rbbt-util 5.34.24 → 5.34.25
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc/batch.rb +6 -1
- data/lib/rbbt/workflow/dependencies.rb +3 -1
- data/lib/rbbt/workflow/step/dependencies.rb +1 -1
- data/lib/rbbt/workflow/step/save_load_inputs.rb +7 -0
- data/lib/rbbt/workflow.rb +3 -3
- data/share/rbbt_commands/hpc/orchestrate +2 -1
- data/share/rbbt_commands/lsf/orchestrate +2 -1
- data/share/rbbt_commands/slurm/orchestrate +2 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: f1a0dc0772864a83c7c6b159d53dc1c5d95e7f58619c4e4b0c630e8240a621aa
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4
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+
data.tar.gz: c8a029debfd1ee7c820185aa1dead29575ecd173a1868692751c6a01dc7be01a
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5
5
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SHA512:
|
6
|
-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
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+
metadata.gz: b151561ce56b42af19160eff58a8f45be7fedd6226d960987111e8b9d1147802eb612f96b85a47ad849476b7d4520df457ed70e91e9528d67e9e03a6959f78c4
|
7
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+
data.tar.gz: 60b1a486a88bd2c65a4c003130c7c81de42ce72446420797132d1047be2446fce74f7cb35c80a652a1f56dcc630ba6e32d7c991a524efeab85a05325aaae1024
|
data/lib/rbbt/hpc/batch.rb
CHANGED
@@ -101,6 +101,11 @@ module HPC
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101
101
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|
102
102
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task = Symbol === job.overriden ? job.overriden : job.task_name
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103
103
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|
104
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+
#override_deps = job.overriden_deps.collect do |dep|
|
105
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+
# name = [dep.workflow.to_s, dep.task_name] * "#"
|
106
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+
# [name, dep.path] * "="
|
107
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+
#end.uniq * ","
|
108
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+
|
104
109
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if job.overriden?
|
105
110
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#override_deps = job.rec_dependencies.
|
106
111
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# select{|dep| Symbol === dep.overriden }.
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@@ -568,7 +573,7 @@ env > #{batch_options[:fenv]}
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568
573
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Misc.add_defaults options,
|
569
574
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:batch_dir => batch_dir,
|
570
575
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:inputs_dir => File.join(batch_dir, "inputs_dir"),
|
571
|
-
:workflows => workflows_to_load.uniq * ","
|
576
|
+
:workflows => workflows_to_load.any? ? workflows_to_load.uniq * "," : nil
|
572
577
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|
573
578
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options[:procpath_performance] ||= File.join(batch_dir, "procpath##{procpath.gsub(',', '#')}") if procpath
|
574
579
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@@ -73,8 +73,10 @@ module Workflow
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|
73
73
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return [] if dep == :skip || dep == 'skip'
|
74
74
|
|
75
75
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if not Step === dep
|
76
|
-
located = Open.exists?(dep)
|
76
|
+
located = Open.exists?(dep) || Open.exists?(dep + '.info')
|
77
77
|
dep = Workflow.load_step(dep)
|
78
|
+
else
|
79
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+
located = true
|
78
80
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end
|
79
81
|
|
80
82
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dep.original_workflow ||= dep.workflow if dep.workflow
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@@ -527,7 +527,7 @@ class Step
|
|
527
527
|
|
528
528
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def overriden?
|
529
529
|
return true if @overriden
|
530
|
-
return true if dependencies && dependencies.select{|dep| dep.overriden
|
530
|
+
return true if dependencies && dependencies.select{|dep| TrueClass === dep.overriden }.any?
|
531
531
|
info[:archived_info].each do |f,i|
|
532
532
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next if Symbol === i
|
533
533
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return true if i[:overriden] || i["overriden"]
|
@@ -31,6 +31,8 @@ module Workflow
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|
31
31
|
|
32
32
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type = :step_array if file.split(".").last == 'as_step_array'
|
33
33
|
|
34
|
+
type = :number_array if file.split(".").last == 'as_number_array'
|
35
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+
|
34
36
|
type = :step_file if file.split(".").last == 'as_step_file'
|
35
37
|
|
36
38
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type = :step_file_array if file.split(".").last == 'as_step_file_array'
|
@@ -57,6 +59,9 @@ module Workflow
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|
57
59
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when :step_array
|
58
60
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steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
|
59
61
|
inputs[input.to_sym] = steps
|
62
|
+
when :number_array
|
63
|
+
numbers = Open.read(file).strip.split("\n").collect{|num| num.to_f }
|
64
|
+
inputs[input.to_sym] = numbers
|
60
65
|
when :step
|
61
66
|
steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
|
62
67
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inputs[input.to_sym] = steps.first
|
@@ -176,6 +181,8 @@ class Step
|
|
176
181
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when Step
|
177
182
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path = path + '.as_step_array'
|
178
183
|
value = value.collect{|s| s.path }
|
184
|
+
when Numeric
|
185
|
+
path = path + '.as_number_array'
|
179
186
|
end
|
180
187
|
|
181
188
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value = value * "\n"
|
data/lib/rbbt/workflow.rb
CHANGED
@@ -437,8 +437,8 @@ module Workflow
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|
437
437
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jobname_input = nil
|
438
438
|
end
|
439
439
|
|
440
|
-
if jobname_input &&
|
441
|
-
inputs[jobname_input] = jobname
|
440
|
+
if jobname_input && inputs[jobname_input].nil?
|
441
|
+
inputs[jobname_input] = jobname || DEFAULT_NAME
|
442
442
|
end
|
443
443
|
|
444
444
|
real_inputs = {}
|
@@ -503,7 +503,7 @@ module Workflow
|
|
503
503
|
when :not_overriden_dep
|
504
504
|
job.overriden = true if has_overriden_inputs || true_overriden_deps.any?
|
505
505
|
else
|
506
|
-
job.overriden = true if has_overriden_inputs ||
|
506
|
+
job.overriden = true if has_overriden_inputs || true_overriden_deps.any?
|
507
507
|
end
|
508
508
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|
509
509
|
job.real_inputs = real_inputs.keys
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@@ -61,7 +61,8 @@ class Step
|
|
61
61
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else
|
62
62
|
begin
|
63
63
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Log.debug "Issuing SLURM job for #{self.path}"
|
64
|
-
|
64
|
+
#@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
|
65
|
+
@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options)
|
65
66
|
if no_load
|
66
67
|
self
|
67
68
|
else
|
@@ -61,7 +61,8 @@ class Step
|
|
61
61
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else
|
62
62
|
begin
|
63
63
|
Log.debug "Issuing SLURM job for #{self.path}"
|
64
|
-
|
64
|
+
#@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
|
65
|
+
@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options)
|
65
66
|
if no_load
|
66
67
|
self
|
67
68
|
else
|
@@ -61,7 +61,8 @@ class Step
|
|
61
61
|
else
|
62
62
|
begin
|
63
63
|
Log.debug "Issuing SLURM job for #{self.path}"
|
64
|
-
|
64
|
+
#@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
|
65
|
+
@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options)
|
65
66
|
if no_load
|
66
67
|
self
|
67
68
|
else
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: rbbt-util
|
3
3
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version: !ruby/object:Gem::Version
|
4
|
-
version: 5.34.
|
4
|
+
version: 5.34.25
|
5
5
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platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
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autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2022-12-
|
11
|
+
date: 2022-12-12 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|