Inheritance diagram for Bio::EnsEMBL::Hive::Queen:

Public Member Functions
public	default_table_name ()

public	default_input_column_mapping ()

public	do_not_update_columns ()

public	object_class ()

public Bio::EnsEMBL::Hive::Worker	create_new_worker ()

public	specialize_worker ()

public	register_worker_death ()

public	cached_resource_mapping ()

public	registered_workers_attributes ()

public	get_submitted_worker_counts_by_meadow_type_rc_name_for_meadow_user ()

public	check_for_dead_workers ()

public	find_previous_worker_incarnations ()

public	fetch_preregistered_worker ()

public	check_in_worker ()

public void	reset_job_by_dbID_and_sync ()

public	fetch_overdue_workers ()

public	synchronize_hive ()

public Boolean	safe_synchronize_AnalysisStats ()

public	synchronize_AnalysisStats ()

public	check_nothing_to_run_but_semaphored ()

public	print_status_and_return_reasons_to_exit ()

public	register_all_workers_dead ()

public	interval_workers_with_unknown_usage ()

public	store_resource_usage ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor
public	object_class ()

public	slicer ()

public	objectify ()

public	mark_stored ()

public	keys_to_columns ()

public The	refresh ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor
public	default_table_name ()

public	default_insertion_method ()

public	default_overflow_limit ()

public	default_input_column_mapping ()

public	do_not_update_columns ()

public	new ()

public	db ()

public	dbc ()

public	prepare ()

public	overflow_limit ()

public	input_column_mapping ()

public	table_name ()

public	insertion_method ()

public	column_set ()

public	primary_key ()

public	updatable_column_list ()

public	autoinc_id ()

protected	_table_info_loader ()

public	count_all ()

public	fetch_all ()

public	primary_key_constraint ()

public	fetch_by_dbID ()

public	remove_all ()

public	remove ()

public	update ()

public	store_or_update_one ()

public	check_object_present_in_db_by_content ()

public	class_specific_execute ()

public	store ()

protected	_multi_column_filter ()

public	DESTROY ()

public	AUTOLOAD ()

Detailed Description

Description

    The Queen of the Hive based job control system is responsible to 'birthing' the
    correct number of workers of the right type so that they can find jobs to do.
    It will also free up jobs of Workers that died unexpectantly so that other workers
    can claim them to do.

    Hive based processing is a concept based on a more controlled version
    of an autonomous agent type system.  Each worker is not told what to do
    (like a centralized control system - like the current pipeline system)
    but rather queries a central database for jobs (give me jobs).

    Each worker is linked to an analysis_id, registers its self on creation
    into the Hive, creates a RunnableDB instance of the Analysis->module,
    gets $analysis->batch_size jobs from the job table, does its work,
    creates the next layer of job entries by interfacing to
    the DataflowRuleAdaptor to determine the analyses it needs to pass its
    output data to and creates jobs on the next analysis database.
    It repeats this cycle until it has lived its lifetime or until there are no
    more jobs left.
    The lifetime limit is just a safety limit to prevent these from 'infecting'
    a system.

    The Queens job is to simply birth Workers of the correct analysis_id to get the
    work down.  The only other thing the Queen does is free up jobs that were
    claimed by Workers that died unexpectantly so that other workers can take
    over the work.

    The Beekeeper is in charge of interfacing between the Queen and a compute resource
    or 'compute farm'.  Its job is to query Queens if they need any workers and to
    send the requested number of workers to open machines via the runWorker.pl script.
    It is also responsible for interfacing with the Queen to identify worker which died
    unexpectantly.

Definition at line 47 of file Queen.pm.

