rbbt-util 5.20.2 → 5.20.3
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- checksums.yaml +4 -4
- data/lib/rbbt/association/index.rb +3 -4
- data/lib/rbbt/tsv/accessor.rb +1 -1
- data/lib/rbbt/tsv/manipulate.rb +0 -1
- data/lib/rbbt/tsv/parallel/traverse.rb +8 -2
- data/lib/rbbt/util/cmd.rb +1 -1
- data/lib/rbbt/util/concurrency/processes.rb +4 -3
- data/lib/rbbt/util/concurrency/processes/worker.rb +4 -2
- data/lib/rbbt/util/log/progress/util.rb +20 -1
- data/lib/rbbt/util/misc/bgzf.rb +1 -1
- data/lib/rbbt/util/misc/inspect.rb +7 -3
- data/lib/rbbt/util/misc/multipart_payload.rb +8 -8
- data/lib/rbbt/util/misc/pipes.rb +115 -51
- data/lib/rbbt/util/open.rb +1 -1
- data/lib/rbbt/workflow.rb +1 -0
- data/lib/rbbt/workflow/accessor.rb +86 -15
- data/lib/rbbt/workflow/definition.rb +10 -17
- data/lib/rbbt/workflow/step.rb +4 -16
- data/lib/rbbt/workflow/step/dependencies.rb +451 -0
- data/lib/rbbt/workflow/step/run.rb +43 -226
- data/lib/rbbt/workflow/task.rb +7 -1
- data/share/rbbt_commands/association/subset +6 -1
- data/share/rbbt_commands/workflow/task +21 -9
- data/test/rbbt/util/misc/test_pipes.rb +54 -0
- data/test/rbbt/workflow/step/test_dependencies.rb +206 -0
- metadata +5 -2
data/lib/rbbt/util/open.rb
CHANGED
data/lib/rbbt/workflow.rb
CHANGED
@@ -1,6 +1,14 @@
|
|
1
1
|
require 'rbbt/util/open'
|
2
2
|
require 'yaml'
|
3
3
|
|
4
|
+
module ComputeDependency
|
5
|
+
attr_accessor :compute
|
6
|
+
def self.setup(dep, value)
|
7
|
+
dep.extend ComputeDependency
|
8
|
+
dep.compute = value
|
9
|
+
end
|
10
|
+
end
|
11
|
+
|
4
12
|
class Step
|
5
13
|
|
6
14
|
|
@@ -493,7 +501,7 @@ module Workflow
|
|
493
501
|
wf, t, o = dep
|
494
502
|
wf.rec_dependencies(t).each do |d|
|
495
503
|
if Array === d
|
496
|
-
new = d
|
504
|
+
new = d.dup
|
497
505
|
else
|
498
506
|
new = [dep.first, d]
|
499
507
|
end
|
@@ -513,10 +521,12 @@ module Workflow
|
|
513
521
|
all_deps << dep.dependency if dep.dependency
|
514
522
|
case dep.dependency
|
515
523
|
when Array
|
516
|
-
dep_wf, dep_task = dep.dependency
|
517
|
-
|
518
|
-
|
519
|
-
|
524
|
+
dep_wf, dep_task, dep_options = dep.dependency
|
525
|
+
if dep_task === Symbol
|
526
|
+
dep_rec_dependencies = dep_wf.rec_dependencies(dep_task.to_sym)
|
527
|
+
dep_rec_dependencies.collect!{|d| Array === d ? d : [dep_wf, d]}
|
528
|
+
all_deps.concat dep_rec_dependencies
|
529
|
+
end
|
520
530
|
when Symbol, String
|
521
531
|
all_deps.concat rec_dependencies(dep.dependency.to_sym)
|
522
532
|
end
|
@@ -553,43 +563,84 @@ module Workflow
|
|
553
563
|
end
|
554
564
|
|
555
565
|
def rec_input_defaults(taskname)
|
566
|
+
rec_inputs = rec_inputs(taskname)
|
556
567
|
[taskname].concat(rec_dependencies(taskname)).inject(IndiferentHash.setup({})){|acc, tn|
|
557
|
-
|
568
|
+
if Array === tn and tn.first
|
569
|
+
new = tn.first.tasks[tn[1].to_sym].input_types
|
570
|
+
elsif Symbol === tn
|
571
|
+
new = tasks[tn.to_sym].input_types
|
572
|
+
else
|
573
|
+
next acc
|
574
|
+
end
|
558
575
|
acc = new.merge(acc)
|
576
|
+
acc.delete_if{|input,defaults| not rec_inputs.include? input}
|
577
|
+
acc
|
559
578
|
}.tap{|h| IndiferentHash.setup(h)}
|
560
579
|
end
|
561
580
|
|
562
581
|
def rec_input_types(taskname)
|
582
|
+
rec_inputs = rec_inputs(taskname)
|
563
583
|
[taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
|
564
|
-
|
584
|
+
if Array === tn and tn.first
|
585
|
+
new = tn.first.tasks[tn[1].to_sym].input_types
|
586
|
+
elsif Symbol === tn
|
587
|
+
new = tasks[tn.to_sym].input_types
|
588
|
+
else
|
589
|
+
next acc
|
590
|
+
end
|
565
591
|
acc = new.merge(acc)
|
592
|
+
acc.delete_if{|input,defaults| not rec_inputs.include? input}
|
593
|
+
acc
|
566
594
|
}.tap{|h| IndiferentHash.setup(h)}
|
567
595
|
end
|
568
596
|
|
569
597
|
def rec_input_descriptions(taskname)
|
598
|
+
rec_inputs = rec_inputs(taskname)
|
570
599
|
[taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
|
571
|
-
|
600
|
+
if Array === tn and tn.first
|
601
|
+
new = tn.first.tasks[tn[1].to_sym].input_types
|
602
|
+
elsif Symbol === tn
|
603
|
+
new = tasks[tn.to_sym].input_types
|
604
|
+
else
|
605
|
+
next acc
|
606
|
+
end
|
572
607
|
acc = new.merge(acc)
|
608
|
+
acc.delete_if{|input,defaults| not rec_inputs.include? input}
|
609
|
+
acc
|
573
610
|
}.tap{|h| IndiferentHash.setup(h)}
|
574
611
|
end
|
575
612
|
|
576
613
|
def rec_input_options(taskname)
|
614
|
+
rec_inputs = rec_inputs(taskname)
|
577
615
|
[taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn|
|
578
|
-
|
616
|
+
if Array === tn and tn.first
|
617
|
+
new = tn.first.tasks[tn[1].to_sym].input_types
|
618
|
+
elsif Symbol === tn
|
619
|
+
new = tasks[tn.to_sym].input_types
|
620
|
+
else
|
621
|
+
next acc
|
622
|
+
end
|
579
623
|
acc = new.merge(acc)
|
624
|
+
acc = acc.delete_if{|input,defaults| not rec_inputs.include? input}
|
625
|
+
acc
|
580
626
|
}.tap{|h| IndiferentHash.setup(h)}
|
581
627
|
end
|
582
628
|
|
583
629
|
def real_dependencies(task, jobname, inputs, dependencies)
|
584
630
|
real_dependencies = []
|
631
|
+
path_deps = {}
|
585
632
|
dependencies.each do |dependency|
|
586
|
-
|
633
|
+
real_dep = case dependency
|
587
634
|
when Array
|
588
635
|
workflow, dep_task, options = dependency
|
589
636
|
|
590
637
|
_inputs = IndiferentHash.setup(inputs.dup)
|
638
|
+
compute = options[:compute] if options
|
591
639
|
options.each{|i,v|
|
640
|
+
next if i == :compute or i == "compute"
|
592
641
|
case v
|
642
|
+
when :compute
|
643
|
+
compute = v
|
593
644
|
when Symbol
|
594
645
|
all_d = (real_dependencies + real_dependencies.collect{|d| d.rec_dependencies} ).flatten.compact.uniq
|
595
646
|
rec_dependency = all_d.select{|d| d.task_name.to_sym == v }.first
|
@@ -598,7 +649,7 @@ module Workflow
|
|
598
649
|
_inputs[i] = v unless _inputs.include? i
|
599
650
|
else
|
600
651
|
input_options = workflow.task_info(dep_task)[:input_options][i] || {}
|
601
|
-
if input_options[:stream]
|
652
|
+
if true or input_options[:stream]
|
602
653
|
#rec_dependency.run(true).grace unless rec_dependency.done? or rec_dependency.running?
