rbbt-util 5.28.4 → 5.28.9
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +5 -2
- data/lib/rbbt/persist.rb +1 -0
- data/lib/rbbt/tsv/accessor.rb +10 -2
- data/lib/rbbt/tsv/dumper.rb +10 -2
- data/lib/rbbt/tsv/parallel/traverse.rb +3 -0
- data/lib/rbbt/tsv/util.rb +5 -1
- data/lib/rbbt/util/config.rb +2 -1
- data/lib/rbbt/util/misc/inspect.rb +1 -1
- data/lib/rbbt/util/misc/system.rb +1 -1
- data/lib/rbbt/util/open.rb +1 -1
- data/lib/rbbt/workflow.rb +1 -0
- data/lib/rbbt/workflow/accessor.rb +94 -93
- data/lib/rbbt/workflow/definition.rb +6 -3
- data/lib/rbbt/workflow/integration/cromwell.rb +4 -2
- data/lib/rbbt/workflow/remote_workflow/driver/rest.rb +5 -1
- data/lib/rbbt/workflow/step.rb +17 -5
- data/lib/rbbt/workflow/step/accessor.rb +9 -6
- data/lib/rbbt/workflow/usage.rb +1 -1
- data/lib/rbbt/workflow/util/archive.rb +1 -0
- data/lib/rbbt/workflow/util/orchestrator.rb +215 -0
- data/lib/rbbt/workflow/util/trace.rb +182 -0
- data/share/rbbt_commands/app/start +2 -2
- data/share/rbbt_commands/purge_job +2 -4
- data/share/rbbt_commands/system/status +1 -1
- data/share/rbbt_commands/workflow/forget_deps +1 -3
- data/share/rbbt_commands/workflow/server +2 -0
- data/test/rbbt/tsv/parallel/test_traverse.rb +14 -0
- data/test/rbbt/tsv/test_manipulate.rb +20 -0
- data/test/rbbt/workflow/test_schedule.rb +0 -0
- data/test/rbbt/workflow/util/test_orchestrator.rb +223 -0
- metadata +8 -3
- data/lib/rbbt/workflow/schedule.rb +0 -238
@@ -54,9 +54,9 @@ app = ARGV.shift
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54
54
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55
55
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ENV["RServe-session"] = options[:RServe_session] || app
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56
56
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57
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-
app_dir = Rbbt.etc.app_dir.exists? ? Path.setup(Rbbt.etc.app_dir.read.strip) : Rbbt.apps
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57
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+
app_dir = Rbbt.etc.app_dir.exists? ? Path.setup(Rbbt.etc.app_dir.read.strip) : Rbbt.apps
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58
58
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-
app_dir = app_dir[app]
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59
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+
app_dir = app_dir[app].find
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server = options[:server] || 'puma'
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62
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Misc.in_dir(app_dir) do
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@@ -3,7 +3,6 @@
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3
3
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require 'rbbt-util'
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4
4
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require 'rbbt/util/simpleopt'
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5
5
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require 'rbbt/workflow'
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6
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-
require 'rbbt/workflow/remote/ssh/get'
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7
6
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8
7
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$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
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9
8
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@@ -14,8 +13,7 @@ Remove a job and its dependencies
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13
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$ rbbt purge [options] <job_path>
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15
14
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15
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-h--help Print this help
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-
-
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18
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-
-r--relocate Include relocated dependencies
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+
-r--recursive Remove recursively
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17
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EOF
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21
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if options[:help]
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@@ -31,4 +29,4 @@ path, search_path, _sep, *other = ARGV
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29
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30
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raise ParameterException, "No path given" if path.nil?
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-
Step.purge(path, options[:
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+
Step.purge(path, options[:recursive])
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@@ -25,6 +25,7 @@ $ rbbt workflow server [options] <Workflow>
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25
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--stream Activate streaming of workflow tasks
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26
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-fs--file_server Activate file serving for resources
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-mj--monitor_jobs Monitor jobs (UNSAFE)
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28
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+
-a--app_dir* Application execution directory
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29
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--export_all Export all workflow tasks (use with caution!)
