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From: Deborah P. <pi...@pc...> - 2005-08-09 22:27:14
|
Flat files of Genbank release 148 from June 15 2005, in genbank format, can be found at: ftp://ftp.ncbi.nih.gov/genbank/ |
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From: Steve F. <sfi...@pc...> - 2005-08-09 22:13:00
|
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
|
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: Michael S. <msa...@pc...> - 2005-08-09 17:39:06
|
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 |
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From: <ju...@cs...> - 2005-08-09 17:38:12
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Presently on the SchemaBrowser, links to many of the PROT schema tables display blank pages. |
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From: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-08 16:26:17
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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=20 -----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...,=20 wd...@pc... Subject: [GUSDEV] Re: [WDKDEV] WDK with Postgres? After downloaded WDK from SVN files=3D20 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:=3D20 org.gusdb.wdk.model.WdkModelException: Failed running query: "SELECT * FROM ( select usertest.query_result_4.result_index_column, = =3D20 a.assembly_consistency, a.contains_mrna, = =3D20 a.number_of_contained_sequences, a.sequence = =3D20 from WDKTestAssembly a, WDKTestTaxonName tn = =3D20 , usertest.query_result_4 where a.na_sequence_id =3D3D usertest.query_result_4.na_sequence_id and a.taxon_id =3D3D tn.taxon_id and usertest.query_result_4.result_index_column >=3D3D = 1 and usertest.query_result_4.result_index_column <=3D3D 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- >=3D20 > I have made a lot of progress. >=3D20 > It is clear that the wdk postgres implementation was never tested. I > have fixed many, many things. >=3D20 > Here is where I am at so far. i ran: > % wdkSanityTest -model toyModel >=3D20 > and got this: >=3D20 > ***Sanity test summary*** > 11 queries passed, 1 queries failed > 0 records passed, 2 records failed > Sanity Test FAILED >=3D20 > tomorrow morning i'll look into the remaining problems =3D20 steve = =3D20 >Thiago Satake wrote: >=3D20 > >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=20 > >>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=20 > >>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=20 > >>>driver to postgres. > >>>2- we had to change testTables files to change the numeric data=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=20 > >>>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...>: > >>> > >>> > >>> > >>> > >>>>Folks- > >>>> > >>>>the production uses of wdk so far are in oracle, so we have not=20 > >>>>put m=3D uch > >>>>effort into ensuring the complete functioning of the postgres module. > >>>> > >>>>however, a student did successfully use postgres with the wdk. he > >>>>ma=3D de > >>>>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 =3D 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 > >>>>>!!!!!!!!!!!!!!!!!!! =3D :-) > >>>>> > >>>>>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=20 > >>>>>>use W=3D DK 1.5 to > >>>>>>explore the postgres schema. We noticed that the WDK code is=20 > >>>>>>manipu=3D lating an > >>>>>>Oracle database, due to some type columns, sequence using,=20 > >>>>>>etc... t=3D hat > >>>>>>generates many errors when running wdk programs (wdkCache,=20 > >>>>>>wdkQuery=3D , > >>>>>>wdkRecord,...). > >>>>>> > >>>>>>Because of this, we're having a hard work to debug the code and=20 > >>>>>>set=3D it to work > >>>>>>with the Postgres schema. We would like to know if someone has a > >>>>>>WD=3D K working > >>>>>>with GUS Postgres perfectly. > >>>>>> > >>>>>>Thanks a lot, > >>>>>> > >>>>>>Fabr=3DEDcio. > >>>>>> > >>>>>>---------------------------------------------------------------- > >>>>>>This message was sent using IMP, the Internet Messaging Program. > >>>>>>_______________________________________________ > >>>>>>WDKDev mailing list > >>>>>>WD...@pc... > >>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>> > >>> > >>> > >>> > > > > > > > > >=3D20 --=3D20 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 =3D 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, =3D20 Fabr=3DEDcio. Citando Thiago Satake <ma...@gm...>: > After downloaded WDK from SVN files=3D20 I run: > wdkSanityTest -model toyModel >=3D20 > and got this >=3D20 > ***Sanity test summary*** > 10 queries passed, 4 queries failed > 1 records passed, 1 records failed > Sanity Test FAILED >=3D20 >=3D20 > and I run: > wdkSummary -model toyModel -question RnaQuestions.ByNumSeqs -rows 1 20 >-params NumSeqs 10 ApiTaxon "Neospora caninum" >=3D20 > I got:=3D20 >=3D20 > org.gusdb.wdk.model.WdkModelException: > Failed running query: > "SELECT * FROM ( select usertest.query_result_4.result_index_column, =3D20 > a.assembly_consistency, a.contains_mrna, =3D20 > a.number_of_contained_sequences, a.sequence =3D20 > from WDKTestAssembly a, WDKTestTaxonName tn =3D20 > , usertest.query_result_4 where a.na_sequence_id =3D3D > usertest.query_result_4.na_sequence_id and a.taxon_id > =3D3D tn.taxon_id and usertest.query_result_4.result_index_column = >=3D3D 1 >=3D and > usertest.query_result_4.result_index_column <=3D3D 20 order by =20 >usertest.query_result_4.result_index_column ) ORDER BY =20 >result_index_column" >=3D20 >=3D20 > :-( >=3D20 >=3D20 > Thanks >=3D20 > Thiago Seito Satake >=3D20 >=3D20 >=3D20 >=3D20 >=3D20 >=3D20 > 2005/8/5, Steve Fischer <sfi...@pc...>: > > Folks- > >=3D20 > > I have made a lot of progress. > >=3D20 > > It is clear that the wdk postgres implementation was never tested. =3D I > > have fixed many, many things. > >=3D20 > > Here is where I am at so far. i ran: > > % wdkSanityTest -model toyModel > >=3D20 > > and got this: > >=3D20 > > ***Sanity test summary*** > > 11 queries passed, 1 queries failed > > 0 records passed, 2 records failed > > Sanity Test FAILED > >=3D20 > > tomorrow morning i'll look into the remaining problems =3D20 steve=20 > >=3D20 Thiago Satake wrote: > >=3D20 > > >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=20 > > >>provided=3D 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=20 > > >>s=3D 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=20 > > >>>dri=3D ver > > >>>to postgres. > > >>>2- we had to change testTables files to change the numeric data=20 > > >>>t=3D ype > > >>>( number > numeric ) > > >>>3- and now we are changing java file to adapt to Postgres (=20 > > >>>seque=3D 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=20 > > >>>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=20 > > >>>>p=3D ut > much > > >>>>effort into ensuring the complete functioning of the postgres=20 > > >>>>mod=3D ule. > > >>>> > > >>>>however, a student did successfully use postgres with the wdk. =20 > > >>>>h=3D e > made > > >>>>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 g=3D et=3D20 > 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 > > >>>>>!!!!!!!!!!!!!!!!=3D !!! > :-) > > >>>>> > > >>>>>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=20 > > >>>>>>u=3D 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,=20 > > >>>>>>etc.=3D .. > that > > >>>>>>generates many errors when running wdk programs (wdkCache,=20 > > >>>>>>wdkQ=3D uery, > > >>>>>>wdkRecord,...). > > >>>>>> > > >>>>>>Because of this, we're having a hard work to debug the code=20 > > >>>>>>and=3D set > it to work > > >>>>>>with the Postgres schema. We would like to know if someone has > > >>>>>>=3D a WDK > working > > >>>>>>with GUS Postgres perfectly. > > >>>>>> > > >>>>>>Thanks a lot, > > >>>>>> > > >>>>>>Fabr=3DEDcio. > > >>>>>> > > >>>>>>-------------------------------------------------------------- > > >>>>>>-=3D - > > >>>>>>This message was sent using IMP, the Internet Messaging=20 > > >>>>>>Program=3D . > > >>>>>>_______________________________________________ > > >>>>>>WDKDev mailing list > > >>>>>>WD...@pc... > > >>>>>>https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>> > > >>> > > >>> > > >>> > > > > > > > > > > > > > >=3D20 >=3D20 >=3D20 > --=3D20 > Thiago Seito Satake > !! Tenha um bom dia !! > Tel: (041) 990-55422 >=3D20 > _______________________________________________ > WDKDev mailing list > WD...@pc... > https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >=3D20 ---------------------------------------------------------------- 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=3D:14783 Content-Type: TEXT/PLAIN; charset=3DISO-8859-1; format=3Dflowed Content-Transfer-Encoding: QUOTED-PRINTABLE Hi Thiago, Usually you should get stable released versions from the download=3D20 site. Steve and I have beening working on the svn trunk and we have more=3D20 work to do before we release version 1.6 - sorry for the inconvenience.=3D20 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 ,=20 > usertest.query_result_4 where a.na_sequence_id =3D3D > usertest.query_result_4.na_sequence_id and a.taxon_id > =3D3D tn.taxon_id and usertest.query_result_4.result_index_column = >=3D3D 1 > an=3D d > usertest.query_result_4.result_index_column <=3D3D 20 order by=20 > usertest.query_result_4.result_index_column ) ORDER BY=20 > 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=20 >>>> 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=20 >>>>> driver to postgres. >>>>> 2- we had to change testTables files to change the numeric data=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=20 >>>>> 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...>: >>>>> >>>>> >>>>> >>>>> >>>>>> Folks- >>>>>> >>>>>> the production uses of wdk so far are in oracle, so we have not=20 >>>>>> put =3D much >>>>>> effort into ensuring the complete functioning of the postgres=20 >>>>>> module=3D =3D2E >>>>>> >>>>>> however, a student did successfully use postgres with the wdk. =20 >>>>>> he m=3D ade >>>>>> 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 =3D 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 >>>>>>> !!!!!!!!!!!!!!!!!!!=3D :-) >>>>>>> >>>>>>> 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=20 >>>>>>>> use =3D WDK 1.5 to >>>>>>>> explore the postgres schema. We noticed that the WDK code is=20 >>>>>>>> manip=3D ulating an >>>>>>>> Oracle database, due to some type columns, sequence using,=20 >>>>>>>> etc... =3D that >>>>>>>> generates many errors when running wdk programs (wdkCache,=20 >>>>>>>> wdkQuer=3D y, >>>>>>>> wdkRecord,...). >>>>>>>> >>>>>>>> Because of this, we're having a hard work to debug the code and >>>>>>>> se=3D t it to work >>>>>>>> with the Postgres schema. We would like to know if someone has=20 >>>>>>>> a W=3D DK working >>>>>>>> with GUS Postgres perfectly. >>>>>>>> >>>>>>>> Thanks a lot, >>>>>>>> >>>>>>>> Fabr=3DEDcio. >>>>>>>> >>>>>>>> --------------------------------------------------------------- >>>>>>>> - This message was sent using IMP, the Internet Messaging=20 >>>>>>>> Program. >>>>>>>> _______________________________________________ >>>>>>>> WDKDev mailing list >>>>>>>> WD...@pc... >>>>>>>> https://mail.pcbi.upenn.edu/mailman/listinfo/wdkdev >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>> >>>>> >>>>> >>>>> >>> >>> >>> >>> >> > > > --=3D20 > Thiago Seito Satake > !! Tenha um bom dia !! > Tel: (041) 990-55422 > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO=20 > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 > Practic=3D es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing=20 > & Q=3D A > Security * Process Improvement & Measurement *=20 > http://www.sqe.com/bsce5sf=20 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > --2074436185-2060476898-1123513372=3D: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...,=20 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 =20 >site. Steve and I have beening working on the svn trunk and we have=20 >more work to do before we release version 1.6 - sorry for the inconvenience. > Please look out for release announcement soon. >=3D20 > -Thomas >=3D20 >=3D20 >=3D20 > On Mon, 8 Aug 2005, Thiago Satake wrote: >=3D20 > > 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 > > 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 ,=20 > > usertest.query_result_4 where a.na_sequence_id =3D3D > > usertest.query_result_4.na_sequence_id and a.taxon_id > > =3D3D tn.taxon_id and usertest.query_result_4.result_index_column = >=3D3D > > 1 =3D and > > usertest.query_result_4.result_index_column <=3D3D 20 order by=20 > > usertest.query_result_4.result_index_column ) ORDER BY=20 > > 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. =3D 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=20 > >> 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=20 > >>>> provided =3D 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=3D 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=20 > >>>>> driv=3D er > >>>>> to postgres. > >>>>> 2- we had to change testTables files to change the numeric data > >>>>> ty=3D pe > >>>>> ( number > numeric ) > >>>>> 3- and now we are changing java file to adapt to Postgres (=20 > >>>>> sequen=3D 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=20 > >>>>> 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...>: > >>>>> > >>>>> > >>>>> > >>>>> > >>>>>> Folks- > >>>>>> > >>>>>> the production uses of wdk so far are in oracle, so we have not > >>>>>> pu=3D t much > >>>>>> effort into ensuring the complete functioning of the postgres=20 > >>>>>> modu=3D le. > >>>>>> > >>>>>> however, a student did successfully use postgres with the wdk. > >>>>>> he=3D 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=3D 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=20 > >>>>>>> !!!!!!!!!!!!!!!!!=3D !! :-) > >>>>>>> > >>>>>>> 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=3D e WDK 1.5 to > >>>>>>>> explore the postgres schema. We noticed that the WDK code is=20 > >>>>>>>> man=3D ipulating an > >>>>>>>> Oracle database, due to some type columns, sequence using,=20 > >>>>>>>> etc..=3D . that > >>>>>>>> generates many errors when running wdk programs (wdkCache,=20 > >>>>>>>> wdkQu=3D ery, > >>>>>>>> wdkRecord,...). > >>>>>>>> > >>>>>>>> Because of this, we're having a hard work to debug the code=20 > >>>>>>>> and =3D set it to work > >>>>>>>> with the Postgres schema. We would like to know if someone=20 > >>>>>>>> has a=3D WDK working > >>>>>>>> with GUS Postgres perfectly. > >>>>>>>> > >>>>>>>> Thanks a lot, > >>>>>>>> > >>>>>>>> Fabr=3DEDcio. > >>>>>>>> > >>>>>>>> ------------------------------------------------------------- > >>>>>>>> --- This message was sent using IMP, the Internet Messaging=20 > >>>>>>>> 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=20 > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 > > Pract=3D ices > > Agile & Plan-Driven Development * Managing Projects & Teams *=20 > > Testing &=3D QA > > Security * Process Improvement & Measurement *=20 > > http://www.sqe.com/bsce5=3D sf > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > >=3D20 --=3D20 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 |
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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: 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 > |
|
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. |
|
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: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-05 14:41:52
|
Hi,
I am having issue in running newly registered plugin.
