rbbt-util 5.21.39 → 5.21.42

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 97680be71c7f39a7c72f307cf0fa154ef8fbb524
-  data.tar.gz: 50b7802d5af30c133c85092bef090eff33ae44bd
+  metadata.gz: d7e3095c61e3d45f4d025495616012edd657e844
+  data.tar.gz: f009065701ca1bb5fc077352d950a41c1448fd6f
 SHA512:
-  metadata.gz: 41a0673225580d3bb28ab960edcdf85a5a5564ddf044ff7445e3267cf3697a7af0d0d2b0b4b10214a489f8fdf16d2055e35bf4ef17dd644744af9c857ba41716
-  data.tar.gz: 9b5211a011ac1fc4bf7c338a372781d41e2471679802cad0e4ca4047a7a498344922a088ad957bb606c867e8ba1f625587beea688ddc0bbfa211a907ca052107
+  metadata.gz: b6761bc6d733ef4f82e18069314df062512f53ef0f8aefdea400a6cfe63dc64939feb0570d77ff1ad1dd1edb92273024b2c240348bf11c16352b29a87953b383
+  data.tar.gz: c2e35aea73309e61fcd0d20df6e8d88b7412f7e7d513b99199e8bd9fbcb8b73d8a406d966f5505f6d52b458df5c02e697e57b3f1c717a810ba899dfe56ffe44e

data/lib/rbbt/util/concurrency/processes/worker.rb

@@ -21,6 +21,12 @@ class RbbtProcessQueue
           @stop = true
         }
 
+        @abort = false
+        Signal.trap(:USR2){ 
+          @abort = true
+        }
+
+
         loop do
           p = @queue.pop
           next if p.nil?
@@ -34,6 +40,7 @@ class RbbtProcessQueue
             raise $!
           end
           raise Respawn if @stop
+          raise Aborted if @abort
         end
         Kernel.exit! 0
       rescue Respawn
@@ -103,7 +110,6 @@ class RbbtProcessQueue
       rescue Aborted, Interrupt
         Log.warn "Worker #{Process.pid} aborted"
         Kernel.exit! 0
-        Process.kill "INT", @current 
       rescue Exception
         Log.exception $!
         raise $!
@@ -148,13 +154,16 @@ class RbbtProcessQueue
 
     def join
       Process.waitpid @pid
-      raise ProcessFailed unless $?.success?
+      raise ProcessFailed if not $?.success?
     end
 
     def abort
       begin
+        Process.kill :USR2, @pid
         Process.kill :INT, @pid
-      rescue
+      rescue Errno::ESRCH 
+      rescue Exception
+        Log.exception $!
       end
     end
 

data/lib/rbbt/workflow/accessor.rb

@@ -339,7 +339,7 @@ class Step
     return false unless error?
     begin
       klass = Kernel.const_get(info[:exception][:class])
-      not RbbtException === klass
+      not (RbbtException == klass or RbbtException === klass)
     rescue Exception
       false
     end
@@ -350,7 +350,7 @@ class Step
   end
 
   def dirty?
-    rec_dependencies.collect{|dependency| dependency.path }.uniq.reject{|path| not Path === path or path.exists?}.any?
+    rec_dependencies.collect{|dependency| dependency.path unless dependency.error? and not dependency.recoverable_error? }.compact.uniq.reject{|path| not Path === path or path.exists?}.any?
   end
 
   def done?
@@ -366,6 +366,8 @@ class Step
     pid = info[:pid]
     return nil if pid.nil?
 
+    return false if done? or error? or aborted? or not started?
+
     if Misc.pid_exists?(pid) 
       pid
     else

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

@@ -199,8 +199,12 @@ class Step
           begin
             step.produce
           rescue Exception
-            step.abort
-            raise $!
+            step.exception $!
+            if step.recoverable_error?
+              raise $!
+            else
+              raise StopInsist.new($!)
+            end
           end
         end
         nil
@@ -221,7 +225,12 @@ class Step
             raise $!
           rescue Exception
             dep.exception $!
-            raise StopInsist.new($!)
+            dep.exception $!
+            if dep.recoverable_error?
+              raise $!
+            else
+              raise StopInsist.new($!)
+            end
           end
         end
         nil

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

@@ -54,7 +54,12 @@ class Step
   def _exec
     resolve_input_steps
     @exec = true if @exec.nil?
-    @task.exec_in((bindings ? bindings : self), *@inputs)
+    begin
+      old = Signal.trap("INT"){ Thread.current.raise Aborted }
+      @task.exec_in((bindings ? bindings : self), *@inputs)
+    ensure
+      Signal.trap("INT", old)
+    end
   end
 
   def exec(no_load=false)
@@ -119,6 +124,7 @@ class Step
           rescue Exception
             FileUtils.rm pid_file if File.exist?(pid_file)
             stop_dependencies
+            Log.exception $!
             raise $!
           end
 
@@ -237,6 +243,8 @@ class Step
       exception $!
       stop_dependencies
       raise $!
+    ensure 
+      set_info :pid, nil
     end
   end
 
@@ -248,11 +256,16 @@ class Step
       if force or aborted? or recoverable_error?
         clean
       else
-        raise "Error in job: #{status} - #{self.path}"
+        e = get_exception
+        if e
+          raise e
+        else
+          raise "Error in job: #{self.path}"
+        end
       end
     end
 
-    clean if dirty? or (not running? and not done?)
+    clean if dirty?
 
     if dofork
       fork(true) unless started?

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.39
+  version: 5.21.42
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-10-04 00:00:00.000000000 Z
+date: 2016-10-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -487,82 +487,82 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
+- test/rbbt/test_workflow.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_setup.rb
 - test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_open.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_pipes.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_association.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/test_persist.rb
+- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
+- test/test_helper.rb