autoflow 0.9.2 → 0.9.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 03a2fce5cddce218e8903d7b7cff49acd3c6962c
-  data.tar.gz: 1c2019a7d65d8710bc37baa649301c43a1b61585
+  metadata.gz: d00ffd44b18b2ba6bff750522f11da332378e57f
+  data.tar.gz: 4ebda34a7cd6c968cfbf4c81164fb8fac1fb243e
 SHA512:
-  metadata.gz: a52c86fde55c4854e587710c1969e62c282d7fbdd51f645c9a94ce1454882097cecf8f58566f1711cd6c6f4fb92fc02f6e4aef9a3fa46154453b6c09b8a01c6e
-  data.tar.gz: 1d8efc8bd847a2c1fea463497a0a02637582cd744d4654951551759a0e425dd74839622ec23f25a94b938c0a21e35edec129188a04409d9f84079c6171345486
+  metadata.gz: f4d0ed9038fe26031413bd81131b10f91f2bf4f7d297c8f070a04e347439d3b044bb48dffcd0abd639c46ff8a992f32d13a1d147ea8d74a133b43012eb8e5d29
+  data.tar.gz: '008f6891d2267ca10b8f0e97da622c069bbfc774f1e7bdd933b051a30fb83f9e1eaef126a998d9b7e38582e6e17b78e1a43bf05c5ce9a1e18fd409754b7646e3'

data/bin/AutoFlow

@@ -108,6 +108,11 @@ optparse = OptionParser.new do |opts|
                 options[:external_dependencies] = external_dependencies.split(',')
         end
 
+        options[:extended_logging] = false
+        opts.on( '-e', '--extended_logging', 'If set the command /usr/bin/time will be used instead of shell built-in version. Data will be saved in process_data file of task folder' ) do 
+                options[:extended_logging] = true
+        end
+
         options[:retry] = false
         opts.on( '-f', '--force', 'Execute all jobs, including any job commented with %' ) do 
                 options[:retry] = true

data/bin/flow_logger

@@ -296,6 +296,15 @@ OptionParser.new do |opts|
   opts.on("-H", "--html", "Make a workflow execution full report in html format") do |opt|
     options[:html] = true
   end  
+
+	 # Set a banner, displayed at the top of the help screen.
+	opts.banner = "Usage: flow_logger [options] \n\n"
+
+	# This displays the help screen
+	opts.on( '-h', '--help', 'Display this screen' ) do
+	        puts opts
+	        exit
+	end
 end.parse!
 
 #################################################################################################

data/lib/autoflow/queue_manager.rb

@@ -15,6 +15,7 @@ class QueueManager
 		@write_sh = options[:write_sh]
 		@external_dependencies = options[:external_dependencies]
 		@active_jobs = []
+		@extended_logging = options[:extended_logging]
 	end
 
 	########################################################################################
@@ -267,7 +268,12 @@ class QueueManager
 
 	def write_job(job, sh_name)	
 		write_file(sh_name, job.initialization) if !job.initialization.nil?
-		write_file(sh_name, 'time ' + job.parameters)
+		if @extended_logging
+			log_command = '/usr/bin/time -o process_data -v '
+		else
+			log_command = 'time '
+		end
+		write_file(sh_name, log_command + job.parameters)
 	end
 
 	def get_dependencies(job, id = nil)

data/lib/autoflow/version.rb

@@ -1,3 +1,3 @@
 module Autoflow
-  VERSION = "0.9.2"
+  VERSION = "0.9.4"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: autoflow
 version: !ruby/object:Gem::Version
-  version: 0.9.2
+  version: 0.9.4
 platform: ruby
 authors:
 - Pedro Seoane
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-10-24 00:00:00.000000000 Z
+date: 2019-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: net-ssh