Member Function Documentation

◆ cached_resource_mapping()

public Bio::EnsEMBL::Hive::Queen::cached_resource_mapping ( )

Undocumented method

Code:

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◆ check_for_dead_workers()

public Bio::EnsEMBL::Hive::Queen::check_for_dead_workers ( )

Undocumented method

Code:

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sub check_for_dead_workers {    # scans the whole Valley for lost Workers (but ignores unreachable ones)
    my ($self, $valley, $check_buried_in_haste, $bury_unkwn_workers) = @_;
    my $last_few_seconds            = 5;    # FIXME: It is probably a good idea to expose this parameter for easier tuning.
    print "GarbageCollector:\tChecking for lost Workers...\n";
    # all non-DEAD workers found in the database, with their meadow status
    my $reconciled_worker_statuses          = $valley->query_worker_statuses( $self->registered_workers_attributes );
    # selects the workers available in this valley. does not query the database / meadow
    my $signature_and_pid_to_worker_status  = $valley->status_of_all_our_workers_by_meadow_signature( $reconciled_worker_statuses );
    # this may pick up workers that have been created since the last fetch
    my $queen_overdue_workers               = $self->fetch_overdue_workers( $last_few_seconds );    # check the workers we have not seen active during the $last_few_seconds
    if (@$queen_overdue_workers) {
        print "GarbageCollector:\tOut of the ".scalar(@$queen_overdue_workers)." Workers that haven't checked in during the last $last_few_seconds seconds...\n";
    } else {
        print "GarbageCollector:\tfound none (all have checked in during the last $last_few_seconds seconds)\n";
    }
    my $this_meadow_user            = whoami();
    my %meadow_status_counts        = ();
    my %mt_and_pid_to_lost_worker   = ();
    foreach my $worker (@$queen_overdue_workers) {
        my $meadow_signature    = $worker->meadow_type.'/'.$worker->meadow_name;
        if(my $pid_to_worker_status = $signature_and_pid_to_worker_status->{$meadow_signature}) {   # the whole Meadow subhash is either present or the Meadow is unreachable
            my $meadow_type = $worker->meadow_type;
            my $process_id  = $worker->process_id;
            my $status = $pid_to_worker_status->{$process_id} // 'DEFERRED_CHECK';  # Workers that have been created between registered_workers_attributes and fetch_overdue_workers
            if($bury_unkwn_workers and ($status eq 'UNKWN')) {
                if( my $meadow = $valley->find_available_meadow_responsible_for_worker( $worker ) ) {
                    if($meadow->can('kill_worker')) {
                        if($worker->meadow_user eq $this_meadow_user) {  # if I'm actually allowed to kill the worker...
                            print "GarbageCollector:\tKilling/forgetting the UNKWN worker by process_id $process_id";
                            $meadow->kill_worker($worker, 1);
                            $status = 'LOST';
                        }
                    }
                }
            }
            $meadow_status_counts{$meadow_signature}{$status}++;
            if(($status eq 'LOST') or ($status eq 'SUBMITTED')) {
                $mt_and_pid_to_lost_worker{$meadow_type}{$process_id} = $worker;
            } elsif ($status eq 'DEFERRED_CHECK') {
                # do nothing now, wait until the next pass to check on this worker
            } else {
                # RUN|PEND|xSUSP handling
                my $update_when_seen_sql = "UPDATE worker SET when_seen=CURRENT_TIMESTAMP WHERE worker_id='".$worker->dbID."'";
                $self->dbc->protected_prepare_execute( [ $update_when_seen_sql ],
                    sub { my ($after) = @_; $self->db->get_LogMessageAdaptor->store_worker_message( $worker, "see_worker".$after, 'INFO' ); }

◆ check_in_worker()

public Bio::EnsEMBL::Hive::Queen::check_in_worker ( )

Undocumented method

Code:

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◆ check_nothing_to_run_but_semaphored()

public Bio::EnsEMBL::Hive::Queen::check_nothing_to_run_but_semaphored ( )

  Arg [1]    : $list_of_analyses
  Example    :

$self->check_nothing_to_run_but_semaphored( [ $analysis_A, $analysis_B ] );

  Description: Counts the number of immediately runnable jobs in the given analyses.
  Exceptions : none
  Caller     : Scheduler

Code:

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◆ create_new_worker()

public Bio::EnsEMBL::Hive::Worker Bio::EnsEMBL::Hive::Queen::create_new_worker ( )

  Description: Creates an entry in the worker table,
               populates some non-storable attributes
               and returns a Worker object based on that insert.
               This guarantees that each worker registered in this Queen's hive is properly registered.
  Returntype : Bio::EnsEMBL::Hive::Worker
  Caller     : runWorker.pl