|
603
654
|
_inputs[i] = rec_dependency
|
604
655
|
else
|
@@ -617,8 +668,9 @@ module Workflow
|
|
617
668
|
end
|
618
669
|
} if options
|
619
670
|
|
620
|
-
|
621
|
-
|
671
|
+
job = workflow.job(dep_task, jobname, _inputs)
|
672
|
+
ComputeDependency.setup(job, compute) if compute
|
673
|
+
job
|
622
674
|
when Step
|
623
675
|
dependency
|
624
676
|
when Symbol
|
@@ -626,10 +678,28 @@ module Workflow
|
|
626
678
|
job(dependency, jobname, _inputs)
|
627
679
|
when Proc
|
628
680
|
_inputs = IndiferentHash.setup(inputs.dup)
|
629
|
-
dependency.call jobname, _inputs, real_dependencies
|
681
|
+
dep = dependency.call jobname, _inputs, real_dependencies
|
682
|
+
|
683
|
+
if DependencyBlock === dependency
|
684
|
+
orig_dep = dependency.dependency
|
685
|
+
if Hash === orig_dep.last
|
686
|
+
options = orig_dep.last
|
687
|
+
compute = options[:compute]
|
688
|
+
|
689
|
+
if Array === dep
|
690
|
+
dep.each{|d| ComputeDependency.setup(d, compute)}
|
691
|
+
elsif dep
|
692
|
+
ComputeDependency.setup(dep, compute)
|
693
|
+
end if compute
|
694
|
+
end
|
695
|
+
end
|
696
|
+
|
697
|
+
dep
|
630
698
|
else
|
631
699
|
raise "Dependency for #{task.name} not understood: #{Misc.fingerprint dependency}"
|
632
700
|
end
|
701
|
+
|
702
|
+
real_dependencies << real_dep
|
633
703
|
end
|
634
704
|
real_dependencies.flatten.compact
|
635
705
|
end
|
@@ -641,7 +711,7 @@ module Workflow
|
|
641
711
|
if inputs.any? or dependencies.any?
|
642
712
|
tagged_jobname = case TAG
|
643
713
|
when :hash
|
644
|
-
hash_str = Misc.
|
714
|
+
hash_str = Misc.obj2digest({:inputs => inputs, :dependencies => dependencies})
|
645
715
|
jobname + '_' << hash_str
|
646
716
|
else
|
647
717
|
jobname
|
@@ -679,4 +749,5 @@ module Workflow
|
|
679
749
|
dir = File.dirname(path)
|
680
750
|
Misc.path_relative_to(workdir_find, dir).sub(/([^\/]+)\/.*/,'\1')
|
681
751
|
end
|
752
|
+
|
682
753
|
end
|
@@ -34,25 +34,16 @@ module Workflow
|
|
34
34
|
@result_description = description
|
35
35
|
end
|
36
36
|
|
37
|
-
#def dep(*dependency_list, &block)
|
38
|
-
# @dependencies ||= []
|
39
|
-
# if Module === dependency_list.first or Hash === dependency_list.last
|
40
|
-
# @dependencies << dependency_list
|
41
|
-
# else
|
42
|
-
# @dependency_list ||= []
|
43
|
-
# if block_given?
|
44
|
-
# dependency_list.unshift self if dependency_list.length == 1
|
45
|
-
# dependency_list << block
|
46
|
-
# end
|
47
|
-
# dependencies.concat dependency_list
|
48
|
-
# end
|
49
|
-
#end
|
50
|
-
|
51
37
|
def dep(*dependency, &block)
|
52
38
|
@dependencies ||= []
|
53
39
|
if block_given?
|
54
|
-
|
55
|
-
|
40
|
+
if dependency.any?
|
41
|
+
wf, task, opt = dependency
|
42
|
+
|
43
|
+
opt, wf = wf, nil if Hash === wf
|
44
|
+
wf, task = self, wf if task.nil? and wf
|
45
|
+
DependencyBlock.setup block, [wf, task, opt]
|
46
|
+
end
|
56
47
|
@dependencies << block
|
57
48
|
else
|
58
49
|
if Module === dependency.first or
|
@@ -76,7 +67,7 @@ module Workflow
|
|
76
67
|
end
|
77
68
|
|
78
69
|
name = name.to_sym
|
79
|
-
|
70
|
+
|
80
71
|
block = self.method(name) unless block_given?
|
81
72
|
|
82
73
|
task_info = {
|
@@ -117,4 +108,6 @@ module Workflow
|
|
117
108
|
synchronous_exports.uniq!
|
118
109
|
synchronous_exports
|
119
110
|
end
|
111
|
+
|
112
|
+
alias export export_asynchronous
|
120
113
|
end
|
data/lib/rbbt/workflow/step.rb
CHANGED
@@ -155,7 +155,7 @@ class Step
|
|
155
155
|
|
156
156
|
dep_hash ||= begin
|
157
157
|
h = {}
|
158
|
-
rec_dependencies.each{|dep| h[dep.
