Queen.pm 25.1 KB
Newer Older
Jessica Severin's avatar
Jessica Severin committed
1
2
3
4
5
6
7
8
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code

=pod 

=head1 NAME
9

10
  Bio::EnsEMBL::Hive::Queen
Jessica Severin's avatar
Jessica Severin committed
11
12

=head1 SYNOPSIS
13

14
  The Queen of the Hive based job control system
Jessica Severin's avatar
Jessica Severin committed
15
16

=head1 DESCRIPTION
17

18
19
20
21
22
23
24
25
26
27
28
29
  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,
30
  gets $worker->batch_size() jobs from the analysis_job table, does its
31
  work, creates the next layer of analysis_job entries by interfacing to
32
33
34
  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
35
36
37
38
39
40
41
42
43
44
  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
45
  or 'compute farm'.  Its job is to query Queens if they need any workers and to
46
47
48
  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.
Jessica Severin's avatar
Jessica Severin committed
49
50

=head1 CONTACT
51

52
53
  Contact Jessica Severin on EnsEMBL::Hive implemetation/design detail: jessica@ebi.ac.uk
  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
Jessica Severin's avatar
Jessica Severin committed
54
55

=head1 APPENDIX
56

57
58
  The rest of the documentation details each of the object methods. 
  Internal methods are usually preceded with a _
Jessica Severin's avatar
Jessica Severin committed
59
60
61
62
63
64

=cut

package Bio::EnsEMBL::Hive::Queen;

use strict;
65
use POSIX;
66
67
68
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;

Jessica Severin's avatar
Jessica Severin committed
69
70
71
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Sys::Hostname;
72
use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
Jessica Severin's avatar
Jessica Severin committed
73

74

Jessica Severin's avatar
Jessica Severin committed
75
76
our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);

77
############################
Jessica Severin's avatar
Jessica Severin committed
78
#
79
# PUBLIC API for Workers
Jessica Severin's avatar
Jessica Severin committed
80
#
81
############################
Jessica Severin's avatar
Jessica Severin committed
82
83
84

=head2 create_new_worker

85
  Arg [1]    : $analysis_id (optional)
Jessica Severin's avatar
Jessica Severin committed
86
  Example    :
87
88
89
90
91
92
  Description: If analysis_id is specified it will try to create a worker based
               on that analysis.  If not specified the queen will analyze the hive
               and pick the analysis that has the most amount of work to be done.
               It creates an entry in the hive table, and returns a Worker object 
               based on that insert.  This guarantees that each worker registered
               in this queens hive is properly registered.
Jessica Severin's avatar
Jessica Severin committed
93
94
95
96
97
98
99
  Returntype : Bio::EnsEMBL::Hive::Worker
  Exceptions :
  Caller     :

=cut

sub create_new_worker {
100
101
  my ($self, @args) = @_;

102
103
  my ($analysis_id, $beekeeper ,$pid) =
     rearrange([qw(analysis_id beekeeper process_id) ], @args);
Jessica Severin's avatar
Jessica Severin committed
104

105
  my $analStatsDBA = $self->db->get_AnalysisStatsAdaptor;
106
  return undef unless($analStatsDBA);
107

108
  return undef if($self->get_hive_current_load() >= 1.5);
109
  
110
111
112
113
  my $analysisStats;
  if($analysis_id) {
    $analysisStats = $analStatsDBA->fetch_by_analysis_id($analysis_id);
  } else {
114
    $analysisStats = $self->_pick_best_analysis_for_new_worker;
115
  }
116
117
  
  return undef unless($analysisStats);
118
  $analStatsDBA->decrement_needed_workers($analysisStats->analysis_id);
119
120
121
122
123
124
125
126
127
  $analysisStats->print_stats;
  
  if($analysisStats->status eq 'BLOCKED') {
    print("Analysis is BLOCKED, can't create workers\n");
    return undef;
  }
  if($analysisStats->status eq 'DONE') {
    print("Analysis is DONE, don't need to create workers\n");
    return undef;
Jessica Severin's avatar
Jessica Severin committed
128
129
130
  }

  my $host = hostname;
131
  $pid = $$ unless($pid);
132
  $beekeeper = '' unless($beekeeper);
Jessica Severin's avatar
Jessica Severin committed
133

134
135
136
  my $sql = q{INSERT INTO hive 
              (born, last_check_in, process_id, analysis_id, beekeeper, host)
              VALUES (NOW(), NOW(), ?,?,?,?)};
Jessica Severin's avatar
Jessica Severin committed
137
138

  my $sth = $self->prepare($sql);
139
  $sth->execute($pid, $analysisStats->analysis_id, $beekeeper, $host);
Jessica Severin's avatar
Jessica Severin committed
140
141
142
143
144
145
  my $hive_id = $sth->{'mysql_insertid'};
  $sth->finish;

  my $worker = $self->_fetch_by_hive_id($hive_id);
  $worker=undef unless($worker and $worker->analysis);

146
  if($worker and $analysisStats) {
147
    $analysisStats->update_status('WORKING');
Jessica Severin's avatar
Jessica Severin committed
148
149
150
151
152
153
154
155
156
  }
  return $worker;
}


sub register_worker_death {
  my ($self, $worker) = @_;

  return unless($worker);
157
158
159
160

  # if called without a defined cause_of_death, assume catastrophic failure
  $worker->cause_of_death('FATALITY') unless(defined($worker->cause_of_death));
  
Jessica Severin's avatar
Jessica Severin committed
161
162
163
164
165
166
167
168
  my $sql = "UPDATE hive SET died=now(), last_check_in=now()";
  $sql .= " ,work_done='" . $worker->work_done . "'";
  $sql .= " ,cause_of_death='". $worker->cause_of_death ."'";
  $sql .= " WHERE hive_id='" . $worker->hive_id ."'";

  my $sth = $self->prepare($sql);
  $sth->execute();
  $sth->finish;
169
170

  if($worker->cause_of_death eq "NO_WORK") {
171
    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, "ALL_CLAIMED");
172
173
174
  }
  if($worker->cause_of_death eq "FATALITY") {
    #print("FATAL DEATH Arrrrgggghhhhhhhh (hive_id=",$worker->hive_id,")\n");
175
    $self->db->get_AnalysisJobAdaptor->reset_dead_jobs_for_worker($worker);
176
  }
177
  
178
  # re-sync the analysis_stats when a worker dies as part of dynamic sync system
179
  if($self->safe_synchronize_AnalysisStats($worker->analysis->stats)->status ne 'DONE') {
180
181
182
183
184
    # since I'm dying I should make sure there is someone to take my place after I'm gone ...
    # above synch still sees me as a 'living worker' so I need to compensate for that
    $self->db->get_AnalysisStatsAdaptor->increment_needed_workers($worker->analysis->dbID);
  }

Jessica Severin's avatar
Jessica Severin committed
185
186
187
}


188
sub worker_check_in {
Jessica Severin's avatar
Jessica Severin committed
189
190
191
192
  my ($self, $worker) = @_;

  return unless($worker);
  my $sql = "UPDATE hive SET last_check_in=now()";
193
  $sql .= " ,work_done='" . $worker->work_done . "'";
Jessica Severin's avatar
Jessica Severin committed
194
195
196
197
198
  $sql .= " WHERE hive_id='" . $worker->hive_id ."'";

  my $sth = $self->prepare($sql);
  $sth->execute();
  $sth->finish;
199
  
200
  $self->safe_synchronize_AnalysisStats($worker->analysis->stats);
Jessica Severin's avatar
Jessica Severin committed
201
202
203
}


204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
=head2 worker_grab_jobs

  Arg [1]           : Bio::EnsEMBL::Hive::Worker object $worker
  Example: 
    my $jobs  = $queen->worker_grab_jobs();
  Description: 
    For the specified worker, it will search available jobs, 
    and using the workers requested batch_size, claim/fetch that
    number of jobs, and then return them.
  Returntype : 
    reference to array of Bio::EnsEMBL::Hive::AnalysisJob objects
  Exceptions :
  Caller     :

