Re: [Gusdev-gusdev] GenBank, Gene Ontology questions

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hi,

I tried following after getting the latest tarball from cvs sanger:

1)
[chetna@mango Plugin]$ ga +update GUS::Common::Plugin::GBParser 
--commit
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/chetna/.gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation 

in Autolib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.

USER ERROR: GUS::PluginMgr::GusApplication revision 1.37 has not been 
registered
Please use 'ga +meta --commit'

2)
[chetna@mango Plugin]$ ga +meta commit
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/chetna/.gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation 

in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at 
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation 

in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at 
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
  <Core::Algorithm>
    <algorithm_id>54</algorithm_id>
    <name>GA-Plugin</name>
    <description>GUS application framework for plugins</description>
    <modification_date>24-MAR-03</modification_date>
    <Core::AlgorithmImplementation>
      <cvs_revision>1.37</cvs_revision>
      <cvs_tag> </cvs_tag>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <executable_md5>4bdb2e1291247ddfd653d63876c3eb7c</executable_md5>
      <description>update for GUS 3.0</description>
      <Core::AlgorithmInvocation>
        <start_time>sysdate</start_time>
        <end_time>sysdate</end_time>
        <machine_id>0</machine_id>
        <cpus_used>1</cpus_used>
        <result>meta</result>
      </Core::AlgorithmInvocation>
    </Core::AlgorithmImplementation>
    <user_read>1</user_read>
    <user_write>1</user_write>
    <group_read>1</group_read>
    <group_write>1</group_write>
    <other_read>1</other_read>
    <other_write>0</other_write>
    <row_user_id>2</row_user_id>
    <row_group_id>2</row_group_id>
    <row_project_id>2</row_project_id>
    <row_alg_invocation_id>1</row_alg_invocation_id>
  </Core::Algorithm>
  <Core::Algorithm>
    <algorithm_id>54</algorithm_id>
    <name>GA-Plugin</name>
    <description>GUS application framework for plugins</description>
    <modification_date>24-MAR-03</modification_date>
    <Core::AlgorithmImplementation>
      <algorithm_implementation_id>78</algorithm_implementation_id>
      <algorithm_id>54</algorithm_id>
      <cvs_revision>1.37</cvs_revision>
      <cvs_tag> </cvs_tag>
      <executable>GUS::PluginMgr::GusApplication</executable>
      <executable_md5>4bdb2e1291247ddfd653d63876c3eb7c</executable_md5>
      <description>update for GUS 3.0</description>
      <modification_date>SYSDATE</modification_date>
      <Core::AlgorithmInvocation>
        <algorithm_invocation_id>119</algorithm_invocation_id>
        <algorithm_implementation_id>78</algorithm_implementation_id>
        <start_time>sysdate</start_time>
        <end_time>sysdate</end_time>
        <machine_id>0</machine_id>
        <cpus_used>1</cpus_used>
        <result>meta</result>
        <modification_date>SYSDATE</modification_date>
        <user_read>1</user_read>
        <user_write>1</user_write>
        <group_read>1</group_read>
        <group_write>1</group_write>
        <other_read>1</other_read>
        <other_write>0</other_write>
        <row_user_id>2</row_user_id>
        <row_group_id>2</row_group_id>
        <row_project_id>2</row_project_id>
        <row_alg_invocation_id>1</row_alg_invocation_id>
     </Core::AlgorithmInvocation>
     <user_read>1</user_read>
      <user_write>1</user_write>
      <group_read>1</group_read>
      <group_write>1</group_write>
      <other_read>1</other_read>
      <other_write>0</other_write>
      <row_user_id>2</row_user_id>
      <row_group_id>2</row_group_id>
      <row_project_id>2</row_project_id>
      <row_alg_invocation_id>1</row_alg_invocation_id>
    </Core::AlgorithmImplementation>
    <user_read>1</user_read>
    <user_write>1</user_write>
    <group_read>1</group_read>
    <group_write>1</group_write>
    <other_read>1</other_read>
    <other_write>0</other_write>
    <row_user_id>2</row_user_id>
    <row_group_id>2</row_group_id>
    <row_project_id>2</row_project_id>
    <row_alg_invocation_id>1</row_alg_invocation_id>
  </Core::Algorithm>
[chetna@mango Plugin]$