I have one new plug in which I registered and I tested it , it ran =
fine.
AFter that I fixed some bug and then tried to run it gave me error =
saying that plugin has change I need to update it. But when I am trying =
to update the plug in it is not letting me do so. Errors are listed =
below :
***************************************
[oragus35@rdevse02 oragus35]$ ga GUS::Supported::Plugin::LoadPrositeDB=20
--file /home/oragus35/prosite.dat --commit
USER ERROR: The md5 checksum of GUS::Supported::Plugin::LoadPrositeDB's=20
executable file (cvs revision 2943) doesn't match the md5 checksum in=20
the database for that plugin and revision. IE, the plugin has been=20
changed but not commited and updated. Please:
- cvs commit the plugin file
- use the build system to install it
- run 'ga +update=20
GUS::Supported::Plugin::LoadPrositeDB --commit'
Aborting
Issuing rollback() for database handle being DESTROY'd without explicit=20
disconnect().
Issuing rollback() for database handle being DESTROY'd without explicit=20
disconnect().
[oragus35@rdevse02 oragus35]$ ga +update=20
GUS::Supported::Plugin::LoadPrositeDB --commit;
Error: GUS::Supported::Plugin::LoadPrositeDB with CVS revision 2943 is =
already registered. You don't need to do a +update.
******************************************************************
Pl. suggest me what needs to be done.
Thanks
Sanjeev
|
|
From: Steve F. <sfi...@pc...> - 2005-08-05 13:46:21
|
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...> - 2005-08-05 11:55:39
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Hello all, We installed GUS 3.5 with Postgres: there is a bug know to fix before instalation: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D47 And there is a bug know did not fix yet: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D41 WDK does not work with postgres but comming soon: http://sourceforge.net/mailarchive/forum.php?thread_id=3D7890981&forum_id= =3D9903 :-) Thiago Satake 2005/8/5, juan perin <bi...@ge...>: > I'm currently working on a test implementation of RAD through the use of > Postgres and GUS. I will be working with a relatively small data set, > probably just a few gigs. We have been running Oracle with the older > GUS release, but will be upgrading the machine and need to decide on > using Oracle or Postgres. Depending on our success with the test > installation and Postgres, we may make the switch to Postgres on our > production machine. I'll keep those interested posted with our successes= . >=20 > Juan Perin > Children's Hospital of Philadelphia > Bioinformatics Core > Chris Stoeckert wrote: >=20 > > Sounds like Fabricio and Thiago have Postgres working from their > > postings earlier today (and hopefully WDK soon) but I believe there > > are others. > > Chris > > > > On Aug 4, 2005, at 10:52 AM, michael chaplin wrote: > > > >> has anyone gotten 3.5 to install with postgres? > >> > >> > >> > >> ------------------------------------------------------- > >> 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 > >> > > > > > > > > ------------------------------------------------------- > > 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/bsce5= sf > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > >=20 >=20 >=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 >=20 --=20 Thiago Seito Satake !! Tenha um bom dia !! Tel: (041) 990-55422 |
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From: juan p. <bi...@ge...> - 2005-08-05 00:11:09
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I'm currently working on a test implementation of RAD through the use of Postgres and GUS. I will be working with a relatively small data set, probably just a few gigs. We have been running Oracle with the older GUS release, but will be upgrading the machine and need to decide on using Oracle or Postgres. Depending on our success with the test installation and Postgres, we may make the switch to Postgres on our production machine. I'll keep those interested posted with our successes. Juan Perin Children's Hospital of Philadelphia Bioinformatics Core Chris Stoeckert wrote: > Sounds like Fabricio and Thiago have Postgres working from their > postings earlier today (and hopefully WDK soon) but I believe there > are others. > Chris > > On Aug 4, 2005, at 10:52 AM, michael chaplin wrote: > >> has anyone gotten 3.5 to install with postgres? >> >> >> >> ------------------------------------------------------- >> 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 >> > > > > ------------------------------------------------------- > 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 > > |
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From: Jian Lu <jl...@vb...> - 2005-08-04 22:55:33
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Hi Chris, I don't have real feature relationship use cases. AAFeatureRelationship and AAFeatRelationshipType are completely based on consideration of consistency of NA and AA. I agree with you if this is not higher priority from community-wide need. Thank you. Jian Chris Stoeckert wrote: > Dear Jian, > No problem with your first two proposals to add comment_name_id and > AAFeatureComment. Should be able to address in an upcoming minor > release. However, these will be ALTER TABLE to add comment_name_id to > existing tables NAComment and NAFeatureComment rather than creating > tables. > Should also be no problem accepting the third proposal for > AAFeatureRelationship and AAFeatRelationshipType however our policy > has been to NOT add tables just for consistency in order to avoid > schema bloat with tables that no one uses. Do you (or anyone else) > have use cases for these? It will help in the documentation. > > Thanks, > Chris > > To store curation comments has been our concern for a while. By > looking at NA > and AA comment tables, they couldn't meet such needs. > 1. there is no way you can tell the type of comments from NAComment and > NAFeatureComment tables so that comment_name_id is needed as a foreign key > reference to CommentName table. > 2. To add curation comments to AA features from protein annotation, > new table > AAFeatureComment is needed. > 3. To keep feature relationship, there are tables > NAFEATRELATIONSHIPTYPE and > NAFEATURERELATIONSHIP. But there are no such tables on AA. To make > consistent > and systematic schema and have potential relationship between AA features, > similar tables AAFEATRELATIONSHIPTYPE and AAFEATURERELATIONSHIP are > needed. > > Following are SQL for those changes. > > CREATE TABLE DoTS.NAComment ( > NA_COMMENT_ID NUMBER(10,0) NOT NULL, > NA_SEQUENCE_ID NUMBER(10,0) NOT NULL, > COMMENT_NAME_ID(10,0), > COMMENT_STRING CLOB NOT NULL, > MODIFICATION_DATE DATE NOT NULL, > USER_READ NUMBER(1,0) NOT NULL, > USER_WRITE NUMBER(1,0) NOT NULL, > GROUP_READ NUMBER(1,0) NOT NULL, > GROUP_WRITE NUMBER(1,0) NOT NULL, > OTHER_READ NUMBER(1,0) NOT NULL, > OTHER_WRITE NUMBER(1,0) NOT NULL, > ROW_USER_ID NUMBER(12,0) NOT NULL, > ROW_GROUP_ID NUMBER(4,0) NOT NULL, > ROW_PROJECT_ID NUMBER(4,0) NOT NULL, > ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL); > ALTER TABLE DOTS.NAComment ADD CONSTRAINT NAComment_FK > FOREIGN KEY (COMMENT_NAME_ID) REFERENCES DOTS.CommentName > (COMMENT_NAME_ID); > > CREATE TABLE DoTS.NAFeatureComment ( > NA_Feature_COMMENT_ID NUMBER(10,0) NOT NULL, > NA_Feature_ID NUMBER(10,0) NOT NULL, > COMMENT_NAME_ID(10,0), > COMMENT_STRING CLOB NOT NULL, > MODIFICATION_DATE DATE NOT NULL, > USER_READ NUMBER(1,0) NOT NULL, > USER_WRITE NUMBER(1,0) NOT NULL, > GROUP_READ NUMBER(1,0) NOT NULL, > GROUP_WRITE NUMBER(1,0) NOT NULL, > OTHER_READ NUMBER(1,0) NOT NULL, > OTHER_WRITE NUMBER(1,0) NOT NULL, > ROW_USER_ID NUMBER(12,0) NOT NULL, > ROW_GROUP_ID NUMBER(4,0) NOT NULL, > ROW_PROJECT_ID NUMBER(4,0) NOT NULL, > ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL); > ALTER TABLE DOTS.NAFeatureComment ADD CONSTRAINT NAFeatureComment_FK > FOREIGN KEY (COMMENT_NAME_ID) REFERENCES DOTS.CommentName > (COMMENT_NAME_ID); > > CREATE TABLE DoTS.AAFeatureComment ( > AA_Feature_COMMENT_ID NUMBER(10,0) NOT NULL, > AA_Feature_ID NUMBER(10,0) NOT NULL, > COMMENT_NAME_ID(10,0), > COMMENT_STRING CLOB NOT NULL, > MODIFICATION_DATE DATE NOT NULL, > USER_READ NUMBER(1,0) NOT NULL, > USER_WRITE NUMBER(1,0) NOT NULL, > GROUP_READ NUMBER(1,0) NOT NULL, > GROUP_WRITE NUMBER(1,0) NOT NULL, > OTHER_READ NUMBER(1,0) NOT NULL, > OTHER_WRITE NUMBER(1,0) NOT NULL, > ROW_USER_ID NUMBER(12,0) NOT NULL, > ROW_GROUP_ID NUMBER(4,0) NOT NULL, > ROW_PROJECT_ID NUMBER(4,0) NOT NULL, > ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL); > ALTER TABLE DOTS.AAFeatureComment ADD CONSTRAINT AAFeatureComment_FK > FOREIGN KEY (COMMENT_NAME_ID) REFERENCES DOTS.CommentName > (COMMENT_NAME_ID); > > CREATE TABLE DoTS.AAFeatRelationshipType ( > AA_FEAT_RELATIONSHIP_TYPE_ID NUMBER(10,0) PRIMARY KEY, > NAME VARCHAR2(255) NOT NULL, > DESCRIPTION CLOB NOT NULL, > MODIFICATION_DATE DATE NOT NULL, > USER_READ NUMBER(1,0) NOT NULL, > USER_WRITE NUMBER(1,0) NOT NULL, > GROUP_READ NUMBER(1,0) NOT NULL, > GROUP_WRITE NUMBER(1,0) NOT NULL, > OTHER_READ NUMBER(1,0) NOT NULL, > OTHER_WRITE NUMBER(1,0) NOT NULL, > ROW_USER_ID NUMBER(12,0) NOT NULL, > ROW_GROUP_ID NUMBER(4,0) NOT NULL, > ROW_PROJECT_ID NUMBER(4,0) NOT NULL, > ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL); > > CREATE TABLE DoTS.AAFeatureRelationship ( > AA_Feature_RELATIONSHIP_ID NUMBER(10,0) PRIMARY KEY, > PARENT_AA_Feature_ID NUMBER(10,0) NOT NULL, > CHILD_AA_Feature_ID NUMBER(10,0) NOT NULL, > AA_FEAT_RELATIONSHIP_TYPE_ID NUMBER(10,0) NOT NULL, > ORDINAL NUMBER(10,0) , > MODIFICATION_DATE DATE NOT NULL, > USER_READ NUMBER(1,0) NOT NULL, > USER_WRITE NUMBER(1,0) NOT NULL, > GROUP_READ NUMBER(1,0) NOT NULL, > GROUP_WRITE NUMBER(1,0) NOT NULL, > OTHER_READ NUMBER(1,0) NOT NULL, > OTHER_WRITE NUMBER(1,0) NOT NULL, > ROW_USER_ID NUMBER(12,0) NOT NULL, > ROW_GROUP_ID NUMBER(4,0) NOT NULL, > ROW_PROJECT_ID NUMBER(4,0) NOT NULL, > ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL); > ALTER TABLE DoTS.AAFeatureRelationship ADD CONSTRAINT > AAFeatureRELATIONSHIP_FK1 > FOREIGN KEY (PARENT_AA_Feature_ID) REFERENCES DoTS.AAFeatureImp > (AA_Feature_ID); > > ALTER TABLE DoTS.AAFeatureRelationship ADD CONSTRAINT > AAFeatureRELATIONSHIP_FK2 > FOREIGN KEY (CHILD_AA_Feature_ID) REFERENCES DoTS.AAFeatureImp > (AA_Feature_ID); > > ALTER TABLE DoTS.AAFeatureRelationship ADD CONSTRAINT > AAFeatureRELATIONSHIP_FK3 > FOREIGN KEY (AA_FEAT_RELATIONSHIP_TYPE_ID) REFERENCES > DoTS.AAFeatRelationshipType (AA_FEAT_RELATIONSHIP_TYPE_ID); |