|
158
|
+
rec_dependencies.each{|dep| h[dep.task_name.to_s] ||= dep }
|
159
159
|
h
|
160
160
|
end
|
161
161
|
dep = dep_hash[a]
|
@@ -204,7 +204,7 @@ class Step
|
|
204
204
|
pid_file = Step.pid_file path
|
205
205
|
files_dir = Step.files_dir path
|
206
206
|
|
207
|
-
if Open.exists?(path) or Open.exists?(pid_file)
|
207
|
+
if Open.exists?(path) or Open.exists?(pid_file) or Open.exists?(info_file)
|
208
208
|
|
209
209
|
@result = nil
|
210
210
|
@pid = nil
|
@@ -245,22 +245,10 @@ class Step
|
|
245
245
|
end
|
246
246
|
|
247
247
|
def recursive_clean
|
248
|
-
clean
|
249
|
-
rec_dependencies.each do |step|
|
250
|
-
if Open.exists?(step.info_file)
|
251
|
-
step.clean
|
252
|
-
end
|
253
|
-
end
|
254
|
-
self
|
255
|
-
end
|
256
|
-
|
257
|
-
def recursive_clean
|
258
|
-
clean
|
259
248
|
dependencies.each do |step|
|
260
|
-
|
261
|
-
step.recursive_clean
|
262
|
-
end
|
249
|
+
step.recursive_clean
|
263
250
|
end
|
251
|
+
clean if Open.exists?(self.info_file)
|
264
252
|
self
|
265
253
|
end
|
266
254
|
|
@@ -0,0 +1,451 @@
|
|
1
|
+
|
2
|
+
class Step
|
3
|
+
|
4
|
+
##STREAM_CACHE = {}
|
5
|
+
##STREAM_CACHE_MUTEX = Mutex.new
|
6
|
+
##def self.purge_stream_cache
|
7
|
+
## Log.medium "Purging dup. stream cache"
|
8
|
+
## STREAM_CACHE_MUTEX.synchronize do
|
9
|
+
## #STREAM_CACHE.collect{|k,s|
|
10
|
+
## # Thread.new do
|
11
|
+
## # Misc.consume_stream s
|
12
|
+
## # end
|
13
|
+
## #}
|
14
|
+
## STREAM_CACHE.clear
|
15
|
+
## end
|
16
|
+
##end
|
17
|
+
|
18
|
+
##def self.dup_stream(stream)
