rbbt-util 5.13.13 → 5.13.14

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 3dd0c58cb609fc0e2f23f44c0346c3b11c0dc33b
+  metadata.gz: 5399e9cd15518ddd19400ba2cf089758cb0e60d2
+  data.tar.gz: 8adfd1f1ec5293cfcd1aa4749ed8ba84aba078c4
 SHA512:
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+  metadata.gz: 132f5a6172cd496d7cadc66affcfc73251fc35b73f1cf458521d08726f766597957d095d029ddc6f3a14cb6f880599ba6576a6c91fbee2fcda7bbde8919c1ca9
+  data.tar.gz: 3cd484b4a5cdf42edae4d19698f8ee780812785d033ccac47b26e9f326fbe5413c977f922344d59a1b715ed703fdfe48a0cce494f312c2f7047281532afedbc5

data/lib/rbbt/persist.rb

@@ -360,8 +360,11 @@ module Persist
       Log.low "Persist up-to-date: #{ path } - #{Misc.fingerprint persist_options}"
       return path if persist_options[:no_load]
       return load_file(path, type) 
+    else
+      Open.rm path if Open.exists? path
     end
 
+
     begin
 
       lock_filename = Persist.persistence_path(path + '.persist', {:dir => Persist.lock_dir})

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

@@ -257,6 +257,7 @@ module TSV
       Log.medium "Aborted traversing 2 #{stream_name(obj)}"
     rescue Exception
       Log.medium "Exception traversing #{stream_name(obj)}"
+      Log.exception $!
       stream = obj_stream(obj)
       stream.abort if stream and stream.respond_to? :abort
       stream = obj_stream(options[:into])

data/lib/rbbt/tsv/stream.rb

@@ -95,8 +95,8 @@ module TSV
 
       sin.puts TSV.header_lines(key_field, fields, options)
 
-      empty.each do |stream|
-        i = streams.index stream
+      empty_pos = empty.collect{|stream| streams.index stream }
+      empty_pos.sort.reverse.each do |i|
         lines.delete_at i
         fields.delete_at i
         key_fields.delete_at i

data/lib/rbbt/tsv/util.rb

@@ -91,8 +91,11 @@ module TSV
       end
       file
     when String
-      raise "Could not open file given by String: #{Misc.fingerprint file}" unless Open.remote?(file) or File.exists? file
-      Open.open(file, open_options)
+      if Open.remote?(file) or File.exists? file
+        Open.open(file, open_options)
+      else
+        StringIO.new file
+      end
     when (defined? Step and Step)
       file.grace
       stream = file.get_stream

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

@@ -48,8 +48,8 @@ module Misc
 
   def self.format_definition_list_item(dt, dd, size = 80, indent = 20, color = :yellow)
     dd = "" if dd.nil?
-    dt = dt.to_s + ":" unless dd.empty?
     dt = Log.color color, dt if color
+    dt = dt.to_s + ":" unless dd.empty?
     len = Log.uncolor(dt).length
 
     if indent < 0

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

@@ -198,7 +198,6 @@ module Misc
   end
 
   def self.sensiblewrite(path, content = nil, &block)
-
     return if Open.exists? path
     tmp_path = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_dir})
     Misc.lock tmp_path do

data/lib/rbbt/util/simpleopt/doc.rb

@@ -80,7 +80,7 @@ module SOPT
 
 #{ Log.color :magenta, "## SYNOPSYS"}
 
-#{synopsys}
+#{Log.color :blue, synopsys}
 
 #{ Log.color :magenta, "## DESCRIPTION"}
 

data/lib/rbbt/workflow/accessor.rb

@@ -391,7 +391,7 @@ module Workflow
         if Array === dep 
           dep.first.rec_dependencies(dep.last).each do |d|
             if Array === d
-              d
+              all_deps << d
             else
               all_deps << [dep.first, d]
             end

data/lib/rbbt/workflow/examples.rb

@@ -19,7 +19,7 @@ module Workflow
   end
 
   def example(task_name, example)
-    tasks[task_name.to_sym].input_types.collect do |input,type|
+    task_info(task_name.to_sym)[:input_types].collect do |input,type|
       next unless example_dir[task_name][example][input].exists?
       [input, type, example_dir[task_name][example][input].find]
     end.compact

data/lib/rbbt/workflow/usage.rb

@@ -2,7 +2,7 @@ require 'rbbt/util/simpleopt'
 
 module Task
   def doc(deps = nil)
-    puts Log.color :magenta, "## #{ name }:"
+    puts Log.color(:yellow, "## #{ name }") << ":"
     puts "\n" << description  << "\n" if description and not description.empty?
     puts
 
@@ -19,21 +19,23 @@ module Task
       puts
     end
 
-    puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults, true)
-    puts
+    if inputs.any?
+      puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults, true)
+      puts
+    end
 
     if deps and deps.any?
-      puts "From dependencies:"
+      puts Log.color(:magenta, "Inputs from dependencies:")
       puts
       deps.each do |dep|
-        puts "  #{Log.color :magenta, dep.name.to_s}:"
+        puts "  #{Log.color :yellow, dep.name.to_s}:"
         puts
         puts SOPT.input_doc((dep.inputs - self.inputs), dep.input_types, dep.input_descriptions, dep.input_defaults, true)
         puts
       end
     end
 
-    puts "Returns: " << Log.color(:blue, result_type.to_s) << "\n"
+    puts Log.color(:magenta, "Returns: ") << Log.color(:blue, result_type.to_s) << "\n"
     puts
   end
 end
@@ -71,6 +73,7 @@ module Workflow
         task_name = task
         task = self.tasks[task_name]
       end
+
       dependencies = self.rec_dependencies(task_name).collect{|dep_name| Array === dep_name ? dep_name.first.tasks[dep_name.last.to_sym] : self.tasks[dep_name.to_sym]}
 
       task.doc(dependencies)
@@ -78,18 +81,20 @@ module Workflow
       if self.examples.include? task_name
           self.examples[task_name].each do |example|
 
-            puts Log.color(:magenta, "Example " << example) + " -- " + Log.color(:blue, example_dir[task_name][example])
+            puts Log.color(:magenta, "Example ") << Log.color(:green, example) + " -- " + Log.color(:blue, example_dir[task_name][example])
 
             inputs = self.example(task_name, example)
 
             inputs.each do |input, type, file|
                 case type
                 when :tsv, :array, :text
-                  head = file.read.split("\n")[0..5].compact * "\n\n"
+                  lines = file.read.split("\n")
+                  head = lines[0..5].compact * "\n\n"
                   head = head[0..500]
-                  puts Misc.format_definition_list_item(input, head, 100, -1).gsub(/\n\s*\n/,"\n")
+                  puts Misc.format_definition_list_item(input, head, 1000, -1, :blue).gsub(/\n\s*\n/,"\n") 
+                  puts '...' if lines.length > 6
                 else
-                  puts Misc.format_definition_list_item(input, file.read)
+                  puts Misc.format_definition_list_item(input, file.read, 80, 20, :blue)
                 end
             end
             puts

data/share/rbbt_commands/workflow/task

@@ -413,7 +413,6 @@ when Step
   if IO === res.result
     begin
       io = res.result
-      Thread.pass while IO.select([io]).nil?
       while block = io.read(2048) do
         out.write block
       end #unless io.closed? 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.13
+  version: 5.13.14
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-16 00:00:00.000000000 Z
+date: 2014-05-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake