Raw content of Bio::EnsEMBL::Pipeline::DBSQL::Finished::JobAdaptor
<![CDATA[# Mar 9, 2006 11:11:17 AM
#
# Created by Mustapha Larbaoui <ml6@sanger.ac.uk>
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Pipeline::DBSQL::Finished::JobAdaptor
=head1 SYNOPSIS
=head1 DESCRIPTION
Module which inherits from JobAdaptor and return a Finished Job object
=head1 FEEDBACK
=head1 AUTHOR - Mustapha Larbaoui
Mustapha Larbaoui E<lt>ml6@sanger.ac.ukE<gt>
=head1 CONTACT
Post general queries to B<anacode@sanger.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Pipeline::DBSQL::Finished::JobAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Pipeline::Finished::Job;
use Bio::EnsEMBL::Pipeline::DBSQL::JobAdaptor;
@ISA = qw(Bio::EnsEMBL::Pipeline::DBSQL::JobAdaptor);
=head2 _objFromHashref
Title : _objFromHashref
Usage : my $job = $self->objFromHashref( $queryResult )
Function: Creates a Finished Job object from given hash reference.
The hash contains column names and content of the column.
Returns : the object or undef if that wasnt possible
Args : a hash reference
=cut
sub _objFromHashref {
# create the appropriate job object
my $self = shift;
my $hashref = shift;
my $job;
my $analysis;
$analysis =
$self->db->get_AnalysisAdaptor->
fetch_by_dbID( $hashref->{analysis_id} );
$job = Bio::EnsEMBL::Pipeline::Finished::Job->new
(
'-dbobj' => $self->db,
'-adaptor' => $self,
'-id' => $hashref->{'job_id'},
'-submission_id' => $hashref->{'submission_id'},
'-input_id' => $hashref->{'input_id'},
'-stdout' => $hashref->{'stdout_file'},
'-stderr' => $hashref->{'stderr_file'},
'-analysis' => $analysis,
'-retry_count' => $hashref->{'retry_count'},
'-exec_host' => $hashref->{'exec_host'},
'-temp_dir' => $hashref->{'temp_dir'},
);
return $job;
}
sub fetch_by_Status_not_like {
my ($self, $status, $start, $end) = @_;
throw("Require status for fetch_by_Status")
unless ($status);
my $query = q{
SELECT j.job_id, j.input_id, j.analysis_id, j.submission_id,
j.stdout_file, j.stderr_file, j.retry_count, j.temp_dir,
j.exec_host
FROM job j, job_status js
WHERE j.job_id = js.job_id
AND js.status != ?
AND js.is_current = 'y'
ORDER BY time desc
};
$query .= " LIMIT $start, $end" if ($start && $end);
my $sth = $self->prepare($query);
my $res = $sth->execute($status);
my @jobs;
while (my $row = $sth->fetchrow_hashref)
{
my $job = $self->_objFromHashref($row);
push(@jobs,$job);
}
return @jobs;
}
1;
]]>