Commit b6542054 authored by Jessica Severin's avatar Jessica Severin
Browse files

refactored reset_job to reset_job_by_dbID to take a dbID rather than an object.

added method reset_all_jobs_for_analysis_id to facilitate re-flowing data through new dataflow rules.
extended perldoc
changed the 'retry count' to 7 (so runs 1 + 7 retrys)
parent 23d89c1b
......@@ -194,6 +194,26 @@ sub fetch_all {
return $self->_generic_fetch();
=head2 fetch_all_failed_jobs
Arg [1] : (optional) int $analysis_id
Example : $failed_jobs = $adaptor->fetch_all_failed_jobs;
$failed_jobs = $adaptor->fetch_all_failed_jobs($analysis->dbID);
Description: Returns a list of all jobs with status 'FAILED'. If an $analysis_id
is specified it will limit the search accordingly.
Returntype : reference to list of Bio::EnsEMBL::Hive::AnalysisJob objects
Exceptions : none
Caller : user processes
sub fetch_all_failed_jobs {
my ($self,$analysis_id) = @_;
my $constraint = "a.status='FAILED'";
$constraint .= " AND a.analysis_id=$analysis_id" if($analysis_id);
return $self->_generic_fetch($constraint);
......@@ -350,7 +370,7 @@ sub update_status {
=head2 store_out_files
Arg [1] : Bio::EnsEMBL::Compar::Hive::AnalysisJob $job
Arg [1] : Bio::EnsEMBL::Hive::AnalysisJob $job
Example :
Description: if files are non-zero size, will update DB with location
Returntype :
......@@ -402,6 +422,20 @@ sub claim_jobs_for_worker {
return $claim;
=head2 reset_dead_jobs_for_worker
Arg [1] : Bio::EnsEMBL::Hive::Worker object
Example :
Description: If a worker has died some of its jobs need to be reset back to 'READY'
so they can be rerun.
Jobs in state CLAIMED as simply reset back to READY.
If jobs was in a 'working' state (GET_INPUT, RUN, WRITE_OUTPUT))
the retry_count is incremented and the status set back to READY.
If the retry_count >=7 the job is set to 'FAILED' and not rerun again.
Exceptions : $worker must be defined
Caller : Bio::EnsEMBL::Hive::Queen
sub reset_dead_jobs_for_worker {
my $self = shift;
......@@ -426,7 +460,7 @@ sub reset_dead_jobs_for_worker {
$sql = "UPDATE analysis_job SET job_claim='', status='READY'".
" ,retry_count=retry_count+1".
" WHERE status in ('GET_INPUT','RUN','WRITE_OUTPUT')".
" AND retry_count<5".
" AND retry_count<7".
" AND hive_id='" . $worker->hive_id ."'";
$sth = $self->prepare($sql);
......@@ -436,7 +470,7 @@ sub reset_dead_jobs_for_worker {
$sql = "UPDATE analysis_job SET status='FAILED'".
" ,retry_count=retry_count+1".
" WHERE status in ('GET_INPUT','RUN','WRITE_OUTPUT')".
" AND retry_count>=5".
" AND retry_count>=7".
" AND hive_id='" . $worker->hive_id ."'";
$sth = $self->prepare($sql);
......@@ -446,22 +480,63 @@ sub reset_dead_jobs_for_worker {
#print(" done update BROKEN jobs\n");
=head2 reset_job_by_dbID
Arg [1] : int $analysis_job_id
Example :
Description: Forces a job to be reset to 'READY' so it can be run again.
Will also reset a previously 'BLOCKED' jobs to READY.
Exceptions : $job must be defined
Caller : user process
sub reset_job {
sub reset_job_by_dbID {
my $self = shift;
my $job = shift;
throw("must define job") unless($job);
my $analysis_job_id = shift;
throw("must define job") unless($analysis_job_id);
my ($sql, $sth);
#first just reset the claimed jobs, these don't need a retry_count index increment
$sql = "UPDATE analysis_job SET job_claim='', status='READY' WHERE analysis_job_id=?";
$sth = $self->prepare($sql);
#print(" done update CLAIMED\n");
=head2 reset_all_jobs_for_analysis_id
Arg [1] : int $analysis_id
Example :
Description: Resets all not BLOCKED jobs back to READY so they can be rerun.
Needed if an analysis/runnableDB modifies the dataflow rules as the
system runs. The jobs that are flowed 'from' will need to be reset so
that the output data can be flowed through the new rule.
If one is designing a system based on a need to change rules mid-process
it is best to make sure such 'from' analyses that need to be reset are 'Dummy'
types so that they can 'hold' the output from the previous step and not require
the system to actually redo processing.
Exceptions : $analysis_id must be defined
Caller : user RunnableDB subclasses which build dataflow rules on the fly
sub reset_all_jobs_for_analysis_id {
my $self = shift;
my $analysis_id = shift;
throw("must define analysis_id") unless($analysis_id);
my ($sql, $sth);
$sql = "UPDATE analysis_job SET job_claim='', status='READY' WHERE status!='BLOCKED' and analysis_id=?";
$sth = $self->prepare($sql);
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