Re: [Gusdev-gusdev] Re: LoadTaxon.pm

[Deborah F. P. <pi...@pc...>]

I didn't experience this problem. However, in looking over the
LoadTaxon.pm code I noticed that there was still a commented out line
that should have been corrected. This line is used only for restarting.
I have uncommented it and submitted to cvs. Please update your file.

                                             Deborah Pinney



On
Fri, 7 Mar 2003, Arnaud Kerhornou wrote:

> Hi
>
> I've tried to populate the taxonomy files from NCBI into GUS3. it's
> working fine until it reaches the last node entry, ie the line 173295 in
> the nodes.dmp file.
> I now have these 2 errors when populating the nodes file:
>
>  > oerr ora 03113
>     03113, 00000, "end-of-file on communication channel"
>     // *Cause:
>     // *Action:
>
>  > oerr ora 01041
>     01041, 00000, "internal error. hostdef extension doesn't exist"
>     // *Cause: Pointer to hstdef extension in hstdef is null.
>     // *Action: Report as a bug
>
> Have you come across the same problem ?
> Any idea about the cause of this 'end-of-file on communication channel'
> error ?
>
> cheers
> Arnaud
>
> ./bin/ga GUS::Common::Plugin::LoadTaxon
> --nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
> --names=/nfs/pathsoft/databases/NCBI/names.dmp
> --gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
>
> --------------------------->
> [...]
>
> RetrieveFromDB: select * from SRes.Taxon where  ncbi_tax_id = ?
>   bindValues (89410)
>
> sqlExec:
>     INSERT INTO SRes.Taxon (  row_user_id, user_write, group_write,
> genetic_code_id, row_project_id, taxon_id, group_r
> ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> modification_date, user_read, row_alg_invocation_id, oth
> er_write, ncbi_tax_id, rank )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>   bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> processed ncbi_tax_id : 89410
>
> ^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
> communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
> team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 242, <NODES> line 173295.
> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> (perhaps you need to call execute first) at /nfs/t
> eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 243, <NODES> line 173295.
>
> RetrieveFromDB: select * from SRes.Taxon where  ncbi_tax_id = ?
>   bindValues (110556)
>
>
> sqlExec:
>     INSERT INTO SRes.Taxon (  row_user_id, user_write, group_write,
> genetic_code_id, row_project_id, taxon_id, group_r
> ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> modification_date, user_read, row_alg_invocation_id, oth
> er_write, ncbi_tax_id, rank )
>     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>   bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> processed ncbi_tax_id : 110556
> DBD::Oracle::db prepare failed: Error while trying to retrieve text for
> error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
> cribe) at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 241, <NODES> line 1
> 73295.
>
>
> sqlExec:
>     UPDATE  Core.AlgorithmInvocation
>     SET
>         end_time = SYSDATE,
>         row_alg_invocation_id = ?,
>         modification_date = SYSDATE
>     WHERE   algorithm_invocation_id = ?
>   bindValues (9, 9)
>  DbiHandle:sqlExec:insert succeeded 1 row(s)
> Can't call method "execute" on an undefined value at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
> lugin/LoadTaxon.pm line 242, <NODES> line 173295.
> <------------------------------------
>
>
>
>
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