Commit 25e17d9a authored by Leo Gordon's avatar Leo Gordon
Browse files

removed rearrange() and throw() from AnalysisJobAdaptor by removing the unused...

removed rearrange() and throw() from AnalysisJobAdaptor by removing the unused CreateNewJob() method
parent ddf0e576
......@@ -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
......
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