autoflow 0.8.0 → 0.8.4

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 94220cd6f51e6b8715d6f89e7bf8e7fcc081651d
+  data.tar.gz: b823cce8cd1125752a9fb9328aa687c72ebc0c81
+SHA512:
+  metadata.gz: 6b3479c881c662937922a604eb993dfd2f2ee4b340075753b33710b54a710f8a515c02a1dac1688c3e0ba55aa4256468d5c9ccb4e7f0a1db5e14d9d1bd41efa9
+  data.tar.gz: cc737f01685322374f41b482ac3e97f12c11fab420d2050a2812ceb0197ad652b3f1bc8df004e316a35399b5dc4f7515dd56bfdb95aae863d7b5803c77fab37c

data/bin/AutoFlow

@@ -171,6 +171,11 @@ optparse = OptionParser.new do |opts|
                 options[:use_ntasks] = TRUE
         end
 
+        options[:show_submit_command] = FALSE
+        opts.on( '-S', '--show_submit_command', 'Show the command line used to submit the job' ) do 
+                options[:show_submit_command] = TRUE
+        end
+
         options[:time] = '20:00:00'
         opts.on( '-t', '--time STRING', 'Max time that can be needed in a task. Format: dd-hh:mm:ss' ) do |time|
                 options[:time] = time

data/bin/flow_logger

@@ -36,7 +36,7 @@ def report_log(log, initial_flow_attribs, mode, workflow_status, no_size)
 	puts Terminal::Table.new :headings => ['Status', 'Folder', 'Time', 'Size', 'Job Name'], :rows => rows
 end
 
-def launch_failed_jobs(log, initial_flow_attribs, exec_folder, batch)
+def launch_failed_jobs(log, initial_flow_attribs, exec_folder, batch, pending = false)
 	options = {
 		:verbose => FALSE,
 		:identifier => nil,
@@ -47,6 +47,7 @@ def launch_failed_jobs(log, initial_flow_attribs, exec_folder, batch)
 		:write_sh => FALSE
 	}
 	failed_jobs = get_failed_jobs(log)
+	failed_jobs.concat(get_pending_jobs(log, failed_jobs, initial_flow_attribs)) if pending
 	jobs = {}
 	create_jobs(jobs, failed_jobs, initial_flow_attribs)
 	get_all_dependencies(jobs, failed_jobs, initial_flow_attribs)
@@ -86,8 +87,24 @@ def get_all_dependencies(jobs, failed_jobs, initial_flow_attribs)
 	end
 end
 
+def get_pending_jobs(log, failed_jobs, initial_flow_attribs)
+	pending = []
+	log.each do |task, attribs|
+		if attribs['start'].last == 0  && attribs['end'].last == 0
+			pending << task
+		end
+	end
+	pending_to_launch = [] #PENDING jobs that for some reason has not been launched although their depedencies has been executed succesful.
+	pending.each do |job|
+		folder, dependencies = initial_flow_attribs[job]
+		if (dependencies & failed_jobs).length == 0 || (dependencies & pending).length == 0
+			pending_to_launch << job
+		end
+	end
+	return pending_to_launch
+end
+
 def get_failed_jobs(log)
-	failed_jobs = [] 
 	position = 0
 	fails = []
 	log.each do |task, attribs|
@@ -97,13 +114,7 @@ def get_failed_jobs(log)
 			fails << [task, abort]
 		end
 	end
-	if !fails.empty?
-		fails.each do |task, index| 
-			if position == index
-				failed_jobs << task
-			end
-		end
-	end
+	failed_jobs = fails.select{|task, index| index == position}.map{|t, i| t}
 	return failed_jobs
 end
 
@@ -272,10 +283,15 @@ OptionParser.new do |opts|
 	end
 
   options[:launch_failed_jobs] = FALSE
-  opts.on("-l", "--launch_failed_jobs", "Launch jobs tagges as ABORT and NOT. This option only works when the -w flag is enabled") do |opt|
+  opts.on("-l", "--launch_failed_jobs", "Launch jobs tagged as ABORT and NOT. This option only works when the -w flag is enabled") do |opt|
     options[:launch_failed_jobs] = TRUE
   end 
 
+  options[:pending] = FALSE
+  opts.on("-p", "--pending", "Launch jobs tagged as NOT. This option only works when the -w flag is enabled") do |opt|
+    options[:pending] = TRUE
+  end 
+
   options[:html] = FALSE
   opts.on("-H", "--html", "Make a workflow execution full report in html format") do |opt|
     options[:html] = TRUE
@@ -310,6 +326,6 @@ else
 	elsif options[:html]
 		report_html(log, attribs)
 	elsif options[:workflow_status] && options[:launch_failed_jobs]
-		launch_failed_jobs(log, attribs, options[:workflow_execution], options[:batch])
+		launch_failed_jobs(log, attribs, options[:workflow_execution], options[:batch], options[:pending])
 	end
 end

data/lib/autoflow/batch.rb

@@ -174,6 +174,7 @@ class Batch
 		resources_line = nil
 		command.each_line do |line|
 			if line.include?('resources:')
+				line = line.chomp
 				resources_line = line
 				fields = line.split(' ')
 				fields.each_with_index do |field, index|

data/lib/autoflow/queue_manager.rb

@@ -7,6 +7,7 @@ class QueueManager
 		@commands = commands
 		@persist_variables = persist_variables
 		@verbose = options[:verbose]
+		@show_submit = options[:show_submit_command]
 		@job_identifier = options[:identifier]
 		@files = {}
 		@remote = options[:remote]

data/lib/autoflow/queue_managers/slurm_manager.rb

@@ -20,6 +20,7 @@ class SlurmManager < QueueManager
 		dependencies = nil
 		dependencies='--dependency=afterok:'+final_dep.join(':') if !final_dep.empty?  
 		cmd = "sbatch #{dependencies} #{job.name}.sh"
+		STDOUT.puts cmd if @show_submit
 		queue_id = get_queue_system_id(system_call(cmd, job.attrib[:exec_folder]))
 		return queue_id
 	end

data/lib/autoflow/version.rb

@@ -1,3 +1,3 @@
 module Autoflow
-  VERSION = "0.8.0"
+  VERSION = "0.8.4"
 end

metadata

@@ -1,113 +1,100 @@
 --- !ruby/object:Gem::Specification
 name: autoflow
 version: !ruby/object:Gem::Version
-  version: 0.8.0
-  prerelease: 
+  version: 0.8.4
 platform: ruby
 authors:
 - Pedro Seoane
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-25 00:00:00.000000000 Z
+date: 2017-07-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: net-ssh
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.8.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 2.8.0
 - !ruby/object:Gem::Dependency
   name: git
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: colorize
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 0.7.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 0.7.3
 - !ruby/object:Gem::Dependency
   name: terminal-table
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.6.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.6.0
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: ! '"Autoflow makes easy to launch big pipelines on a queue system. Only
+description: '"Autoflow makes easy to launch big pipelines on a queue system. Only
   works with SLURM & PBS"'
 email:
 - seoanezonjic@hotmail.com
@@ -119,7 +106,7 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
+- ".gitignore"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -143,28 +130,27 @@ files:
 homepage: ''
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.4.8
 signing_key: 
-specification_version: 3
-summary: ! '"This gem take a pipeline and launch it on a queue system"'
+specification_version: 4
+summary: '"This gem take a pipeline and launch it on a queue system"'
 test_files:
 - test/stack_test.rb
 - test/test_helper.rb