rbbt-util 5.25.56 → 5.26.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/workflow/prepare.rb +23 -0
- data/share/rbbt_commands/workflow/task +11 -0
- metadata +2 -1
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: 2e46da3a8f9a6af1484317f1b072ec5b7ce9b896
|
|
4
|
+
data.tar.gz: b62b161eb2202bde09d7368d104621c968b4fdff
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 4acc4980955ab32ebc68ce730d27cd03c58ea84a7e7b5764e744f0b197b756317e442692ed00d83ec84f698064be5447a46964f7611e46774ca846fb529ce88c
|
|
7
|
+
data.tar.gz: e5c8196ba18b2aedd92f48b2cdb41a59bd6b44f38bb8caa4943e7bc7bc4d2c43a772dbb88251947a6e54c24e5f7f3d6774d35f84246d421e43410c65e8c87348
|
|
@@ -0,0 +1,23 @@
|
|
|
1
|
+
class Step
|
|
2
|
+
def self.prepare_dependencies(jobs, tasks, cpus)
|
|
3
|
+
deps = []
|
|
4
|
+
|
|
5
|
+
jobs = [jobs] unless Array === jobs
|
|
6
|
+
tasks = [tasks] unless Array === tasks
|
|
7
|
+
tasks = tasks.collect{|t| t.to_s}
|
|
8
|
+
|
|
9
|
+
jobs.each do |job|
|
|
10
|
+
job.rec_dependencies.each do |dep|
|
|
11
|
+
next if dep.done?
|
|
12
|
+
deps << dep if tasks.include?(dep.task_name.to_s) or tasks.include?([dep.workflow.to_s, dep.task_name] * "#")
|
|
13
|
+
end
|
|
14
|
+
end
|
|
15
|
+
|
|
16
|
+
cpus = jobs.length if cpus.to_s == "max"
|
|
17
|
+
cpus = cpus.to_i if String === cpus
|
|
18
|
+
TSV.traverse deps.collect{|dep| dep.path}, :type => :array, :cpus => cpus, :bar => "Prepare dependencies #{Misc.fingerprint tasks} for #{Misc.fingerprint job}" do |path|
|
|
19
|
+
dep = deps.select{|dep| dep.path == path}.first
|
|
20
|
+
dep.produce
|
|
21
|
+
end
|
|
22
|
+
end
|
|
23
|
+
end
|
|
@@ -190,6 +190,8 @@ the job dependencies recursively.
|
|
|
190
190
|
-prov--provenance Report the jobs provenance
|
|
191
191
|
-W--workflows* Load a list of workflows
|
|
192
192
|
-R--requires* Require a list of files
|
|
193
|
+
-pre--prepare* Prepare dependencies
|
|
194
|
+
-prec--prepare_cpus* Number of dependencies prepared in parallel
|
|
193
195
|
-rwt--remote_workflow_tasks* Load a yaml file describing remote workflow tasks
|
|
194
196
|
-od--override_deps* Override deps using 'Workflow#task=<path>' array_separated
|
|
195
197
|
EOF
|
|
@@ -370,6 +372,15 @@ begin
|
|
|
370
372
|
exit 0
|
|
371
373
|
end
|
|
372
374
|
|
|
375
|
+
if tasks = options.delete(:prepare)
|
|
376
|
+
require 'rbbt/workflow/prepare'
|
|
377
|
+
tasks = tasks.split(",")
|
|
378
|
+
prepare_cpus = (options[:prepare_cpus] || 1)
|
|
379
|
+
puts Step.prepare_dependencies(job, tasks, prepare_cpus)
|
|
380
|
+
exit 0
|
|
381
|
+
end
|
|
382
|
+
|
|
383
|
+
|
|
373
384
|
if do_fork
|
|
374
385
|
ENV["RBBT_NO_PROGRESS"] = "true"
|
|
375
386
|
if detach
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: rbbt-util
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 5.
|
|
4
|
+
version: 5.26.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Miguel Vazquez
|
|
@@ -323,6 +323,7 @@ files:
|
|
|
323
323
|
- lib/rbbt/workflow/definition.rb
|
|
324
324
|
- lib/rbbt/workflow/doc.rb
|
|
325
325
|
- lib/rbbt/workflow/examples.rb
|
|
326
|
+
- lib/rbbt/workflow/prepare.rb
|
|
326
327
|
- lib/rbbt/workflow/provenance.rb
|
|
327
328
|
- lib/rbbt/workflow/soap.rb
|
|
328
329
|
- lib/rbbt/workflow/step.rb
|