Code:

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sub create_new_worker {
    my $self    = shift @_;
    my %flags   = @_;
    my ($preregistered, $resource_class_id, $resource_class_name, $beekeeper_id,
            $no_write, $debug, $worker_log_dir, $hive_log_dir, $job_limit, $life_span, $no_cleanup, $retry_throwing_jobs, $can_respecialize,
            $worker_delay_startup_seconds, $worker_crash_on_startup_prob, $config_files)
     = @flags{qw(-preregistered -resource_class_id -resource_class_name -beekeeper_id
            -no_write -debug -worker_log_dir -hive_log_dir -job_limit -life_span -no_cleanup -retry_throwing_jobs -can_respecialize
            -worker_delay_startup_seconds -worker_crash_on_startup_prob -config_files)};
    sleep( $worker_delay_startup_seconds // 0 );    # NB: undefined parameter would have caused eternal sleep!
    if( defined( $worker_crash_on_startup_prob ) ) {
        if( rand(1) < $worker_crash_on_startup_prob ) {
            die "This is a requested crash of the Worker (with probability=$worker_crash_on_startup_prob)";
        }
    }
    my $default_config = Bio::EnsEMBL::Hive::Utils::Config->new(@$config_files);
    my ($meadow, $process_id, $meadow_host, $meadow_user) = Bio::EnsEMBL::Hive::Valley->new( $default_config )->whereami();
    die "Valley is not fully defined" unless ($meadow && $process_id && $meadow_host && $meadow_user);
    my $meadow_type = $meadow->type;
    my $meadow_name = $meadow->cached_name;
    foreach my $prev_worker_incarnation (@{ $self->find_previous_worker_incarnations($meadow_type, $meadow_name, $process_id) }) {
            # So far 'RELOCATED events' has been detected on LSF 9.0 in response to sending signal #99 or #100
            # Since I don't know how to avoid them, I am trying to register them when they happen.
            # The following snippet buries the previous incarnation of the Worker before starting a new one.
            #
            # FIXME: if GarabageCollector (beekeeper -dead) gets to these processes first, it will register them as DEAD/UNKNOWN.
            #       LSF 9.0 does not report "rescheduling" events in the output of 'bacct', but does mention them in 'bhist'.
            #       So parsing 'bhist' output would probably yield the most accurate & confident registration of these events.
        $prev_worker_incarnation->cause_of_death( 'RELOCATED' );
        $self->register_worker_death( $prev_worker_incarnation );
    }
    my $worker;
    if($preregistered) {
        my $max_registration_seconds    = $meadow->config_get('MaxRegistrationSeconds');
        my $seconds_waited              = 0;
        my $seconds_more                = 5;    # step increment
        until( $worker = $self->fetch_preregistered_worker($meadow_type, $meadow_name, $process_id) ) {
            my $log_message_adaptor = $self->db->get_LogMessageAdaptor;
            if( defined($max_registration_seconds) and ($seconds_waited > $max_registration_seconds) ) {
                my $msg = "Preregistered Worker $meadow_type/$meadow_name:$process_id timed out waiting to occupy its entry, bailing out";
                $log_message_adaptor->store_hive_message($msg, 'WORKER_ERROR' );
                die $msg;
            } else {
                $log_message_adaptor->store_hive_message("Preregistered Worker $meadow_type/$meadow_name:$process_id waiting $seconds_more more seconds to fetch itself...", 'WORKER_CAUTION' );
                sleep($seconds_more);
                $seconds_waited += $seconds_more;
            }
        }
            # only update the fields that were not available at the time of submission:
        $worker->meadow_host( $meadow_host );
        $worker->meadow_user( $meadow_user );
        $worker->when_born(   'CURRENT_TIMESTAMP' );
        $worker->status(      'READY' );
        $self->update( $worker );
    } else {
        my $resource_class;
        if( defined($resource_class_name) ) {
            $resource_class = $self->db->hive_pipeline->collection_of('ResourceClass')->find_one_by('name' => $resource_class_name)
                or die "resource_class with name='$resource_class_name' could not be fetched from the database";
        } elsif( defined($resource_class_id) ) {
            $resource_class = $self->db->hive_pipeline->collection_of('ResourceClass')->find_one_by('dbID', $resource_class_id)
                or die "resource_class with dbID='$resource_class_id' could not be fetched from the database";
        }
        $worker = Bio::EnsEMBL::Hive::Worker->new(
            'meadow_type'       => $meadow_type,
            'meadow_name'       => $meadow_name,
            'process_id'        => $process_id,
            'resource_class'    => $resource_class,
            'beekeeper_id'      => $beekeeper_id,
            'meadow_host'       => $meadow_host,
            'meadow_user'       => $meadow_user,
        );
        if (ref($self)) {
            $self->store( $worker );
            $worker->when_born(   'CURRENT_TIMESTAMP' );
            $self->update_when_born( $worker );
            $self->refresh( $worker );
        }
    }
    $worker->set_log_directory_name($hive_log_dir, $worker_log_dir);
    $worker->init;
    if(defined($job_limit)) {
      $worker->job_limiter($job_limit);
      $worker->life_span(0);
    }
    $worker->life_span($life_span * 60)                 if($life_span); # $life_span min -> sec
    $worker->execute_writes(0)                          if($no_write);
    $worker->perform_cleanup(0)                         if($no_cleanup);
    $worker->debug($debug)                              if($debug);
    $worker->retry_throwing_jobs($retry_throwing_jobs)  if(defined $retry_throwing_jobs);
    $worker->can_respecialize($can_respecialize)        if(defined $can_respecialize);
    return $worker;
}

