rbbt-util 5.25.56 → 5.26.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 0c46454a4604e7ac3622114c04ae9667b602f751
-  data.tar.gz: f32e35b8f21e4e1b6c0affed3f4c1344afcd9615
+  metadata.gz: 2e46da3a8f9a6af1484317f1b072ec5b7ce9b896
+  data.tar.gz: b62b161eb2202bde09d7368d104621c968b4fdff
 SHA512:
-  metadata.gz: 526540540bec4f2771b7a6b32e806ecdb7de1b36b28ddefcc9610c8939258e8f1025b390d95276ab3cae4de26e86ac8971b58a28876ce89ffb206c9acb649f31
-  data.tar.gz: e3d04b79a7a8e951bc4b89b0f65fea70b4d3ad5921021fd05c8707a1436862e7847bba192b5cfe80d88232defef938efcfe026329c8e4808bda7b398e459aa8b
+  metadata.gz: 4acc4980955ab32ebc68ce730d27cd03c58ea84a7e7b5764e744f0b197b756317e442692ed00d83ec84f698064be5447a46964f7611e46774ca846fb529ce88c
+  data.tar.gz: e5c8196ba18b2aedd92f48b2cdb41a59bd6b44f38bb8caa4943e7bc7bc4d2c43a772dbb88251947a6e54c24e5f7f3d6774d35f84246d421e43410c65e8c87348

data/lib/rbbt/workflow/prepare.rb

@@ -0,0 +1,23 @@
+class Step
+  def self.prepare_dependencies(jobs, tasks, cpus)
+    deps = []
+
+    jobs = [jobs] unless Array === jobs
+    tasks = [tasks] unless Array === tasks
+    tasks = tasks.collect{|t| t.to_s}
+
+    jobs.each do |job|
+      job.rec_dependencies.each do |dep|
+        next if dep.done?
+        deps << dep if tasks.include?(dep.task_name.to_s) or tasks.include?([dep.workflow.to_s, dep.task_name] * "#")
+      end
+    end
+
+    cpus = jobs.length if cpus.to_s == "max"
+    cpus = cpus.to_i if String === cpus
+    TSV.traverse deps.collect{|dep| dep.path}, :type => :array, :cpus => cpus, :bar => "Prepare dependencies #{Misc.fingerprint tasks} for #{Misc.fingerprint job}" do |path|
+      dep = deps.select{|dep| dep.path == path}.first
+      dep.produce
+    end
+  end
+end

data/share/rbbt_commands/workflow/task

@@ -190,6 +190,8 @@ the job dependencies recursively.
 -prov--provenance Report the jobs provenance
 -W--workflows* Load a list of workflows
 -R--requires* Require a list of files
+-pre--prepare* Prepare dependencies
+-prec--prepare_cpus* Number of dependencies prepared in parallel
 -rwt--remote_workflow_tasks* Load a yaml file describing remote workflow tasks
 -od--override_deps* Override deps using 'Workflow#task=<path>' array_separated
 EOF
@@ -370,6 +372,15 @@ begin
     exit 0
   end
 
+  if tasks = options.delete(:prepare)
+    require 'rbbt/workflow/prepare'
+    tasks = tasks.split(",")
+    prepare_cpus = (options[:prepare_cpus] || 1)
+    puts Step.prepare_dependencies(job, tasks,  prepare_cpus)
+    exit 0
+  end
+
+
   if do_fork
     ENV["RBBT_NO_PROGRESS"] = "true"
     if detach

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.56
+  version: 5.26.0
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -323,6 +323,7 @@ files:
 - lib/rbbt/workflow/definition.rb
 - lib/rbbt/workflow/doc.rb
 - lib/rbbt/workflow/examples.rb
+- lib/rbbt/workflow/prepare.rb
 - lib/rbbt/workflow/provenance.rb
 - lib/rbbt/workflow/soap.rb
 - lib/rbbt/workflow/step.rb