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Re: [Gusdev-gusdev] Re: LoadTaxon.pm
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From: Chetna W. <ch...@ar...> - 2003-03-07 15:06:42
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Hi,
That is because without --commit option the table TaxonName is empty and
thats why the loading stops. Oracle checks that is the specified row
present in the table TaxonName and only when this check is sucessful it
will allow loading of data into the table under consideration. This way
RDBMS's keep consistency in the database.
Thanks
Chetna
> 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.
> >><------------------------------------
> >>
> >>
> >>
> >>
> >>
>
>
>
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