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30
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--export* Export workflow tasks (asynchronous)
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31
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--export_asynchronous* Export workflow tasks as asynchronous
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@@ -74,6 +75,7 @@ sync_exports = options[:export_synchronous].split(/\s*,/) if options[:export_syn
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74
75
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exec_exports = options[:export_exec].split(/\s*,/) if options[:export_exec]
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75
76
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76
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TmpFile.with_file do |app_dir|
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78
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+
app_dir = options[:app_dir] if options[:app_dir]
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Misc.in_dir(app_dir) do
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78
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app_dir = Path.setup(app_dir.dup)
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Open.write(app_dir.etc.target_workflow.find, workflow)
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@@ -392,6 +392,20 @@ class TestTSVParallelThrough < Test::Unit::TestCase
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assert_equal size, stream.read.split("\n").length
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end
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394
394
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395
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+
def test_traverse_into_path
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size = 100
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397
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+
array = (1..size).to_a.collect{|n| n.to_s}
|
398
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+
TmpFile.with_file do |tmpfile|
|
399
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Path.setup(tmpfile)
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400
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io = TSV.traverse array, :into => tmpfile do |e|
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e
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402
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end
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403
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io.join
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404
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assert_equal size, Open.read(tmpfile).split("\n").length
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405
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end
|
406
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+
end
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407
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+
|
408
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+
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395
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def test_traverse_progress
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396
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size = 1000
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array = (1..size).to_a.collect{|n| n.to_s}
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@@ -117,6 +117,26 @@ row2 A B C
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end
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118
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end
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119
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120
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+
def test_slice_empty
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content =<<-EOF
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#ID ValueA ValueB Comment
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row1 a b c
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row2 A B C
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EOF
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TmpFile.with_file(content) do |filename|
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tsv = TSV.open(File.open(filename), :type => :list, :sep => /\s/)
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129
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tsv = tsv.slice []
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assert tsv.fields.empty?
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TmpFile.with_file do |tmpfile|
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iii tsv.to_s
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Open.write(tmpfile, tsv.to_s)
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134
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tsv = TSV.open tmpfile
|
135
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assert tsv.fields.empty?
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136
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+
end
|
137
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+
end
|
138
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+
end
|
139
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+
|
120
140
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def test_select
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121
141
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content =<<-EOF
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122
142
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#Id ValueA ValueB OtherID
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File without changes
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@@ -0,0 +1,223 @@
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1
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+
require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
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2
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+
require 'rbbt/workflow/util/orchestrator'
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3
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+
require 'rbbt/workflow/util/trace'
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4
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+
require 'rbbt-util'
|
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require 'rbbt/workflow'
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7
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module TestWF
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8
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extend Workflow
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9
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+
|
10
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MULT = 0.1
|
11
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task :a => :text do
|
12
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sleep(TestWF::MULT * (rand(10) + 2))
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13
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+
end
|
14
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+
|
15
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dep :a
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16
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task :b => :text do
|
17
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+
sleep(TestWF::MULT * (rand(10) + 2))
|
18
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+
end
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19
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+
|
20
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dep :a
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21
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+
dep :b
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22
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+
task :c => :text do
|
23
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+
sleep(TestWF::MULT * (rand(10) + 2))
|
24
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+
end
|
25
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+
|
26
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dep :c
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27
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+
task :d => :text do
|
28
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+
sleep(TestWF::MULT * (rand(10) + 2))
|
29
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+
end
|
30
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+
end
|
31
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+
|
32
|
+
class TestClass < Test::Unit::TestCase
|
33
|
+
def test_orchestrate_resources
|
34
