Raw content of Bio::EnsEMBL::Pipeline::DBSQL::Finished::StateInfoContainer
<![CDATA[# Mar 6, 2006 5:20:22 PM
#
# Created by Mustapha Larbaoui <ml6@sanger.ac.uk>
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Pipeline::DBSQL::Finished::StateinfoContainer
=head1 SYNOPSIS
my $dbobj = Bio::EnsEMBL::Pipeline::DBSQL::Finished::DBAdaptor->new(
-host => $dbhost,
-dbname => $dbname,
-user => $dbuser,
-pass => $dbpass,
-port => $dbport,
);
$sic = $dbobj->get_StateInfoContainer;
=head1 DESCRIPTION
Module which inherits from StateInfoContainer and overrides specific methods to implement the incremental
updating of the Blast analysis used in the Finished Pipeline.
=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::StateInfoContainer;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Pipeline::DBSQL::StateInfoContainer;
@ISA = qw( Bio::EnsEMBL::Pipeline::DBSQL::StateInfoContainer );
=head2 fetch_db_version
Fetches the db version of a specific input ID and analysis
which have been completed.
Takes one string - input ID
and one analysis object - Bio::EnsEMBL::Analysis
and returns the db version as a string.
Throws an exception if the analysis object does not have a type.
=cut
sub fetch_db_version {
my ( $self, $inputId, $analysis) = @_;
my $db_version = '';
throw("[$analysis] is not a Bio::EnsEMBL::Pipeline::Analysis object")
unless $analysis->isa("Bio::EnsEMBL::Pipeline::Analysis");
my $sth = $self->prepare(
q {
SELECT db_version
FROM input_id_analysis
WHERE input_id = ?
AND analysis_id = ? }
);
$sth->execute($inputId,$analysis->dbID);
while ( my $row = $sth->fetchrow_arrayref ) {
$db_version = $row->[0];
}
return $db_version;
}
=head2 fetch_analysis_by_input_id
Fetches all analyses on a specific input ID
which have been completed and don't need to be updated
Takes one string - input ID
and returns a ref to a list of Bio::EnsEMBL::Analysis.
=cut
sub fetch_analysis_by_input_id {
my ( $self, $inputId ) = @_;
my @result;
my @row;
my $anaAd = $self->db->get_AnalysisAdaptor();
my $sth = $self->prepare(
q{
SELECT analysis_id , db_version
FROM input_id_analysis
WHERE input_id = ? }
);
$sth->execute($inputId);
while ( my $row = $sth->fetchrow_arrayref ) {
my $analysis = $anaAd->fetch_by_dbID( $row->[0] );
my $version = $row->[1];
next unless ($analysis);
if ( !$version
|| $analysis->logic_name =~ /Halfwise/
|| $analysis->db_version eq $version )
{
#print "Analysis " . $analysis->logic_name . " V. $version\n";
push( @result, $analysis );
}
else {
#print "Analysis ". $analysis->logic_name." V. $version need to be updated to V. ". $analysis->db_version."\n";
}
}
return \@result;
}
=head2 store_input_id_analysis
Stores an input ID, type, analysis and db version searched [optionally runtime info].
Takes an input ID (as string), Bio::EnsEMBL::Analysis object, is_dbversion_saved Boolean
and [optionally runtime_info as string].
Throws an exception if any of the inputs are invalid or if
the analysis object does not have a type.
called by: Job->run_module
=cut
sub store_input_id_analysis {
my ( $self, $inputId, $analysis, $host, $is_dbversion_saved, $run_time ) =
@_;
throw("[$analysis] is not a Bio::EnsEMBL::Pipeline::Analysis object")
unless $analysis->isa("Bio::EnsEMBL::Pipeline::Analysis");
throw("Invalid inputId [$inputId]")
unless $inputId;
throw("No type defined in analysis obj")
unless defined( $analysis->input_id_type );
if ( defined($run_time) ) {
my $db_version = $is_dbversion_saved ? $analysis->db_version : 0;
my $sth = $self->prepare(
qq{
REPLACE INTO input_id_analysis
(input_id, input_id_type, analysis_id, created, runhost, db_version , result)
values (?, ?, ?, now(), ?, ? , ?)
}
);
$sth->execute( $inputId, $analysis->input_id_type, $analysis->dbID,
$host, $db_version, $run_time );
}
else {
my $db_version = $is_dbversion_saved ? $analysis->db_version : 0;
my $sth = $self->prepare(
qq{
REPLACE INTO input_id_analysis
(input_id, input_id_type, analysis_id, created, runhost, db_version)
values (?, ?, ?, now(), ?, ?)
}
);
$sth->execute( $inputId, $analysis->input_id_type, $analysis->dbID,
$host, $db_version );
}
}
1;
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