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From: Chris S. <sto...@pc...> - 2005-08-04 22:23:28
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Sounds like Fabricio and Thiago have Postgres working from their postings earlier today (and hopefully WDK soon) but I believe there are others. Chris On Aug 4, 2005, at 10:52 AM, michael chaplin wrote: > has anyone gotten 3.5 to install with postgres? > > > > ------------------------------------------------------- > 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 > |
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From: Chris S. <sto...@pc...> - 2005-08-04 22:18:04
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It doesn't work as a feature as these are tied to one sequence. Depending on how much you want to load, you can just go with Aaron's solution and load base information in DBRef and associate sequences to it with AASequenceDBRef. If you need to store more than what fits in DBRef, you might propose creating a new table along the lines of DoTS.PfamEntry or DoTS.NRDBEntry. Cheers, Chris On Aug 4, 2005, at 3:13 PM, Aaron J. Mackey wrote: > A Prosite entry is a (regular expression or profile-based) sequence > motif. So it's none of the above. > > I believe we are going to handle Prosite (and other InterProScan- > related datasets) simply as DbRefs, and not try to store their > actual definitions (thus linking out to expasy, etc. as necessary). > > -Aaron > > On Aug 4, 2005, at 2:56 PM, Chris Stoeckert wrote: > > >> Hi Sanjeev, >> I guess the first thing to decide is if this entry represents a >> sequence, a feature, or an annotation. Do you (or anyone else) >> have strong opinions on this? Can you send an example entry? >> Thanks, >> Chris >> >> On Aug 4, 2005, at 12:35 PM, Kumar, Sanjeev (Contr) wrote: >> >> >> >>> Hi, >>> Now let us figure out which GUS table to used to store >>> PrositeDB master data. >>> Can any one help me in that please? >>> Following type of information it contains: >>> ID Identification (Begins each entry; 1 per entry) >>> AC Accession number (1 per entry) >>> DT Date (1 per entry) >>> DE Short description (1 per entry) >>> PA Pattern (>1 per entry) >>> MA Matrix/profile (>1 per entry) >>> RU Rule (>1 per entry) >>> NR Numerical results (>1 per entry) >>> CC Comments (>=1 per entry) >>> DR Cross-references to Swiss-Prot (>1 per entry) >>> 3D Cross-references to PDB (>1 per entry) >>> DO Pointer to the documentation file (1 per entry) >>> >>> Any help on this will be appreciated. >>> >>> >>> Thanks >>> Sanjeev >>> >>> -----Original Message----- >>> From: gus...@li... >>> [mailto:gus...@li...]On Behalf Of >>> gus...@li... >>> Sent: Tuesday, August 02, 2005 11:09 PM >>> To: gus...@li... >>> Subject: Gusdev-gusdev digest, Vol 1 #637 - 1 msg >>> >>> >>> 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: Loading Prosite DB (Kumar, Sanjeev (Contr)) >>> >>> --__--__-- >>> >>> Message: 1 >>> Subject: RE: [GUSDEV] Loading Prosite DB >>> Date: Tue, 2 Aug 2005 17:04:05 -0400 >>> From: "Kumar, Sanjeev \(Contr\)" <San...@ng...> >>> To: "Aaron J. Mackey" <am...@pc...> >>> Cc: "Jian Lu" <jl...@vb...>, >>> <gus...@li...> >>> >>> So, The PlugIn which you are writing will not be taking care >>> detail = >>> Prosite data, right? >>> If yes then I will write a separate plugin to load detail Prosite >>> master = >>> data. >>> >>> Thanks >>> Sanjeev >>> >>> -----Original Message----- >>> From: Aaron J. Mackey [mailto:am...@pc...] >>> Sent: Tuesday, August 02, 2005 5:01 PM >>> To: Kumar, Sanjeev (Contr) >>> Cc: Jian Lu; gus...@li... >>> Subject: Re: [GUSDEV] Loading Prosite DB >>> >>> >>> Yes, InterProScan only provides domain analysis results, not the =20 >>> actual domain/pattern/motif databases themselves. >>> >>> -Aaron >>> >>> On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote: >>> >>> >>> >>> >>>> Hi Aaron/Jian, >>>> The Interproscan data has only PrositeID and description in >>>> it. =20 >>>> But to load other information for a prosite ID, we need to load >>>> the =20 >>>> Prosite data which comes in different format than Interpro. >>>> That is what I found, Do you copy? >>>> >>>> Thanks >>>> Sanjeev >>>> >>>> -----Original Message----- >>>> From: Aaron J. Mackey [mailto:am...@pc...] >>>> Sent: Tuesday, August 02, 2005 4:43 PM >>>> To: Jian Lu >>>> Cc: Kumar, Sanjeev (Contr) >>>> Subject: Re: [GUSDEV] Loading Prosite DB >>>> >>>> >>>> >>>> From http://www.ebi.ac.uk/interpro/README1.html >>>> >>>> PROSITE patterns. >>>> >>>> Some biologically significant amino acid patterns can be summarised >>>> in the form of regular expressions. >>>> >>>> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R. >>>> 1994) . >>>> >>>> PROSITE profile. >>>> >>>> There are a number of protein families as well as functional or >>>> structural domains that cannot be detected using patterns due to >>>> their extreme sequence divergence; the use of techniques based on >>>> weight matrices (also known as profiles) allows the detection of >>>> such >>>> domains. >>>> >>>> pfscan from thePftools package (by >>>> Phi...@is...). >>>> >>>> PRINTS. >>>> The PRINTS database houses a collection of protein family >>>> fingerprints. These are groups of motifs that together are >>>> diagnostically more potent than single motifs by making use of the >>>> biological context inherent in a multiple-motif method. >>>> >>>> FingerPRINTScan (Scordis, P. et al. 1999) . >>>> >>>> PFAM. >>>> Pfam is a database of protein domain families. Pfam contains >>>> curated >>>> multiple sequence alignments for each family and corresponding >>>> profile hidden Markov models (HMMs). >>>> >>>> hmmpfam from theHMMER2.1 package (by Sean Eddy, >>>> ed...@ge..., http://hmmer.wustl.edu), >>>> DeCypher=99 (TimeLogic) implementation of HMM search. >>>> >>>> PRODOM. >>>> ProDom families are built by an automated process based on a >>>> recursive use ofPSI-BLAST homology searches. >>>> >>>> BlastProDom.pl (by Florence Servant, >>>> fse...@to...) >>>> =96 a filter on top of theBlast package (Altschul, S. F. et al. >>>> 1997) = >>>> >>>> >>>> >>> . >>> >>> >>> >>>> >>>> SMART. >>>> SMART domains are extensively annotated with respect to phyletic >>>> distributions, functional class, tertiary structures and >>>> functionally >>>> important residues. SMART alignments are optimised manually and >>>> following construction of corresponding hidden Markov models >>>> (HMMs). >>>> >>>> hmmpfam from theHMMER2.1 package. >>>> >>>> TIGRFAMs. >>>> TIGRFAMs are a collection of protein families featuring curated >>>> multiple sequence alignments, Hidden Markov Models (HMMs) and >>>> associated information designed to support the automated functional >>>> identification of proteins by sequence homology. Classification by >>>> equivalog family (see below), where achievable, complements >>>> classification by orthologs, superfamily, domain or motif. It >>>> provides the information best suited for automatic assignment of >>>> specific functions to proteins from large scale genome sequencing >>>> projects >>>> >>>> =D8 hmmpfam from theHMMER2.1 package. >>>> >>>> Optionally, predictions for coiled-coil, signal peptide cleavage >>>> sites (SignalP v2) and TM helices (TMHMM v2) are supported. >>>> >>>> >>>> >>>> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote: >>>> >>>> >>>> >>>> >>>> >>>>> I don't think so. Here is the data sheet from InterProScan. >>>>> >>>>> Kumar, Sanjeev (Contr) wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> Hi Aaron/Jian, >>>>>> What all types of data we are talking in IterProScan plugin? >>>>>> Does it include Prosite data. >>>>>> Thanks >>>>>> Sanjeev >>>>>> >>>>>> -----Original Message----- >>>>>> From: Jian Lu [mailto:jl...@vb...] >>>>>> Sent: Tuesday, August 02, 2005 2:02 PM >>>>>> To: Aaron J. Mackey >>>>>> Cc: Kumar, Sanjeev (Contr); gus...@li... >>>>>> Subject: Re: [GUSDEV] Loading Prosite DB >>>>>> >>>>>> >>>>>> Aaron, >>>>>> >>>>>> We are also working on InterProScan and other analysis tools. But >>>>>> we haven't got a plugin yet. If your plugin is ready, I would >>>>>> like >>>>>> to play it. Here is the view that we created for InterProScan. >>>>>> Please comment it. Thanks. >>>>>> >>>>>> -- >>>>>> -- VIEW DOTS.INTERPROSCAN >>>>>> -- used to store outputs from InterProScan >>>>>> -- June 29, 2005 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> <InterProScan_OUTPUT.pdf> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Aaron J. Mackey, Ph.D. >>>> Project Manager, ApiDB Bioinformatics Resource Center >>>> Penn Genomics Institute, University of Pennsylvania >>>> email: am...@pc... >>>> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) >>>> fax: 215-746-6697 >>>> postal: Penn Genomics Institute >>>> Goddard Labs 212 >>>> 415 S. University Avenue >>>> Philadelphia, PA 19104-6017 >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> SF.Net email is sponsored by: Discover Easy Linux Migration >>>> Strategies >>>> from IBM. Find simple to follow Roadmaps, straightforward articles, >>>> informative Webcasts and more! Get everything you need to get up to >>>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >>>> >>> >>> -- >>> Aaron J. Mackey, Ph.D. >>> Project Manager, ApiDB Bioinformatics Resource Center >>> Penn Genomics Institute, University of Pennsylvania >>> email: am...@pc... >>> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) >>> fax: 215-746-6697 >>> postal: Penn Genomics Institute >>> Goddard Labs 212 >>> 415 S. University Avenue >>> Philadelphia, PA 19104-6017 >>> >>> >>> >>> >>> >>> --__--__-- >>> >>> _______________________________________________ >>> 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 >>> >>> >>> >> >> >> >> ------------------------------------------------------- >> 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 >> >> > > -- > Aaron J. Mackey, Ph.D. > Project Manager, ApiDB Bioinformatics Resource Center > Penn Genomics Institute, University of Pennsylvania > email: am...@pc... > office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) > fax: 215-746-6697 > postal: Penn Genomics Institute > Goddard Labs 212 > 415 S. University Avenue > Philadelphia, PA 19104-6017 > > |
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From: Chris S. <sto...@pc...> - 2005-08-04 22:05:33
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Dear Jian,
No problem with your first two proposals to add comment_name_id and
AAFeatureComment. Should be able to address in an upcoming minor
release. However, these will be ALTER TABLE to add comment_name_id to
existing tables NAComment and NAFeatureComment rather than creating
tables.
