[GUSDEV] schema documentation and the plugins

[Josef J. <ju...@cs...>]

Often, it is difficult to understand the intended use of many
of the schema tables and columns as the documentation on
this is still incomplete.

Recently, it struck me that many of the supported plugins are
a sort of schema documentation by themselves and with that,
I have been trying to run the recently discussed
InsertSequenceFeatures plugin, though I have yet to be successful.
I have been running this plugin with the following arguments:

 ga GUS::Supported::Plugin::InsertSequenceFeatures \
    --mapFile $HOME/xml/genbank2gus.xml \
    --seqFile AT_chr5_T2I1.gbk \
    --fileFormat genbank \
    --soCvsVersion 1.42 \
    --extDbName ncbi \
    --extDbRlsVer genbank \
    --sqlVerbose \
    --commit

and depending on the genbank file (I have tried several)
the plugin bombs at one of two errors.  Either:

   Can't locate object method "value" via package "Bio::Annotation::Comment" at
     /home2/gus5/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 655,
       <GEN14> line 77428.

or

   SQL ERROR!! involving
   INSERT INTO DoTS.Keyword (  keyword, group_write, other_read, group_read, user_read,
      row_user_id, other_write, modification_date, row_alg_invocation_id, row_project_id,
      row_group_id, keyword_id, user_write )
     VALUES   (  null, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
   Values: 1, 1, 1, 1, 1, 0, 88, 1, 1, 7, 1 at
     /home2/gus5/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166

where the plugin trys to insert a row into DoTS.Keyword leaving the
column "keyword" NULL.


Can someone just suggest a genbank file that is known to have
worked with this plugin in the recent past?

What of "Bio::Annotation::Comment" error?  Is this a known bug?

On a related note; concerning the SRes.SequenceOntology table and
the InsertSequenceOntology plugin, what is the difference between
the columns so_version and so_cvs_version?

Thank you for your insight.

Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

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