rbbt-util 5.25.10 → 5.25.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 13bac11c495886a59c36af1b96806cd378cfed87
-  data.tar.gz: 73b4586d838d9ada0e7d3f156b25bd42d3f53614
+  metadata.gz: 6ae58162f37a549950ca17612244b5dc6e557369
+  data.tar.gz: d87001e2b5313efe465e6f55a6d7a38a631dab15
 SHA512:
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-  data.tar.gz: e672b0531ab5f6c44ec7b8c676e43d2cd7022be89eea22b5446e22572d766f7cba0ad909d018f530a4b157fe4cde84f95ebd120268702090cb23bef03af8bdbe
+  metadata.gz: dbd7d9e31a15cc49014c5539247188dd036fbee214c67068a9c398c72fa4b4999b575d4fd7751b90ff5dfa40c29b513400e4148a11f43f5f1ce8c44c1a4b54f4
+  data.tar.gz: 6538afe285d095537e301a5a749b3aa80543da58b5fc73f523986215c7b3c2602555d38d6c6b8cbccba4056ecf2b8e1636e5ebc56410d43855a2ba364f0bafca

data/lib/rbbt/hpc.rb

@@ -7,7 +7,6 @@ module Marenostrum
 
     def self.template(args, options = {})
 
-      dry_run          = options.delete :dry_run
       development      = options.delete :drbbt
       contain          = options.delete :contain
       sync             = options.delete :sync
@@ -228,12 +227,15 @@ EOF
 
       workdir = options[:workdir]
       Open.mkdir workdir
-      fout = File.join(workdir, 'std.out')
-      ferr = File.join(workdir, 'std.err')
-      fjob = File.join(workdir, 'job.id')
+
+      dry_run = options.delete :dry_run
+
+      fout  = File.join(workdir, 'std.out')
+      ferr  = File.join(workdir, 'std.err')
+      fjob  = File.join(workdir, 'job.id')
       fexit = File.join(workdir, 'exit.status')
       fsync = File.join(workdir, 'sync.log')
-      fcmd = File.join(workdir, 'command.slurm')
+      fcmd  = File.join(workdir, 'command.slurm')
 
       job = nil
       if options[:clean_job]
@@ -253,6 +255,10 @@ EOF
       else
         if File.exists?(fout)
           return
+        elsif dry_run
+          STDERR.puts Log.color(:magenta, "Prepared work directory: ")
+          puts workdir
+          STDERR.puts Log.color(:magenta, "To execute run: sbatch '#{workdir}/command.slurm'")
         else
           Open.rm fsync
           Open.rm fexit

data/lib/rbbt/rest/client/step.rb

@@ -207,7 +207,9 @@ class WorkflowRESTClient
       @done = false
       get_streams
       @name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
-        WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(other_params).merge(:jobname => @name||@base_name, :_cache_type => cache_type))
+        Misc.insist do
+          WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(other_params).merge(:jobname => @name||@base_name, :_cache_type => cache_type))
+        end
       end
       if Open.remote? @name
         @url = @name

data/lib/rbbt/util/concurrency/processes.rb

@@ -146,7 +146,7 @@ class RbbtProcessQueue
 
       @callback_queue.close_read if @callback_queue
 
-      num_processes.times do |i|
+      num_processes.to_i.times do |i|
         @total += 1 
         process_mutex.synchronize do
           processes << RbbtProcessQueueWorker.new(@queue, @callback_queue, @cleanup, @respawn, (@offset ? @total : false), &@init_block)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.10
+  version: 5.25.12
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-20 00:00:00.000000000 Z
+date: 2019-01-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake