Re: [Gusdev-gusdev] error loading data using plugin

[Steve F. <sfi...@pc...>]

it needs to be in the TableInfo table.   and, you probably need to 
regenerate the perl objects.  to do so, touch the file 
$PROJECT_HOME/GUS/Model/schema/VERSION and then do a "build GUS install 
-append"

steve

D. Brent Weatherly wrote:

>Hello folks.
>
>This is probably an easy question, but I'm unable to use a
>plugin on our most recent GUS instance that worked fine on a
>previous instance. The table in question is:
>
>Dots.MassSpecSummary 
>
>which we had to manually add to Oracle. The
>"MassSpecSummary.pm" perl module does exist in
>GUS::Common::DoTS.  Do these modules need a special
>initialization that we've yet to perform?
>
>Thanks for any help!
>
>Brent Weatherly
>
>
>
>[brentw@mkiwi brentw]$ ga
>GUS::Common::Plugin::LoadTcruziDBMassSpecSummary
>--filename=/scratch/brentw/TcruziDB_data/TSKTSC_ver3_proteome_TcruziDB_data.txt
>--loadSummary --verbose --veryVerbose
>Thu Sep  9 08:55:46 2004        ALGINVID        10254
>Thu Sep  9 08:55:46 2004        COMMIT  commit off
>Thu Sep  9 08:55:46 2004        ARGS    algoinvo        1
>Thu Sep  9 08:55:46 2004        ARGS    algorithm       PROVALT
>Thu Sep  9 08:55:46 2004        ARGS    algorithmId     82
>Thu Sep  9 08:55:46 2004        ARGS    comment
>Thu Sep  9 08:55:46 2004        ARGS    commit
>Thu Sep  9 08:55:46 2004        ARGS    debug
>Thu Sep  9 08:55:46 2004        ARGS    extDbRelId      222
>Thu Sep  9 08:55:46 2004        ARGS    filename       
>/scratch/brentw/TcruziDB_data/TSKTSC_ver3_proteome_TcruziDB_data.txt
>Thu Sep  9 08:55:46 2004        ARGS    forceLookUp
>Thu Sep  9 08:55:46 2004        ARGS    gfExtDbRelId    208
>Thu Sep  9 08:55:46 2004        ARGS    group
>Thu Sep  9 08:55:46 2004        ARGS    gusconfigfile  
>/home/brentw/brentw/.gus.properties
>Thu Sep  9 08:55:46 2004        ARGS    loadSpans       0
>Thu Sep  9 08:55:46 2004        ARGS    loadSummary     1
>Thu Sep  9 08:55:46 2004        ARGS    lookUpFile
>Thu Sep  9 08:55:46 2004        ARGS    project TcruziDB3.0
>Thu Sep  9 08:55:46 2004        ARGS    projectId       22
>Thu Sep  9 08:55:46 2004        ARGS    restart
>Thu Sep  9 08:55:46 2004        ARGS    sqlVerbose
>Thu Sep  9 08:55:46 2004        ARGS    testnumber
>Thu Sep  9 08:55:46 2004        ARGS    usage
>Thu Sep  9 08:55:46 2004        ARGS    user
>Thu Sep  9 08:55:46 2004        ARGS    verbose 1
>Thu Sep  9 08:55:46 2004        ARGS    veryVerbose     1
>COMMIT TURNED OFF
>Thu Sep  9 08:55:46 2004        II parsing entry:
>Peptide Group: 1        TOP     11788.t00001    alpha tubulin
>          3919
>
>
>PepGroup: Peptide Group: 1, Source: TOP, GeneID: 11788.t00001,
>GeneName: alpha tubulin, Tot Score: 
>
>
>
>PepGroup: Peptide Group: 1, Source: TOP, GeneID: 11788.t00001,
>GeneName: alpha tubulin, Tot Score: 
>
>Thu Sep  9 08:55:46 2004        II      got new protein (count
>0)  with geneId: 11788.t00001...
>select tas.* from dots.genefeature gf, dots.rnafeature rnaf,
>dots.translatedaafeature taf, dots.translatedaasequence tas 
>           where gf.external_database_release_id = 208 
>           and rnaf.parent_id = gf.na_feature_id 
>           and rnaf.na_feature_id = taf.na_feature_id
>           and taf.aa_sequence_id = tas.aa_sequence_id 
>           and gf.source_id='11788.t00001' 
>Thu Sep  9 08:55:58 2004        II aa_sequence_id for
>11788.t00001 is 4276057
>
>INFO: 4276057  
>MREAICIHIGQAGCQVGNACWELFCLEHGIQPDGAMPSDKTIGVEDDAFNTFFSETGAGKHVPRAVFLDLEPTVVDEIRTGTYRQLFHPEQLISGKEDAANNYARGHYTIGKEIVDLCLDRIRKLADNCTGLQGFLVYHAVGGGTGSGLGALLLERLSVDYGKKSKLGYTVYPSPQVSTAVVEPYNSVLSTHSLLEHTDVAAMLDNEAIYDLTRRNLDIERPTYTNLNRLIGQVVSALTASLRFDGALNVDLTEFQTNLVPYPRIHFVLTSYAPVISAEKAYHEQLSVSEISNAVFEPASMMTKCDPRHGKYMACCLMYRGDVVPKDVNAAVATIKTKRTIQFVDWSPTGFKCGINYQPPTVVPGGDLAKVQRAVCMIANSTAIAEVFARIDHKFDLMYSKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGAESADMEGEEDVEEY
>
>II      parsing:
>Amastigote      2064    255     38      57
>
>Here: 4276057   Amastigote      38      208     82      38   
>  255     451     1       0       57
>
>
>Can't locate object method "new" via package "_Table" (perhaps
>you forgot to load "_Table"?) at 
>
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line
>201, <F> line 2.
>
>
>
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