◆ default_input_column_mapping()

public Bio::EnsEMBL::Hive::Queen::default_input_column_mapping ( )

Undocumented method

Code:

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◆ default_table_name()

public Bio::EnsEMBL::Hive::Queen::default_table_name ( )

Undocumented method

Code:

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◆ do_not_update_columns()

public Bio::EnsEMBL::Hive::Queen::do_not_update_columns ( )

Undocumented method

Code:

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◆ fetch_overdue_workers()

public Bio::EnsEMBL::Hive::Queen::fetch_overdue_workers ( )

Undocumented method

Code:

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◆ fetch_preregistered_worker()

public Bio::EnsEMBL::Hive::Queen::fetch_preregistered_worker ( )

Undocumented method

Code:

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◆ find_previous_worker_incarnations()

public Bio::EnsEMBL::Hive::Queen::find_previous_worker_incarnations ( )

Undocumented method

Code:

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◆ get_submitted_worker_counts_by_meadow_type_rc_name_for_meadow_user()

public Bio::EnsEMBL::Hive::Queen::get_submitted_worker_counts_by_meadow_type_rc_name_for_meadow_user ( )

Undocumented method

Code:

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◆ interval_workers_with_unknown_usage()

public Bio::EnsEMBL::Hive::Queen::interval_workers_with_unknown_usage ( )

Undocumented method

Code:

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◆ object_class()

public Bio::EnsEMBL::Hive::Queen::object_class ( )

Undocumented method

Code:

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◆ print_status_and_return_reasons_to_exit()

public Bio::EnsEMBL::Hive::Queen::print_status_and_return_reasons_to_exit ( )

  Arg [1]    : $list_of_analyses
  Arg [2]    : $debug
  Example    :

my $reasons_to_exit = $queen->print_status_and_return_reasons_to_exit( [ $analysis_A, $analysis_B ] );
            : foreach my $reason_to_exit (@$reasons_to_exit) {
            :     my $exit_message  = $reason_to_exit->{'message'};
            :     my $exit_status   = $reason_to_exit->{'exit_status'};

  Description: Runs through all analyses in the given list, reports failed analyses, and computes some totals.
             : It returns a list of exit messages and status codes. Each element of the list is a hashref,
             : with the exit message keyed by 'message' and the status code keyed by 'exit_status'
             :
             : Possible status codes are:
             :   'JOB_FAILED'
             :   'ANALYSIS_FAILED'
             :   'NO_WORK'
             :
             : If $debug is set, the list will contain all analyses. Otherwise, empty and done analyses
             : will not be listed
  Exceptions : none
  Caller     : beekeeper.pl

