rbbt-util 5.23.38 → 5.23.39

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 30801ee36aab9d59c5e918783021efd8c7239af4
+  metadata.gz: 32c23558db95c8f8705eb13a20976b239298f57c
+  data.tar.gz: 0ddc962a3b40fdb2833b45e214a5184a823d0c90
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+  data.tar.gz: 957b85fc91e9fdd5cc4913eda388cdb60b22c55424b55e9d304726769ba277bf88b2e926a5ebbceb46ea834923457591ecfc178f0ae2e4b71959c6656b60986a

data/lib/rbbt/util/cmd.rb

@@ -127,14 +127,6 @@ module CMD
         rescue
           Log.error "Error in CMD  [#{pid}] #{cmd}: #{$!.message}"
           raise $!
-        #  begin
-        #    Process.kill "INT", pid
-        #    #parent.raise $!
-        #  ensure
-        #    raise $!
-        #  end
-        #ensure
-        #  #sin.close  unless sin.closed?
         end
       end
     else

data/lib/rbbt/workflow/accessor.rb

@@ -912,12 +912,9 @@ module Workflow
     _inputs
   end
 
-  def real_dependencies(task, orig_jobname, inputs, dependencies)
-    real_dependencies = []
-    path_deps = {}
-
+  def override_dependencies(inputs)
     override_dependencies = IndiferentHash.setup({})
-
+    return override_dependencies if inputs.nil?
     inputs.each do |key,value|
       if String === key && m = key.match(/(.*)#(.*)/)
         workflow, task = m.values_at 1, 2
@@ -926,6 +923,14 @@ module Workflow
         override_dependencies[workflow][task] = value
       end
     end
+    override_dependencies
+  end
+
+  def real_dependencies(task, orig_jobname, inputs, dependencies)
+    real_dependencies = []
+    path_deps = {}
+
+    override_dependencies = override_dependencies(inputs)
 
     dependencies.each do |dependency|
       _inputs = IndiferentHash.setup(inputs.dup)
@@ -938,8 +943,9 @@ module Workflow
 
                    if override_dependencies[workflow.to_s] && value = override_dependencies[workflow.to_s][dep_task]
                      d_ = Step === value ? value : Workflow.load_step(value)
-                     d_.task = workflow.tasks[dep_task]
-                     d_.workflow = workflow
+                     d_.task_name = dep_task
+                     #d_.task = workflow.tasks[dep_task]
+                     #d_.workflow = workflow
                      d_.overriden = true
                      d_
                    else
@@ -960,8 +966,9 @@ module Workflow
                  when Symbol
                    if override_dependencies[self.to_s] && value = override_dependencies[self.to_s][dependency]
                      d_ = Step === value ? value : Workflow.load_step(value)
-                     d_.task = self.tasks[dependency]
-                     d_.workflow = self
+                     d_.task_name = dependency
+                     #d_.task = self.tasks[dependency]
+                     #d_.workflow = self
                      d_.overriden = true
                      d_
                    else
@@ -988,8 +995,9 @@ module Workflow
                          d[:task] ||= task_name
                          if override_dependencies[d[:workflow].to_s] && value = override_dependencies[d[:workflow].to_s][d[:task]]
                            d = (Step === value ? value : Workflow.load_step(value))
-                           d.task = d[:workflow].tasks[d[:task]]
-                           d.workflow = self
+                           d.task_name = d[:task]
+                           #d.task = d[:workflow].tasks[d[:task]]
+                           #d.workflow = self
                            d.overriden = true
                            d
                          else
@@ -1010,9 +1018,11 @@ module Workflow
                        dep[:workflow] ||= wf  || self
                        if override_dependencies[dep[:workflow].to_s] && value = override_dependencies[dep[:workflow].to_s][dep[:task]]
                          dep = (Step === value ? value : Workflow.load_step(value))
-                         dep.task = d[:workflow].tasks[d[:task]]
-                         dep.workflow = self
+                         dep.task_name = d[:task]
+                         #dep.task = d[:workflow].tasks[d[:task]]
+                         #dep.workflow = self
                          dep.overriden = true
+                         dep
                        else
                          task_info = (dep[:task] && dep[:workflow]) ? dep[:workflow].task_info(dep[:task]) : nil
                          inputs = assign_dep_inputs({}, dep[:inputs], real_dependencies, task_info)

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

@@ -674,8 +674,9 @@ class Step
         dependencies.each{|dep| dep.join }
       else
         begin
+          pid = pid.to_i if String === pid
           Log.debug{"Waiting for pid: #{pid}"}
-          Process.waitpid pid 
+          Process.waitpid pid
         rescue Errno::ECHILD
           Log.debug{"Process #{ pid } already finished: #{ path }"}
         end if Misc.pid_exists? pid

data/lib/rbbt/workflow/step.rb

@@ -104,8 +104,12 @@ class Step
     rec_dependencies.each do |dep|
       next unless NamedArray === dep.inputs
       dep.inputs.zip(dep.inputs.fields).each do |v,f|
-        next if i.include?(f)
-        i[f] = v
+        if i.include?(f) && i[f] != v
+          Log.debug "Conflict in #{ f }: #{[i[f].inspect, v.inspect] * " <-> "}"
+          i[f] = nil
+        else 
+          i[f] = v
+        end
       end
     end
     #dependencies.each do |dep|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.38
+  version: 5.23.39
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-03 00:00:00.000000000 Z
+date: 2018-12-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake