[GUSDEV] InsertSequenceOntology bug?

[Nicolas J. <nic...@gm...>]

Hello,

I am proceeding with inserting data into my gusdb.
I downloaded the latest so.obo file from www.sequenceontology.org and added
that data to the db (see output below).

Once that done, I tried to insert sequence features but ran into the
following error message: ERROR: Can't find primary key for SO term 'gene'

Going through the code to find the error, I've manually checked the output
of the following sql code:
select term_name, sequence_ontology_id from sres.SequenceOntology where
so_cvs_version = '$soCvsVersion'

In my case the soCvsVersion is 1.324. And the result was nothing. So I
checked the table in question, and found it full of data, but with an
erroneous soCvsVersion: the InsertSequenceOntologyOBO plugin seems to have
used the soVersion as both the soVersion and the soCvsVersion.

Is this a bug in that plugin or is it supposed to be that way?

If it is a bug, I found in the InsertSequenceOntologyOBO.pm file the
following code (lines 170 to 178):

   my $soTerm = GUS::Model::SRes::SequenceOntology->
     new({'so_id' => $obo->{'id'},
  'ontology_name' => 'sequence',
  'so_version' => $soVer,
  *'so_cvs_version' => $soVer,*
  'term_name' => $obo->{'name'},
  'definition' => $definition });

   return $soTerm;


Is there a specific way to update the table (I don't see any UNDO for this
plugin)? Or should I just use plain sql UPDATE for this?

Best regards,
Nicolas



Nicolas-work-iMac:~ Nicolas$ ga
GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile
~/Data_for_GUS/so.obo --soVersion 1.2 --soCvsVersion 1.324 --commit
Wed Apr 11 15:51:53 2012 DSN dbi:Pg:dbname=varDB_2012
Wed Apr 11 15:51:53 2012 PLUGIN
GUS::Supported::Plugin::InsertSequenceOntologyOBO
Wed Apr 11 15:51:53 2012 ARG algoinvo 1
Wed Apr 11 15:51:53 2012 ARG comment
Wed Apr 11 15:51:53 2012 ARG commit 1
Wed Apr 11 15:51:53 2012 ARG debug 0
Wed Apr 11 15:51:53 2012 ARG group
Wed Apr 11 15:51:53 2012 ARG gusconfigfile
/Users/Nicolas/GUS/gus_home/config/gus.config
Wed Apr 11 15:51:53 2012 ARG help 0
Wed Apr 11 15:51:53 2012 ARG helpHTML 0
Wed Apr 11 15:51:53 2012 ARG inputFile /Data_for_GUS/so.obo
Wed Apr 11 15:51:53 2012 ARG project
Wed Apr 11 15:51:53 2012 ARG soCvsVersion 1.324
Wed Apr 11 15:51:53 2012 ARG soExtDbRlsName
Wed Apr 11 15:51:53 2012 ARG soVersion 1.2
Wed Apr 11 15:51:53 2012 ARG sqlVerbose 0
Wed Apr 11 15:51:53 2012 ARG user
Wed Apr 11 15:51:53 2012 ARG verbose 0
Wed Apr 11 15:51:53 2012 ARG veryVerbose 0
Wed Apr 11 15:51:53 2012 ARG workflowstepid 0
Wed Apr 11 15:51:53 2012 AlgInvocationId 29
Wed Apr 11 15:51:53 2012 COMMIT commit on
Wed Apr 11 15:51:54 2012 Submitted 100 terms
Wed Apr 11 15:51:54 2012 Submitted 200 terms
Wed Apr 11 15:51:54 2012 Submitted 300 terms
Wed Apr 11 15:51:54 2012 Submitted 400 terms
Wed Apr 11 15:51:54 2012 Submitted 500 terms
Wed Apr 11 15:51:54 2012 Submitted 600 terms
Wed Apr 11 15:51:54 2012 Submitted 700 terms
Wed Apr 11 15:51:54 2012 Submitted 800 terms
Wed Apr 11 15:51:54 2012 Submitted 900 terms
Wed Apr 11 15:51:55 2012 Submitted 1000 terms
Wed Apr 11 15:51:55 2012 Submitted 1100 terms
Wed Apr 11 15:51:55 2012 Submitted 1200 terms
Wed Apr 11 15:51:55 2012 Submitted 1300 terms
Wed Apr 11 15:51:55 2012 Submitted 1400 terms
Wed Apr 11 15:51:55 2012 Submitted 1500 terms
Wed Apr 11 15:51:55 2012 Submitted 1600 terms
Wed Apr 11 15:51:55 2012 Submitted 1700 terms
Wed Apr 11 15:51:55 2012 Submitted 1800 terms
Wed Apr 11 15:51:56 2012 Submitted 1900 terms
Wed Apr 11 15:51:56 2012 Submitted 2000 terms
Wed Apr 11 15:51:56 2012 Submitted 2100 terms
Wed Apr 11 15:51:56 2012 TIME 3 sec  (0:00:03)
Wed Apr 11 15:51:56 2012 RESULT Inserted 2120 terms into SequenceOntology
Wed Apr 11 15:51:56 2012 Rows Written SRes.SequenceOntology: 2120
Wed Apr 11 15:51:56 2012 AlgInvocationId 29
Wed Apr 11 15:51:56 2012 COMMIT commit on