autoflow 0.5.1 → 0.5.3

data/bin/AutoFlow

@@ -107,6 +107,11 @@ optparse = OptionParser.new do |opts|
                 options[:identifier] = identifier
         end
 
+        options[:key_name] = FALSE
+        opts.on( '-k', '--use_key_name', 'Use job names like folder name' ) do
+                options[:key_name] = TRUE
+        end
+
         options[:list] = nil
         opts.on( 'l', '--list_repository STRING', 'List template names in repository') do |name|
                 options[:list] = name

data/lib/autoflow/batch.rb

@@ -13,6 +13,11 @@ class Batch
 		:multinode => nil,
 		:ntask => nil
 	}
+	@@folder_name = :program_name # can  :job_name
+
+	def self.set_job_folder_definition(definition)
+		@@folder_name = definition
+	end
 
 	def self.set_general_attrib(attrib_hash)
 		@@general_computation_attrib = attrib_hash
@@ -141,7 +146,7 @@ class Batch
 	end
 
 
-	def asign_folder(local_command = nil)
+	def asign_folder(name, local_command = nil)
 		if local_command.nil? #we check a simple job
 			command = @main_command
 		else #we check a cloned job
@@ -150,12 +155,16 @@ class Batch
 		if command.class.to_s == 'Array'
 			folder = nil
 		elsif @attrib[:folder]
-			program = File.join(@attrib[:exec_folder], command.split(' ', 2).first) 			
-			count = 0
-			folder = program + "_#{"%04d" % count}"
-			while @@all_jobs_relations.values.include?(folder)
+			if @@folder_name == :program_name
+				program = File.join(@attrib[:exec_folder], command.split(' ', 2).first) 			
+				count = 0
 				folder = program + "_#{"%04d" % count}"
-				count += 1
+				while @@all_jobs_relations.values.include?(folder)
+					folder = program + "_#{"%04d" % count}"
+					count += 1
+				end
+			elsif @@folder_name == :job_name
+				folder = File.join(@attrib[:exec_folder], name)
 			end
 		else
 			folder = @attrib[:exec_folder]
@@ -170,7 +179,7 @@ class Batch
 		new_job.dependencies = tmp_j.dependencies.clone
 		new_job.initialization = tmp_j.initialization.clone
 		new_job.parameters = tmp_j.parameters.clone
-		new_job.attrib[:exec_folder] = asign_folder(new_job.parameters)
+		new_job.attrib[:exec_folder] = asign_folder(new_job.name, new_job.parameters)
 		return new_job
 	end
 
@@ -211,7 +220,7 @@ class Batch
 					job_attrib[:done] = done if !@attrib[:done] # To keep attrib priority in batch on job
 				end
 				name = "#{@name}#{iter}"
-				job_attrib[:exec_folder] = asign_folder if @parent.nil? #Don't asign folder to nested batches (iterative batchs)
+				job_attrib[:exec_folder] = asign_folder(name) if @parent.nil? #Don't asign folder to nested batches (iterative batchs)
 				job_dependencies = []
 				initialization = replace_dependencies(@initialization, job_dependencies, iter, num)
 				parameters = replace_dependencies(@main_command, job_dependencies, iter, num)

data/lib/autoflow/queue_manager.rb

@@ -70,10 +70,10 @@ class QueueManager
 				rm_done_dependencies(job)
 			end	
 			buffered_jobs = launch_job_in_folder(job, name, buffered_jobs)
-		end
+		end 
 	end
 
-	def sort_jobs_by_dependencies
+	def sort_jobs_by_dependencies # We need job ids from queue system so we ask for each job and we give the previous queue system ids as dependencies if necessary
 		ar_jobs = @commands.to_a
 		sorted_jobs = []
 		jobs_without_dep = ar_jobs.select{|job| job.last.dependencies.empty?}

data/lib/autoflow/stack.rb

@@ -17,12 +17,14 @@ class Stack
 			:node => options[:node_type],
 			:multinode => options[:use_multinode],
 			:ntask => options[:use_ntasks]
-		}) 
+		})
+		Batch.set_job_folder_definition(:job_name) if options[:key_name]
 		@commands = {}	
 		@variables = {}
 		@persist_variables = {}
 		@exec_folder = exec_folder
 		@do_retry = options[:retry]
+		@options = options
 		parse(options[:workflow], options[:Variables])
 		@jobs = get_jobs_relations
 	end
@@ -142,8 +144,10 @@ class Stack
 			new_batch = Batch.new(tag, init, command, index, @exec_folder)			
 
 			#Dependencies
+			#-- Check initialize
 			scan_dependencies(init, new_batch.dependencies, dinamic_variables)
 			dinamic_variables.concat(collect_dinamic_variables(init, tag))
+			#-- Check command
 			if command.class.to_s == 'String'
 				scan_dependencies(command, new_batch.dependencies, dinamic_variables)
 				dinamic_variables.concat(collect_dinamic_variables(command, tag))
@@ -151,6 +155,8 @@ class Stack
 
 			@commands[new_batch.name] = new_batch
 		end
+
+		# link each parent batch to a child batch
 		@commands.each do |name, batch|
 			batch.main_command = asign_child_batch(batch.main_command, batch.name) if batch.main_command.class.to_s == 'Array'
 		end
@@ -245,7 +251,7 @@ class Stack
 		@commands.each do |name, batch|
 			next if batch.has_jobs?
 			batch.get_jobs.each do |j|
-				set_path(j, all_jobs_relations) 
+				set_path(j, all_jobs_relations)
 				jobs << [j.name, j]
 			end
 		end

data/lib/autoflow/version.rb

@@ -1,3 +1,3 @@
 module Autoflow
-  VERSION = "0.5.1"
+  VERSION = "0.5.3"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: autoflow
 version: !ruby/object:Gem::Version
-  version: 0.5.1
+  version: 0.5.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-11-05 00:00:00.000000000 Z
+date: 2015-04-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: net-ssh