From 25e17d9a223224c80d5bc46c50d8309b3483ca76 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Thu, 6 Feb 2014 12:11:57 +0000
Subject: [PATCH] removed rearrange() and throw() from AnalysisJobAdaptor by
removing the unused CreateNewJob() method
---
.../EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm | 69 -------------------
1 file changed, 69 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index 88cb0611b..9a9ff7cb6 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -43,9 +43,6 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use strict;
-use Bio::EnsEMBL::Utils::Argument ('rearrange');
-use Bio::EnsEMBL::Utils::Exception ('throw');
-
use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::Hive::AnalysisJob;
use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
@@ -73,72 +70,6 @@ sub default_overflow_limit {
}
-
-###############################################################################
-#
-# CLASS method
-#
-###############################################################################
-
-=head2 CreateNewJob
-
- Args : -input_id => string of input_id which will be passed to run the job (or a Perl hash that will be automagically stringified)
- -analysis => Bio::EnsEMBL::Hive::Analysis object stored in the database
- -prev_job_id => (optional) job_id of job that is creating this job.
- Used purely for book keeping.
- Example : $job_id = Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor->CreateNewJob(
- -input_id => 'my input data',
- -analysis => $myAnalysis);
- Description: uses the analysis object to get the db connection from the adaptor to store a new
- job in a hive. This is a class level method since it does not have any state.
- Also updates corresponding analysis_stats by incrementing total_job_count,
- ready_job_count and flagging the incremental update by changing the status
- to 'LOADING' (but only if the analysis is not blocked).
- NOTE: no AnalysisJob object is created in memory as the result of this call; it is simply a "fast store".
- Returntype : int job_id on database analysis is from.
- Exceptions : thrown if either -input_id or -analysis are not properly defined
- Caller : general
- Status : DEPRECATED. Please use $job_adaptor->store_jobs_and_adjust_counters( \@jobs_to_store ) instead
-
-=cut
-
-sub CreateNewJob {
- my ($class, @args) = @_;
-
- my ($prev_job, $prev_job_id, $analysis, $input_id, $param_id_stack, $accu_id_stack, $semaphore_count, $semaphored_job_id, $push_new_semaphore) =
- rearrange([qw(prev_job prev_job_id analysis input_id param_id_stack accu_id_stack semaphore_count semaphored_job_id push_new_semaphore)], @args);
-
- warn "CreateNewJob() method is deprecated. Please use \$job_adaptor->store_jobs_and_adjust_counters() instead.\n";
-
- throw("must define input_id") unless($input_id);
- throw("must define analysis") unless($analysis);
- throw("analysis must be [Bio::EnsEMBL::Hive::Analysis] not a [$analysis]") unless($analysis->isa('Bio::EnsEMBL::Hive::Analysis'));
- throw("analysis must have adaptor connected to database") unless($analysis->adaptor and $analysis->adaptor->db);
- throw("Please specify prev_job object instead of prev_job_id if available") if ($prev_job_id); # 'obsolete' message
-
- my $job = Bio::EnsEMBL::Hive::AnalysisJob->new(
- -prev_job_id => $prev_job && $prev_job->dbID,
- -analysis_id => $analysis->dbID,
- -input_id => $input_id,
- -param_id_stack => $param_id_stack,
- -accu_id_stack => $accu_id_stack,
- -semaphore_count => $semaphore_count,
- -semaphored_job_id => $semaphored_job_id,
- );
-
- my ($job_id) = @{ $analysis->adaptor->db->get_AnalysisJobAdaptor->store_jobs_and_adjust_counters( [ $job ], $push_new_semaphore ) };
-
- return $job_id;
-}
-
-
-###############################################################################
-#
-# INSTANCE methods
-#
-###############################################################################
-
-
=head2 store_jobs_and_adjust_counters
Arg [1] : arrayref of Bio::EnsEMBL::Hive::AnalysisJob $jobs_to_store
--
GitLab