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+
|
35
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+
jobs =[]
|
36
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+
|
37
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+
num = 10
|
38
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+
num.times do |i|
|
39
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+
jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
|
40
|
+
end
|
41
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+
jobs.each do |j| j.recursive_clean end
|
42
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+
|
43
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+
rules = YAML.load <<-EOF
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44
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+
defaults:
|
45
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+
log: 4
|
46
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+
default_resources:
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47
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+
IO: 1
|
48
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+
TestWF:
|
49
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+
a:
|
50
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+
resources:
|
51
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+
cpus: 7
|
52
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b:
|
53
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+
resources:
|
54
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+
cpus: 2
|
55
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+
c:
|
56
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+
resources:
|
57
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+
cpus: 10
|
58
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+
d:
|
59
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+
resources:
|
60
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+
cpus: 15
|
61
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+
EOF
|
62
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+
|
63
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+
orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
|
64
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+
Log.with_severity 0 do
|
65
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orchestrator.process(rules, jobs)
|
66
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+
end
|
67
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+
|
68
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+
data = Workflow.trace jobs, :plot_data => true
|
69
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+
eend = data.column("End.second").values.collect{|v| v.to_f}.max
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70
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+
second_cpus = TSV.setup({}, "Second~CPUS#:type=:single#:cast=:to_f")
|
71
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+
(0..eend.to_i).each do |second|
|
72
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+
tasks = data.select("Start.second"){|s| s <= second}.select("End.second"){|s| s > second}
|
73
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+
cpus = 0
|
74
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+
tasks.through :key, ["Workflow", "Task"] do |k, values|
|
75
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+
workflow, task = values
|
76
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+
cpus += rules[workflow][task.to_s]["resources"]["cpus"]
|
77
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+
end
|
78
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+
second_cpus[second] = cpus
|
79
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+
end
|
80
|
+
|
81
|
+
assert Misc.mean(second_cpus.values) > 15
|
82
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+
assert Misc.mean(second_cpus.values) < 30
|
83
|
+
end
|
84
|
+
|
85
|
+
def test_orchestrate_erase
|
86
|
+
|
87
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+
jobs =[]
|
88
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+
|
89
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+
num = 10
|
90
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+
num.times do |i|
|
91
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+
jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
|
92
|
+
end
|
93
|
+
jobs.each do |j| j.recursive_clean end
|
94
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+
|
95
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+
rules = YAML.load <<-EOF
|
96
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+
defaults:
|
97
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+
log: 4
|
98
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+
default_resources:
|
99
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+
IO: 1
|
100
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TestWF:
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101
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a:
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102
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erase: true
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103
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resources:
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104
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+
cpus: 7
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105
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b:
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106
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erase: true
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107
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resources:
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108
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cpus: 2
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109
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c:
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resources:
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cpus: 10
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d:
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113
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resources:
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114
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+
cpus: 15
|
115
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EOF
|
116
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+
|
117
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+
orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
|
118
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+
Log.with_severity 3 do
|
119
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+
orchestrator.process(rules, jobs)
|
120
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+
end
|
121
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+
|
122
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+
jobs.each do |job|
|
123
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+
assert job.step(:c).dependencies.empty?
|
124
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+
assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/a/")}.any?
|
125
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+
assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/b/")}.any?
|
126
|
+
end
|
127
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+
|
128
|
+
end
|
129
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+
|
130
|
+
def test_orchestrate_default
|
131
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+
|
132
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+
jobs =[]
|
133
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+
|
134
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num = 3
|
135
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+
num.times do |i|
|
136
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+
jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
|
137
|
+
end
|
138
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+
jobs.each do |j| j.recursive_clean end
|
139
|
+
|
140
|
+
rules = YAML.load <<-EOF
|
141
|
+
defaults:
|
142
|
+
erase: true
|
143
|
+
log: 4
|
144
|
+
default_resources:
|
145
|
+
IO: 1
|
146
|
+
TestWF:
|
147
|
+
a:
|
148
|
+
erase: true
|
149
|
+
resources:
|
150
|
+
cpus: 7
|
151
|
+
b:
|
152
|
+
erase: true
|
153
|
+
resources:
|
154
|
+
cpus: 2
|
155
|
+
c:
|
156
|
+
erase: false
|
157
|
+
resources:
|
158
|
+
cpus: 10
|
159
|
+
d:
|
160
|
+
resources:
|
161
|
+
cpus: 15
|
162
|
+
EOF
|
163
|
+
|
164
|
+
orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
|
165
|
+
Log.with_severity 3 do
|
166
|
+
orchestrator.process(rules, jobs)
|
167
|
+
end
|
168
|
+
|
169
|
+
jobs.each do |job|
|
170
|
+
assert job.step(:c).dependencies.empty?
|
171
|
+
assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/a/")}.any?
|
172
|
+
assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/b/")}.any?