=cut

sub worker_grab_jobs {
  my $self            = shift;
  my $worker          = shift;
  
  my $jobDBA = $self->db->get_AnalysisJobAdaptor;
  my $claim = $jobDBA->claim_jobs_for_worker($worker);
  my $jobs = $jobDBA->fetch_by_claim_analysis($claim, $worker->analysis->dbID);
  return $jobs;
}

230
=head2 reset_and_fetch_job_by_dbID
231
232
233

  Arg [1]: int $analysis_job_id
  Example: 
234
    my $job = $queen->reset_and_fetch_job_by_dbID($analysis_job_id);
235
236
  Description: 
    For the specified analysis_job_id it will fetch just that job, 
237
238
239
    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 
240
241
    same job simultaneously (use only for debugging).
  Returntype : 
242
    Bio::EnsEMBL::Hive::AnalysisJob object
243
  Exceptions :
244
  Caller     : beekeepers, runWorker.pl scripts
245
246
247

=cut

248
249
sub reset_and_fetch_job_by_dbID {
  my $self = shift;
250
  my $analysis_job_id = shift;
251
  
252
  my $jobDBA = $self->db->get_AnalysisJobAdaptor;
253
254
255
256
257
  $jobDBA->reset_job_by_dbID($analysis_job_id); 

  my $job = $jobDBA->fetch_by_dbID($analysis_job_id); 
  my $stats = $self->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($job->analysis_id);
  $self->synchronize_AnalysisStats($stats);
258
  
259
260
261
262
263
264
265
266
267
268
269
270
  return $job;
}


sub worker_reclaim_job {
  my $self   = shift;
  my $worker = shift;
  my $job    = shift;

  return undef unless($job and $worker);
  $job->hive_id($worker->hive_id);
  $self->db->get_AnalysisJobAdaptor->reclaim_job($job);
271
272
273
274
275
276
277
278
279
280
281
282
  return $job;
}


sub worker_register_job_done {
  my $self = shift;
  my $worker = shift;
  my $job = shift;
  
  return unless($job);
  return unless($job->dbID and $job->adaptor and $job->hive_id);
  return unless($worker and $worker->analysis and $worker->analysis->dbID);
283
  
284
  $job->update_status('DONE');
285
286

  $self->flow_output_job($job);
287
288
289
290
291
292
293
294
}


sub flow_output_job {
  my $self = shift;
  my $job = shift;
  
  return unless($job);
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
  
  my $rules = $self->db->get_DataflowRuleAdaptor->fetch_from_analysis_job($job);
  foreach my $rule (@{$rules}) {
    Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor->CreateNewJob (
        -input_id       => $job->input_id,
        -analysis       => $rule->to_analysis,
        -input_job_id   => $job->dbID,
    );
  }
}


######################################
#
# Public API interface for beekeeper
#
######################################

313
314
315
316
317
318
319
320
321
322
sub fetch_overdue_workers {
  my ($self,$overdue_secs) = @_;

  $overdue_secs = 3600 unless(defined($overdue_secs));

  my $constraint = "h.cause_of_death='' ".
                   "AND (UNIX_TIMESTAMP()-UNIX_TIMESTAMP(h.last_check_in))>$overdue_secs";
  return $self->_generic_fetch($constraint);
}

323
324
325
326
327
328
sub fetch_failed_workers {
  my $self = shift;
  my $constraint = "h.cause_of_death='FATALITY' ";
  return $self->_generic_fetch($constraint);
}

Jessica Severin's avatar
Jessica Severin committed
329

330
331
332
333
334
335
336
337
338
339
340
341
342
=head2 synchronize_hive

  Example    : $queen->synchronize_hive();
  Description: Runs through all analyses in the system and synchronizes
              the analysis_stats summary with the states in the analysis_job 
              and hive tables.  Then follows by checking all the blocking rules
              and blocks/unblocks analyses as needed.
  Exceptions : none
  Caller     : general

=cut

sub synchronize_hive {
343
344
  my $self = shift;