|
19
|
+
## case stream
|
20
|
+
## when IO, File, Step
|
21
|
+
## return stream if stream.respond_to?(:closed?) and stream.closed?
|
22
|
+
## return stream if stream.respond_to?(:done?) and stream.done?
|
23
|
+
|
24
|
+
## STREAM_CACHE_MUTEX.synchronize do
|
25
|
+
## stream_key = Misc.fingerprint(stream)
|
26
|
+
## current = STREAM_CACHE[stream_key]
|
27
|
+
## case current
|
28
|
+
## when nil
|
29
|
+
## Log.medium "Not duplicating stream #{stream_key}"
|
30
|
+
## STREAM_CACHE[stream_key] = stream
|
31
|
+
## when File
|
32
|
+
## if Open.exists? current.path
|
33
|
+
## Log.medium "Reopening file #{stream_key}"
|
34
|
+
## Open.open(current.path)
|
35
|
+
## else
|
36
|
+
## new = Misc.dup_stream(current)
|
37
|
+
## Log.medium "Duplicating file #{stream_key} #{current.inspect} => #{Misc.fingerprint(new)}"
|
38
|
+
## new
|
39
|
+
## end
|
40
|
+
## when Step
|
41
|
+
## job = current
|
42
|
+
## current = job.result
|
43
|
+
## new = Misc.dup_stream(current)
|
44
|
+
## job.result = current
|
45
|
+
## Log.medium "Duplicating step #{stream_key} #{current.inspect} => #{Misc.fingerprint(new)}"
|
46
|
+
## new
|
47
|
+
## else
|
48
|
+
## new = Misc.dup_stream(current)
|
49
|
+
## Log.medium "Duplicating stream #{stream_key} #{ Misc.fingerprint(stream) } => #{Misc.fingerprint(new)}"
|
50
|
+
## new
|
51
|
+
## end
|
52
|
+
## end
|
53
|
+
## when TSV::Dumper#, TSV::Parser
|
54
|
+
## stream = stream.stream
|
55
|
+
## return stream if stream.closed?
|
56
|
+
|
57
|
+
## STREAM_CACHE_MUTEX.synchronize do
|
58
|
+
## if STREAM_CACHE[stream].nil?
|
59
|
+
## Log.high "Not duplicating dumper #{ stream.inspect }"
|
60
|
+
## STREAM_CACHE[stream] = stream
|
61
|
+
## else
|
62
|
+
## new = Misc.dup_stream(STREAM_CACHE[stream])
|
63
|
+
## Log.high "Duplicating dumper #{ stream.inspect } into #{new.inspect}"
|
64
|
+
## new
|
65
|
+
## end
|
66
|
+
## end
|
67
|
+
## else
|
68
|
+
## stream
|
69
|
+
## end
|
70
|
+
##end
|
71
|
+
|
72
|
+
def self.prepare_for_execution(job)
|
73
|
+
return if (job.done? and not job.dirty?) or
|
74
|
+
(job.streaming? and job.running?) or
|
75
|
+
(defined? WorkflowRESTClient and WorkflowRESTClient::RemoteStep === job and not (job.error? or job.aborted?))
|
76
|
+
|
77
|
+
job.clean if job.error? or job.aborted? or (job.started? and not job.running? and not job.error?)
|
78
|
+
|
79
|
+
raise DependencyError, job if job.error?
|
80
|
+
end
|
81
|
+
|
82
|
+
def log_dependency_exec(dependency, action)
|
83
|
+
task_name = self.task_name
|
84
|
+
|
85
|
+
str = Log.color(:reset, "")
|
86
|
+
str << Log.color(:yellow, task_name.to_s || "")
|
87
|
+
str << " "
|
88
|
+
str << Log.color(:magenta, action.to_s)
|
89
|
+
str << " "
|
90
|
+
str << Log.color(:yellow, dependency.task_name.to_s || "")
|
91
|
+
str << " -- "
|
92
|
+
str << "#{Log.color :blue, dependency.path}"
|
93
|
+
|
94
|
+
Log.info str
|
95
|
+
end
|
96
|
+
|
97
|
+
def execute_dependency(dependency, log = true)
|
98
|
+
task_name = self.task_name
|
99
|
+
begin
|
100
|
+
|
101
|
+
dependency.resolve_input_steps
|
102
|
+
|
103
|
+
if dependency.done?
|
104
|
+
log_dependency_exec(dependency, :done) if log
|
105
|
+
return
|
106
|
+
end
|
107
|
+
|
108
|
+
if not dependency.started?
|
109
|
+
log_dependency_exec(dependency, :starting)
|
110
|
+
dependency.run(:stream)
|
111
|
+
raise TryAgain
|
112
|
+
end
|
113
|
+
|
114
|
+
dependency.grace
|
115
|
+
|
116
|
+
if dependency.aborted?
|
117
|
+
log_dependency_exec(dependency, "aborted (clean)")
|
118
|
+
dependency.clean
|
119
|
+
raise TryAgain
|
120
|
+
end
|
121
|
+
|
122
|
+
if dependency.error?
|
123
|
+
log_dependency_exec(dependency, :error)
|
124
|
+
raise DependencyError, [dependency.path, dependency.messages.last] * ": " if dependency.error?
|
125
|
+
end
|
126
|
+
|
127
|
+
if dependency.streaming?
|
128
|
+
log_dependency_exec(dependency, :streaming) if log
|
129
|
+
return
|
130
|
+
end
|
131
|
+
|
132
|
+
begin
|
133
|
+
log_dependency_exec(dependency, :joining)
|
134
|
+
dependency.join
|
135
|
+
raise TryAgain unless dependency.done?
|
136
|
+
rescue Aborted
|
137
|
+
raise TryAgain
|
138
|
+
end
|
139
|
+
|
140
|
+
rescue TryAgain
|
141
|
+
retry
|
142
|
+
rescue Aborted, Interrupt
|
143
|
+
Log.error "Aborted dep. #{Log.color :red, dependency.task_name.to_s}"
|
144
|
+
raise $!
|
145
|
+
rescue Interrupt
|
146
|
+
Log.error "Interrupted while in dep. #{Log.color :red, dependency.task_name.to_s}"
|
147
|
+
raise $!
|
148
|
+
rescue Exception
|
149
|
+
Log.error "Exception in dep. #{ Log.color :red, dependency.task_name.to_s }"
|
150
|
+
Log.exception $!
|
151
|
+
raise $!
