Re: [Gusdev-gusdev] Problem loading EMBL files into GUS

[Madhura S. <sma...@st...>]

Hi Paul

After reading your email, I setted up Dots.SequenceType tables with required
ds-DNA entries and then tried loading EMBL files again, this time it made
progress, it didn't give "can't fine sequence type ds-DNA" error, but it
went ahead and gave following error:

**********************************************
buildRNA() : DoTS.RNA created.
buildRNAInstance() : $rna_object->getId() =
buildRNAInstance() : Creating brand new RNAInstance
Object type is 'GUS::Model::DoTS::GeneFeature', $object =
GUS::Model::DoTS::Gene
Feature=HASH(0x173113c)
DBD::Oracle::st execute failed: ORA-02291: integrity constraint
(DOTS.NAFEATUREI
MP_FK08) violated - parent key not found (DBD ERROR: OCIStmtExecute) at
/afs/ir/
users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.

 SQL ERROR!! involving

    INSERT INTO DoTS.GeneFeature (  gene_type, row_user_id, user_write,
group_wr
ite, na_sequence_id, row_project_id, name, is_partial, product, is_pseudo,
revie
w_status_id, subclass_view, group_read, row_group_id, other_read,
modification_d
ate, is_predicted, user_read, row_alg_invocation_id, other_write,
na_feature_id,
 number_of_exons )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
?, ?
, ?, ? )
 Values: protein coding, 1, 1, 1, 49, 1, BP0001, 0, glucose inhibited
division p
rotein A, 0, 5, GeneFeature, 1, 1, 1, 1, 1, 99, 0, 1, 1 at
/afs/ir/users/s/m/sma
dhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0xb791a
8)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.GeneFeature (
ge...') c
alled at
/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm l
ine 148
**********************************************

Madhura



----- Original Message ----- 
From: <pj...@sa...>
To: "Madhura Sharangpani" <sma...@st...>
Cc: <gus...@li...>
Sent: Thursday, May 20, 2004 3:25 AM
Subject: Re: [Gusdev-gusdev] Problem loading EMBL files into GUS


> Madhura,
>
> Did you setup the DoTS.SequenceType tables?
> I presume it can't find ds-DNA in there (and doesn't report it - I shall
improve
> the plugin).
> See: GUS/Website/htdocs/documentation/installguide_UGA.html
> and do a search for ds-DNA to find all the INSERT statements for ss-DNA,
ds-DNA,
> ss-RNA etc. I'm guessing we used those statements here at Sanger.
>
> All,
>
> On a slightly related note, I do have a collection of XML files that
populate
> dictionary tables such as ExternalDatabase, ExternalDatabaseRelease.
Someone
> emailed the list and said it would be good to have this somewhere, perhaps
CVS.
> I agree, although we would need to have "common" and "center specific"
> dirctories. I am in the process of setting up a new GUS instance so I will
soon
> be in a better position to propose something.
>
> Paul.
>
> Quoting Madhura Sharangpani <sma...@st...>:
>
> > Hi All
> >
> > I am trying to load EMBL files into GUS, but having some problems,
> > when I try to execute the command :
> >
> > ga GUS::Common::Plugin::GenericParser2Gus --filetype=embl
> > -filepath=b.pertussis.embl -sequencetype=ds-DNA
> >
> > without commit, I get the following error:
> >
> > *********************************************************
> > ***COMMIT TURNED OFF***
> > Dumping log: $VAR1 = '/tmp//GenericParser2Gusdev.pid28608.log';
> >
> > embl file to parse, b.bronchiseptica.embl...
> > ID line fine!!!
> > source feature found, FT   source          1..5339179!!
> > processing bioperl sequence, BB...
> > sequence not in GUS yet
> > can't find SequenceType, ds-DNA
> > number of features = 5009
> > organism, taxon id: Bordetella bronchiseptica,
> > DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> > ("DOTS"."NASE
> > QUENCEIMP"."SEQUENCE_TYPE_ID") (DBD ERROR: OCIStmtExecute) at
> > /afs/ir/users/s/m/
> > smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
> >
> > (after this along sequence is printed)
> >
> >
ATCGTACGGATTACAGGGCTTACGATGTTTCACGTGAAACGCCGAACGAGGTGCCACTATAATGGCCTCGGAACGC
TCTT
> > TCATCTCTCCCCATC, 1, 1, 1, 5339179, 850606, 0, chr. 1, 853819, 1, 86,
1825282,
> > 0
> > at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line
> > 18
> > 5
> >
> >
***************************************************************************
> > Can someone tell me why this error is occuring?
> >
> > Thanks!
> >
> > Madhura
> >
>
>
>