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

[<ja...@op...>]

"Michael Pear" <mic...@ho...> writes:

> Found the following errors so far with xml2db.pl
> 
> 1) Stopped on a contact "genex" that was in the initial database
>    (not added by me) when looking up the record. 
> 
> DBD::Pg::st execute failed: ERROR:  parser: parse error at or near ""
> 7Contact: SELECT con_pk from Contact where contact_person = 'genex' AND   at /var/genex/local/bin/xml2db.pl line 1656.
> 
> Response: I removed the offending <contact> </contact> from the submitted XML
> file with an editor and went on.

The 'genex' contact is used by the DB as the contact person for the
installation. It is the corresponding Contact entry for the 'genex'
UserSec entry. That UserSec entry is specified as the owner of all the
NCGR curated data in the DB. 

The problem seems to be that even though Contact:organization is
specified to be NOT NULL in the DB, the 'genex' Contact entry has a
blank organization... This will have to come out in the DB update.

> 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.