autoflow 0.8.4 → 0.8.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 94220cd6f51e6b8715d6f89e7bf8e7fcc081651d
-  data.tar.gz: b823cce8cd1125752a9fb9328aa687c72ebc0c81
+  metadata.gz: f312d125afdd65f9895264cda8383258bd155fb3
+  data.tar.gz: 005f0219a73e5f38811df45b30d5fdaba7f243ae
 SHA512:
-  metadata.gz: 6b3479c881c662937922a604eb993dfd2f2ee4b340075753b33710b54a710f8a515c02a1dac1688c3e0ba55aa4256468d5c9ccb4e7f0a1db5e14d9d1bd41efa9
-  data.tar.gz: cc737f01685322374f41b482ac3e97f12c11fab420d2050a2812ceb0197ad652b3f1bc8df004e316a35399b5dc4f7515dd56bfdb95aae863d7b5803c77fab37c
+  metadata.gz: 2106ec11e38495b7338bef9cf94a02f2df9a9ddaea8a464167872d4a5919ace690dfd9624ea68f60d3fde74fda5d4aab606f4905c3241eb434697b14049628f2
+  data.tar.gz: 2f046987dd54bee1c4c256e5475c7a544ecbaf5735b4b01677f841188457fe5eaf644dcbc2d0089a0f6ea30cc0cbe4c310f333d73b6a2b673a3be8bb11755033

data/bin/AutoFlow

@@ -83,9 +83,9 @@ optparse = OptionParser.new do |opts|
                 options[:add] = add
         end
 
-        options[:batch] = FALSE
+        options[:batch] = false
         opts.on( '-b', '--batch', 'Workflow execution using batch' ) do 
-                options[:batch] = TRUE
+                options[:batch] = true
         end
 
         options[:cpus] = 16
@@ -93,9 +93,9 @@ optparse = OptionParser.new do |opts|
                 options[:cpus] = cpus.to_i
         end
 
-        options[:comment] = FALSE
+        options[:comment] = false
         opts.on( '-C', '--comment_main_command', 'Comment first line of main command job' ) do 
-                options[:comment] = TRUE
+                options[:comment] = true
         end
 
         options[:external_dependencies] = []
@@ -103,9 +103,9 @@ optparse = OptionParser.new do |opts|
                 options[:external_dependencies] = external_dependencies.split(',')
         end
 
-        options[:retry] = FALSE
+        options[:retry] = false
         opts.on( '-f', '--force', 'Execute all jobs, including any job commented with %' ) do 
-                options[:retry] = TRUE
+                options[:retry] = true
         end
 
         options[:graph] = nil
@@ -118,14 +118,14 @@ optparse = OptionParser.new do |opts|
                 options[:get_template_repository] = url
         end
 
-        options[:identifier] = FALSE
+        options[:identifier] = false
         opts.on( '-i', '--job_identifier STRING', 'Identifier tag for each launching script' ) do |identifier|
                 options[:identifier] = identifier
         end
 
-        options[:key_name] = FALSE
+        options[:key_name] = false
         opts.on( '-k', '--use_key_name', ' Use job names as folder names' ) do
-                options[:key_name] = TRUE
+                options[:key_name] = true
         end
 
         options[:list] = nil
@@ -153,9 +153,9 @@ optparse = OptionParser.new do |opts|
                 options[:pull] = pull
         end    
 
-        options[:remote] = FALSE
+        options[:remote] = false
         opts.on( '-r', '--remote', 'Connect with remote machine and launch the workflow' ) do 
-                options[:remote] = TRUE
+                options[:remote] = true
                 puts 'Host to connect and launch workflow:'
                 host = gets.chomp
                 puts 'User:'
@@ -166,14 +166,14 @@ optparse = OptionParser.new do |opts|
                 puts options[:ssh].exec!('hostname')
         end
 
-        options[:use_ntasks] = FALSE
+        options[:use_ntasks] = false
         opts.on( '-s', '--use_ntasks', 'Use several nodes on execution' ) do 
-                options[:use_ntasks] = TRUE
+                options[:use_ntasks] = true
         end
 
-        options[:show_submit_command] = FALSE
+        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
+                options[:show_submit_command] = true
         end
 
         options[:time] = '20:00:00'
@@ -187,9 +187,9 @@ optparse = OptionParser.new do |opts|
         end     
 
 
-        options[:verbose] = FALSE
+        options[:verbose] = false
         opts.on( '-v', '--verbose', 'Show info without launching jobs' ) do 
-                options[:verbose] = TRUE
+                options[:verbose] = true
         end
 
         options[:Variables] = nil
@@ -197,7 +197,7 @@ optparse = OptionParser.new do |opts|
                 options[:Variables] = [mem]
         end
 
-        options[:workflow] = FALSE
+        options[:workflow] = false
         opts.on( '-w', '--workflow FILE', 'Input workflow file' ) do |workflow|
                 options[:workflow] = workflow
                 template_file = workflow
@@ -338,7 +338,7 @@ if !options[:graph].nil?
 else
         stack.inspect if options[:verbose]
         stack.comment_main_command if options[:comment]
-        options[:write_sh] = TRUE # Set in flow logger to FALSE, it is used for relaunch failed jobs 
+        options[:write_sh] = true # Set in flow logger to FALSE, it is used for relaunch failed jobs 
         manager = QueueManager.select_queue_manager(stack.exec_folder, options, stack.jobs, stack.persist_variables)
         manager.exec
 end

data/bin/flow_logger

@@ -267,34 +267,34 @@ OptionParser.new do |opts|
     options[:report] = opt
   end
 
