gusdev-gusdev

[Gusdev-gusdev] increasing space for externalaasequence.name

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

Dear group,

I am now uploading data to the externalaasequence, and frequently it gets
interrupted because the name has data type varchar2(255), where as some of
the names are much longer than that.I was wondering if the table
definition can be changed in the distribution to handle this OR is there a
reason why this should be kept as varchar2(255)?

Thanks

Sucheta

-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

Re: [Gusdev-gusdev] increasing space for externalaasequence.name

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

"Sucheta Tripathy" <su...@vb...> writes:
>
> I am now uploading data to the externalaasequence, and frequently it gets
> interrupted because the name has data type varchar2(255), where as some of
> the names are much longer than that.I was wondering if the table
> definition can be changed in the distribution to handle this OR is there a
> reason why this should be kept as varchar2(255)?

The description column of ExternalNASequence is of type varchar2(2000),
which should be long enough for the full name of your sequence.

A problem we have run into is that the table DoTS.NAFeature
only has the field "name" to describe the feature:

   column          nulls?  type
   name            no      varchar2(30)

and could really use a description field such as:

   description        varchar2(2000)

as the genbank description for many features significantly
exceeds 30 characters.  Sure, the table DoTS.NAFeatureComment
with its "comment_string clob(4000)" column exists, but that
NAFeature lacks a description column is inconsistent with other
GUS tables.


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

Re: [Gusdev-gusdev] increasing space for externalaasequence.name

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

can you provide an example of such a name?

steve

Sucheta Tripathy wrote:

>Dear group,
>
>I am now uploading data to the externalaasequence, and frequently it gets
>interrupted because the name has data type varchar2(255), where as some of
>the names are much longer than that.I was wondering if the table
>definition can be changed in the distribution to handle this OR is there a
>reason why this should be kept as varchar2(255)?
>
>Thanks
>
>Sucheta
>
>  
>

Re: [Gusdev-gusdev] increasing space for externalaasequence.name

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

Well, As Josef rightly pointed , I guess that can go to description instead 
of name field. Though I don't find a clear demarcation between the two.

For example in this case:

cold inducible similar to other osmotic stress induced gene products 
includin: Tomato abscisic stress ripening protein 1 encoded by GenBank 
Accession Number L08255, Solanum lycopersicum ABA- and ripening-induced 
protein encoded by GenBank Accession Number L20756 and to Solanum chacoense 
abscisic stress ripening protein encoded by GenBank Accession Number U12439 
[Solanum tuberosum]

This happens when I give a --regex_source_id="gi\|(\w+)\|(.*)" 
--regex_secondary_id="gb|emb|dbj|ref|pir|sp\|(\w+)" --regex_name=".*\|(.+)$"
in the insertnewexternalsequence plugin.





At 01:20 PM 11/22/2004 -0500, Steve Fischer wrote:
>can you provide an example of such a name?
>
>steve
>
>Sucheta Tripathy wrote:
>
>>Dear group,
>>
>>I am now uploading data to the externalaasequence, and frequently it gets
>>interrupted because the name has data type varchar2(255), where as some of
>>the names are much longer than that.I was wondering if the table
>>definition can be changed in the distribution to handle this OR is there a
>>reason why this should be kept as varchar2(255)?
>>
>>Thanks
>>
>>Sucheta
>>
>>

[Gusdev-gusdev] Error in LoadBlastSimFast plugin

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

Hello again,

I am trying the LoadBlastSimFast plugin, but after inserting some values to 
the database, an error message comes saying
the following:
_____

         result: []
DBD::Oracle::st execute failed: ORA-01407: cannot update 
("CORE"."ALGORITHMINVOC
ATION"."RESULT") to NULL (DBD ERROR: OCIStmtExecute) [for Statement "
     UPDATE  Core.AlgorithmInvocation
     SET
         modification_date = SYSDATE,
         end_time = SYSDATE,
         row_alg_invocation_id = ?,
         result = ''
     WHERE   algorithm_invocation_id = ?" with ParamValues: :p1='20174', 
:p2='201
74'] at /home/apps/GUS/dev/gushome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 
145.

  SQL ERROR!! involving

     UPDATE  Core.AlgorithmInvocation
     SET
         modification_date = SYSDATE,
         end_time = SYSDATE,
         row_alg_invocation_id = ?,
         result = ''
     WHERE   algorithm_invocation_id = ?
  Values: 20174, 20174 at 
/home/apps/GUS/dev/gushome/lib/perl/GUS/ObjRelP/DbiDbHa
ndle.pm line 185
         GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86564
cc)','\x{a} SQL ERROR!! involving\x{a} 
\x{a}    UPDATE  Core.AlgorithmInvocatio.
..') called at 
/home/apps/GUS/dev/gushome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm li
ne 148
         GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x865
64cc)','GUS::ObjRelP::DbiDbHandle::st=HASH(0x85edde0)','ARRAY(0x85ebc08)','\x{a}
     UPDATE  Core.AlgorithmInvocation\x{a}    SET 
\x{a}\x{9}modificat...') ca
lled at /home/apps/GUS/dev/gushome/lib/perl/GUS/ObjRelP/DbiRow.pm line 726
         GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvoc
ation=HASH(0x87a0d3c)','HASH(0x82ee7a4)','HASH(0x85ebb30)') called at 
/home/apps
/GUS/dev/gushome/lib/perl/GUS/ObjRelP/DbiRow.pm line 592
______


Any idea what could be going wrong?

Thanks

Sucheta

At 01:40 PM 11/22/2004 -0500, Sucheta Tripathy wrote:

>Well, As Josef rightly pointed , I guess that can go to description 
>instead of name field. Though I don't find a clear demarcation between the two.
>
>For example in this case:
>
>cold inducible similar to other osmotic stress induced gene products 
>includin: Tomato abscisic stress ripening protein 1 encoded by GenBank 
>Accession Number L08255, Solanum lycopersicum ABA- and ripening-induced 
>protein encoded by GenBank Accession Number L20756 and to Solanum 
>chacoense abscisic stress ripening protein encoded by GenBank Accession 
>Number U12439 [Solanum tuberosum]
>
>This happens when I give a --regex_source_id="gi\|(\w+)\|(.*)" 
>--regex_secondary_id="gb|emb|dbj|ref|pir|sp\|(\w+)" --regex_name=".*\|(.+)$"
>in the insertnewexternalsequence plugin.
>
>
>
>
>
>At 01:20 PM 11/22/2004 -0500, Steve Fischer wrote:
>>can you provide an example of such a name?
>>
>>steve
>>
>>Sucheta Tripathy wrote:
>>
>>>Dear group,
>>>
>>>I am now uploading data to the externalaasequence, and frequently it gets
>>>interrupted because the name has data type varchar2(255), where as some of
>>>the names are much longer than that.I was wondering if the table
>>>definition can be changed in the distribution to handle this OR is there a
>>>reason why this should be kept as varchar2(255)?
>>>
>>>Thanks
>>>
>>>Sucheta
>>>
>
>
>
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