[Gusdev-gusdev] RE: LoadTaxon.pm

[Martin W. <md...@sa...>]

Hi Arnaud,

If the whole file except the last part is processing into the DB OK, it
suggest the end of the file is corrupt.

Ora 1041 is an internal error that looks like you have hut an internal
oracle bug, but in fact is often a result of 3113, losing your
connection to the DB.

I take it 99.99% of what you are processing is getting into the DB?

Martin

-----Original Message-----
From: Arnaud Kerhornou [mailto:ax...@sa...] 
Sent: 07 March 2003 10:57
To: gusdev-gusdev
Cc: db...@sa...
Subject: Re: LoadTaxon.pm


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/LoadTa
xon.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/LoadTax
on.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/L
oadTaxon.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.
<------------------------------------