It would be great if somebody could help,
Thanks
Chetna

>---------Included Message----------
>>Date: Mon, 12 May 2003 13:39:17 -0400 (EDT)
>>From: "Deborah F. Pinney" <pi...@pc...>
>>To: "Chetna D. Warade" <ch...@ug...>
>>Cc: <gus...@li...>
>>Subject: Re: [Gusdev-gusdev] GenBank, Gene Ontology questions
>>
>>Hi Chetna,
>>
>>Is your GBParser.pm updated from CVS? There were several changes made 

>to 
>>the plugin for GUS3.0. I used the plugin in it's current form and it 
>>performed well. 
>>
>>Here is a sample command line I used when testing the plugin:
>>
>>ga GUS::Common::Plugin::GBParser --gbRel 132 --file 
>>/ptolemy/share/data/thirdparty/genbank/133/gbrod4.seq.gz --debug --log 

>
>>gbrod5.seq.log --db_rel_id 6547 > & gbrod5.err &
>>
>>
>>Your command is missing the --db_rel_id option which is the 
>>external_database_release_id of GenBank release 133 from the 
>>ExternalDatabaseRelease table. I just made this a required option so 
>you 
>>can update from CVS to get that change. 
>>
>>Can you e-mail the actual errors you get? It should not be necessary 
>for 
>>the dbref table to be filled to run GBParser.
>>
>>                                                  Debbie 
>>
>>
>>
>>
>>
>>
>>
>>On Mon, 12 May 2003, Chetna D. Warade wrote:
>>
>>> Hi all,
>>> 
>>> It would be great if I can get insight into following:
>>> 
>>> 1) GenBank
>>> 
>>> I am trying to load data from GenBank with the  command
>>> 
>>> ga GUS::Common::Plugin::GBParser --gbRel=133 
>>> --file=/home/gusdev/GenBank/TcNCBIgenomic.gb
>>> 
>>> I am getting SQL Error: foreign  key violation for tables SRes.DbRef 

>and 
>>> DoTS.ExternalNASequence.
>>> 
>>> I wanted to know more about how to solve the dependencies in these 
>>> tables.
>>> 
>>> In order to solve this dependency I might need the 
>>> InsertDbRefAndDbRefNASequence.pm and thats not functional as of yet. 

>I 
>>> was wondering if its up and running.
>>> 
>>> 2) GeneOntology
>>> 
>>> We have successfully  installed Taxonomy in the gus 3.0 database at 

>this 
>>> end. I need to know what version and files do I need to put all the 
3 
>
>>> ontologies in the database.  Also what are the dependencies in 
>loading 
>>> Gene Ontology in terms of data.
>>> 
>>> 3) Following is the list of tables we have filled in to work with 
>gus:
>>> Core.Algorithm
>>> Core.AlgorithmInvocation
>>> Core.Userinfo
>>> Core.Projectinfo
>>> Core.Groupinfo
>>> Core.Machine
>>> SRes.Taxon
>>> SRes.Taxonname
>>> SRes.GeneticCode
>>> 
>>> I would be very happy to call you guys over phone (if possible) at a 

>
>>> good time if you think that the answers are really long and complex 

>to 
>>> talk over email.
>>> 
>>> Hope to hear from you all,
>>> Thanks,
>>> Chetna
>>> 
>>> 
>>> 
>>> 
>>> -------------------------------------------------------
>>> Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa 
>Clara
>>> The only event dedicated to issues related to Linux enterprise 
>solutions
>>> www.enterpriselinuxforum.com
>>> 
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> 
>>
>>
>---------End of Included Message----------
>
>
>
---------End of Included Message----------