|
173
|
+
end
|
174
|
+
|
175
|
+
end
|
176
|
+
|
177
|
+
def test_orchestrate_top_level
|
178
|
+
|
179
|
+
jobs =[]
|
180
|
+
|
181
|
+
num = 3
|
182
|
+
num.times do |i|
|
183
|
+
jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
|
184
|
+
jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:c, name + " #{i}") }
|
185
|
+
end
|
186
|
+
jobs.each do |j| j.recursive_clean end
|
187
|
+
|
188
|
+
rules = YAML.load <<-EOF
|
189
|
+
defaults:
|
190
|
+
erase: true
|
191
|
+
log: 4
|
192
|
+
default_resources:
|
193
|
+
IO: 1
|
194
|
+
TestWF:
|
195
|
+
a:
|
196
|
+
resources:
|
197
|
+
cpus: 7
|
198
|
+
b:
|
199
|
+
resources:
|
200
|
+
cpus: 2
|
201
|
+
c:
|
202
|
+
resources:
|
203
|
+
cpus: 10
|
204
|
+
d:
|
205
|
+
resources:
|
206
|
+
cpus: 15
|
207
|
+
EOF
|
208
|
+
|
209
|
+
orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
|
210
|
+
Log.with_severity 3 do
|
211
|
+
orchestrator.process(rules, jobs)
|
212
|
+
end
|
213
|
+
|
214
|
+
jobs.each do |job|
|
215
|
+
next unless job.task_name.to_s == 'd'
|
216
|
+
assert job.step(:c).dependencies.empty?
|
217
|
+
assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/a/")}.any?
|
218
|
+
assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/b/")}.any?
|
219
|
+
end
|
220
|
+
|
221
|
+
end
|
222
|
+
end
|
223
|
+
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.28.
|
4
|
+
version: 5.28.9
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2020-
|
11
|
+
date: 2020-11-04 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -327,7 +327,6 @@ files:
|
|
327
327
|
- lib/rbbt/workflow/remote_workflow/remote_step.rb
|
328
328
|
- lib/rbbt/workflow/remote_workflow/remote_step/rest.rb
|
329
329
|
- lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb
|
330
|
-
- lib/rbbt/workflow/schedule.rb
|
331
330
|
- lib/rbbt/workflow/soap.rb
|
332
331
|
- lib/rbbt/workflow/step.rb
|
333
332
|
- lib/rbbt/workflow/step/accessor.rb
|
@@ -337,7 +336,9 @@ files:
|
|
337
336
|
- lib/rbbt/workflow/task.rb
|
338
337
|
- lib/rbbt/workflow/usage.rb
|
339
338
|
- lib/rbbt/workflow/util/archive.rb
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339
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+
- lib/rbbt/workflow/util/orchestrator.rb
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340
340
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- lib/rbbt/workflow/util/provenance.rb
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- lib/rbbt/workflow/util/trace.rb
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- share/Rlib/plot.R
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- share/Rlib/svg.R
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- share/Rlib/util.R
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@@ -516,8 +517,10 @@ files:
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517
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- test/rbbt/workflow/step/test_dependencies.rb
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518
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- test/rbbt/workflow/test_doc.rb
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519
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- test/rbbt/workflow/test_remote_workflow.rb
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520
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+
- test/rbbt/workflow/test_schedule.rb
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521
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- test/rbbt/workflow/test_step.rb
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522
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- test/rbbt/workflow/test_task.rb
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+
- test/rbbt/workflow/util/test_orchestrator.rb
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524
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- test/test_helper.rb
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homepage: http://github.com/mikisvaz/rbbt-util
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526
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licenses:
|
@@ -545,7 +548,9 @@ summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
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548
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test_files:
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549
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- test/rbbt/test_entity.rb
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550
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- test/rbbt/workflow/test_remote_workflow.rb
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551
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+
- test/rbbt/workflow/util/test_orchestrator.rb
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552
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- test/rbbt/workflow/test_doc.rb
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553
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+
- test/rbbt/workflow/test_schedule.rb
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549
554
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- test/rbbt/workflow/test_step.rb
|
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555
|
- test/rbbt/workflow/remote/test_client.rb
|
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556
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- test/rbbt/workflow/step/test_dependencies.rb
|
@@ -1,238 +0,0 @@
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1
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class Step
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class ResourceManager
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class NotEnoughResources < Exception
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end
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attr_accessor :cpus, :memory
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def initialize(cpus = nil, memory = nil)
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@cpus = cpus
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@memory = memory
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-
@sem_file = "ResourceManager-" + rand(10000).to_s
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@semaphore = RbbtSemaphore.create_semaphore(@sem_file, 1)
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end
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def allocate(cpus = nil, memory = nil, &block)
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RbbtSemaphore.synchronize(@semaphore) do
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if (@cpus && cpus && @cpus < cups) ||
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(@memory && memory && @memory < memory)
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raise NotEnoughResources
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end
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begin
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@cpus -= cpus
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@memory -= memory
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yield
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rescue
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@cpus += cpus
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@memory += memory
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end
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end
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end
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def finalize(manager)
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RbbtSemaphore.delete_semaphore(@sem_file)
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end
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def self.finalize(manager)
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proc { manager.finalize }
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end
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end
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class Scheduler
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attr_accessor :jobs, :cpus, :dep_jobs, :job_deps, :jobps
|
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def initialize(jobs, cpus)
|
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@jobs = jobs
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@cpus = cpus
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-
|
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@job_deps = {}
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-
|
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with_deps = jobs.dup
|
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@dep_jobs = {}
|
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@job_deps = {}
|
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@jobps = {}
|
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@missing = Set.new
|
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while with_deps.any?