345
  my $start_time = time();
346

347
348
349
350
351
352
  my $allAnalysis = $self->db->get_AnalysisAdaptor->fetch_all;
  print("analyze ", scalar(@$allAnalysis), "\n");
  foreach my $analysis (@$allAnalysis) {
    my $stats = $analysis->stats;
    $self->synchronize_AnalysisStats($stats);
  }
353
  foreach my $analysis (@$allAnalysis) {
354
355
356
357
    $self->check_blocking_control_rules_for_AnalysisStats($analysis->stats);
  }
  print((time() - $start_time), " secs to synchronize_hive\n");
}
358

359

360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
=head2 safe_synchronize_AnalysisStats

  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
  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.
  Exceptions : none
  Caller     : general

=cut

sub safe_synchronize_AnalysisStats {
  my $self = shift;
  my $stats = shift;

  return $stats unless($stats);
  return $stats unless($stats->analysis_id);
  return $stats if($stats->status eq 'SYNCHING');
  return $stats if($stats->status eq 'DONE');
  return $stats if($stats->sync_lock);
  return $stats if(($stats->status eq 'WORKING') and
                   ($stats->seconds_since_last_update < 5*60));

  # OK try to claim the sync_lock
  my $sql = "UPDATE analysis_stats SET status='SYNCHING', sync_lock=1 ".
            "WHERE sync_lock=0 and analysis_id=" . $stats->analysis_id;
  print("$sql\n");
  my $row_count = $self->dbc->do($sql);  
  return $stats unless($row_count == 1);
  printf("got sync_lock on analysis_stats(%d)\n", $stats->analysis_id);
  
  #OK have the lock, go and do the sync
  $self->synchronize_AnalysisStats($stats);
  
  return $stats;
}


399
=head2 synchronize_AnalysisStats
400

401
402
403
404
405
406
407
408
  Arg [1]    : Bio::EnsEMBL::Hive::AnalysisStats object
  Example    : $self->synchronize($analysisStats);
  Description: Queries the analysis_job and hive tables to get summary counts
               and rebuilds the AnalysisStats object.  Then updates the
               analysis_stats table with the new summary info
  Returntype : newly synced Bio::EnsEMBL::Hive::AnalysisStats object
  Exceptions : none
  Caller     : general
409

410
=cut
411

412
sub synchronize_AnalysisStats {
413
  my $self = shift;
414
  my $analysisStats = shift;
415

416
  return $analysisStats unless($analysisStats);
417
  return $analysisStats unless($analysisStats->analysis_id);
418
  
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
  $analysisStats->total_job_count(0);
  $analysisStats->unclaimed_job_count(0);
  $analysisStats->done_job_count(0);
  $analysisStats->failed_job_count(0);
  $analysisStats->num_required_workers(0);

  my $sql = "SELECT status, count(*) FROM analysis_job ".
            "WHERE analysis_id=? GROUP BY status";
  my $sth = $self->prepare($sql);
  $sth->execute($analysisStats->analysis_id);

  while (my ($status, $count)=$sth->fetchrow_array()) {

    my $total = $analysisStats->total_job_count();
    $analysisStats->total_job_count($total + $count);

    if($status eq 'READY') {
      $analysisStats->unclaimed_job_count($count);
437
438
439
      my $numWorkers = POSIX::ceil($count * $analysisStats->avg_msec_per_job / 300000); 
        # guess num needed workers by total jobs / (num jobs a worker could do in 5 minutes)
      $numWorkers=$count if($numWorkers==0);
440
441
442
443
444
445
446
447
448
      if($analysisStats->hive_capacity>0 and $numWorkers > $analysisStats->hive_capacity) {
        $numWorkers=$analysisStats->hive_capacity;
      }
      $analysisStats->num_required_workers($numWorkers);
    }
    if($status eq 'DONE') { $analysisStats->done_job_count($count); }
    if($status eq 'FAILED') { $analysisStats->failed_job_count($count); }
  }
  $sth->finish;
449
450

