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Re: [GUSDEV] Question regarding GUS3.0
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From: Michael S. <msa...@pc...> - 2005-08-09 17:39:06
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Hi Sanjeev, The easiest thing is to install GUS in separate locations, i.e. ~/gusdev and ~/gustest. Each will have it's own $GUS_HOME, $PROJECT_HOME, and $GUS_CONFIG_FILE (as well as the appropriate $PATH and $PERL5LIB settings). I find it's easiest to place all environment variables in a file for each GUS installation, and then (in Bash) I just "source" the file for the installation I wish to use. Since the installations will be identical, you could also just have two $GUS_CONFIG_FILEs, and update the environment variable to point to the one specifying test or dev as needed. Just be careful under both options since it can become difficult to remember which db you're working with. --Mike On 8/8/05 12:25 PM, "Kumar, Sanjeev (Contr)" <San...@ng...> wrote: > Hi, > I have GUS3.0 installed and pointed to dev database.Now I want to use > the same GUS installation to point to different database 'Test' which > parameter do I need to change. > I have already copied all the GUS database objects from Dev to Test > database. > > Thanks > Sanjeev > > -----Original Message----- > From: gus...@li... > [mailto:gus...@li...] On Behalf Of > gus...@li... > Sent: Monday, August 08, 2005 11:15 AM > To: gus...@li... > Subject: Gusdev-gusdev digest, Vol 1 #644 - 4 msgs > > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > gus...@li... > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of Gusdev-gusdev digest..." > > > Today's Topics: > > 1. Re: [WDKDEV] WDK with Postgres? (Thiago Satake) > 2. Re: [WDKDEV] WDK with Postgres? (fab...@de...) > 3. Re: Re: [WDKDEV] WDK with Postgres? (Y. Thomas Gan) > 4. Re: Re: [WDKDEV] WDK with Postgres? (Thiago Satake) > > --__--__-- > > Message: 1 > Date: Mon, 8 Aug 2005 11:54:18 -0300 > From: Thiago Satake <ma...@gm...> > To: Steve Fischer <sfi...@pc...>, > gus...@li..., > wd...@pc... > Subject: [GUSDEV] Re: [WDKDEV] WDK with Postgres? > > 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 > > > --__--__-- > > Message: 2 > Date: Mon, 08 Aug 2005 12:02:39 -0300 > From: fab...@de... > To: Thiago Satake <ma...@gm...> > Cc: gus...@li..., wd...@pc..., > Steve Fischer <sfi...@pc...> > Subject: [GUSDEV] Re: [WDKDEV] WDK with Postgres? > > Thiago, > > I'm having this problem too. In wdkSummary it seems that the schema name > = 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. > > > --__--__-- > > Message: 3 > Date: Mon, 8 Aug 2005 11:02:52 -0400 (EDT) > From: "Y. Thomas Gan" <yon...@pc...> > To: Thiago Satake <ma...@gm...> > cc: Steve Fischer <sfi...@pc...>, > gus...@li..., wd...@pc... > Subject: Re: [GUSDEV] Re: [WDKDEV] WDK with Postgres? > > This message is in MIME format. The first part should be readable > text, > while the remaining parts are likely unreadable without MIME-aware > tools. > > --2074436185-2060476898-1123513372=:14783 > Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: QUOTED-PRINTABLE > > 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 >> > --2074436185-2060476898-1123513372=:14783-- > > > --__--__-- > > Message: 4 > Date: Mon, 8 Aug 2005 12:14:24 -0300 > From: Thiago Satake <ma...@gm...> > To: "Y. Thomas Gan" <yon...@pc...> > Subject: Re: [GUSDEV] Re: [WDKDEV] WDK with Postgres? > Cc: Steve Fischer <sfi...@pc...>, > gus...@li..., > wd...@pc... > > :-) > > Ok ..... I am waiting for new release version !!! > > > Thiago Seito Satake > > 2005/8/8, Y. Thomas Gan <yon...@pc...>: >> Hi Thiago, >> Usually you should get stable released versions from the download >> 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 > > > > --__--__-- > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > End of Gusdev-gusdev Digest > > > ------------------------------------------------------- > 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/bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