Should also be no problem accepting the third proposal for
AAFeatureRelationship and AAFeatRelationshipType however our policy
has been to NOT add tables just for consistency in order to avoid
schema bloat with tables that no one uses. Do you (or anyone else)
have use cases for these? It will help in the documentation.
Thanks,
Chris
To store curation comments has been our concern for a while. By
looking at NA
and AA comment tables, they couldn't meet such needs.
1. there is no way you can tell the type of comments from NAComment and
NAFeatureComment tables so that comment_name_id is needed as a
foreign key
reference to CommentName table.
2. To add curation comments to AA features from protein annotation,
new table
AAFeatureComment is needed.
3. To keep feature relationship, there are tables
NAFEATRELATIONSHIPTYPE and
NAFEATURERELATIONSHIP. But there are no such tables on AA. To make
consistent
and systematic schema and have potential relationship between AA
features,
similar tables AAFEATRELATIONSHIPTYPE and AAFEATURERELATIONSHIP are
needed.
Following are SQL for those changes.
CREATE TABLE DoTS.NAComment (
NA_COMMENT_ID NUMBER(10,0) NOT NULL,
NA_SEQUENCE_ID NUMBER(10,0) NOT NULL,
COMMENT_NAME_ID(10,0),
COMMENT_STRING CLOB NOT NULL,
MODIFICATION_DATE DATE NOT NULL,
USER_READ NUMBER(1,0) NOT NULL,
USER_WRITE NUMBER(1,0) NOT NULL,
GROUP_READ NUMBER(1,0) NOT NULL,
GROUP_WRITE NUMBER(1,0) NOT NULL,
OTHER_READ NUMBER(1,0) NOT NULL,
OTHER_WRITE NUMBER(1,0) NOT NULL,
ROW_USER_ID NUMBER(12,0) NOT NULL,
ROW_GROUP_ID NUMBER(4,0) NOT NULL,
ROW_PROJECT_ID NUMBER(4,0) NOT NULL,
ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL);
ALTER TABLE DOTS.NAComment ADD CONSTRAINT NAComment_FK
FOREIGN KEY (COMMENT_NAME_ID) REFERENCES DOTS.CommentName
(COMMENT_NAME_ID);
CREATE TABLE DoTS.NAFeatureComment (
NA_Feature_COMMENT_ID NUMBER(10,0) NOT NULL,
NA_Feature_ID NUMBER(10,0) NOT NULL,
COMMENT_NAME_ID(10,0),
COMMENT_STRING CLOB NOT NULL,
MODIFICATION_DATE DATE NOT NULL,
USER_READ NUMBER(1,0) NOT NULL,
USER_WRITE NUMBER(1,0) NOT NULL,
GROUP_READ NUMBER(1,0) NOT NULL,
GROUP_WRITE NUMBER(1,0) NOT NULL,
OTHER_READ NUMBER(1,0) NOT NULL,
OTHER_WRITE NUMBER(1,0) NOT NULL,
ROW_USER_ID NUMBER(12,0) NOT NULL,
ROW_GROUP_ID NUMBER(4,0) NOT NULL,
ROW_PROJECT_ID NUMBER(4,0) NOT NULL,
ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL);
ALTER TABLE DOTS.NAFeatureComment ADD CONSTRAINT NAFeatureComment_FK
FOREIGN KEY (COMMENT_NAME_ID) REFERENCES DOTS.CommentName
(COMMENT_NAME_ID);
CREATE TABLE DoTS.AAFeatureComment (
AA_Feature_COMMENT_ID NUMBER(10,0) NOT NULL,
AA_Feature_ID NUMBER(10,0) NOT NULL,
COMMENT_NAME_ID(10,0),
COMMENT_STRING CLOB NOT NULL,
MODIFICATION_DATE DATE NOT NULL,
USER_READ NUMBER(1,0) NOT NULL,
USER_WRITE NUMBER(1,0) NOT NULL,
GROUP_READ NUMBER(1,0) NOT NULL,
GROUP_WRITE NUMBER(1,0) NOT NULL,
OTHER_READ NUMBER(1,0) NOT NULL,
OTHER_WRITE NUMBER(1,0) NOT NULL,
ROW_USER_ID NUMBER(12,0) NOT NULL,
ROW_GROUP_ID NUMBER(4,0) NOT NULL,
ROW_PROJECT_ID NUMBER(4,0) NOT NULL,
ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL);
ALTER TABLE DOTS.AAFeatureComment ADD CONSTRAINT AAFeatureComment_FK
FOREIGN KEY (COMMENT_NAME_ID) REFERENCES DOTS.CommentName
(COMMENT_NAME_ID);
CREATE TABLE DoTS.AAFeatRelationshipType (
AA_FEAT_RELATIONSHIP_TYPE_ID NUMBER(10,0) PRIMARY KEY,
NAME VARCHAR2(255) NOT NULL,
DESCRIPTION CLOB NOT NULL,
MODIFICATION_DATE DATE NOT NULL,
USER_READ NUMBER(1,0) NOT NULL,
USER_WRITE NUMBER(1,0) NOT NULL,
GROUP_READ NUMBER(1,0) NOT NULL,
GROUP_WRITE NUMBER(1,0) NOT NULL,
OTHER_READ NUMBER(1,0) NOT NULL,
OTHER_WRITE NUMBER(1,0) NOT NULL,
ROW_USER_ID NUMBER(12,0) NOT NULL,
ROW_GROUP_ID NUMBER(4,0) NOT NULL,
ROW_PROJECT_ID NUMBER(4,0) NOT NULL,
ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL);
CREATE TABLE DoTS.AAFeatureRelationship (
AA_Feature_RELATIONSHIP_ID NUMBER(10,0) PRIMARY KEY,
PARENT_AA_Feature_ID NUMBER(10,0) NOT NULL,
CHILD_AA_Feature_ID NUMBER(10,0) NOT NULL,
AA_FEAT_RELATIONSHIP_TYPE_ID NUMBER(10,0) NOT NULL,
ORDINAL NUMBER(10,0) ,
MODIFICATION_DATE DATE NOT NULL,
USER_READ NUMBER(1,0) NOT NULL,
USER_WRITE NUMBER(1,0) NOT NULL,
GROUP_READ NUMBER(1,0) NOT NULL,
GROUP_WRITE NUMBER(1,0) NOT NULL,
OTHER_READ NUMBER(1,0) NOT NULL,
OTHER_WRITE NUMBER(1,0) NOT NULL,
ROW_USER_ID NUMBER(12,0) NOT NULL,
ROW_GROUP_ID NUMBER(4,0) NOT NULL,
ROW_PROJECT_ID NUMBER(4,0) NOT NULL,
ROW_ALG_INVOCATION_ID NUMBER(12,0) NOT NULL);
ALTER TABLE DoTS.AAFeatureRelationship ADD CONSTRAINT
AAFeatureRELATIONSHIP_FK1
FOREIGN KEY (PARENT_AA_Feature_ID) REFERENCES DoTS.AAFeatureImp
(AA_Feature_ID);
ALTER TABLE DoTS.AAFeatureRelationship ADD CONSTRAINT
AAFeatureRELATIONSHIP_FK2
FOREIGN KEY (CHILD_AA_Feature_ID) REFERENCES DoTS.AAFeatureImp
(AA_Feature_ID);
ALTER TABLE DoTS.AAFeatureRelationship ADD CONSTRAINT
AAFeatureRELATIONSHIP_FK3
FOREIGN KEY (AA_FEAT_RELATIONSHIP_TYPE_ID) REFERENCES
DoTS.AAFeatRelationshipType (AA_FEAT_RELATIONSHIP_TYPE_ID); |
|
From: Aaron J. M. <am...@pc...> - 2005-08-04 19:14:41
|
A Prosite entry is a (regular expression or profile-based) sequence motif. So it's none of the above. I believe we are going to handle Prosite (and other InterProScan- related datasets) simply as DbRefs, and not try to store their actual definitions (thus linking out to expasy, etc. as necessary). -Aaron On Aug 4, 2005, at 2:56 PM, Chris Stoeckert wrote: > Hi Sanjeev, > I guess the first thing to decide is if this entry represents a > sequence, a feature, or an annotation. Do you (or anyone else) have > strong opinions on this? Can you send an example entry? > Thanks, > Chris > > On Aug 4, 2005, at 12:35 PM, Kumar, Sanjeev (Contr) wrote: > > >> Hi, >> Now let us figure out which GUS table to used to store PrositeDB >> master data. >> Can any one help me in that please? >> Following type of information it contains: >> ID Identification (Begins each entry; 1 per entry) >> AC Accession number (1 per entry) >> DT Date (1 per entry) >> DE Short description (1 per entry) >> PA Pattern (>1 per entry) >> MA Matrix/profile (>1 per entry) >> RU Rule (>1 per entry) >> NR Numerical results (>1 per entry) >> CC Comments (>=1 per entry) >> DR Cross-references to Swiss-Prot (>1 per entry) >> 3D Cross-references to PDB (>1 per entry) >> DO Pointer to the documentation file (1 per entry) >> >> Any help on this will be appreciated. >> >> >> Thanks >> Sanjeev >> >> -----Original Message----- >> From: gus...@li... >> [mailto:gus...@li...]On Behalf Of >> gus...@li... >> Sent: Tuesday, August 02, 2005 11:09 PM >> To: gus...@li... >> Subject: Gusdev-gusdev digest, Vol 1 #637 - 1 msg >> >> >> 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: Loading Prosite DB (Kumar, Sanjeev (Contr)) >> >> --__--__-- >> >> Message: 1 >> Subject: RE: [GUSDEV] Loading Prosite DB >> Date: Tue, 2 Aug 2005 17:04:05 -0400 >> From: "Kumar, Sanjeev \(Contr\)" <San...@ng...> >> To: "Aaron J. Mackey" <am...@pc...> >> Cc: "Jian Lu" <jl...@vb...>, >> <gus...@li...> >> >> So, The PlugIn which you are writing will not be taking care detail = >> Prosite data, right? >> If yes then I will write a separate plugin to load detail Prosite >> master = >> data. >> >> Thanks >> Sanjeev >> >> -----Original Message----- >> From: Aaron J. Mackey [mailto:am...@pc...] >> Sent: Tuesday, August 02, 2005 5:01 PM >> To: Kumar, Sanjeev (Contr) >> Cc: Jian Lu; gus...@li... >> Subject: Re: [GUSDEV] Loading Prosite DB >> >> >> Yes, InterProScan only provides domain analysis results, not the =20 >> actual domain/pattern/motif databases themselves. >> >> -Aaron >> >> On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote: >> >> >> >>> Hi Aaron/Jian, >>> The Interproscan data has only PrositeID and description in >>> it. =20 >>> But to load other information for a prosite ID, we need to load >>> the =20 >>> Prosite data which comes in different format than Interpro. >>> That is what I found, Do you copy? >>> >>> Thanks >>> Sanjeev >>> >>> -----Original Message----- >>> From: Aaron J. Mackey [mailto:am...@pc...] >>> Sent: Tuesday, August 02, 2005 4:43 PM >>> To: Jian Lu >>> Cc: Kumar, Sanjeev (Contr) >>> Subject: Re: [GUSDEV] Loading Prosite DB >>> >>> >>> >>> From http://www.ebi.ac.uk/interpro/README1.html >>> >>> PROSITE patterns. >>> >>> Some biologically significant amino acid patterns can be summarised >>> in the form of regular expressions. >>> >>> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R. >>> 1994) . >>> >>> PROSITE profile. >>> >>> There are a number of protein families as well as functional or >>> structural domains that cannot be detected using patterns due to >>> their extreme sequence divergence; the use of techniques based on >>> weight matrices (also known as profiles) allows the detection of >>> such >>> domains. >>> >>> pfscan from thePftools package (by Phi...