rbbt-util 5.24.0 → 5.24.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: b937c979d3515e7a923f2f229c64dd734f5ae2c6
+  metadata.gz: 4785253a5733137474410b83536a9a079b1fda64
+  data.tar.gz: 44f40786114ad60851366238366bbb5ef09bd577
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+  metadata.gz: 6cfd642943afb2e512cdf69c2cd02d4ea91180152e0a09134e0312de688e055d7a90138219b97475836855cf97e311516cf8c6a648f381422253d2559bee4ff6
+  data.tar.gz: 38e50f7448597c9d309918aa81aba0fc05bbb6a1489c3087177bd6bff4b7988ab11bc0e5e6cd4f2cc36079c882dcdf071988e0f0165b96d4080a8a8b4d9a57a3

data/lib/rbbt/util/misc/inspect.rb

@@ -261,10 +261,11 @@ module Misc
             "{"<< obj.collect{|k,v| obj2str(k) + '=>' << obj2str(v)}*"," << "}"
           when Symbol 
             obj.to_s
-          when (defined? Path and Path)
+          when (defined?(Path) and Path)
             if obj.exists?
               if obj.directory?
-                "directory: #{obj.glob("**/*")}"
+                files = obj.glob("**/*")
+                "directory: #{files}"
               else
                 "file: " << obj << "--" << mtime_str(obj)
               end
@@ -272,7 +273,7 @@ module Misc
               obj + " (file missing)"
             end
           when String
-            if Misc.is_filename?(obj) 
+            if Misc.is_filename?(obj) and ! %w(. ..).include?(obj)
               obj2str Path.setup(obj.dup)
             else
               obj = obj.chomp if String === obj

data/lib/rbbt/util/misc/pipes.rb

@@ -204,7 +204,7 @@ module Misc
 
         stream.close unless stream.closed?
         #stream.join if stream.respond_to? :join
-        in_pipes.first.close
+        in_pipes.first.close unless in_pipes.first.closed?
         #Log.medium "Tee done #{Misc.fingerprint stream}"
       rescue Aborted, Interrupt
         stream.abort if stream.respond_to? :abort

data/lib/rbbt/util/open.rb

@@ -362,6 +362,14 @@ module Open
     end
   end
 
+  def self.link(source, target, options = {})
+    begin
+      Open.ln(source, target, options)
+    rescue
+      Open.ln_s(source, target, options)
+    end
+  end
+
   #def self.cp(source, target, options = {})
   #  source = source.find if Path === source
   #  target = target.find if Path === target
@@ -733,6 +741,11 @@ module Open
     end
   end
 
+  def self.realpath(file)
+    file = file.find if Path === file
+    Pathname.new(File.expand_path(file)).realpath.to_s 
+  end
+
   def self.mtime(file)
     if (dir_sub_path = find_repo_dir(file))
       get_time_from_repo(*dir_sub_path)

data/lib/rbbt/workflow/definition.rb

@@ -63,6 +63,16 @@ module Workflow
     end
   end
 
+  def dep_task(name, *dependency, &block)
+    dep(*dependency, &block)
+    task name do
+      dep = dependencies.last.join
+      set_info :result_type, dep.info[:result_type]
+      Open.link dep.path, self.path
+      nil
+    end
+  end
+
   def task(name, &block)
     if Hash === name
       type = name.first.last

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

@@ -94,7 +94,8 @@ class Step
         job.clean 
       end
 
-      (job.init_info and job.dup_inputs) unless status == 'done' or job.started?
+      job.dup_inputs unless status == 'done' or job.started?
+      job.init_info unless status == 'noinfo' or status == 'done' or job.started?
 
       canfail = ComputeDependency === job && job.canfail?
     end
@@ -194,10 +195,8 @@ class Step
         return unless other_steps.length > 1
         log_dependency_exec(step, "duplicating #{other_steps.length}") 
         copies = Misc.tee_stream_thread_multiple(stream, other_steps.length)
-        other_steps.zip(copies).each do |other,dupped_stream|
-          stream.annotate(dupped_stream) if stream.respond_to?(:annotate)
-          other.instance_variable_set("@result", dupped_stream)
-        end
+        copies.extend StreamArray
+        step.instance_variable_set("@result", copies)
       end
     end
   end
@@ -356,7 +355,7 @@ class Step
       step.dependencies.each do |step_dep|
         next if step_dep.done? or step_dep.running? or (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore))
         dep_step[step_dep.path] ||= []
-        dep_step[step_dep.path] << step
+        dep_step[step_dep.path] << step_dep
       end
       step.inputs.each do |inputs|
         inputs = [inputs] unless Array === inputs
@@ -364,7 +363,7 @@ class Step
           next unless Step === step_dep
           next if step_dep.done? or step_dep.running? or (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore))
           dep_step[step_dep.path] ||= []
-          dep_step[step_dep.path] << step
+          dep_step[step_dep.path] << step_dep
         end
       end
     end

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

@@ -1,5 +1,8 @@
 require 'rbbt/workflow/step/dependencies'
 
+
+module StreamArray; end
+
 class Step
 
   attr_reader :stream, :dupped, :saved_stream
@@ -8,10 +11,12 @@ class Step
     @mutex.synchronize do
       Log.low "Getting stream from #{path} #{!@saved_stream} [#{object_id}-#{Misc.fingerprint(@result)}]"
       begin
-        return nil if @saved_stream
         if IO === @result 
+          return nil if @saved_stream
           @saved_stream = @result 
-        else 
+        elsif StreamArray === @result and @result.any?
+          @saved_stream = @result.pop 
+        else
           nil
         end
       end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.24.0
+  version: 5.24.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-05 00:00:00.000000000 Z
+date: 2018-12-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake