From 0411ab954d8ec17efffd5e60eb3db6dbff6eb4ea Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Tue, 14 Jan 2014 16:31:44 +0000
Subject: [PATCH] JobAdaptor now inherits from ObjectAdaptor
---
.../EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm | 213 +++---------------
1 file changed, 34 insertions(+), 179 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index 0de5da3dd..2d4b3b420 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -50,7 +50,28 @@ use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::Hive::AnalysisJob;
use Bio::EnsEMBL::Hive::Utils ('stringify');
-use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
+use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
+
+
+sub default_table_name {
+ return 'job';
+}
+
+
+sub object_class {
+ return 'Bio::EnsEMBL::Hive::AnalysisJob';
+}
+
+
+sub default_overflow_limit {
+ return {
+ 'input_id' => 255,
+ 'param_id_stack' => 64,
+ 'accu_id_stack' => 64,
+ };
+}
+
+
###############################################################################
#
@@ -174,37 +195,6 @@ sub CreateNewJob {
#
###############################################################################
-=head2 fetch_by_dbID
-
- Arg [1] : int $id
- the unique database identifier for the feature to be obtained
- Example : $feat = $adaptor->fetch_by_dbID(1234);
- Description: Returns the AnalysisJob defined by the job_id $id.
- Returntype : Bio::EnsEMBL::Hive::AnalysisJob
- Exceptions : thrown if $id is not defined
- Caller : general
-
-=cut
-
-sub fetch_by_dbID {
- my ($self,$id) = @_;
-
- unless(defined $id) {
- throw("fetch_by_dbID must have an id");
- }
-
- my @tabs = $self->_tables;
-
- my ($name, $syn) = @{$tabs[0]};
-
- #construct a constraint like 't1.table1_id = 1'
- my $constraint = "${syn}.${name}_id = $id";
-
- #return first element of _generic_fetch list
- my ($obj) = @{$self->_generic_fetch($constraint)};
- return $obj;
-}
-
=head2 fetch_all_by_analysis_id_status
@@ -222,25 +212,26 @@ sub fetch_all_by_analysis_id_status {
my ($self, $analysis_id, $status, $retry_count_at_least) = @_;
my @constraints = ();
- push @constraints, "j.analysis_id=$analysis_id" if ($analysis_id);
- push @constraints, "j.status='$status'" if ($status);
- push @constraints, "j.retry_count >= $retry_count_at_least" if ($retry_count_at_least);
- return $self->_generic_fetch( join(" AND ", @constraints) );
+ push @constraints, "analysis_id=$analysis_id" if ($analysis_id);
+ push @constraints, "status='$status'" if ($status);
+ push @constraints, "retry_count >= $retry_count_at_least" if ($retry_count_at_least);
+
+ return $self->fetch_all( join(" AND ", @constraints) );
}
sub fetch_some_by_analysis_id_limit {
my ($self, $analysis_id, $limit) = @_;
- return $self->_generic_fetch( "j.analysis_id = '$analysis_id'", undef, "LIMIT $limit" );
+ return $self->fetch_all( "analysis_id = '$analysis_id' LIMIT $limit" );
}
sub fetch_all_incomplete_jobs_by_worker_id {
my ($self, $worker_id) = @_;
- my $constraint = "j.status IN ('COMPILATION','PRE_CLEANUP','FETCH_INPUT','RUN','WRITE_OUTPUT','POST_CLEANUP') AND j.worker_id='$worker_id'";
- return $self->_generic_fetch($constraint);
+ my $constraint = "status IN ('COMPILATION','PRE_CLEANUP','FETCH_INPUT','RUN','WRITE_OUTPUT','POST_CLEANUP') AND worker_id='$worker_id'";
+ return $self->fetch_all($constraint);
}
@@ -258,144 +249,11 @@ sub fetch_by_url_query {
}
}
-#
-# INTERNAL METHODS
-#
-###################
-
-sub _generic_fetch {
- my ($self, $constraint, $join, $final_clause) = @_;
-
- my @tables = $self->_tables;
- my $columns = join(', ', $self->_columns());
-
- if ($join) {
- foreach my $single_join (@{$join}) {
- my ($tablename, $condition, $extra_columns) = @{$single_join};
- if ($tablename && $condition) {
- push @tables, $tablename;
-
- if($constraint) {
- $constraint .= " AND $condition";
- } else {
- $constraint = " $condition";
- }
- }
- if ($extra_columns) {
- $columns .= ", " . join(', ', @{$extra_columns});
- }
- }
- }
-
- #construct a nice table string like 'table1 t1, table2 t2'
- my $tablenames = join(', ', map({ join(' ', @$_) } @tables));
-
- my $sql = "SELECT $columns FROM $tablenames";
-
- my $default_where = $self->_default_where_clause;
-
- #append a where clause if it was defined
- if($constraint) {
- $sql .= " WHERE $constraint ";
- if($default_where) {
- $sql .= " AND $default_where ";
- }
- } elsif($default_where) {
- $sql .= " WHERE $default_where ";
- }
-
- #append additional clauses which may have been defined
- $sql .= " $final_clause" if($final_clause);
-
- my $sth = $self->prepare($sql);
- $sth->execute;
-
- #print STDOUT $sql,"\n";
-
- return $self->_objs_from_sth($sth);
-}
-
-
-sub _tables {
- my $self = shift;
-
- return (['job', 'j']);
-}
-
-
-sub _columns {
- my $self = shift;
-
- return qw (j.job_id
- j.prev_job_id
- j.analysis_id
- j.input_id
- j.param_id_stack
- j.accu_id_stack
- j.worker_id
- j.status
- j.retry_count
- j.completed
- j.runtime_msec
- j.query_count
- j.semaphore_count
- j.semaphored_job_id
- );
-}
-
-
-sub _objs_from_sth {
- my ($self, $sth) = @_;
-
- my %column;
- $sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));
-
- my @jobs = ();
-
- while ($sth->fetch()) {
-
- my $input_id = ($column{'input_id'} =~ /^_ext(?:\w+)_data_id (\d+)$/)
- ? $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1)
- : $column{'input_id'};
-
- my $param_id_stack = ($column{'param_id_stack'} =~ /^_ext(?:\w+)_data_id (\d+)$/)
- ? $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1)
- : $column{'param_id_stack'};
-
- my $accu_id_stack = ($column{'accu_id_stack'} =~ /^_ext(?:\w+)_data_id (\d+)$/)
- ? $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1)
- : $column{'accu_id_stack'};
-
-
- my $job = Bio::EnsEMBL::Hive::AnalysisJob->new(
- -dbID => $column{'job_id'},
- -analysis_id => $column{'analysis_id'},
- -input_id => $input_id,
- -param_id_stack => $param_id_stack,
- -accu_id_stack => $accu_id_stack,
- -worker_id => $column{'worker_id'},
- -status => $column{'status'},
- -retry_count => $column{'retry_count'},
- -completed => $column{'completed'},
- -runtime_msec => $column{'runtime_msec'},
- -query_count => $column{'query_count'},
- -semaphore_count => $column{'semaphore_count'},
- -semaphored_job_id => $column{'semaphored_job_id'},
- -adaptor => $self,
- );
-
- push @jobs, $job;
- }
- $sth->finish;
-
- return \@jobs
-}
-
-
+########################
#
# STORE / UPDATE METHODS
#
-################
+########################
sub decrease_semaphore_count_for_jobid { # used in semaphore annihilation or unsuccessful creation
@@ -525,8 +383,7 @@ sub reset_or_grab_job_by_dbID {
or die "Could not run\n\t$sql\nwith data:\n\t(".join(',', @values).')';
$sth->finish;
- my $constraint = "j.job_id='$job_id' AND j.status='$new_status'";
- my ($job) = @{ $self->_generic_fetch($constraint) };
+ my $job = $self->fetch_by_job_id_AND_status($job_id, $new_status) ;
return $job;
}
@@ -590,9 +447,7 @@ sub grab_jobs_for_worker {
}
}
-# my $constraint = "j.analysis_id='$analysis_id' AND j.worker_id='$worker_id' AND j.status='CLAIMED'";
- my $constraint = "j.worker_id='$worker_id' AND j.status='CLAIMED'";
- return $self->_generic_fetch($constraint);
+ return $self->fetch_all_by_worker_id_AND_status($worker_id, 'CLAIMED') ;
}
--
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