[ensembl-dev] problem on interacting with mysql

[Zhang Di]

more info:

Seems that the pipeline LOCKed  TABLE 'sequence' just before the DELETE
statement.

But no sequence really inserted into the TABLE 'sequence', and no 'UNLOCK
TABLES' executed.

still working...

On Sun, Nov 20, 2011 at 2:23 PM, Zhang Di <aureliano.jz at gmail.com> wrote:

> Hi,
>    Strange things here.
>    I have run ensembl-compara pipeline for whole genome alignment
> successfully a week before.
>    When I try to run it again on yesterday, It stoped at StoreSequence
> step, compaining that:
>
>   DBI::mysql::do do failed: 'job_file' was not locked with LOCK TABLES at:
> /mydir/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 769.
>   DBI::mysql::do do failed: 'job_file' was not locked with LOCK TABLES at:
> /mydir/ensembl/modules/Bio/EnsEMBL/DBSQL/DBConnection.pm line 769.
>
> After some debug work, I found that it could not execute the sql statement
> 'DELETE from job_file WHERE job_id=xxx AND worker_id=xx';
> I tried to work around it by modify the DBConnection.pm, replaced line 769:
>
>                      my $result = $self->db_handle->do($string);
>
>                      TO:
>                      my $result;
>                      system "mysql -ppassword $self>{_dbname} -e
> '$string'";
>                      $result=1;
>
> It worked! But the pipeline still stoped complaining that:
> DBD::mysql::st execute failed: Table 'job_file' was not locked with LOCK
> TABLES at
> /mydir/ensembl-hive/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
> line 466.
> DBD::mysql::st execute failed: Table 'job_file' was not locked with LOCK
> TABLES at
> /mydir/ensembl-hive/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
> line 466.
>
> Seems another place failed to execute some sql statement related to
> 'job_file'.
>
>
> ---------------------------------------------------------------------------------------------
>
> When I terminate (Ctrl-C) the pipeline.  The same statement ran without
> any problem in a test perl script:
>
> #!/usr/bin/perl -w
> use DBI;
> my $dbh = DBI->connect("DBI:mysql:mydb:localhost","user","pass");
> my $string = "DELETE FROM job_file WHERE job_id=xxx AND worker_id=xx";
> $dbh->do($string);
>
>
> ---------------------------------------------------------------------------------------------
> Any suggestions?
>
>
> Best Reguards.
>
>
>
>
> --
> Zhang Di
>



-- 
Zhang Di
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