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

[Jiaye Z. <ze...@in...>]

Hi michael,

Quoting Michael Pear <mic...@ho...>:

> 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.

Hmmmm, why is genex in the contact info? -U option is only used for 
initializing the connection string. The above error occured when the program is 
checking for existing data in the database.


> 2)  XML Parser error on a special character in the USF file.
> Known problem from before. I'm leaving it in the data I'm working with
> so that we can reproduce it in the future. 
> 
> Response: Edited non-ascii char out and went on.

I should add this to the realease note or a README file.


> 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});
>   }
> 

Oh, I see. Michael, the addition of above code can be avoided, here's why. If 
you look at line 900-910, you will see that the program is checking for the two 
attributes that don't exist anymore. Just remove these ten lines, we'll be ok. 
(this was there was because since the two attributes still existed in the 
database until early this week, with not null option. I used it as sort of a 
hack)

> at the top of pgInsert (after   my ($table, $contentRef) = @_; )
> to remove the keys.
> 
> 
> Then: Success! dataset added.


Thanks for pointing this out.

Jiaye