|
152
|
+
end
|
153
|
+
end
|
154
|
+
|
155
|
+
#def dup_inputs
|
156
|
+
# return if true or @dupped or ENV["RBBT_NO_STREAM"] == 'true'
|
157
|
+
# Log.low "Dupping inputs for #{path}"
|
158
|
+
# dupped_inputs = @inputs.collect do |input|
|
159
|
+
# Step.dup_stream input
|
160
|
+
# end
|
161
|
+
# @inputs.replace dupped_inputs
|
162
|
+
# @dupped = true
|
163
|
+
#end
|
164
|
+
|
165
|
+
def consolidate_dependencies(path_deps = {})
|
166
|
+
return false if @consolidated or dependencies.nil? or dependencies.empty?
|
167
|
+
consolidated_deps = dependencies.collect do |dep|
|
168
|
+
dep.consolidate_dependencies(path_deps)
|
169
|
+
path = dep.path
|
170
|
+
path_deps[path] ||= dep
|
171
|
+
end
|
172
|
+
dependencies.replace consolidated_deps
|
173
|
+
@consolidated = true
|
174
|
+
end
|
175
|
+
|
176
|
+
#def prepare_dependencies
|
177
|
+
# dep_step = {}
|
178
|
+
|
179
|
+
# all_deps = rec_dependencies + [self]
|
180
|
+
|
181
|
+
# seen_paths = Set.new
|
182
|
+
# all_deps.uniq.each do |step|
|
183
|
+
# next if seen_paths.include? step.path
|
184
|
+
# Step.prepare_for_execution(step)
|
185
|
+
# seen_paths << step.path
|
186
|
+
# step.dependencies.each do |step_dep|
|
187
|
+
# dep_step[step_dep.path] ||= []
|
188
|
+
# dep_step[step_dep.path] << step_dep
|
189
|
+
# end
|
190
|
+
# end
|
191
|
+
|
192
|
+
# seen_paths = Set.new
|
193
|
+
# rec_dependencies.uniq.each do |step|
|
194
|
+
# next if seen_paths.include? step.path
|
195
|
+
# = {} seen_paths << step.path
|
196
|
+
# execute_dependency(step)
|
197
|
+
# if step.streaming? and step.result
|
198
|
+
# if dep_step[step.path] and dep_step[step.path].length > 1
|
199
|
+
# stream = step.result
|
200
|
+
# other_steps = dep_step[step.path] - [step]
|
201
|
+
# copies = Misc.dup_stream_multiple(stream, other_steps.length)
|
202
|
+
# other_steps.zip(copies).each do |other,dupped_stream|
|
203
|
+
# other.instance_variable_set(:@result, dupped_stream)
|
204
|
+
# end
|
205
|
+
# end
|
206
|
+
# end
|
207
|
+
# end
|
208
|
+
|
209
|
+
# Step.purge_stream_cache
|
210
|
+
#end
|
211
|
+
|
212
|
+
def execute_and_dup(step, dep_step, log = true)
|
213
|
+
dup = ! step.result
|
214
|
+
execute_dependency(step, log)
|
215
|
+
if dup and step.streaming? and step.result
|
216
|
+
if dep_step[step.path] and dep_step[step.path].length > 1
|
217
|
+
stream = step.result
|
218
|
+
other_steps = dep_step[step.path] - [step]
|
219
|
+
copies = Misc.dup_stream_multiple(stream, other_steps.length)
|
220
|
+
log_dependency_exec(step, "duplicating #{copies.length}")
|
221
|
+
other_steps.zip(copies).each do |other,dupped_stream|
|
222
|
+
other.instance_variable_set(:@result, dupped_stream)
|
223
|
+
end
|
224
|
+
end
|
225
|
+
end
|
226
|
+
end
|
227
|
+
|
228
|
+
def run_compute_dependencies(type, list, dep_step = {})
|
229
|
+
if Array === type
|
230
|
+
type, *rest = type
|
231
|
+
end
|
232
|
+
|
233
|
+
case type
|
234
|
+
when :produce, :no_dup
|
235
|
+
list.each do |step|
|
236
|
+
step.produce
|
237
|
+
nil
|
238
|
+
end
|
239
|
+
when :bootstrap
|
240
|
+
cpus = rest.nil? ? nil : rest.first
|
241
|
+
cpus = 30 if cpus.nil?