@is...). >>> >>> PRINTS. >>> The PRINTS database houses a collection of protein family >>> fingerprints. These are groups of motifs that together are >>> diagnostically more potent than single motifs by making use of the >>> biological context inherent in a multiple-motif method. >>> >>> FingerPRINTScan (Scordis, P. et al. 1999) . >>> >>> PFAM. >>> Pfam is a database of protein domain families. Pfam contains curated >>> multiple sequence alignments for each family and corresponding >>> profile hidden Markov models (HMMs). >>> >>> hmmpfam from theHMMER2.1 package (by Sean Eddy, >>> ed...@ge..., http://hmmer.wustl.edu), >>> DeCypher=99 (TimeLogic) implementation of HMM search. >>> >>> PRODOM. >>> ProDom families are built by an automated process based on a >>> recursive use ofPSI-BLAST homology searches. >>> >>> BlastProDom.pl (by Florence Servant, >>> fse...@to...) >>> =96 a filter on top of theBlast package (Altschul, S. F. et al. >>> 1997) = >>> >>> >> . >> >> >>> >>> SMART. >>> SMART domains are extensively annotated with respect to phyletic >>> distributions, functional class, tertiary structures and >>> functionally >>> important residues. SMART alignments are optimised manually and >>> following construction of corresponding hidden Markov models (HMMs). >>> >>> hmmpfam from theHMMER2.1 package. >>> >>> TIGRFAMs. >>> TIGRFAMs are a collection of protein families featuring curated >>> multiple sequence alignments, Hidden Markov Models (HMMs) and >>> associated information designed to support the automated functional >>> identification of proteins by sequence homology. Classification by >>> equivalog family (see below), where achievable, complements >>> classification by orthologs, superfamily, domain or motif. It >>> provides the information best suited for automatic assignment of >>> specific functions to proteins from large scale genome sequencing >>> projects >>> >>> =D8 hmmpfam from theHMMER2.1 package. >>> >>> Optionally, predictions for coiled-coil, signal peptide cleavage >>> sites (SignalP v2) and TM helices (TMHMM v2) are supported. >>> >>> >>> >>> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote: >>> >>> >>> >>> >>>> I don't think so. Here is the data sheet from InterProScan. >>>> >>>> Kumar, Sanjeev (Contr) wrote: >>>> >>>> >>>> >>>> >>>> >>>>> Hi Aaron/Jian, >>>>> What all types of data we are talking in IterProScan plugin? >>>>> Does it include Prosite data. >>>>> Thanks >>>>> Sanjeev >>>>> >>>>> -----Original Message----- >>>>> From: Jian Lu [mailto:jl...@vb...] >>>>> Sent: Tuesday, August 02, 2005 2:02 PM >>>>> To: Aaron J. Mackey >>>>> Cc: Kumar, Sanjeev (Contr); gus...@li... >>>>> Subject: Re: [GUSDEV] Loading Prosite DB >>>>> >>>>> >>>>> Aaron, >>>>> >>>>> We are also working on InterProScan and other analysis tools. But >>>>> we haven't got a plugin yet. If your plugin is ready, I would like >>>>> to play it. Here is the view that we created for InterProScan. >>>>> Please comment it. Thanks. >>>>> >>>>> -- >>>>> -- VIEW DOTS.INTERPROSCAN >>>>> -- used to store outputs from InterProScan >>>>> -- June 29, 2005 >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> <InterProScan_OUTPUT.pdf> >>>> >>>> >>>> >>>> >>> >>> -- >>> Aaron J. Mackey, Ph.D. >>> Project Manager, ApiDB Bioinformatics Resource Center >>> Penn Genomics Institute, University of Pennsylvania >>> email: am...@pc... >>> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) >>> fax: 215-746-6697 >>> postal: Penn Genomics Institute >>> Goddard Labs 212 >>> 415 S. University Avenue >>> Philadelphia, PA 19104-6017 >>> >>> >>> >>> >>> ------------------------------------------------------- >>> SF.Net email is sponsored by: Discover Easy Linux Migration >>> Strategies >>> from IBM. Find simple to follow Roadmaps, straightforward articles, >>> informative Webcasts and more! Get everything you need to get up to >>> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >> >> -- >> Aaron J. Mackey, Ph.D. >> Project Manager, ApiDB Bioinformatics Resource Center >> Penn Genomics Institute, University of Pennsylvania >> email: am...@pc... >> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) >> fax: 215-746-6697 >> postal: Penn Genomics Institute >> Goddard Labs 212 >> 415 S. University Avenue >> Philadelphia, PA 19104-6017 >> >> >> >> >> >> --__--__-- >> >> _______________________________________________ >> 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 >> >> > > > > ------------------------------------------------------- > 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 > -- Aaron J. Mackey, Ph.D. Project Manager, ApiDB Bioinformatics Resource Center Penn Genomics Institute, University of Pennsylvania email: am...@pc... office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) fax: 215-746-6697 postal: Penn Genomics Institute Goddard Labs 212 415 S. University Avenue Philadelphia, PA 19104-6017 |
|
From: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-04 19:02:24
|
Hi Chris, Here is the sample example, It doesn't have any sequence.=20 ID ASX_HYDROXYL; PATTERN. AC PS00010; DT APR-1990 (CREATED); APR-1990 (DATA UPDATE); APR-2005 (INFO UPDATE). DE Aspartic acid and asparagine hydroxylation site. PA C-x-[DN]-x(4)-[FY]-x-C-x-C. NR /RELEASE=3D46.6,180652; NR /TOTAL=3D1358(269); /POSITIVE=3D1342(260); /UNKNOWN=3D0(0); = /FALSE_POS=3D16(9); NR /FALSE_NEG=3D0; /PARTIAL=3D0; CC /TAXO-RANGE=3D??E??; /MAX-REPEAT=3D43; CC /SITE=3D3,hydroxylation; CC /VERSION=3D1; DR P31696, AGRN_CHICK , T; Q90404, AGRN_DISOM , T; P13497, BMP1_HUMAN = , T; DR P98063, BMP1_MOUSE , T; P98070, BMP1_XENLA , T; P98069, BMPH_STRPU = , T; DR Q9NPY3, C1QR1_HUMAN, T; O89103, C1QR1_MOUSE, T; Q9ET61, C1QR1_RAT = , T; DR P00736, C1R_HUMAN , T; Q8CG16, C1R_MOUSE , T; Q5R1W3, C1R_PANTR = , T; DR P09871, C1S_HUMAN , T; P15156, CASP_MESAU , T; Q8SQA4, CD97_BOVIN = , T; DR P48960, CD97_HUMAN , T; Q9Z0M6, CD97_MOUSE , T; Q9NYQ6, = CELR1_HUMAN, T; DR O35161, CELR1_MOUSE, T; Q9HCU4, CELR2_HUMAN, T; Q9R0M0, = CELR2_MOUSE, T; DR Q9QYP2, CELR2_RAT , T; Q9NYQ7, CELR3_HUMAN, T; Q91ZI0, = CELR3_MOUSE, T; DR O88278, CELR3_RAT , T; Q86T13, CN027_HUMAN, T; Q8VCP9, = CN027_MOUSE, T; DR P10040, CRB_DROME , T; P82279, CRUM1_HUMAN, T; P81282, = CSPG2_BOVIN, T; DR Q90953, CSPG2_CHICK, T; P13611, CSPG2_HUMAN, T; Q28858, = CSPG2_MACNE, T; DR Q62059, CSPG2_MOUSE, T; Q9ERB4, CSPG2_RAT , T; O14594, = CSPG3_HUMAN, T; DR P55066, CSPG3_MOUSE, T; Q5IS41, CSPG3_PANTR, T; P55067, CSPG3_RAT = , T; DR P80370, DLK_HUMAN , T; Q09163, DLK_MOUSE , T; O00548, DLL1_HUMAN = , T; DR Q61483, DLL1_MOUSE , T; P97677, DLL1_RAT , T; Q9NR61, DLL4_HUMAN = , T; DR Q9JI71, DLL4_MOUSE , T; P10041, DL_DROME , T; O43854, = EDIL3_HUMAN, T; DR O35474, EDIL3_MOUSE, T; O75095, EGFL3_HUMAN, T; O88281, EGFL3_RAT = , T; DR Q7Z7M0, EGFL4_HUMAN, T; P60882, EGFL4_MOUSE, T; Q9QYP0, EGFL4_RAT = , T; DR Q9UHF1, EGFL7_HUMAN, T; Q6AZ60, EGFL7_RAT , T; Q99944, = EGFL8_HUMAN, T; DR Q6GUQ1, EGFL8_MOUSE, T; Q6MG84, EGFL8_RAT , T; Q6UY11, = EGFL9_HUMAN, T; DR Q8K1E3, EGFL9_MOUSE, T; Q9BEA0, EGF_CANFA , T; Q95ND4, EGF_FELCA = , T; DR P01133, EGF_HUMAN , T; P01132, EGF_MOUSE , T; Q00968, EGF_PIG = , T; DR P07522, EGF_RAT , T; Q9HBW9, ELTD1_HUMAN, T; Q923X1, = ELTD1_MOUSE, T; DR Q9ESC1, ELTD1_RAT , T; Q14246, EMR1_HUMAN , T; Q61549, EMR1_MOUSE = , T; DR Q9UHX3, EMR2_HUMAN , T; Q9BY15, EMR3_HUMAN , T; Q86SQ3, EMR4_HUMAN = , T; DR Q91ZE5, EMR4_MOUSE , T; P00743, FA10_BOVIN , T; P25155, FA10_CHICK = , T; DR P83370, FA10_HOPST , T; P00742, FA10_HUMAN , T; O88947, FA10_MOUSE = , T; DR O19045, FA10_RABIT , T; Q63207, FA10_RAT , T; P81428, FA10_TROCA = , T; DR P22457, FA7_BOVIN , T; P08709, FA7_HUMAN , T; P70375, FA7_MOUSE = , T; DR P98139, FA7_RABIT , T; Q8K3U6, FA7_RAT , T; P00741, FA9_BOVIN = , T; DR P19540, FA9_CANFA , T; Q804X6, FA9_CHICK , T; Q6SA95, FA9_FELCA = , T; DR P00740, FA9_HUMAN , T; P16294, FA9_MOUSE , T; Q95ND7, FA9_PANTR = , T; DR P16293, FA9_PIG , T; Q9VW71, FAT2_DROME , T; Q14517, FATH_HUMAN = , T; DR O42182, FBLN1_BRARE, T; O77469, FBLN1_CAEEL, T; Q8MJJ9, = FBLN1_CERAE, T; DR O73775, FBLN1_CHICK, T; P23142, FBLN1_HUMAN, T; Q08879, = FBLN1_MOUSE, T; DR P98095, FBLN2_HUMAN, T; P37889, FBLN2_MOUSE, T; Q12805, = FBLN3_HUMAN, T; DR Q7YQD7, FBLN3_MACFA, T; Q8BPB5, FBLN3_MOUSE, T; O35568, FBLN3_RAT = , T; DR O55058, FBLN4_CRIGR, T; O95967, FBLN4_HUMAN, T; Q9WVJ9, = FBLN4_MOUSE, T; DR Q9UBX5, FBLN5_HUMAN, T; Q9WVH9, FBLN5_MOUSE, T; Q9WVH8, FBLN5_RAT = , T; DR P98133, FBN1_BOVIN , T; P35555, FBN1_HUMAN , T; Q61554, FBN1_MOUSE = , T; DR Q9TV36, FBN1_PIG , T; P35556, FBN2_HUMAN , T; Q61555, FBN2_MOUSE = , T; DR Q75N90, FBN3_HUMAN , T; P10079, FBP1_STRPU , T; P49013, FBP3_STRPU = , T; DR Q25464, FP2_MYTGA , T; Q14393, GAS6_HUMAN , T; Q61592, GAS6_MOUSE = , T; DR Q63772, GAS6_RAT , T; P13508, GLP1_CAEEL , T; Q90Y57, = JAG1A_BRARE, T; DR Q90Y54, JAG1B_BRARE, T; P78504, JAG1_HUMAN , T; Q9QXX0, JAG1_MOUSE = , T; DR Q63722, JAG1_RAT , T; Q9Y219, JAG2_HUMAN , T; Q9QYE5, JAG2_MOUSE = , T; DR P97607, JAG2_RAT , T; Q99087, LDLR1_XENLA, T; Q99088, = LDLR2_XENLA, T; DR P35950, LDLR_CRIGR , T; P01130, LDLR_HUMAN , T; P35951, LDLR_MOUSE = , T; DR Q28832, LDLR_PIG , T; P20063, LDLR_RABIT , T; P35952, LDLR_RAT = , T; DR P14585, LIN12_CAEEL, T; Q9NZR2, LRP1B_HUMAN, T; Q9JI18, = LRP1B_MOUSE, T; DR P98157, LRP1_CHICK , T; Q07954, LRP1_HUMAN , T; P98164, LRP2_HUMAN = , T; DR P98158, LRP2_RAT , T; O75096, LRP4_HUMAN , T; Q8VI56, LRP4_MOUSE = , T; DR Q9QYP1, LRP4_RAT , T; Q98931, LRP8_CHICK , T; Q14114, LRP8_HUMAN = , T; DR Q924X6, LRP8_MOUSE , T; Q04833, LRP_CAEEL , T; Q14766, = LTB1L_HUMAN, T; DR Q8CG19, LTB1L_MOUSE, T; P22064, LTB1S_HUMAN, T; Q8CG18, = LTB1S_MOUSE, T; DR Q00918, LTBP1_RAT , T; Q28019, LTBP2_BOVIN, T; Q14767, = LTBP2_HUMAN, T; DR O08999, LTBP2_MOUSE, T; O35806, LTBP2_RAT , T; Q9NS15, = LTBP3_HUMAN, T; DR Q61810, LTBP3_MOUSE, T; Q8K4G1, LTBP4_MOUSE, T; P48740, = MASP1_HUMAN, T; DR P98064, MASP1_MOUSE, T; O00187, MASP2_HUMAN, T; O00339, = MATN2_HUMAN, T; DR O08746, MATN2_MOUSE, T; O95460, MATN4_HUMAN, T; O89029, = MATN4_MOUSE, T; DR P34576, MUA3_CAEEL , T; Q20176, NAS39_CAEEL, T; Q92832, = NELL1_HUMAN, T; DR Q62919, NELL1_RAT , T; Q99435, NELL2_HUMAN, T; Q61220, = NELL2_MOUSE, T; DR Q62918, NELL2_RAT , T; Q90827, NEL_CHICK , T; Q14112, NID2_HUMAN = , T; DR O88322, NID2_MOUSE , T; P14543, NIDO_HUMAN , T; P10493, NIDO_MOUSE = , T; DR P08460, NIDO_RAT , T; P46530, NOTC1_BRARE, T; P46531, = NOTC1_HUMAN, T; DR Q01705, NOTC1_MOUSE, T; Q07008, NOTC1_RAT , T; Q04721, = NOTC2_HUMAN, T; DR O35516, NOTC2_MOUSE, T; Q9QW30, NOTC2_RAT , T; Q9UM47, = NOTC3_HUMAN, T; DR Q61982, NOTC3_MOUSE, T; Q9R172, NOTC3_RAT , T; Q99466, = NOTC4_HUMAN, T; DR P31695, NOTC4_MOUSE, T; P07207, NOTCH_DROME, T; P21783, = NOTCH_XENLA, T; DR Q28146, NRX1A_BOVIN, T; Q9DDD0, NRX1A_CHICK, T; Q9ULB1, = NRX1A_HUMAN, T; DR Q63372, NRX1A_RAT , T; Q9Y4C0, NRX3A_HUMAN, T; Q07310, NRX3A_RAT = , T; DR Q8HYB7, PERT_CANFA , T; P07202, PERT_HUMAN , T; P35419, PERT_MOUSE = , T; DR P14650, PERT_RAT , T; P13608, PGCA_BOVIN , T; Q28343, PGCA_CANFA = , T; DR P07898, PGCA_CHICK , T; P00745, PROC_BOVIN , T; Q28278, PROC_CANFA = , T; DR P04070, PROC_HUMAN , T; P33587, PROC_MOUSE , T; Q9GLP2, PROC_PIG = , T; DR Q28661, PROC_RABIT , T; P31394, PROC_RAT , T; P07224, PROS_BOVIN = , T; DR P07225, PROS_HUMAN , T; Q28520, PROS_MACMU , T; Q08761, PROS_MOUSE = , T; DR P98118, PROS_RABIT , T; P53813, PROS_RAT , T; P00744, PROZ_BOVIN = , T; DR P22891, PROZ_HUMAN , T; Q9CQW3, PROZ_MOUSE , T; P18168, SERR_DROME = , T; DR O94813, SLIT2_HUMAN, T; P24014, SLIT_DROME , T; Q07929, SP63_STRPU = , T; DR Q26627, SUREJ_STRPU, T; P25723, TLD_DROME , T; O57460, TLL1_BRARE = , T; DR P06579, TRBM_BOVIN , T; Q5W7P8, TRBM_CANFA , T; P07204, TRBM_HUMAN = , T; DR P15306, TRBM_MOUSE , T; Q71U07, TRBM_SAISC , T; P48733, UROM_BOVIN = , T; DR Q862Z3, UROM_CANFA , T; P07911, UROM_HUMAN , T; Q91X17, UROM_MOUSE = , T; DR P27590, UROM_RAT , T; P98165, VLDLR_CHICK, T; P98155, = VLDLR_HUMAN, T; DR P98156, VLDLR_MOUSE, T; P35953, VLDLR_RABIT, T; P98166, VLDLR_RAT = , T; DR P41950, YLK2_CAEEL , T; P98163, YL_DROME , T; DR O15943, CADN_DROME , F; Q13201, MMRN1_HUMAN, F; O75093, = SLIT1_HUMAN, F; DR Q80TR4, SLIT1_MOUSE, F; O88279, SLIT1_RAT , F; Q9R1B9, = SLIT2_MOUSE, F; DR O75094, SLIT3_HUMAN, F; Q9WVB4, SLIT3_MOUSE, F; O88280, SLIT3_RAT = , F; 3D 1APO; 1APQ; 1AUT; 1BF9; 1CCF; 1DAN; 1DVA; 1DX5; 1EDM; 1EMN; 1EMO; = 1F7E; 3D 1F7M; 1FAK; 1FF7; 1FFM; 1GL4; 1HJ7; 1HZ8; 1I0U; 1IXA; 1J9C; 1LMJ; = 1N7D; 3D 1NL8; 1NZI; 1O5D; 1PFX; 1QFK; 1SZB; 1TOZ; 1UZJ; 1UZP; 1UZQ; 1W0Y; = 1WHE; 3D 1WHF; 1XFE; 1XKA; 1XKB; DO PDOC00010; // =20 Thanks Sanjeev -----Original Message----- From: Chris Stoeckert [mailto:sto...@pc...] Sent: Thursday, August 04, 2005 2:56 PM To: Kumar, Sanjeev (Contr) Cc: gus...@li... Subject: Re: [GUSDEV] RE: Gusdev-gusdev digest, Vol 1 #637 - 1 msg Hi Sanjeev, I guess the first thing to decide is if this entry represents a =20 sequence, a feature, or an annotation. Do you (or anyone else) have =20 strong opinions on this? Can you send an example entry? Thanks, Chris On Aug 4, 2005, at 12:35 PM, Kumar, Sanjeev (Contr) wrote: > Hi, > Now let us figure out which GUS table to used to store PrositeDB =20 > master data. > Can any one help me in that please? > Following type of information it contains: > ID Identification (Begins each entry; 1 per entry) > AC Accession number (1 per entry) > DT Date (1 per entry) > DE Short description (1 per entry) > PA Pattern (>1 per entry) > MA Matrix/profile (>1 per entry) > RU Rule (>1 per entry) > NR Numerical results (>1 per entry) > CC Comments (>=3D1 per entry) > DR Cross-references to Swiss-Prot (>1 per entry) > 3D Cross-references to PDB (>1 per entry) > DO Pointer to the documentation file (1 per entry) > > Any help on this will be appreciated. > > > Thanks > Sanjeev > > -----Original Message----- > From: gus...@li... > [mailto:gus...@li...]On Behalf Of > gus...@li... > Sent: Tuesday, August 02, 2005 11:09 PM > To: gus...@li... > Subject: Gusdev-gusdev digest, Vol 1 #637 - 1 msg > > > 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: Loading Prosite DB (Kumar, Sanjeev (Contr)) > > --__--__-- > > Message: 1 > Subject: RE: [GUSDEV] Loading Prosite DB > Date: Tue, 2 Aug 2005 17:04:05 -0400 > From: "Kumar, Sanjeev \(Contr\)" <San...@ng...> > To: "Aaron J. Mackey" <am...@pc...> > Cc: "Jian Lu" <jl...@vb...>, > <gus...@li...> > > So, The PlugIn which you are writing will not be taking care detail = =3D > Prosite data, right? > If yes then I will write a separate plugin to load detail Prosite =20 > master =3D > data. > > Thanks > Sanjeev > > -----Original Message----- > From: Aaron J. Mackey [mailto:am...@pc...] > Sent: Tuesday, August 02, 2005 5:01 PM > To: Kumar, Sanjeev (Contr) > Cc: Jian Lu; gus...@li... > Subject: Re: [GUSDEV] Loading Prosite DB > > > Yes, InterProScan only provides domain analysis results, not the =3D20 > actual domain/pattern/motif databases themselves. > > -Aaron > > On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote: > > >> Hi Aaron/Jian, >> The Interproscan data has only PrositeID and description in it. =20 >> =3D20 >> But to load other information for a prosite ID, we need to load =20 >> the =3D20 >> Prosite data which comes in different format than Interpro. >> That is what I found, Do you copy? >> >> Thanks >> Sanjeev >> >> -----Original Message----- >> From: Aaron J. Mackey [mailto:am...@pc...] >> Sent: Tuesday, August 02, 2005 4:43 PM >> To: Jian Lu >> Cc: Kumar, Sanjeev (Contr) >> Subject: Re: [GUSDEV] Loading Prosite DB >> >> >> >> From http://www.ebi.ac.uk/interpro/README1.html >> >> PROSITE patterns. >> >> Some biologically significant amino acid patterns can be summarised >> in the form of regular expressions. >> >> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R. >> 1994) . >> >> PROSITE profile. >> >> There are a number of protein families as well as functional or >> structural domains that cannot be detected using patterns due to >> their extreme sequence divergence; the use of techniques based on >> weight matrices (also known as profiles) allows the detection of such >> domains. >> >> pfscan from thePftools package (by Phi...@is...). >> >> PRINTS. >> The PRINTS database houses a collection of protein family >> fingerprints. These are groups of motifs that together are >> diagnostically more potent than single motifs by making use of the >> biological context inherent in a multiple-motif method. >> >> FingerPRINTScan (Scordis, P. et al. 1999) . >> >> PFAM. >> Pfam is a database of protein domain families. Pfam contains curated >> multiple sequence alignments for each family and corresponding >> profile hidden Markov models (HMMs). >> >> hmmpfam from theHMMER2.1 package (by Sean Eddy, >> ed...@ge..., http://hmmer.wustl.edu), >> DeCypher=3D99 (TimeLogic) implementation of HMM search. >> >> PRODOM. >> ProDom families are built by an automated process based on a >> recursive use ofPSI-BLAST homology searches. >> >> BlastProDom.pl (by Florence Servant, fse...