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From: Madhura S. <sma...@st...> - 2004-05-06 19:31:13
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Hi I am trying again to load Pfam data into GUS using LoadPfam plugin, but = after registering the LoadPfam plugin successfully, when I try loading = data into database, I get the following error: *************************************************** elaine15:~/RA/pfam> ga GUS::Common::Plugin::LoadPfam --parse_only --flat_file=3DPfam-A.full.gz = --rele ase=3D13.0 Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop Reading properties from = /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties ImportPfam: COMMIT OFF ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz 0: PF00244.7 Unable to find most recent ExternalDatabaseRelease for ExternalDatabase medline at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm line 417, <PFAM> line 590. gunzip: stdout: Broken pipe *************************************************** I have downloaded latest release 13.0 from website Do I need to also specify external_database_release_id or something in = the command? =20 Thanks! Madhura |
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From: Steve F. <sfi...@pc...> - 2004-05-06 20:19:13
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madhura- i am real busy right now, so, quickly, i think the problem is that the data has links to medline entries. the plugin wants to insert that link, and do it in a formal way. we represent external links in two tables (the ones mentioned in the error message). you need to add a row in ExternalDatabase for medline, and one in ExternalDatabaseRelease. I'll write shortly with what we have in our db for this. steve Madhura Sharangpani wrote: > Hi > > I am trying again to load Pfam data into GUS using LoadPfam plugin, > but after registering the LoadPfam plugin successfully, when I try > loading data into database, I get the following error: > > *************************************************** > elaine15:~/RA/pfam> ga > GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz > --rele > ase=13.0 > Reading properties from > /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop > Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties > ImportPfam: COMMIT OFF > ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz > 0: PF00244.7 > Unable to find most recent ExternalDatabaseRelease for ExternalDatabase > medline at > /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm > line 417, <PFAM> line 590. > > gunzip: stdout: Broken pipe > *************************************************** > > I have downloaded latest release 13.0 from website > > Do I need to also specify external_database_release_id or something in the > command? > > Thanks! > > Madhura |
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From: Deborah F. P. <pi...@pc...> - 2004-05-06 20:37:25
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Hi Madhura,
The error you're seeing is due to there not being an external_database_id
and external_database_release_id for medline in your database's
sres.externaladatabase and sres.externaladatabaserelease tables.
You will have to insert those rows with the appropriate information. I
generally use UpdateGusFromXML to enter rows into the db but I think you
can use SubmitRow also.
sres.externaladatabase is pretty minimal with only the name (MEDLINE) and
lowercasename (medline)
Entries in sres.externaladatabaserelease only require an
external_database_id and version but the other fields are useful to track
your data source properly.
Debbie
On Thu, 6 May 2004, Madhura Sharangpani wrote:
> Hi
>
> I am trying again to load Pfam data into GUS using LoadPfam plugin, but after registering the LoadPfam plugin successfully, when I try loading data into database, I get the following error:
>
> ***************************************************
> elaine15:~/RA/pfam> ga
> GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz --rele
> ase=13.0
> Reading properties from
> /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop
> Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties
> ImportPfam: COMMIT OFF
> ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz
> 0: PF00244.7
> Unable to find most recent ExternalDatabaseRelease for ExternalDatabase
> medline at
> /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> line 417, <PFAM> line 590.
>
> gunzip: stdout: Broken pipe
> ***************************************************
>
> I have downloaded latest release 13.0 from website
>
> Do I need to also specify external_database_release_id or something in the
> command?
>
> Thanks!