|
242
|
+
cpus = list.length / 2 if cpus > list.length / 2
|
243
|
+
|
244
|
+
Misc.bootstrap(list, cpus, :bar => "Bootstrapping dependencies for #{path}", :_respawn => :always) do |dep|
|
245
|
+
dep.produce
|
246
|
+
nil
|
247
|
+
end
|
248
|
+
else
|
249
|
+
list.each do |step|
|
250
|
+
execute_and_dup(step, dep_step, false)
|
251
|
+
end
|
252
|
+
end
|
253
|
+
end
|
254
|
+
|
255
|
+
def run_dependencies
|
256
|
+
dep_step = {}
|
257
|
+
|
258
|
+
all_deps = rec_dependencies + [self]
|
259
|
+
|
260
|
+
dependencies.each do |dep|
|
261
|
+
next unless ComputeDependency === dep
|
262
|
+
if dep.compute == :produce
|
263
|
+
dep.produce
|
264
|
+
end
|
265
|
+
end
|
266
|
+
|
267
|
+
compute_deps = rec_dependencies.collect do |dep|
|
268
|
+
next unless ComputeDependency === dep
|
269
|
+
dep.rec_dependencies
|
270
|
+
end.compact.flatten.uniq
|
271
|
+
|
272
|
+
seen_paths = Set.new
|
273
|
+
all_deps.uniq.each do |step|
|
274
|
+
next if seen_paths.include? step.path
|
275
|
+
seen_paths << step.path
|
276
|
+
Step.prepare_for_execution(step) unless step == self
|
277
|
+
next unless step.dependencies and step.dependencies.any?
|
278
|
+
step.dependencies.each do |step_dep|
|
279
|
+
next if step_dep.done? or step_dep.running? or (ComputeDependency === step_dep and step_dep.compute == :nodup)
|
280
|
+
dep_step[step_dep.path] ||= []
|
281
|
+
dep_step[step_dep.path] << step_dep
|
282
|
+
end
|
283
|
+
end
|
284
|
+
|
285
|
+
required_dep_paths = []
|
286
|
+
dep_step.each do |path,list|
|
287
|
+
required_dep_paths << path if list.length > 1
|
288
|
+
end
|
289
|
+
|
290
|
+
required_dep_paths.concat dependencies.collect{|dep| dep.path }
|
291
|
+
|
292
|
+
log :dependencies, "Dependencies for step #{Log.color :yellow, task.name.to_s || ""}"
|
293
|
+
|
294
|
+
pre_deps = []
|
295
|
+
compute_pre_deps = {}
|
296
|
+
last_deps = []
|
297
|
+
compute_last_deps = {}
|
298
|
+
seen_paths = Set.new
|
299
|
+
rec_dependencies.uniq.each do |step|
|
300
|
+
next if seen_paths.include? step.path
|
301
|
+
seen_paths << step.path
|
302
|
+
next unless required_dep_paths.include? step.path
|
303
|
+
if dependencies.include?(step) and step.inputs.flatten.select{|i| Step === i}.any?
|
304
|
+
if ComputeDependency === step
|
305
|
+
compute_last_deps[step.compute] ||= []
|
306
|
+
compute_last_deps[step.compute] << step
|
307
|
+
else
|
308
|
+
last_deps << step
|
309
|
+
end
|
310
|
+
else
|
311
|
+
if ComputeDependency === step
|
312
|
+
compute_pre_deps[step.compute] ||= []
|
313
|
+
compute_pre_deps[step.compute] << step
|
314
|
+
else
|
315
|
+
pre_deps << step #if dependencies.include?(step)
|
316
|
+
end
|
317
|
+
end
|
318
|
+
end
|
319
|
+
|
320
|
+
pre_deps.each do |step|
|
321
|
+
next if compute_deps.include? step
|
322
|
+
execute_and_dup(step, dep_step, false)
|
323
|
+
end
|
324
|
+
|
325
|
+
compute_pre_deps.each do |type,list|
|
326
|
+
run_compute_dependencies(type, list, dep_step)
|
327
|
+
end
|
328
|
+
|
329
|
+
last_deps.each do |step|
|
330
|
+
next if compute_deps.include? step
|
331
|
+
execute_and_dup(step, dep_step)
|
332
|
+
end
|
333
|
+
|
334
|
+
compute_last_deps.each do |type,list|
|
335
|
+
run_compute_dependencies(type, list, dep_step)