@to...) >> =3D96 a filter on top of theBlast package (Altschul, S. F. et al. =20 >> 1997) =3D >> > . > >> >> SMART. >> SMART domains are extensively annotated with respect to phyletic >> distributions, functional class, tertiary structures and functionally >> important residues. SMART alignments are optimised manually and >> following construction of corresponding hidden Markov models (HMMs). >> >> hmmpfam from theHMMER2.1 package. >> >> TIGRFAMs. >> TIGRFAMs are a collection of protein families featuring curated >> multiple sequence alignments, Hidden Markov Models (HMMs) and >> associated information designed to support the automated functional >> identification of proteins by sequence homology. Classification by >> equivalog family (see below), where achievable, complements >> classification by orthologs, superfamily, domain or motif. It >> provides the information best suited for automatic assignment of >> specific functions to proteins from large scale genome sequencing >> projects >> >> =3DD8 hmmpfam from theHMMER2.1 package. >> >> Optionally, predictions for coiled-coil, signal peptide cleavage >> sites (SignalP v2) and TM helices (TMHMM v2) are supported. >> >> >> >> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote: >> >> >> >>> I don't think so. Here is the data sheet from InterProScan. >>> >>> Kumar, Sanjeev (Contr) wrote: >>> >>> >>> >>> >>>> Hi Aaron/Jian, >>>> What all types of data we are talking in IterProScan plugin? >>>> Does it include Prosite data. >>>> Thanks >>>> Sanjeev >>>> >>>> -----Original Message----- >>>> From: Jian Lu [mailto:jl...@vb...] >>>> Sent: Tuesday, August 02, 2005 2:02 PM >>>> To: Aaron J. Mackey >>>> Cc: Kumar, Sanjeev (Contr); gus...@li... >>>> Subject: Re: [GUSDEV] Loading Prosite DB >>>> >>>> >>>> Aaron, >>>> >>>> We are also working on InterProScan and other analysis tools. But >>>> we haven't got a plugin yet. If your plugin is ready, I would like >>>> to play it. Here is the view that we created for InterProScan. >>>> Please comment it. Thanks. >>>> >>>> -- >>>> -- VIEW DOTS.INTERPROSCAN >>>> -- used to store outputs from InterProScan >>>> -- June 29, 2005 >>>> >>>> >>>> >>>> >>> >>> >>> <InterProScan_OUTPUT.pdf> >>> >>> >>> >> >> -- >> Aaron J. Mackey, Ph.D. >> Project Manager, ApiDB Bioinformatics Resource Center >> Penn Genomics Institute, University of Pennsylvania >> email: am...@pc... >> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) >> fax: 215-746-6697 >> postal: Penn Genomics Institute >> Goddard Labs 212 >> 415 S. University Avenue >> Philadelphia, PA 19104-6017 >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration =20 >> Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=3D16492&op=3DCCk >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > -- > Aaron J. Mackey, Ph.D. > Project Manager, ApiDB Bioinformatics Resource Center > Penn Genomics Institute, University of Pennsylvania > email: am...@pc... > office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) > fax: 215-746-6697 > postal: Penn Genomics Institute > Goddard Labs 212 > 415 S. University Avenue > Philadelphia, PA 19104-6017 > > > > > > --__--__-- > > _______________________________________________ > 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 =20 > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * =20 > Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/=20 > bsce5sf > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Chris S. <sto...@pc...> - 2005-08-04 18:56:39
|
Hi Sanjeev, I guess the first thing to decide is if this entry represents a sequence, a feature, or an annotation. Do you (or anyone else) have strong opinions on this? Can you send an example entry? Thanks, Chris On Aug 4, 2005, at 12:35 PM, Kumar, Sanjeev (Contr) wrote: > Hi, > Now let us figure out which GUS table to used to store PrositeDB > master data. > Can any one help me in that please? > Following type of information it contains: > ID Identification (Begins each entry; 1 per entry) > AC Accession number (1 per entry) > DT Date (1 per entry) > DE Short description (1 per entry) > PA Pattern (>1 per entry) > MA Matrix/profile (>1 per entry) > RU Rule (>1 per entry) > NR Numerical results (>1 per entry) > CC Comments (>=1 per entry) > DR Cross-references to Swiss-Prot (>1 per entry) > 3D Cross-references to PDB (>1 per entry) > DO Pointer to the documentation file (1 per entry) > > Any help on this will be appreciated. > > > Thanks > Sanjeev > > -----Original Message----- > From: gus...@li... > [mailto:gus...@li...]On Behalf Of > gus...@li... > Sent: Tuesday, August 02, 2005 11:09 PM > To: gus...@li... > Subject: Gusdev-gusdev digest, Vol 1 #637 - 1 msg > > > 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: Loading Prosite DB (Kumar, Sanjeev (Contr)) > > --__--__-- > > Message: 1 > Subject: RE: [GUSDEV] Loading Prosite DB > Date: Tue, 2 Aug 2005 17:04:05 -0400 > From: "Kumar, Sanjeev \(Contr\)" <San...@ng...> > To: "Aaron J. Mackey" <am...@pc...> > Cc: "Jian Lu" <jl...@vb...>, > <gus...@li...> > > So, The PlugIn which you are writing will not be taking care detail = > Prosite data, right? > If yes then I will write a separate plugin to load detail Prosite > master = > data. > > Thanks > Sanjeev > > -----Original Message----- > From: Aaron J. Mackey [mailto:am...@pc...] > Sent: Tuesday, August 02, 2005 5:01 PM > To: Kumar, Sanjeev (Contr) > Cc: Jian Lu; gus...@li... > Subject: Re: [GUSDEV] Loading Prosite DB > > > Yes, InterProScan only provides domain analysis results, not the =20 > actual domain/pattern/motif databases themselves. > > -Aaron > > On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote: > > >> Hi Aaron/Jian, >> The Interproscan data has only PrositeID and description in it. >> =20 >> But to load other information for a prosite ID, we need to load >> the =20 >> Prosite data which comes in different format than Interpro. >> That is what I found, Do you copy? >> >> Thanks >> Sanjeev >> >> -----Original Message----- >> From: Aaron J. Mackey [mailto:am...@pc...] >> Sent: Tuesday, August 02, 2005 4:43 PM >> To: Jian Lu >> Cc: Kumar, Sanjeev (Contr) >> Subject: Re: [GUSDEV] Loading Prosite DB >> >> >> >> From http://www.ebi.ac.uk/interpro/README1.html >> >> PROSITE patterns. >> >> Some biologically significant amino acid patterns can be summarised >> in the form of regular expressions. >> >> ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R. >> 1994) . >> >> PROSITE profile. >> >> There are a number of protein families as well as functional or >> structural domains that cannot be detected using patterns due to >> their extreme sequence divergence; the use of techniques based on >> weight matrices (also known as profiles) allows the detection of such >> domains. >> >> pfscan from thePftools package (by Phi...@is...). >> >> PRINTS. >> The PRINTS database houses a collection of protein family >> fingerprints. These are groups of motifs that together are >> diagnostically more potent than single motifs by making use of the >> biological context inherent in a multiple-motif method. >> >> FingerPRINTScan (Scordis, P. et al. 1999) . >> >> PFAM. >> Pfam is a database of protein domain families. Pfam contains curated >> multiple sequence alignments for each family and corresponding >> profile hidden Markov models (HMMs). >> >> hmmpfam from theHMMER2.1 package (by Sean Eddy, >> ed...@ge..., http://hmmer.wustl.edu), >> DeCypher=99 (TimeLogic) implementation of HMM search. >> >> PRODOM. >> ProDom families are built by an automated process based on a >> recursive use ofPSI-BLAST homology searches. >> >> BlastProDom.pl (by Florence Servant, fse...@to...) >> =96 a filter on top of theBlast package (Altschul, S. F. et al. >> 1997) = >> > . > >> >> SMART. >> SMART domains are extensively annotated with respect to phyletic >> distributions, functional class, tertiary structures and functionally >> important residues. SMART alignments are optimised manually and >> following construction of corresponding hidden Markov models (HMMs). >> >> hmmpfam from theHMMER2.1 package. >> >> TIGRFAMs. >> TIGRFAMs are a collection of protein families featuring curated >> multiple sequence alignments, Hidden Markov Models (HMMs) and >> associated information designed to support the automated functional >> identification of proteins by sequence homology. Classification by >> equivalog family (see below), where achievable, complements >> classification by orthologs, superfamily, domain or motif. It >> provides the information best suited for automatic assignment of >> specific functions to proteins from large scale genome sequencing >> projects >> >> =D8 hmmpfam from theHMMER2.1 package. >> >> Optionally, predictions for coiled-coil, signal peptide cleavage >> sites (SignalP v2) and TM helices (TMHMM v2) are supported. >> >> >> >> On Aug 2, 2005, at 4:32 PM, Jian Lu wrote: >> >> >> >>> I don't think so. Here is the data sheet from InterProScan. >>> >>> Kumar, Sanjeev (Contr) wrote: >>> >>> >>> >>> >>>> Hi Aaron/Jian, >>>> What all types of data we are talking in IterProScan plugin? >>>> Does it include Prosite data. >>>> Thanks >>>> Sanjeev >>>> >>>> -----Original Message----- >>>> From: Jian Lu [mailto:jl...@vb...] >>>> Sent: Tuesday, August 02, 2005 2:02 PM >>>> To: Aaron J. Mackey >>>> Cc: Kumar, Sanjeev (Contr); gus...