rbbt-util 5.9.4 → 5.9.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2cf8e981590ec75d716c3b173786a1d9d49751af
-  data.tar.gz: c48d0c459d08b67b68a5caf94d31bef4ea10e4c4
+  metadata.gz: 485bac99517b86329c91a69142f4b38c8405cc8f
+  data.tar.gz: f8f7fee0f9f2ceccc294431d31d1f9e14983b903
 SHA512:
-  metadata.gz: 7687ee59c28372845dfb2d9d3606c2aa3409fcc299566530dcec737b48ef764bfadb49504d5dd0256fac2f85d8ddf10a5780642034ed6f05ccfa2a73e5b187c1
-  data.tar.gz: f47bb2989be8fa6f39e15551caf8cd35d4506ba07092b61716e6b7a14efff001b5e12509e34266fd572f0f22cef07f4d138cd3e518c4243e6e493792027ab6b6
+  metadata.gz: 2b3897bc88326b032537c45579f6d6236da05b47683fd4d802cd61032c4d12c7cf35ee35898d05e19bb8a63d505c495a282206ab55a0740461b630c4cc303f92
+  data.tar.gz: 15680565e5cf2e61dc0770ae9b8949d890a5c13dd27a93e60eabad2c4ad3a18754056f145edc72763630d573119f9b64b6773a8bb9de9397c565bc5f4e7acc6b

data/lib/rbbt/workflow/step.rb

@@ -180,8 +180,8 @@ class Step
   def fork(semaphore = nil)
     raise "Can not fork: Step is waiting for proces #{@pid} to finish" if not @pid.nil?
     @pid = Process.fork do
-      trap(:INT) { raise Aborted.new "INT signal recieved" }
       begin
+        #trap(:INT) { raise Aborted.new "INT signal recieved" }
         RbbtSemaphore.wait_semaphore(semaphore) if semaphore
         FileUtils.mkdir_p File.dirname(path) unless Open.exists? File.dirname(path)
         begin
@@ -219,19 +219,22 @@ class Step
         RbbtSemaphore.post_semaphore(semaphore) if semaphore
       end
     end
+    set_info :forked, true
     Process.detach(@pid)
     self
   end
 
   def abort
     @pid ||= info[:pid]
-    if @pid.nil?
+    if @pid.nil? and info[:forked]
       Log.medium "Could not abort #{path}: no pid"
       false
     else
       Log.medium "Aborting #{path}: #{ @pid }"
       begin
-        Process.kill("INT", @pid)
+        Process.kill("TERM", @pid)
+        sleep 1
+        Process.kill("KILL", @pid)
         Process.waitpid @pid
       rescue Exception
         Log.debug("Aborted job #{@pid} was not killed: #{$!.message}")

data/share/rbbt_commands/workflow/task

@@ -3,6 +3,7 @@
 require 'rbbt/util/simpleopt'
 require 'rbbt/workflow'
 require 'rbbt/workflow/usage'
+require 'time'
 
 def report_options(options)
   if options.nil? or options.empty?
@@ -265,34 +266,58 @@ begin
   end
 
   if do_fork
-    job.fork
     if detach
-      Process.detach job.pid
-      puts Log.color(:magenta, "Issued: ") + Log.color(:magenta, job.pid.to_s) + ' -- ' + job.path
+      job.fork
+      Process.detach job.pid if job.pid
+      puts Log.color(:magenta, "Issued: ") + Log.color(:magenta, job.pid ? job.pid.to_s : 'no pid') + ' -- ' + job.path
+      exit 0
+    end
+
+    Signal.trap(:INT) do
+      begin
+        job.abort if job.info[:pid] == job.pid
+      rescue
+      end
       exit 0
     end
+
+    job.fork
+
     puts 
     puts
+    size = Log.tty_size
+    size = 100 if size.nil?
+
     while not job.done?
       message = (job.messages and job.messages.any?) ? job.messages.last.strip : "no message"
       status = job.status || "no status"
-      time = Time.now - job.info[:issued] if job.info and job.info.include? :issued
-      size = Log.tty_size
-      size = 100 if size.nil?
+      if job.info and job.info.include? :issued
+        issued = job.info[:issued]
+        issued = Time.parse(issued) unless Time === issued
+        time = Time.now - issued
+      end
       puts Log.return_line << " " * size << Log.return_line 
       puts Log.return_line << " " * size << Log.return_line 
       puts "#{Log.color :blue, job.path}"
-      puts "Waiting on #{Log.color :blue, job.info[:pid] || job.pid} (+#{time.to_i if time}) " << [Log.color(:cyan, status.to_s),message.strip].compact*" " 
+      puts "Waiting on #{Log.color :blue, job.info[:pid] || job.pid} (#{time ? time.to_i : '?'} sec. ago) " << [Log.color(:cyan, status.to_s),message.strip].compact*" " 
       sleep 2
     end
-    #Signal.trap(:INT){ job.abort }
     raise job.messages.last if job.error?
-    res = job.load
+
+    if job.info and job.info.include? :issued
+      issued = job.info[:issued]
+      issued = Time.parse(issued) unless Time === issued
+      time = Time.now - issued
+    end
+    puts Log.return_line << " " * size << Log.return_line 
+    puts Log.return_line << " " * size << Log.return_line 
+    puts job.path
+    exit 0
   else
-    res = job.run(true)
+    job.run(true)
+    res = job
   end
 
-  puts res
 
   if options.delete(:provenance)
     pp job.provenance
@@ -332,12 +357,14 @@ if job_file = options.delete(:job_file)
   out.puts Path === file ? file.read : file
   exit 0
 end
-ddd 1
 
-if Step === res and not res.exec
+case res
+when (defined?(WorkflowRESTClient) and WorkflowRESTClient::RemoteStep)
+  out.puts res.load
+when Step
   out.puts Open.read(res.path) if File.exists? res.path
 else
-  out.puts res
+  out.puts res.to_s
 end
 
 exit 0

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.9.4
+  version: 5.9.5
 platform: ruby
 authors:
 - Miguel Vazquez