|
336
|
+
end
|
337
|
+
|
338
|
+
end
|
339
|
+
|
340
|
+
def stop_dependencies
|
341
|
+
dependencies.each do |dep|
|
342
|
+
dep.abort
|
343
|
+
end
|
344
|
+
kill_children
|
345
|
+
end
|
346
|
+
|
347
|
+
#def run_dependencies
|
348
|
+
# @seen ||= []
|
349
|
+
# seen_paths ||= Set.new
|
350
|
+
#
|
351
|
+
# consolidate_dependencies
|
352
|
+
# dependencies.uniq.each do |dependency|
|
353
|
+
# dependency_path = dependency.path
|
354
|
+
# next if seen_paths.include? dependency_path
|
355
|
+
# @seen.concat dependency.rec_dependencies
|
356
|
+
# seen_paths.union(dependency.rec_dependencies.collect{|d| d.path})
|
357
|
+
# @seen << dependency
|
358
|
+
# seen_paths << dependency_path
|
359
|
+
# end
|
360
|
+
|
361
|
+
# @seen.uniq!
|
362
|
+
# @seen.delete self
|
363
|
+
|
364
|
+
# return if @seen.empty?
|
365
|
+
|
366
|
+
# log :dependencies, "#{Log.color :magenta, "Dependencies"} for step #{Log.color :yellow, task.name.to_s || ""}"
|
367
|
+
|
368
|
+
# @seen.each do |dependency|
|
369
|
+
# Step.prepare_for_execution(dependency)
|
370
|
+
# end
|
371
|
+
|
372
|
+
# pre_deps = []
|
373
|
+
# compute_pre_deps = {}
|
374
|
+
# last_deps = []
|
375
|
+
# compute_last_deps = {}
|
376
|
+
# @seen.each do |dependency|
|
377
|
+
# if dependencies.include?(dependency) and dependency.inputs.flatten.select{|i| Step === i}.any?
|
378
|
+
# if ComputeDependency === dependency
|
379
|
+
# compute_last_deps[dependency.compute] ||= []
|
380
|
+
# compute_last_deps[dependency.compute] << dependency
|
381
|
+
# else
|
382
|
+
# last_deps << dependency
|
383
|
+
# end
|
384
|
+
# else
|
385
|
+
# if ComputeDependency === dependency
|
386
|
+
# compute_pre_deps[dependency.compute] ||= []
|
387
|
+
# compute_pre_deps[dependency.compute] << dependency
|
388
|
+
# else
|
389
|
+
# pre_deps << dependency if dependencies.include?(dependency)
|
390
|
+
# end
|
391
|
+
# end
|
392
|
+
# end
|
393
|
+
|
394
|
+
# pre_deps.each do |dependency|
|
395
|
+
# dependency.dup_inputs
|
396
|
+
# execute_dependency(dependency)
|
397
|
+
# end
|
398
|
+
|
399
|
+
# compute_pre_deps.each do |type,list|
|
400
|
+
# if Array === type
|
401
|
+
# type, *rest = type
|
402
|
+
# end
|
403
|
+
|
404
|
+
# case type
|
405
|
+
# when :bootstrap
|
406
|
+
# cpus = rest.nil? ? nil : rest.first
|
407
|
+
# cpus = 10 if cpus.nil?
|
408
|
+
|
409
|
+
# list.each do |dependency|
|
410
|
+
# dependency.dup_inputs
|
411
|
+
# end
|
412
|
+
|
413
|
+
# Misc.bootstrap(list, cpus, :bar => "Bootstrapping dependencies for #{path}", :_respawn => :always) do |dep|
|
414
|
+
# dep.produce
|
415
|
+
# nil
|
416
|
+
# end
|
417
|
+
# else
|
418
|
+
# list.each do |dependency|
|
419
|
+
# dependency.dup_inputs
|
420
|
+
# execute_dependency(dependency)
|
421
|
+
# end
|
422
|
+
# end
|
423
|
+
# end
|
424
|
+
|
425
|
+
# last_deps.each do |dependency|
|
426
|
+
# dependency.dup_inputs
|
427
|
+
# end
|
428
|
+
|
429
|
+
# last_deps.each do |dependency|
|
430
|
+
# execute_dependency(dependency)
|
431
|
+
# end
|
432
|
+
|
433
|
+
# compute_last_deps.each do |type,list|
|
434
|
+
# case type
|
435
|
+
# when :_bootstrap
|
436
|
+
# list.each do |dependency|
|
437
|
+
# dependency.dup_inputs
|
438
|
+
# end
|
439
|
+
# Misc.bootstrap(list, 3, :bar => "Boostrapping dependencies for #{path}", :respawn => :always) do |dependency|
|
440
|
+
# dependency.produce
|
441
|
+
# nil
|
442
|
+
# end
|
443
|
+
# else
|
444
|
+
# list.each do |dependency|
|
445
|
+
# dependency.dup_inputs
|
446
|
+
# execute_dependency(dependency)
|
447
|
+
# end
|
448
|
+
# end
|
449
|
+
# end
|
450
|
+
#end
|
451
|
+
end
|