rbbt-util 5.20.14 → 5.20.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7b5585c1845795e5a7c874e332091305114e4ee7
-  data.tar.gz: 9b66bcf3e909d67e240419b4492ebfb5a418185a
+  metadata.gz: 8acdb68bc077ef40aa93cc0bd822e2a03e634d7f
+  data.tar.gz: 5aeb1004ef167478f65659794dbc2c93d294cd10
 SHA512:
-  metadata.gz: a4b43d8d9cf4506820dfbb6171527a98dd2cdfde10da40291f63c0ebb6c30c7359b1464ec35199d1d370da8175263986c957ccd72d684bed0f53be0e378f6202
-  data.tar.gz: 8439f337004a4b65353b63535343e42fa1f37075a2f71dfccf90c130615e4a9c46eefb93e7c60b2b23ab7e11d3a4b991a6680faff6593914719344e611258250
+  metadata.gz: c5bb2dc2c484251bc7d41b88d3869eeea5d179724bf4ff46403fdd7e3c84be1c28bb31c8bd5d4412f51027221e3fd41139acd1b444fbb1829adcd8baa49560e6
+  data.tar.gz: 1c82abfa22a27807250e030c22f03a586327d10cee8baea5bc70644275e71ad7f69cff72c4327df9ff4f6f0f05b8e788a5c1ff28b949bdae1ab9d5791f519672

data/lib/rbbt/resource.rb

@@ -160,6 +160,8 @@ module Resource
                 Misc.sensiblewrite(final_path, data * "\n")
               when TSV
                 Misc.sensiblewrite(final_path, data.dumper_stream) 
+              when TSV::Dumper
+                Misc.sensiblewrite(final_path, data.stream) 
               when nil
               else
                 raise "Unkown object produced: #{Misc.fingerprint data}"

data/lib/rbbt/rest/client/step.rb

@@ -34,8 +34,19 @@ class WorkflowRESTClient
       inputs.each do |k,v|
         stream = stream_input.to_s == k.to_s
         if Step === v 
-          v.run(true) and v.grace unless v.done? or v.streaming?
-          new_inputs[k] = stream ? TSV.get_stream(v) : v.load
+          unless (v.done? or v.streaming? or RestClient::Step === v)
+            v.run(true) and v.grace 
+          end
+
+          begin
+            if stream
+              new_inputs[k] = TSV.get_stream(v)
+            else
+              new_inputs[k] = v.load
+            end
+          rescue Exception
+            raise $!
+          end
         else
           new_inputs[k] = v
         end

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -352,6 +352,8 @@ module TSV
 
   def self.traverse_cpus(num, obj, options, &block)
     begin
+      error = false
+      
       callback, cleanup, join, respawn, bar = Misc.process_options options, :callback, :cleanup, :join, :respawn, :bar
       respawn = true if ENV["RBBT_RESPAWN"] and ENV["RBBT_RESPAWN"] == "true"
 
@@ -369,6 +371,7 @@ module TSV
       q.join
 
     rescue Interrupt, Aborted
+      error = true
       q.abort
       Log.medium{"Aborted traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}: #{$!.backtrace*","}"}
       stream = obj_stream(obj)
@@ -377,6 +380,7 @@ module TSV
       stream.abort if stream.respond_to? :abort
       raise "Traversal aborted"
     rescue Exception
+      error = true
       q.abort
       Log.medium "Exception during traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}: #{$!.message}"
       stream = obj_stream(obj)
@@ -386,7 +390,7 @@ module TSV
       raise $!
     ensure
       q.clean
-      Log::ProgressBar.remove_bar(bar) if bar
+      Log::ProgressBar.remove_bar(bar, error) if bar
     end
   end
 

data/lib/rbbt/util/log/progress/report.rb

@@ -147,5 +147,21 @@ module Log
       print(io, up_lines(@depth) << done_msg << down_lines(@depth)) 
       Open.rm @file if @file and Open.exists? @file
     end
+
+    def error(io = STDERR)
+      done_msg = Log.color(:magenta, desc) << " " << Log.color(:red, "error")
+      if @start
+        ellapsed = (Time.now - @start).to_i
+      else
+        ellapsed = 0
+      end
+      ellapsed = [ellapsed/3600, ellapsed/60 % 60, ellapsed % 60].map{|t| "%02i" % t }.join(':')
+      done_msg << " " << Log.color(:blue, (@ticks).to_s) << " in " << Log.color(:green, ellapsed)
+      @last_count = 0
+      @last_time = @start
+      done_msg << " (" << thr_msg << ")"
+      print(io, up_lines(@depth) << done_msg << down_lines(@depth)) 
+      Open.rm @file if @file and Open.exists? @file
+    end
   end
 end

data/lib/rbbt/util/log/progress/util.rb

@@ -57,8 +57,12 @@ module Log
       end
     end
 
-    def self.remove_bar(bar)
-      bar.done if bar.respond_to? :done
+    def self.remove_bar(bar, error = false)
+      if error
+        bar.error if bar.respond_to? :error
+      else
+        bar.done if bar.respond_to? :done
+      end
       BAR_MUTEX.synchronize do
         REMOVE << bar
       end

data/lib/rbbt/workflow/accessor.rb

@@ -22,7 +22,7 @@ class Step
       threads = jobs.collect do |j| 
         Thread.new do
           begin
-            j.join 
+            j.join unless j.done?
           rescue Exception
             Log.error "Exception waiting for job: #{Log.color :blue, j.path}"
             raise $!

data/lib/rbbt/workflow/step/dependencies.rb

@@ -184,7 +184,14 @@ class Step
     case type
     when :produce, :no_dup
       list.each do |step|
-        step.produce
+        Misc.insist do
+          begin
+            step.produce
+          rescue
+            step.abort
+            raise $!
+          end
+        end
         nil
       end
     when :bootstrap
@@ -193,7 +200,14 @@ class Step
       cpus = list.length / 2 if cpus > list.length / 2
 
       Misc.bootstrap(list, cpus, :bar => "Bootstrapping dependencies for #{path}", :respawn => :always) do |dep|
-        dep.produce
+        Misc.insist do
+          begin
+            dep.produce
+          rescue
+            dep.abort
+            raise $!
+          end
+        end
         nil
       end
     else

data/share/rbbt_commands/workflow/prov

@@ -46,7 +46,7 @@ end
 
 def report_msg(status, name, path)
 
-  parts = path.sub(/#{Regexp.quote(name)}$/,'').split "/"
+  parts = path.sub(/\{.*/,'').sub(/#{Regexp.quote(name)}$/,'').split "/"
 
   task = Log.color(:yellow, parts.pop)
   workflow = Log.color(:magenta, parts.pop)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.20.14
+  version: 5.20.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-18 00:00:00.000000000 Z
+date: 2016-06-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake