> 3- and now we are changing java file to adapt to Postgres ( >>>>>>>>>>> sequence >>>>>>>>>>> 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.RequestProcess= or >>>>>>>>>>> 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 >>>>>>>>>>>=20 >>>>>>>>>>>=20 >>>>>>>>>>>> Folks- >>>>>>>>>>>>=20 >>>>>>>>>>>> the production uses of wdk so far are in oracle, so we have no= t put >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> much >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> effort into ensuring the complete functioning of the postgres >>>>>>>>>>>> module. >>>>>>>>>>>>=20 >>>>>>>>>>>> however, a student did successfully use postgres with the wdk.= he >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> made >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> improvements in the PostgreSQL.java file, and a small change i= n >>>>>>>>>>>> ResultFactory that are not yet in the release. >>>>>>>>>>>>=20 >>>>>>>>>>>> I will incorporate those changes today and test it. I hope t= o get >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> you >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> a patch by tomorrow. >>>>>>>>>>>>=20 >>>>>>>>>>>> can you describe briefly the problems? >>>>>>>>>>>>=20 >>>>>>>>>>>> steve >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Satake wrote: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=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 >>>>>>>>>>>>=20 >>>>>>> :-) >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> Thanks ............. >>>>>>>>>>>>=20 >>>>>>>>>>>> Thiago Seito Satake >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> 2005/8/4, fab...@de... <fab...@de...>: >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>> Hello all, >>>>>>>>>>>>=20 >>>>>>>>>>>> We have a GUS installation running ok and now we're trying to = use >>>>>>>>>>>> WDK >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> 1.5 to >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> explore the postgres schema. We noticed that the WDK code is >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> manipulating an >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> Oracle database, due to some type columns, sequence using, etc= ... >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> that >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> generates many errors when running wdk programs (wdkCache, >>>>>>>>>>>> wdkQuery, >>>>>>>>>>>> wdkRecord,...). >>>>>>>>>>>>=20 >>>>>>>>>>>> Because of this, we're having a hard work to debug the code an= d set >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> it to work >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> with the Postgres schema. We would like to know if someone has= a >>>>>>>>>>>> WDK >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>>>>>>>=20 >>>>>>> working >>>>>>>=20 >>>>>>>=20 >>>>>>>=20 >>>>>>>>>>>> with GUS Postgres perfectly. >>>>>>>>>>>>=20 >>>>>>>>>>>> Thanks a lot, >>>>>>>>>>>>=20 >>>>>>>>>>>> Fabr=EDcio. >>>>>>>>>>>>=20 >>>>>>>>>>>> --------------------------------------------------------------= -- >>>>>>>>>>>> This message was sent using IMP, the Internet Messaging Progra= m. >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> 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 >>>>>>>>>=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 >>>>>>=20 >>>>>>=20 >>>>> ------------------------------------------------------- >>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>>>> Practices >>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testing= & QA >>>>> Security * Process Improvement & Measurement * http://www.sqe.com/bsc= e5sf >>>>> _______________________________________________ >>>>> Gusdev-gusdev mailing list >>>>> Gus...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>=20 >>>>>=20 >>>>>=20 >>>=20 >>>=20 >>> -- >>> Thiago Seito Satake >>> !! Tenha um bom dia !! >>> Tel: (041) 990-55422 >>>=20 >>>=20 >>>=20 >>>=20 >> _______________________________________________ >> WDKDev mailing list >> WD...@pc... >> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>=20 |
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From: Y. T. G. <yon...@pc...> - 2005-08-10 13:25:29
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Yeah, I remember working with you trying to switch to it but was not able= =20 to get it to work. I can give it another shot soon. -Thomas On Wed, 10 Aug 2005, Michael Saffitz wrote: > > Thomas, > > This is very similar to an issue we had with the Oracle OCI drivers, whic= h > are much more robust that the thin driver in use around the lab. With ou= r > new servers, I'd like websites to begin to use the OCI drivers, so it may= be > worth our while to test with those as well. > > --Mike > > > > On 8/10/05 8:56 AM, "Y. Thomas Gan" <yon...@pc...> wrote: > >> maybe we need to explicitly register pg drivers. i'll try it. we should >> not have to add the driver jar to tomcat'S CLASSPATH. >> >> -thomas >> >> On Wed, 10 Aug 2005, Steve Fischer wrote: >> >>> is it possibly caused by my having commented out this line in >>> PostegeSQL.java: >>> >>> // DriverManager.registerDriver(new org.postgresql.Driver= ()); >>> >>> it didn't seem to make any difference when running outside of tomcat (s= o >>> i took it out). >>> >>> steve >>> >>> Thiago Satake wrote: >>> >>>> We updated WDK release with postgres and WDKToySite Works well. >>>> >>>> >>>>> See bug 114: toySite throws 'No suitable driver' SQLException >>>>> >>>>> >>>> It seems to me that is a tomcat problem,I belive that you must set >>>> $CLASSPATH adding jdbc driver for postgres into >>>> $CATALINA_HOME/bin/setclass.sh..... >>>> as showed bellow: >>>> >>>> >>>>> # Set standard CLASSPATH >>>>> CLASSPATH=3D"$JAVA_HOME"/lib/tools.jar:"$JAVA_HOME"/lib/pg74.216.jdbc= 3.jar >>>>> >>>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> >>>> Thiago Seito Stake >>>> >>>> >>>> >>>> >>>> 2005/8/10, Y. Thomas Gan <yon...@pc...>: >>>> >>>> >>>>> 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' SQLExcepti= on at >>>>> start up against postgres (oracle is ok) although sanityTest succeed= s >>>>> (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 oth= er >>>>>> features, including an improved Sanity Test. the test will now test= all >>>>>> Questions in the model XML file as well as all Queries and all Recor= ds. >>>>>> this was needed to thoroughly test postgres. >>>>>> >>>>>> we're working hard to get this release out... >>>>>> >>>>>> steve >>>>>> >>>>>> fab...@de... wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Thiago, >>>>>>> >>>>>>> >>>> >>>> >>>> >>>> >>>>>>> I'm having this problem too. In wdkSummary it seems that the schema= name >>>>>>> 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...>: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> 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_colum= n, >>>>>>>> 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 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- >>>>>>>>> >>>>>>>>> I have made a lot of progress. >>>>>>>>> >>>>>>>>> It is clear that the wdk postgres implementation was never tested= =2E 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 prov= ided >>>>>>>>>>> by >>>>>>>>>>> the student's fixes. i am starting now to look at them and mer= ge. >>>>>>>>>>> >>>>>>>>>>> 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 da= ta >>>>>>>>>>>> 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.RequestProces= sor >>>>>>>>>>>> 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 n= ot put >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> much >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> effort into ensuring the complete functioning of the postgres >>>>>>>>>>>>> module. >>>>>>>>>>>>> >>>>>>>>>>>>> however, a student did successfully use postgres with the wdk= =2E he >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> 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 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 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> manipulating an >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> Oracle database, due to some type columns, sequence using, et= c... >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> that >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> 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 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> it to work >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> with the Postgres schema. We would like to know if someone ha= s a >>>>>>>>>>>>> WDK >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>> working >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>>>>>> 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 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>> -- >>>>>>>> Thiago Seito Satake >>>>>>>> !! Tenha um bom dia !! >>>>>>>> Tel: (041) 990-55422 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> WDKDev mailing list >>>>>>>> WD...@pc... >>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------- >>>>>>> This message was sent using IMP, the Internet Messaging Program. >>>>>>> >>>>>>> >>>>>>> >>>>>> ------------------------------------------------------- >>>>>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>>>>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>>>>> Practices >>>>>> Agile & Plan-Driven Development * Managing Projects & Teams * Testin= g & QA >>>>>> Security * Process Improvement & Measurement * http://www.sqe.com/bs= ce5sf >>>>>> _______________________________________________ >>>>>> Gusdev-gusdev mailing list >>>>>> Gus...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> -- >>>> Thiago Seito Satake >>>> !! Tenha um bom dia !! >>>> Tel: (041) 990-55422 >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> WDKDev mailing list >>> WD...@pc... >>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>> > > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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