Code:

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sub print_status_and_return_reasons_to_exit {
    my ($self, $list_of_analyses, $debug) = @_;
    my ($total_done_jobs, $total_failed_jobs, $total_jobs, $total_excluded_jobs, $cpumsec_to_do) = (0) x 5;
    my %skipped_analyses = ('EMPTY' => [], 'DONE' => []);
    my @analyses_to_display;
    my @reasons_to_exit;
    foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
        my $stats               = $analysis->stats;
        my $failed_job_count    = $stats->failed_job_count;
        my $is_excluded         = $stats->is_excluded;
        if ($debug or !$skipped_analyses{$stats->status}) {
            push @analyses_to_display, $analysis;
        } else {
            push @{$skipped_analyses{$stats->status}}, $analysis;
        }
        if ($failed_job_count > 0) {
           $self->synchronize_AnalysisStats($stats);
           $stats->determine_status();
            my $exit_status;
            my $failure_message;
            my $logic_name = $analysis->logic_name;
            my $tolerance = $analysis->failed_job_tolerance;
            if( $stats->status eq 'FAILED') {
                $exit_status = 'ANALYSIS_FAILED';
                $failure_message =  "### Analysis '$logic_name' has FAILED  (failed jobs: $failed_job_count, tolerance: $tolerance\%) ###";
            } else {
                $exit_status = 'JOB_FAILED';
                $failure_message = "### Analysis '$logic_name' has failed jobs (failed jobs: $failed_job_count, tolerance: $tolerance\%) ###";
            }
            push (@reasons_to_exit, {'message'     => $failure_message,
                                     'exit_status' => $exit_status});
        }
        if ($is_excluded) {
            my $excluded_job_count = $stats->total_job_count - $stats->done_job_count - $failed_job_count;
            $total_excluded_jobs += $excluded_job_count;
            push @{$skipped_analyses{'EXCLUDED'}}, $analysis;
        }
        $total_done_jobs    += $stats->done_job_count;
        $total_failed_jobs  += $failed_job_count;
        $total_jobs         += $stats->total_job_count;
        $cpumsec_to_do      += $stats->ready_job_count * $stats->avg_msec_per_job;
    }
    my $total_jobs_to_do        = $total_jobs - $total_done_jobs - $total_failed_jobs - $total_excluded_jobs;         # includes SEMAPHORED, READY, CLAIMED, INPROGRESS
    my $cpuhrs_to_do            = $cpumsec_to_do / (1000.0*60*60);
    my $percentage_completed    = $total_jobs
                                    ? (($total_done_jobs+$total_failed_jobs)*100.0/$total_jobs)
                                    : 0.0;
    my $max_logic_name_length = max(map {length($_->logic_name)} @analyses_to_display);
    foreach my $analysis (@analyses_to_display) {
        print $analysis->stats->toString($max_logic_name_length) . "\n";
    }
    print "\n";
    if (@{$skipped_analyses{'EMPTY'}}) {
        printf("%d analyses not shown because they don't have any jobs.\n", scalar(@{$skipped_analyses{'EMPTY'}}));
    }
    if (@{$skipped_analyses{'DONE'}}) {
        printf("%d analyses not shown because all their jobs are done.\n", scalar(@{$skipped_analyses{'DONE'}}));
    }
    printf("total over %d analyses : %6.2f%% complete (< %.2f CPU_hrs) (%d to_do + %d done + %d failed + %d excluded = %d total)\n",
           scalar(@$list_of_analyses), $percentage_completed, $cpuhrs_to_do, $total_jobs_to_do, $total_done_jobs, $total_failed_jobs, $total_excluded_jobs, $total_jobs);
    unless( $total_jobs_to_do ) {
        if ($total_excluded_jobs > 0) {
            push (@reasons_to_exit, {'message' => "### Some analyses are excluded ###",
                                     'exit_status' => 'NO_WORK'});
        }
        push (@reasons_to_exit, {'message' => "### No jobs left to do ###",
                                 'exit_status' => 'NO_WORK'});
    }
    return \@reasons_to_exit;
}

