rbbt-util 5.25.41 → 5.25.42

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 730e709d5f66cb69ee6df6a4e1209492afe98fc1
+  metadata.gz: 8c7c2171a24807d0a7e1f7d33bc6b95c4905ed4d
+  data.tar.gz: 99a0ae12b516bdf954e3128f48c1fb585efc2567
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+  metadata.gz: 9cc824ce02d93292895424f60db1c14da44519a9e373e6064e05317b1c34e6f05efa43703dd8f38326a24d62b9c0edbc4f778866fe88bd772d6c2cd9c2cdb464
+  data.tar.gz: 4fec89ee21e2471dcf091891cada8115ec1d97cb54b689ee0fedfd7f86488379a3d5172c32b7be4305d333bcda2b859fb053ef2df4a2adefe0c2cfd924d235e1

data/lib/rbbt/workflow/accessor.rb

@@ -92,13 +92,19 @@ class Step
       next unless task_inputs.include? name.to_sym
       next if value.nil?
       path = File.join(dir, name.to_s)
-      type = input_types[name]
+      type = input_types[name].to_s
       Log.debug "Saving job input #{name} (#{type}) into #{path}"
       case
       when Array === value
         Open.write(path, value * "\n")
       when IO === value
         Open.write(path, value)
+      when type == "file"
+        if String === value && File.exists?(value)
+          Open.ln(value, path)
+        else
+          Open.write(path + '.read', value.to_s)
+        end
       else
         Open.write(path, value.to_s)
       end
@@ -974,6 +980,7 @@ 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_.info[:name] = d_.name
+                     d_.task = workflow.tasks[dep_task] if workflow.tasks.include?(dep_task)
                      d_.task_name = dep_task
                      d_.overriden = true
                      d_
@@ -995,6 +1002,7 @@ 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] if self.tasks.include?(dependency)
                      d_.info[:name] = d_.name
                      d_.task_name = dependency
                      d_.overriden = true
@@ -1024,6 +1032,12 @@ module Workflow
                          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.info[:name] = d.name
+                           begin
+                             workflow = String === d[:workflow] ? Kernel.const_get(d[:workflow]) : d[:workflow]
+                             d.task = workflow.tasks[d[:task]] if workflow.tasks.include?(d[:task])
+                           rescue
+                             Log.exception $!
+                           end
                            d.task_name = d[:task]
                            d.overriden = true
                            d
@@ -1042,11 +1056,17 @@ module Workflow
                      _inputs = IndiferentHash.setup(_inputs.dup)
                      dep = dependency.call jobname, _inputs, real_dependencies
                      if Hash === dep
-                       dep[:workflow] ||= wf  || self
+                       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.info[:name] = dep.name
-                         dep.task_name = d[:task]
+                         begin
+                           workflow = String === dep[:workflow] ? Kernel.const_get(dep[:workflow]): dep[:workflow]
+                           dep.task = workflow.tasks[dep[:task]] if workflow.tasks.include?(dep[:task])
+                         rescue
+                           Log.exception $!
+                         end
+                         dep.task_name = dep[:task]
                          dep.overriden = true
                          dep
                        else

data/lib/rbbt/workflow/examples.rb

@@ -49,7 +49,11 @@ module Workflow
         case input_types[input]
         when :file
           Log.debug "Pointing #{ input } to #{file}"
-          inputs[input.to_sym]  = file
+          if file =~ /\.read$/
+            inputs[input.to_sym]  = Open.read(file)
+          else
+            inputs[input.to_sym]  = Open.realpath(file)
+          end
         when :text
           Log.debug "Reading #{ input } from #{file}"
           inputs[input.to_sym]  = Open.read(file)

data/lib/rbbt/workflow/step.rb

@@ -167,7 +167,7 @@ class Step
     @result_type ||= if @task.nil?
                        info[:result_type]
                      else
-                       @task.result_type || info[:result_type]
+                       @task.result_type || info[:result_type] || :string
                      end
   end
 

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

@@ -219,8 +219,6 @@ class Step
 
           Open.write(pid_file, Process.pid.to_s) unless Open.exists? pid_file
 
-          config_keys_pre = Rbbt::Config::GOT_KEYS.dup
-
           @exec = false
           init_info(true)
 
@@ -310,7 +308,9 @@ class Step
           set_info :started, (start_time = Time.now)
           log :started, "Starting step #{Log.color :yellow, task.name.to_s || ""}"
 
+          config_keys_pre = Rbbt::Config::GOT_KEYS.dup
           begin
+
             result = _exec
           rescue Aborted, Interrupt
             log(:aborted, "Aborted")

data/test/rbbt/test_workflow.rb

@@ -151,6 +151,11 @@ for this dependency
     "Sum odds: " << step(:sum_odds).load.to_s
   end
 
+  input :file, :file, "Save file"
+  task :reverse_file => :text do |file|
+    Open.read(file).reverse
+  end
+
 
 end
 
@@ -288,8 +293,8 @@ class TestWorkflow < Test::Unit::TestCase
   end
 
   def test_override_dep
-    TmpFile.with_file("OTHER") do |file|
-      assert TestWF.job(:repeat2, nil, :number => 3, "TestWF#str" => file).run.include? "OTHER"
+    TmpFile.with_file("OTHER", false) do |file|
+      assert TestWF.job(:repeat2, nil, :number => 3, "TestWF#str" => file).clean.run.include? "OTHER"
     end
   end
 
@@ -389,4 +394,25 @@ class TestWorkflow < Test::Unit::TestCase
     assert_equal "Sum odds: 24", job.run
   end
 
+  def test_save_inputs
+    TmpFile.with_file("Hi") do |file|
+      job = TestWF.job(:reverse_file, nil, :file => file)
+      TmpFile.with_file do |dir|
+        Path.setup(dir)
+        Step.save_job_inputs(job, dir)
+        assert_equal Dir.glob(dir + "/*"), [dir.file.find]
+      end
+    end
+
+    job = TestWF.job(:reverse_file, nil, :file => "code")
+    TmpFile.with_file do |dir|
+      Path.setup(dir)
+      Step.save_job_inputs(job, dir)
+      assert_equal Dir.glob(dir + "/*"), [dir.file.find + '.read']
+      inputs  = Workflow.load_inputs(dir, [:file], :file => :file)
+      assert_equal inputs, {:file => 'code'}
+    end
+
+  end
+
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.41
+  version: 5.25.42
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-08 00:00:00.000000000 Z
+date: 2019-04-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake