Re: [GUSDEV] schema documentation and the plugins

[Steve F. <sfi...@pc...>]

josef-

thanks.  i think the problem you are having is demonstrating that ISF 
plugin is not fully tested.   We are still gearing up to use it for real 
in-house.   I released it as "beta" but, i think that is optimistic.    
The code to handle comments, i think, has not yet been exercised by our 
testing.  

but, it will very soon, as we have been spending the past few days 
unexpectedly getting straight where we are to get our P.falciparum 
chromosome files from.  

i think we've gotten that straight, so, at last will be running the 
plugin on that data, as further testing.

in your case, the code seems to be calling a method value() that is not 
supported by Bio::AnnotationI.   I'll probably fix it in the next couple 
of days.

thanks,
steve

Josef Jurek wrote:

>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...
>
>voice: (773) 834-3985
>fax:   (773) 702-6648
>
>
>
>
>
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