◆ register_all_workers_dead()

public Bio::EnsEMBL::Hive::Queen::register_all_workers_dead ( )

  Example    :

$queen->register_all_workers_dead();

  Description: Registers all workers dead
  Exceptions : none
  Caller     : beekeeper.pl

Code:

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◆ register_worker_death()

public Bio::EnsEMBL::Hive::Queen::register_worker_death ( )

Undocumented method

Code:

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◆ registered_workers_attributes()

public Bio::EnsEMBL::Hive::Queen::registered_workers_attributes ( )

Undocumented method

Code:

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◆ reset_job_by_dbID_and_sync()

public void Bio::EnsEMBL::Hive::Queen::reset_job_by_dbID_and_sync ( )

  Arg [1]: int $job_id
  Example: 
    my $job = $queen->reset_job_by_dbID_and_sync($job_id);
  Description: 
    For the specified job_id it will fetch just that job, 
    reset it completely as if it has never run, and return it.  
    Specifying a specific job bypasses the safety checks, 
    thus multiple workers could be running the 
    same job simultaneously (use only for debugging).
  Returntype : none
  Exceptions :
  Caller     : beekeeper.pl

Code:

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◆ safe_synchronize_AnalysisStats()

public Boolean Bio::EnsEMBL::Hive::Queen::safe_synchronize_AnalysisStats ( )

  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    :

$self->safe_synchronize_AnalysisStats($stats);

  Description: Prewrapper around synchronize_AnalysisStats that does
               checks and grabs sync_lock before proceeding with sync.
               Used by distributed worker sync system to avoid contention.
               Returns 1 on success and 0 if the lock could not have been obtained,
               and so no sync was attempted.
  Returntype : boolean
  Caller     : general

Code:

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◆ specialize_worker()

public Bio::EnsEMBL::Hive::Queen::specialize_worker ( )

  Description: If analysis_id or logic_name is specified it will try to specialize the Worker into this analysis.
               If not specified the Queen will analyze the hive and pick the most suitable analysis.
  Caller     : Bio::EnsEMBL::Hive::Worker

Code:

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sub specialize_worker {
    my $self    = shift @_;
    my $worker  = shift @_;
    my $flags   = shift @_;
    my ($analyses_pattern, $job_id, $force)
     = @$flags{qw(-analyses_pattern -job_id -force)};
    if( $analyses_pattern and $job_id ) {
        die "At most one of the options {-analyses_pattern, -job_id} can be set to pre-specialize a Worker";
    }
    my $analysis;
    if( $job_id ) {
        $worker->worker_say("resetting and fetching job for job_id '$job_id'");
        my $job_adaptor = $self->db->get_AnalysisJobAdaptor;
        my $job = $job_adaptor->fetch_by_dbID( $job_id )
            or die "Could not fetch job with dbID='$job_id'";
        my $job_status = $job->status();
        if($job_status =~/(CLAIMED|PRE_CLEANUP|FETCH_INPUT|RUN|WRITE_OUTPUT|POST_HEALTHCHECK|POST_CLEANUP)/ ) {
            die "Job with dbID='$job_id' is already in progress, cannot run";   # FIXME: try GC first, then complain
        } elsif($job_status =~/(DONE|SEMAPHORED)/ and !$force) {
            die "Job with dbID='$job_id' is $job_status, please use --force to override";
        }
        $analysis = $job->analysis;
        if(($analysis->stats->status eq 'BLOCKED') and !$force) {
            die "Analysis is BLOCKED, can't specialize a worker. Please use --force to override";
        }
        if(($job_status eq 'DONE') and my $controlled_semaphore = $job->controlled_semaphore) {
            $worker->worker_say("Increasing the semaphore count of the dependent job");
            $controlled_semaphore->increase_by( [ $job ] );
        }
        my %status2counter = ('FAILED' => 'failed_job_count', 'READY' => 'ready_job_count', 'DONE' => 'done_job_count', 'PASSED_ON' => 'done_job_count', 'SEMAPHORED' => 'semaphored_job_count');
        $analysis->stats->adaptor->increment_a_counter( $status2counter{$job->status}, -1, $job->analysis_id );
    } else {
        $analyses_pattern //= '%';  # for printing
        my $analyses_matching_pattern   = $worker->hive_pipeline->collection_of( 'Analysis' )->find_all_by_pattern( $analyses_pattern );
            # refresh the stats of matching analyses before re-specialization:
        foreach my $analysis ( @$analyses_matching_pattern ) {
            $analysis->stats->refresh();
        }
        $self->db->hive_pipeline->invalidate_hive_current_load;
        $analysis = Bio::EnsEMBL::Hive::Scheduler::suggest_analysis_to_specialize_a_worker($worker, $analyses_matching_pattern, $analyses_pattern);
        unless( ref($analysis) ) {
            $worker->cause_of_death('NO_ROLE');
            my $msg = $analysis // "No analysis suitable for the worker was found";
            die "$msg\n";
        }
    }
    my $new_role = Bio::EnsEMBL::Hive::Role->new(
        'worker'        => $worker,
        'analysis'      => $analysis,
    );
    $self->db->get_RoleAdaptor->store( $new_role );
    $worker->current_role( $new_role );
    my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor;
    if($job_id) {
        my $role_id = $new_role->dbID;
        if( my $job = $self->db->get_AnalysisJobAdaptor->reset_or_grab_job_by_dbID($job_id, $role_id) ) {
            $worker->special_batch( [ $job ] );
        } else {
            die "Could not claim job with dbID='$job_id' for Role with dbID='$role_id'";
        }
    } else {    # Note: special batch Workers should avoid flipping the status to 'WORKING' in case the analysis is still 'BLOCKED'
        $analysis_stats_adaptor->update_status($analysis->dbID, 'WORKING');
    }
        # The following increment used to be done only when no specific task was given to the worker,
        # thereby excluding such "special task" workers from being counted in num_running_workers.
        #
        # However this may be tricky to emulate by triggers that know nothing about "special tasks",
        # so I am (temporarily?) simplifying the accounting algorithm.
        #
    $analysis_stats_adaptor->increment_a_counter( 'num_running_workers', 1, $analysis->dbID );
}

