[Gusdev-gusdev] error loading data using plugin

[D. B. W. <db...@ug...>]

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.