|
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job = with_deps.pop
|
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@jobps[job.path] = job
|
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|
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@missing << job.path unless job.done?
|
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-
|
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jdeps = job.dependencies
|
59
|
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jdeps += job.inputs.flatten.select{|i| Step === i}
|
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-
|
61
|
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jdeps.reject!{|dep| dep.done? }
|
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|
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@job_deps[job.path] = []
|
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jdeps.each do |dep|
|
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#next if dep.done?
|
65
|
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@dep_jobs[dep.path] ||= []
|
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|
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@job_deps[job.path] << dep.path
|
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@dep_jobs[dep.path] << job.path
|
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with_deps << dep unless @job_deps.include? dep.path
|
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|
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end
|
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-
end
|
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|
-
|
72
|
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def ready
|
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|
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@job_deps.select do |jobp,deps|
|
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|
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(@missing & deps).empty?
|
75
|
-
end.collect{|jobp,deps| jobp}
|
76
|
-
end
|
77
|
-
|
78
|
-
def used
|
79
|
-
iii @dep_jobs
|
80
|
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@dep_jobs.select do |dep,jobs|
|
81
|
-
iif [dep, @missing.to_a, jobs]
|
82
|
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(@missing & jobs).empty?
|
83
|
-
end.keys
|
84
|
-
end
|
85
|
-
|
86
|
-
def next
|
87
|
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priorities = {}
|
88
|
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@jobs.each do |job|
|
89
|
-
priorities[job.path] = 1
|
90
|
-
end
|
91
|
-
|
92
|
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@missing.each do |jobp|
|
93
|
-
end
|
94
|
-
|
95
|
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ready.first
|
96
|
-
end
|
97
|
-
end
|
98
|
-
end
|
99
|
-
|
100
|
-
#def self._priorities(jobs)
|
101
|
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# job_level = {}
|
102
|
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# jobs.each do |job|
|
103
|
-
# job_level[job.path] = 1.0
|
104
|
-
# end
|
105
|
-
|
106
|
-
# with_deps = jobs.dup
|
107
|
-
# dep_jobs = {}
|
108
|
-
# job_deps = {}
|
109
|
-
# while with_deps.any?
|
110
|
-
# job = with_deps.pop
|
111
|
-
# level = job_level[job.path]
|
112
|
-
# job_deps[job.path] = []
|
113
|
-
# jdeps = job.dependencies
|
114
|
-
# jdeps += job.inputs.flatten.select{|i| Step === i}
|
115
|
-
|
116
|
-
# jdeps.reject!{|dep| dep.done? }
|
117
|
-
# jdeps.each do |dep|
|
118
|
-
# next if dep.done?
|
119
|
-
# dep_jobs[dep.path] ||= []
|
120
|
-
# job_level[dep.path] = level / (10 * jdeps.length) if job_level[dep.path].nil? || job_level[dep.path] < level / (10 * jdeps.length)
|
121
|
-
# job_deps[job.path] << dep.path
|
122
|
-
# dep_jobs[dep.path] << job.path
|
123
|
-
# with_deps << dep unless job_deps.include? dep.path
|
124
|
-
# end
|
125
|
-
# end
|
126
|
-
# [job_level, job_deps, dep_jobs]
|
127
|
-
#end
|
128
|
-
|
129
|
-
#def self.produce_jobs(jobs, cpus, step_cpus = {})
