Re: [GeneX-dev] xml2db.pl errors...

[Michael P. <mic...@ho...>]

On the key removal for putative_csf_fk and nonunique_flag,
I consider what I did as a temporary kludge. I hope there is
a better permanent solution....Jiaye knows better than I how
these keys are set, from XML, programmatically, etc. and what
needs to be done to avoid their original creation.

Regards,

Michael Pear


> > 3) Problem due to missing field related to CSF removal and other
> >    schema changes
> >
> >
> > DBD::Pg::db do failed: ERROR:  Relation 'usersequencefeature' does not have attribute
'putative_csf_fk'
> > 7UserSequenceFeature: INSERT INTO UserSequenceFeature (usf_name, putative_csf_fk,
nonunique_flag, spc_fk, short_description, owner_us_fk, usf_type) VALUES ('E06a', '1', '1', '50',
'bone morphogenetic protein 4  (BMP4) + bone morphogenetic protein 2B  (BMP2B)', '1', 'gene_name')
at /var/genex/local/bin/xml2db.pl line 1609.
> >
> > Inserting UserSequenceFeature, this may take a few minutes...
> > DBD::Pg::db do failed: ERROR:  Relation 'usersequencefeature' does not have attribute
'nonunique_flag'
> > 7UserSequenceFeature: INSERT INTO UserSequenceFeature (usf_name, nonunique_flag, spc_fk,
short_description, owner_us_fk, usf_type) VALUES ('E06a', '1', '50', 'bone morphogenetic protein 4
(BMP4) + bone morphogenetic protein 2B  (BMP2B)', '1', 'gene_name')  at
/var/genex/local/bin/xml2db.pl line 1615.
> >
> > response: Added
> >
> >   if ($table eq 'UserSequenceFeature'){
> >     delete($$contentRef{putative_csf_fk});
> >     delete($$contentRef{nonunique_flag});
> >   }
> >
> > at the top of pgInsert (after   my ($table, $contentRef) = @_; )
> > to remove the keys.
> >
> >
> > Then: Success! dataset added.
>
> Great! I'm glad it was as simple as just removing the keys... Whew!!
> That's an enormous help Michael.
>
> jas.
>
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