  $analysisStats->determine_status();
451

452
453
454
455
  #
  # adjust_stats_for_living_workers
  #
  
456
457
458
459
460
461
462
463
464
465
466
467
468
469
  if($analysisStats->hive_capacity > 0) {
    my $sql = "SELECT count(*) FROM hive WHERE cause_of_death='' and analysis_id=?";
    $sth = $self->prepare($sql);
    $sth->execute($analysisStats->analysis_id);
    my($liveCount)=$sth->fetchrow_array();
    $sth->finish;

    my $numWorkers = $analysisStats->num_required_workers;

    my $capacityAdjust = ($numWorkers + $liveCount) - $analysisStats->hive_capacity;
    $numWorkers -= $capacityAdjust if($capacityAdjust > 0);
    $numWorkers=0 if($numWorkers<0);

    $analysisStats->num_required_workers($numWorkers);
470
471
472
473
  }
  
  $analysisStats->update;
  
474
475
  $self->check_blocking_control_rules_for_AnalysisStats($analysisStats);
  
476
  return $analysisStats;
477
}
478
479


480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
sub check_blocking_control_rules_for_AnalysisStats
{
  my $self = shift;
  my $stats = shift;
  
  return unless($stats);

  #print("check ctrl on analysis ");  $stats->print_stats;
  my $ctrlRules = $self->db->get_AnalysisCtrlRuleAdaptor->
                  fetch_by_ctrled_analysis_id($stats->analysis_id);
  my $allRulesDone = 1;
  if(scalar @$ctrlRules > 0) {
    #print("HAS blocking_ctrl_rules to check\n");
    foreach my $ctrlrule (@{$ctrlRules}) {
      #use this method because the condition_analysis objects can be
      #network distributed to a different database so use it's adaptor to get
      #the AnalysisStats object
      #$ctrlrule->print_rule;
      my $condAnalysis = $ctrlrule->condition_analysis;
      my $condStats = $condAnalysis->stats if($condAnalysis);
      $allRulesDone = 0 unless($condStats and $condStats->status eq 'DONE');
      #print("  "); $condStats->print_stats;
    }
503

504
505
506
    if($allRulesDone) {
      if($stats->status eq 'BLOCKED') {
        #print("  UNBLOCK analysis : all conditions met\n");
507
        $stats->update_status('LOADING'); #trigger sync
508
509
510
511
      }
    } else {
      #print("  RE-BLOCK analysis : some conditions failed\n");
      $stats->update_status('BLOCKED');
512
513
    }
  }
514
515
516
}


517
518
519
sub get_hive_current_load {
  my $self = shift;
  my $sql = "SELECT sum(1/analysis_stats.hive_capacity) FROM hive, analysis_stats ".
520
521
            "WHERE hive.analysis_id=analysis_stats.analysis_id and cause_of_death ='' ".
            "AND analysis_stats.hive_capacity>0";
522
523
524
525
526
527
528
529
530
531
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $load)=$sth->fetchrow_array();
  $sth->finish;
  $load=0 unless($load);
  print("current hive load = $load\n");
  return $load;
}


532
533
534
535
536
537
538
539
540
541
542
543
sub get_num_running_workers {
  my $self = shift;
  my $sql = "SELECT count(*) FROM hive WHERE cause_of_death =''";
  my $sth = $self->prepare($sql);
  $sth->execute();
  (my $runningCount)=$sth->fetchrow_array();
  $sth->finish;
  $runningCount=0 unless($runningCount);
  print("current hive num_running_workers = $runningCount\n");
  return $runningCount;
}

544
545
546
547
548
549
550
=head2 get_num_needed_workers

  Example    : $count = $queen->get_num_needed_workers();
  Description: Runs through the analyses in the system which are waiting
               for workers to be created for them.  Calculates the maximum
               number of workers needed to fill the current needs of the system
  Exceptions : none
551
  Caller     : beekeepers and other external processes
552
553
554

=cut

555
sub get_num_needed_workers {
556
557
  my $self = shift;

558
559
560
561
562
  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
  my $neededAnals = $statsDBA->fetch_by_needed_workers();
  my $deeper_stats_list = $statsDBA->fetch_by_status('LOADING', 'BLOCKED');
  push @$neededAnals, @$deeper_stats_list;

563
  return 0 unless($neededAnals);
564

565
566
567
568
569
  my $availableLoad = 1.0 - $self->get_hive_current_load();
  return 0 if($availableLoad <0.0);

  my $numWorkers = 0;
  foreach my $analysis_stats (@{$neededAnals}) {
570
571
    #$analysis_stats->print_stats();