>
> Madhura
>
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From: <pj...@sa...> - 2004-05-06 21:38:54
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If I remember correctly I got an XML dump from CBIL with all of the ExternalDatabase table entries with the matching ExternalDatabaseRelease rows. I added a few entries that GeneDB needed. Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema is created? I have a copy of those files that I can send to you but I can't access it right now. Quoting Madhura Sharangpani <sma...@st...>: > Hi > > I am trying again to load Pfam data into GUS using LoadPfam plugin, but after > registering the LoadPfam plugin successfully, when I try loading data into > database, I get the following error: > > *************************************************** > elaine15:~/RA/pfam> ga > GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz --rele > ase=13.0 > Reading properties from > /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop > Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties > ImportPfam: COMMIT OFF > ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz > 0: PF00244.7 > Unable to find most recent ExternalDatabaseRelease for ExternalDatabase > medline at > /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm > line 417, <PFAM> line 590. > > gunzip: stdout: Broken pipe > *************************************************** > > I have downloaded latest release 13.0 from website > > Do I need to also specify external_database_release_id or something in the > command? > > Thanks! > > Madhura > |
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From: MICHAEL L. <lu...@cs...> - 2004-05-07 15:30:13
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Hello- Such a thing--an XML from CBIL with all of the ExternalDatabase table entries and matching ExternalDatabaseRelease rows would probably be useful to almost everyone running or with plans to run GUS. So much of the perl plugin codebase already has ties to this. I think making it available as an option in the install would help solve MANY issues that arise in installing/populating/retrieving data from GUS using the perl object layer and the WDK. Are there any issues with having people standardized on an ExternalDatabaseID? Everyone is probably using some subset of a standard set of external databases, and it is easy to add another one. Michael Luchtan http://www.cs.uga.edu/~luchtan On Thu, 6 May 2004 pj...@sa... wrote: > > If I remember correctly I got an XML dump from CBIL with > all of the ExternalDatabase table entries with the matching > ExternalDatabaseRelease rows. I added a few entries that GeneDB needed. > > Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema > is created? > > I have a copy of those files that I can send to you but I can't access it right now. > > > Quoting Madhura Sharangpani <sma...@st...>: > > > Hi > > > > I am trying again to load Pfam data into GUS using LoadPfam plugin, but after > > registering the LoadPfam plugin successfully, when I try loading data into > > database, I get the following error: > > > > *************************************************** > > elaine15:~/RA/pfam> ga > > GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz --rele > > ase=13.0 > > Reading properties from > > /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop > > Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties > > ImportPfam: COMMIT OFF > > ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz > > 0: PF00244.7 > > Unable to find most recent ExternalDatabaseRelease for ExternalDatabase > > medline at > > /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm > > line 417, <PFAM> line 590. > > > > gunzip: stdout: Broken pipe > > *************************************************** > > > > I have downloaded latest release 13.0 from website > > > > Do I need to also specify external_database_release_id or something in the > > command? > > > > Thanks! > > > > Madhura > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by Sleepycat Software > Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver > higher performing products faster, at low TCO. > http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Steve F. <st...@pc...> - 2004-05-07 16:45:54
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ok, we can look into this. it might be that we ask for a volunteer. i don't yet know what is involved. steve MICHAEL LUCHTAN wrote: >Hello- >Such a thing--an XML from CBIL with all of the ExternalDatabase table >entries and matching ExternalDatabaseRelease rows would probably be useful >to almost everyone running or with plans to run GUS. So much of the perl >plugin codebase already has ties to this. I think making it available as >an option in the install would help solve MANY issues that arise in >installing/populating/retrieving data from GUS using the perl object layer >and the WDK. Are there any issues with having people standardized on an >ExternalDatabaseID? Everyone is probably using some subset of a standard >set of external databases, and it is easy to add another one. > >Michael Luchtan >http://www.cs.uga.edu/~luchtan > > >On Thu, 6 May 2004 pj...@sa... wrote: > > > >>If I remember correctly I got an XML dump from CBIL with >>all of the ExternalDatabase table entries with the matching >>ExternalDatabaseRelease rows. I added a few entries that GeneDB needed. >> >>Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema >>is created? >> >>I have a copy of those files that I can send to you but I can't access it right now. >> >> >>Quoting Madhura Sharangpani <sma...@st...>: >> >> >> >>>Hi >>> >>>I am trying again to load Pfam data into GUS using LoadPfam plugin, but after >>>registering the LoadPfam plugin successfully, when I try loading data into >>>database, I get the following error: >>> >>>*************************************************** >>>elaine15:~/RA/pfam> ga >>>GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz --rele >>>ase=13.0 >>>Reading properties from >>>/afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop >>>Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties >>>ImportPfam: COMMIT OFF >>>ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz >>>0: PF00244.7 >>>Unable to find most recent ExternalDatabaseRelease for ExternalDatabase >>>medline at >>>/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm >>>line 417, <PFAM> line 590. >>> >>>gunzip: stdout: Broken pipe >>>*************************************************** >>> >>>I have downloaded latest release 13.0 from website >>> >>>Do I need to also specify external_database_release_id or something in the >>>command? >>> >>>Thanks! >>> >>>Madhura >>> >>> >>> >> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by Sleepycat Software >>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver >>higher performing products faster, at low TCO. >>http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> > > > >------------------------------------------------------- >This SF.Net email is sponsored by Sleepycat Software >Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver >higher performing products faster, at low TCO. >http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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