|
130
|
-
# require 'fc'
|
131
|
-
|
132
|
-
# step_cpus = IndiferentHash.setup(step_cpus || {})
|
133
|
-
|
134
|
-
# deps = []
|
135
|
-
|
136
|
-
# jobs = [jobs] unless Array === jobs
|
137
|
-
|
138
|
-
# job_level, job_deps, dep_jobs = self._priorities(jobs)
|
139
|
-
|
140
|
-
# jobps = {}
|
141
|
-
# (jobs + jobs.collect{|job| job.rec_dependencies}).flatten.uniq.each do |job|
|
142
|
-
# jobps[job.path] = job
|
143
|
-
# end
|
144
|
-
|
145
|
-
# prio_queue = FastContainers::PriorityQueue.new :max
|
146
|
-
|
147
|
-
# job_deps.each do |jobp,depps|
|
148
|
-
# next if depps.any?
|
149
|
-
# level = job_level[jobp]
|
150
|
-
|
151
|
-
# prio_queue.push(jobp, level)
|
152
|
-
# end
|
153
|
-
|
154
|
-
# queue = RbbtProcessQueue.new cpus
|
155
|
-
|
156
|
-
# missing = job_deps.keys
|
157
|
-
# queue.callback do |jobp|
|
158
|
-
# Log.info "Done: #{jobp}"
|
159
|
-
# missing -= [jobp]
|
160
|
-
|
161
|
-
# job_level, job_deps, dep_jobs = self._priorities(jobs)
|
162
|
-
|
163
|
-
# parentsp = dep_jobs[jobp]
|
164
|
-
|
165
|
-
# parentsp.each do |parentp|
|
166
|
-
# next unless job_deps[parentp].include? jobp
|
167
|
-
# job_deps[parentp] -= [jobp]
|
168
|
-
# if job_deps[parentp].empty?
|
169
|
-
# level = job_level[parentp]
|
170
|
-
# prio_queue.push(parentp, level )
|
171
|
-
# end
|
172
|
-
# end if parentsp
|
173
|
-
# prio_queue_new = FastContainers::PriorityQueue.new :max
|
174
|
-
# while prio_queue.any?
|
175
|
-
# elem = prio_queue.pop
|
176
|
-
# prio_queue_new.push(elem, job_level[elem])
|
177
|
-
# end
|
178
|
-
# prio_queue = prio_queue_new
|
179
|
-
# end
|
180
|
-
#
|
181
|
-
# queue.init do |jobp|
|
182
|
-
# Log.info "Processing: #{jobp}"
|
183
|
-
# job = jobps[jobp]
|
184
|
-
# job_cpus = step_cpus[job.task_name] || 1
|
185
|
-
# sleep 0.5
|
186
|
-
# #job.produce
|
187
|
-
# jobp
|
188
|
-
# end
|
189
|
-
|
190
|
-
# while missing.any?
|
191
|
-
# while prio_queue.empty? && missing.any?
|
192
|
-
# sleep 1
|
193
|
-
# end
|
194
|
-
# break if missing.empty?
|
195
|
-
# jobp = prio_queue.pop
|
196
|
-
# queue.process jobp
|
197
|
-
# end
|
198
|
-
|
199
|
-
# queue.join
|
200
|
-
#end
|
201
|
-
end
|
202
|
-
|
203
|
-
|
204
|
-
if __FILE__ == $0
|
205
|
-
require 'rbbt/workflow'
|
206
|
-
|
207
|
-
module TestWF
|
208
|
-
extend Workflow
|
209
|
-
input :num, :integer
|
210
|
-
task :dep => :integer do |num|
|
211
|
-
num
|
212
|
-
end
|
213
|
-
dep :dep, :num => 1
|
214
|
-
dep :dep, :num => 2
|
215
|
-
dep :dep, :num => 3
|
216
|
-
task :test do
|
217
|
-
dependencies.collect{|d| d.load.to_s} * ","
|
218
|
-
end
|
219
|
-
end
|
220
|
-
Log.severity = 0
|
221
|
-
job = TestWF.job(:test)
|
222
|
-
job.recursive_clean
|
223
|
-
|
224
|
-
Rbbt::Config.load_file Rbbt.etc.config_profile.HTS.find
|
225
|
-
Workflow.require_workflow "Sample"
|
226
|
-
Workflow.require_workflow "HTS"
|
227
|
-
|
228
|
-
jobs = []
|
229
|
-
# jobs << Sample.job(:mutect2, "QUINTANA-15")
|
230
|
-
# jobs << Sample.job(:mutect2, "QUINTANA-25")
|
231
|
-
# jobs << Sample.job(:mutect2, "QUINTANA-22")
|
232
|
-
jobs << Sample.job(:mutect2, "small")
|
233
|
-
|
234
|
-
sched = Step::Scheduler.new(jobs, 3)
|
235
|
-
iii sched.ready
|
236
|
-
iii sched.used
|
237
|
-
iii sched.next
|
238
|
-
end
|