@li... >>>> Subject: Re: [GUSDEV] Loading Prosite DB >>>> >>>> >>>> Aaron, >>>> >>>> We are also working on InterProScan and other analysis tools. But >>>> we haven't got a plugin yet. If your plugin is ready, I would like >>>> to play it. Here is the view that we created for InterProScan. >>>> Please comment it. Thanks. >>>> >>>> -- >>>> -- VIEW DOTS.INTERPROSCAN >>>> -- used to store outputs from InterProScan >>>> -- June 29, 2005 >>>> >>>> >>>> >>>> >>> >>> >>> <InterProScan_OUTPUT.pdf> >>> >>> >>> >> >> -- >> Aaron J. Mackey, Ph.D. >> Project Manager, ApiDB Bioinformatics Resource Center >> Penn Genomics Institute, University of Pennsylvania >> email: am...@pc... >> office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) >> fax: 215-746-6697 >> postal: Penn Genomics Institute >> Goddard Labs 212 >> 415 S. University Avenue >> Philadelphia, PA 19104-6017 >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is sponsored by: Discover Easy Linux Migration >> Strategies >> from IBM. Find simple to follow Roadmaps, straightforward articles, >> informative Webcasts and more! Get everything you need to get up to >> speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > -- > Aaron J. Mackey, Ph.D. > Project Manager, ApiDB Bioinformatics Resource Center > Penn Genomics Institute, University of Pennsylvania > email: am...@pc... > office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) > fax: 215-746-6697 > postal: Penn Genomics Institute > Goddard Labs 212 > 415 S. University Avenue > Philadelphia, PA 19104-6017 > > > > > > --__--__-- > > _______________________________________________ > 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 > |
|
From: Kumar, S. \(Contr\) <San...@ng...> - 2005-08-04 16:36:38
|
Hi, Now let us figure out which GUS table to used to store PrositeDB = master data. Can any one help me in that please? Following type of information it contains: ID Identification (Begins each entry; 1 per entry) AC Accession number (1 per entry) DT Date (1 per entry) DE Short description (1 per entry) PA Pattern (>1 per entry) MA Matrix/profile (>1 per entry) RU Rule (>1 per entry) NR Numerical results (>1 per entry) CC Comments (>=3D1 per entry) DR Cross-references to Swiss-Prot (>1 per entry) 3D Cross-references to PDB (>1 per entry) DO Pointer to the documentation file (1 per entry) Any help on this will be appreciated. =20 Thanks Sanjeev -----Original Message----- From: gus...@li... [mailto:gus...@li...]On Behalf Of gus...@li... Sent: Tuesday, August 02, 2005 11:09 PM To: gus...@li... Subject: Gusdev-gusdev digest, Vol 1 #637 - 1 msg 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: Loading Prosite DB (Kumar, Sanjeev (Contr)) --__--__-- Message: 1 Subject: RE: [GUSDEV] Loading Prosite DB Date: Tue, 2 Aug 2005 17:04:05 -0400 From: "Kumar, Sanjeev \(Contr\)" <San...@ng...> To: "Aaron J. Mackey" <am...@pc...> Cc: "Jian Lu" <jl...@vb...>, <gus...@li...> So, The PlugIn which you are writing will not be taking care detail =3D Prosite data, right? If yes then I will write a separate plugin to load detail Prosite master = =3D data. Thanks Sanjeev -----Original Message----- From: Aaron J. Mackey [mailto:am...@pc...] Sent: Tuesday, August 02, 2005 5:01 PM To: Kumar, Sanjeev (Contr) Cc: Jian Lu; gus...@li... Subject: Re: [GUSDEV] Loading Prosite DB Yes, InterProScan only provides domain analysis results, not the =3D20 actual domain/pattern/motif databases themselves. -Aaron On Aug 2, 2005, at 4:54 PM, Kumar, Sanjeev (Contr) wrote: > Hi Aaron/Jian, > The Interproscan data has only PrositeID and description in it. = =3D20 > But to load other information for a prosite ID, we need to load the = =3D20 > Prosite data which comes in different format than Interpro. > That is what I found, Do you copy? > > Thanks > Sanjeev > > -----Original Message----- > From: Aaron J. Mackey [mailto:am...@pc...] > Sent: Tuesday, August 02, 2005 4:43 PM > To: Jian Lu > Cc: Kumar, Sanjeev (Contr) > Subject: Re: [GUSDEV] Loading Prosite DB > > > > From http://www.ebi.ac.uk/interpro/README1.html > > PROSITE patterns. > > Some biologically significant amino acid patterns can be summarised > in the form of regular expressions. > > ScanRegExp (by Wol...@eb...), Ppsearch (Fuchs, R. > 1994) . > > PROSITE profile. > > There are a number of protein families as well as functional or > structural domains that cannot be detected using patterns due to > their extreme sequence divergence; the use of techniques based on > weight matrices (also known as profiles) allows the detection of such > domains. > > pfscan from thePftools package (by Phi...@is...). > > PRINTS. > The PRINTS database houses a collection of protein family > fingerprints. These are groups of motifs that together are > diagnostically more potent than single motifs by making use of the > biological context inherent in a multiple-motif method. > > FingerPRINTScan (Scordis, P. et al. 1999) . > > PFAM. > Pfam is a database of protein domain families. Pfam contains curated > multiple sequence alignments for each family and corresponding > profile hidden Markov models (HMMs). > > hmmpfam from theHMMER2.1 package (by Sean Eddy, > ed...@ge..., http://hmmer.wustl.edu), > DeCypher=3D99 (TimeLogic) implementation of HMM search. > > PRODOM. > ProDom families are built by an automated process based on a > recursive use ofPSI-BLAST homology searches. > > BlastProDom.pl (by Florence Servant, fse...@to...) > =3D96 a filter on top of theBlast package (Altschul, S. F. et al. = 1997) =3D . > > SMART. > SMART domains are extensively annotated with respect to phyletic > distributions, functional class, tertiary structures and functionally > important residues. SMART alignments are optimised manually and > following construction of corresponding hidden Markov models (HMMs). > > hmmpfam from theHMMER2.1 package. > > TIGRFAMs. > TIGRFAMs are a collection of protein families featuring curated > multiple sequence alignments, Hidden Markov Models (HMMs) and > associated information designed to support the automated functional > identification of proteins by sequence homology. Classification by > equivalog family (see below), where achievable, complements > classification by orthologs, superfamily, domain or motif. It > provides the information best suited for automatic assignment of > specific functions to proteins from large scale genome sequencing > projects > > =3DD8 hmmpfam from theHMMER2.1 package. > > Optionally, predictions for coiled-coil, signal peptide cleavage > sites (SignalP v2) and TM helices (TMHMM v2) are supported. > > > > On Aug 2, 2005, at 4:32 PM, Jian Lu wrote: > > >> I don't think so. Here is the data sheet from InterProScan. >> >> Kumar, Sanjeev (Contr) wrote: >> >> >> >>> Hi Aaron/Jian, >>> What all types of data we are talking in IterProScan plugin? >>> Does it include Prosite data. >>> Thanks >>> Sanjeev >>> >>> -----Original Message----- >>> From: Jian Lu [mailto:jl...@vb...] >>> Sent: Tuesday, August 02, 2005 2:02 PM >>> To: Aaron J. Mackey >>> Cc: Kumar, Sanjeev (Contr); gus...@li... >>> Subject: Re: [GUSDEV] Loading Prosite DB >>> >>> >>> Aaron, >>> >>> We are also working on InterProScan and other analysis tools. But >>> we haven't got a plugin yet. If your plugin is ready, I would like >>> to play it. Here is the view that we created for InterProScan. >>> Please comment it. Thanks. >>> >>> -- >>> -- VIEW DOTS.INTERPROSCAN >>> -- used to store outputs from InterProScan >>> -- June 29, 2005 >>> >>> >>> >> >> >> <InterProScan_OUTPUT.pdf> >> >> > > -- > Aaron J. Mackey, Ph.D. > Project Manager, ApiDB Bioinformatics Resource Center > Penn Genomics Institute, University of Pennsylvania > email: am...@pc... > office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) > fax: 215-746-6697 > postal: Penn Genomics Institute > Goddard Labs 212 > 415 S. University Avenue > Philadelphia, PA 19104-6017 > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=3D16492&op=3DCCk > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Aaron J. Mackey, Ph.D. Project Manager, ApiDB Bioinformatics Resource Center Penn Genomics Institute, University of Pennsylvania email: am...@pc... office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) fax: 215-746-6697 postal: Penn Genomics Institute Goddard Labs 212 415 S. University Avenue Philadelphia, PA 19104-6017 --__--__-- _______________________________________________ Gusdev-gusdev mailing list Gus...@li... https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev End of Gusdev-gusdev Digest |
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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: 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: michael c. <cha...@vc...> - 2005-08-04 14:52:43
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has anyone gotten 3.5 to install with postgres? |
30 messages has been excluded from this view by a project administrator.