◆ store_resource_usage()

public Bio::EnsEMBL::Hive::Queen::store_resource_usage ( )

Undocumented method

Code:

click to view

◆ synchronize_AnalysisStats()

public Bio::EnsEMBL::Hive::Queen::synchronize_AnalysisStats ( )

  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    :

$self->synchronize_AnalysisStats( $stats );

  Description: Queries the job and worker tables to get summary counts
               and rebuilds the AnalysisStats object.
               Then updates the analysis_stats table with the new summary info.
  Exceptions : none
  Caller     : general

Code:

click to view

◆ synchronize_hive()

public Bio::EnsEMBL::Hive::Queen::synchronize_hive ( )

  Arg [1]    : $list_of_analyses
  Example    :

$queen->synchronize_hive( [ $analysis_A, $analysis_B ] );

  Description: Runs through all analyses in the given list and synchronizes
              the analysis_stats summary with the states in the job and worker tables.
              Then follows by checking all the blocking rules and blocks/unblocks analyses as needed.
  Exceptions : none
  Caller     : general

Code:

click to view

The documentation for this class was generated from the following file:

modules/Bio/EnsEMBL/Hive/Queen.pm

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ cached_resource_mapping()

◆ check_for_dead_workers()

◆ check_in_worker()

◆ check_nothing_to_run_but_semaphored()

◆ create_new_worker()

◆ default_input_column_mapping()

◆ default_table_name()

◆ do_not_update_columns()

◆ fetch_overdue_workers()

◆ fetch_preregistered_worker()

◆ find_previous_worker_incarnations()

◆ get_submitted_worker_counts_by_meadow_type_rc_name_for_meadow_user()

◆ interval_workers_with_unknown_usage()

◆ object_class()

◆ print_status_and_return_reasons_to_exit()

◆ register_all_workers_dead()

◆ register_worker_death()

◆ registered_workers_attributes()

◆ reset_job_by_dbID_and_sync()

◆ safe_synchronize_AnalysisStats()

◆ specialize_worker()

◆ store_resource_usage()

◆ synchronize_AnalysisStats()

◆ synchronize_hive()