-  options[:workflow_status] = FALSE
+  options[:workflow_status] = false
   opts.on("-w", "--workflow_finished", "When set, logger assumes that the workflow has ended") do |opt|
-    options[:workflow_status] = TRUE
+    options[:workflow_status] = true
   end
   
-  options[:no_size] = FALSE
+  options[:no_size] = false
   opts.on("-n", "--no_size", "When set, logger don't compute the workflow folder sizes") do |opt|
-    options[:no_size] = TRUE
+    options[:no_size] = true
   end
 
-	options[:batch] = FALSE
+	options[:batch] = false
 	opts.on( '-b', '--batch', 'Workflow execution using batch' ) do |opt|
-		options[:batch] = TRUE
+		options[:batch] = true
 	end
 
-  options[:launch_failed_jobs] = FALSE
+  options[:launch_failed_jobs] = false
   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
+    options[:launch_failed_jobs] = true
   end 
 
-  options[:pending] = FALSE
+  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
+    options[:pending] = true
   end 
 
-  options[:html] = FALSE
+  options[:html] = false
   opts.on("-H", "--html", "Make a workflow execution full report in html format") do |opt|
-    options[:html] = TRUE
+    options[:html] = true
   end  
 end.parse!
 

data/lib/autoflow/batch.rb

@@ -34,9 +34,9 @@ class Batch
 		@initialization = init
 		@main_command = main_command
 		@attrib = {
-			:done => FALSE,
-			:folder => TRUE,
-			:buffer => FALSE,
+			:done => false,
+			:folder => true,
+			:buffer => false,
 			:exec_folder => exec_folder,
 			:cpu_asign => nil # number, list or mono
 		}.merge(@@general_computation_attrib)
@@ -150,13 +150,13 @@ class Batch
 		@@batch_iterator_relations[@name] = @iterator
 	end
 
-	def check_execution_modifiers(name, iter_type = FALSE) #The last paremeter iused to indicate tha name is a iterator not an orignal node name
-		done = FALSE
-		folder = TRUE
-		buffer = FALSE
-		done = TRUE if name.include?('%')
-		folder = FALSE if name.include?('!')
-		buffer = TRUE if name.include?('&')
+	def check_execution_modifiers(name, iter_type = false) #The last paremeter iused to indicate tha name is a iterator not an orignal node name
+		done = false
+		folder = true
+		buffer = false
+		done = true if name.include?('%')
+		folder = false if name.include?('!')
+		buffer = true if name.include?('&')
 		if !iter_type
 			name.gsub!(/&|\!|\%|\)/,'')# Delete function characters
 		else
@@ -191,9 +191,9 @@ class Batch
 					end	
 				end
 				if fields.include?('-s')
-					@attrib[:ntask] = TRUE
+					@attrib[:ntask] = true
 				else
-					@attrib[:ntask] = FALSE
+					@attrib[:ntask] = false
 				end
 			end
 		end
@@ -264,7 +264,7 @@ class Batch
 			@iterator.each_with_index do |iter, num|
 				job_attrib = @attrib.dup
 				if !iter.nil?
-					iter, done, job_attrib[:folder], job_attrib[:buffer] = check_execution_modifiers(iter, TRUE)
+					iter, done, job_attrib[:folder], job_attrib[:buffer] = check_execution_modifiers(iter, true)
 					job_attrib[:done] = done if !@attrib[:done] # To keep attrib priority in batch on job
 				end
 				name = "#{@name}#{iter}"
@@ -357,14 +357,14 @@ class Batch
 	end
 
 	def string_overlap(matched_regions, substr, string)
-		match = FALSE
+		match = false
 		range = get_string_position(substr, string)
 		if !range.empty?
 			matched_regions.each do |start, ending|
 				if (range.first >= start && range.first <= ending) || 
 					(range.last >= start && range.last <= ending) ||
 					(range.first <= start && range.last >= ending)
-					match = TRUE
+					match = true
 					break
 				end
 			end
@@ -471,4 +471,4 @@ class Batch
 		return jobs
 	end
 
-end
+end

data/lib/autoflow/stack.rb

@@ -44,14 +44,14 @@ class Stack
 		persist_variables_lines = []
 		node_lines = []
 
-		node_beg = FALSE		
+		node_beg = false		
 		@workflow.each_line do |line|
-			node_beg = TRUE if line.include?('{') 	# This check the context of a variable
+			node_beg = true if line.include?('{') 	# This check the context of a variable
 			if line.include?('}')					# if a variable is within a node,
 				if node_beg							# we consider tha is a bash variable not a static autoflow variable
-					node_beg = FALSE
+					node_beg = false
 				else
-					node_beg = TRUE
+					node_beg = true
 				end
 			end
 			if line =~ /^\$/ && !node_beg

data/lib/autoflow/version.rb

@@ -1,3 +1,3 @@
 module Autoflow
-  VERSION = "0.8.4"
+  VERSION = "0.8.5"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: autoflow
 version: !ruby/object:Gem::Version
-  version: 0.8.4
+  version: 0.8.5
 platform: ruby
 authors:
 - Pedro Seoane
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-07-27 00:00:00.000000000 Z
+date: 2017-11-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: net-ssh