572
573
574
575
576
577
578
579
580
    #digging deeper under the surface so need to sync
    if(($analysis_stats->status eq 'LOADING') or ($analysis_stats->status eq 'BLOCKED')) {
      $self->synchronize_AnalysisStats($analysis_stats);
      $self->check_blocking_control_rules_for_AnalysisStats($analysis_stats);
    }

    next if($analysis_stats->status eq 'BLOCKED');
    next if($analysis_stats->num_required_workers == 0);

581
582
583
584
585
586
    my $thisLoad = 0.0;
    if($analysis_stats->hive_capacity>0) {
      $thisLoad = $analysis_stats->num_required_workers * (1/$analysis_stats->hive_capacity);
    }

    if(($analysis_stats->hive_capacity<=0) or ($thisLoad < $availableLoad)) {
587
588
589
      $numWorkers += $analysis_stats->num_required_workers;
      $availableLoad -= $thisLoad;
      $analysis_stats->print_stats();
590
      printf("  %5d workers (%1.3f remaining-hive-load)\n", $numWorkers, $availableLoad);
591
    } else {
592
      my $workerCount = POSIX::ceil($availableLoad * $analysis_stats->hive_capacity);
593
594
595
      $numWorkers += $workerCount;
      $availableLoad -=  $workerCount * (1/$analysis_stats->hive_capacity);
      $analysis_stats->print_stats();
596
      printf("  %5d workers (%1.3f remaining-hive-load) use only %3d workers\n", $numWorkers, $availableLoad, $workerCount);
597
      last;
598
    }
599
    last if($availableLoad <= 0.0);
600
  }
601

602
  printf("need $numWorkers workers (availLoad=%1.5f)\n", $availableLoad);
603
  return $numWorkers;
604
605
606
}


607
608
609
sub get_hive_progress
{
  my $self = shift;
610
  my $sql = "SELECT sum(done_job_count), sum(failed_job_count), sum(total_job_count) FROM analysis_stats";
611
612
  my $sth = $self->prepare($sql);
  $sth->execute();
613
  my ($done, $failed, $total) = $sth->fetchrow_array();
614
  $sth->finish;
615
  $done=0 unless($done);
616
  $failed=0 unless($failed);
617
618
  $total=0 unless($total);
  my $completed=0.0;
619
620
  $completed = ((100.0 * ($done+$failed))/$total)  if($total>0);
  printf("hive %1.3f%% complete (%d done + %d failed / %d total)\n", $completed, $done, $failed, $total);
621
622
623
  return $done, $total;
}

624
sub print_hive_status
625
626
627
628
629
630
631
632
{
  my $self = shift;
  $self->print_analysis_status;
  $self->print_running_worker_status;
}


sub print_analysis_status
633
634
635
636
{
  my $self = shift;

  my $allStats = $self->db->get_AnalysisStatsAdaptor->fetch_all();
637
 
638
639
640
  foreach my $analysis_stats (@{$allStats}) {
    $analysis_stats->print_stats;
  }
641
642
643
644
645
646
}


sub print_running_worker_status
{
  my $self = shift;
647

648
  my $total = 0;
649
650
651
652
653
654
655
656
  print("HIVE LIVE WORKERS====\n");
  my $sql = "select logic_name, count(*) from hive, analysis ".
            "where hive.analysis_id=analysis.analysis_id and hive.cause_of_death='' ".
            "group by hive.analysis_id";
  my $sth = $self->prepare($sql);
  $sth->execute();
  while((my $logic_name, my $count)=$sth->fetchrow_array()) {
    printf("%20s : %d workers\n", $logic_name, $count);
657
    $total += $count;
658
  }
659
  printf("  %d total workers\n", $total);
660
  print("=====================\n");
661
  $sth->finish;
662
}
663

664

Jessica Severin's avatar
Jessica Severin committed
665
666
667
668
669
#
# INTERNAL METHODS
#
###################

670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
sub _pick_best_analysis_for_new_worker {
  my $self = shift;

  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
  return undef unless($statsDBA);

  my ($stats) = @{$statsDBA->fetch_by_needed_workers(1)};
  return $stats if($stats);

  # ok so no analyses 'need' workers.
  # see if anything needs an update, in case there are
  # hidden jobs that haven't made it into the summary stats

  print("QUEEN: no obvious needed workers, need to dig deeper\n");
  my $stats_list = $statsDBA->fetch_by_status('LOADING', 'BLOCKED');
  foreach $stats (@$stats_list) {
    #$stats->print_stats();
687
    $self->safe_synchronize_AnalysisStats($stats);
688
689
690
691
692
693
694
695
696
697
698
699
700
    $self->check_blocking_control_rules_for_AnalysisStats($stats);   
    #$stats->print_stats();

    return $stats if(($stats->status eq 'READY') and ($stats->num_required_workers > 0));
  }

  ($stats) = @{$statsDBA->fetch_by_needed_workers(1)};
  return $stats if($stats);

  return undef;
}


Jessica Severin's avatar
Jessica Severin committed
701
702
703
704
=head2 _fetch_by_hive_id

  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
705
  Example    : $feat = $queen->fetch_by_dbID(1234);
Jessica Severin's avatar
Jessica Severin committed
706
707
708
709
710
711
712
713
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Hive::Worker
  Exceptions : thrown if $id is not defined
  Caller     : general

=cut

714
sub _fetch_by_hive_id {
Jessica Severin's avatar
Jessica Severin committed
715
716
717
  my ($self,$id) = @_;

  unless(defined $id) {
718
    throw("fetch_by_dbID must have an id");
Jessica Severin's avatar
Jessica Severin committed
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
  }

  my @tabs = $self->_tables;

  my $constraint = "h.hive_id = $id";

  #return first element of _generic_fetch list
  my ($obj) = @{$self->_generic_fetch($constraint)};
  return $obj;
}

=head2 _generic_fetch

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::_generic_fetch

=cut

sub _generic_fetch {
  my ($self, $constraint, $join) = @_;

  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;
  my $final_clause = $self->_final_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";

  my $sth = $self->prepare($sql);
  $sth->execute;

#  print STDERR $sql,"\n";

  return $self->_objs_from_sth($sth);
}

sub _tables {
  my $self = shift;

  return (['hive', 'h']);
}

sub _columns {
  my $self = shift;

  return qw (h.hive_id
             h.analysis_id
809
             h.beekeeper
Jessica Severin's avatar
Jessica Severin committed
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
             h.host
             h.process_id
             h.work_done
             h.born
             h.last_check_in
             h.died
             h.cause_of_death
            );
}

sub _objs_from_sth {
  my ($self, $sth) = @_;

  my %column;
  $sth->bind_columns( \( @column{ @{$sth->{NAME_lc} } } ));

  my @workers = ();

  while ($sth->fetch()) {
    my $worker = new Bio::EnsEMBL::Hive::Worker;
    $worker->init;

    $worker->hive_id($column{'hive_id'});
833
    $worker->beekeeper($column{'beekeeper'});
Jessica Severin's avatar
Jessica Severin committed
834
835
836
837
838
839
840
    $worker->host($column{'host'});
    $worker->process_id($column{'process_id'});
    $worker->work_done($column{'work_done'});
    $worker->born($column{'born'});
    $worker->last_check_in($column{'last_check_in'});
    $worker->died($column{'died'});
    $worker->cause_of_death($column{'cause_of_death'});
841
    $worker->queen($self);
Jessica Severin's avatar
Jessica Severin committed
842
843
    $worker->db($self->db);

844
845
    if($column{'analysis_id'} and $self->db->get_AnalysisAdaptor) {
      $worker->analysis($self->db->get_AnalysisAdaptor->fetch_by_dbID($column{'analysis_id'}));
Jessica Severin's avatar
Jessica Severin committed
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
    }

    push @workers, $worker;
  }
  $sth->finish;

  return \@workers
}

sub _default_where_clause {
  my $self = shift;
  return '';
}

sub _final_clause {
  my $self = shift;
  return '';
}


1;