[Gusdev-gusdev] InsertNewExternalSequences errors

[sucheta T. <su...@vb...>]

Hi Steve,

I  used only one table name but, the plugin does not seem to upload any
data to the externalnasequence table that I specify.

I have used the following option:

ga GUS::Common::Plugin::InsertNewExternalSequences --debug
--external_database_release_id=1  --no_check  --sequencefile=/usr
/local/src/gus-related/seq/soybean_clean.seq
--table_name=DoTS::ExternalNASequence --update --sqlVerbose
--writeFile=/usr/lo
cal/src/gus-related/seq/temp >& /home/apps/oracle/externalna_err1 --commit

It runs for a while and comes out without any error messages. The last few
lines of the error file is :

bindValues (123, Run finished: Processed 3721, inserted 28 and updated 
sequences from file /usr/local/src/gus-related/seq
/soybean_clean.seq, 123)
 DbiHandle:sqlExec:insert succeeded 1 row(s)

the 28 records are inserted into some of the core tables.

Thanks

Sucheta




> sucheta-
>
> looking at the plugin code, it seems that you can only specify one table
> to insert into.
>
> but, you are inserting into two:
>
> --table_name=DoTS::ExternalNASequence, DoTS::VirtualSequence
>
> as far as which table to use, what is the data you are inserting?
>
> steve
>
> sucheta Tripathy wrote:
>
>>Hi Steve,
>>
>>I used the GUS::Common::Plugin::InsertNewExternalSequences for uploading
>>our local nucleotide sequences with the following parameters:
>>
>>ga GUS::Common::Plugin::InsertNewExternalSequences --algoinvo=2
>>--comment=Loading external NA Sequence --debug
>>--external_database_release_id=1 --no_check --seq
>>uence_type_id=1
>>--sequencefile=/usr/local/src/gus-related/seq/soybean_clean.seq
>>--startAt=0 --table_name=DoTS::ExternalNASequence, DoTS::VirtualSequence
>>--taxon
>>_id=143371 --update --sqlVerbose
>>--writeFile=/usr/local/src/gus-related/seq/temp
>> >& /home/apps/oracle/externalna_err1
>>
>>It gives me the following error:
>>
>>Can't locate object method "new" via package "_Table" at
>>/home/apps/gus/gushome/
>>lib/perl/GUS/ObjRelP/DbiDatabase.pm line 179.
>>
>>My assumption is that since we are using a view name in the table_name
>>parameter it gives the error. In case that is the problem, can you please
>>tell us which table the data should go without violating much of the
>>dependencies?
>>
>>Thanks in advance
>>
>>Sucheta
>>
>>
>>
>
>
>
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