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

[Arnaud K. <ax...@sa...>]

It's working now. Just noticed something, when the option --commit is 
not specified, the loading stops on the population of the TaxonName 
table, because of the Foreign Key taxon_id integrity not respected.

with '--commit' option it seems to work fine.

------------->

RetrieveFromDB: select * from SRes.TaxonName where  unique_name_variant 
is NULL and  name_class = ? and  name = ? and
 taxon_id is NULL
  bindValues (synonym, all)


sqlExec:
    INSERT INTO SRes.TaxonName (  row_user_id, other_read, 
unique_name_variant, user_write, group_write, name_class, r
ow_project_id, name, taxon_id, modification_date, user_read, 
row_alg_invocation_id, group_read, other_write, row_group
_id, taxon_name_id )
    VALUES   (  ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
  bindValues (1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1)
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into 
("SRES"."TAXONNAME"."TAXON_ID") (DBD ERROR: OCIStmt
Execute) at 
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm 
line 137, <NODES> line 2.


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)

 SQL ERROR!! involving
 
    INSERT INTO SRes.TaxonName (  row_user_id, other_read, 
unique_name_variant, user_write, group_write, name_class, r
ow_project_id, name, taxon_id, modification_date, user_read, 
row_alg_invocation_id, group_read, other_write, row_group
_id, taxon_name_id )
    VALUES   (  ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? ) 
 Values: 1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1 at 
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Obj
RelP/DbiDbHandle.pm line 177, <NODES> line 2.

<--------------------

Arnaud

Deborah F. Pinney wrote:

>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.
>><------------------------------------
>>
>>
>>
>>    
>>