rbbt-util 5.12.1 → 5.12.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 8a4fd1ba66536df107ae3d23426c79b60801a080
+  metadata.gz: 957c675de87a163f988c6175828d6de03d346987
+  data.tar.gz: 937b879524577ae29d2b41a436ceb0a69e5ba285
 SHA512:
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-  data.tar.gz: f47fffb35b77b270b0a02e1fda74e67d1cc6fd4b67e7cc12ba0881b679fd5a2478cb2e01ea08bcd4e2766df5becbd21f1054fd60998aa6127ce3ea374c1fec61
+  metadata.gz: 6d5959cd1b7e3a412f16f3a28379d8f1cda0e6677b6eefda51072b6b85095567cea8dee27fd9aaa661ff152e5c748a5c90d7f2c6c716c8b177cc57c2b9235c1e
+  data.tar.gz: 6ae212b12a951921efe4405568cf57d1bcb84f9a4393f7eec532e8131ae2e1526b8697540019a7bf98909cb0344c0bc82c7092f868bcea98d7840961a28b5087

data/lib/rbbt/tsv/accessor.rb

@@ -621,7 +621,7 @@ Example:
       else
         self.through do |key,values|
           field_values = values.delete_at field_pos
-          zipped = values.zip_fields
+          zipped = Misc.zip_fields(values)
           field_values.zip(zipped).each do |field_value,rest|
             k = [key,field_value]*":"
             new[k] = rest
@@ -631,11 +631,12 @@ Example:
       end
     end
 
-
-    new.key_field = [self.key_field, self.fields[field_pos]] * ":"
-    new_fields = self.fields.dup
-    new_fields.delete_at field_pos
-    new.fields = new_fields
+    if self.key_field and self.fields
+      new.key_field = [self.key_field, self.fields[field_pos]] * ":" 
+      new_fields = self.fields.dup 
+      new_fields.delete_at field_pos
+      new.fields = new_fields
+    end
 
     new
   end

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

@@ -306,9 +306,9 @@ module TSV
     end
   end
 
-  def self.traverse_stream(obj, threads, cpus, options, &block)
+  def self.traverse_stream(obj, threads = nil, cpus = nil, options = {}, &block)
     into = options[:into]
-    thread = Thread.new(Thread.current, obj) do |parent,obj|
+    thread = Thread.new(Thread.current) do |parent|
       begin
         traverse_run(obj, threads, cpus, options, &block)
         into.close if into.respond_to? :close

data/lib/rbbt/tsv/parser.rb

@@ -277,6 +277,15 @@ module TSV
       end
     end
 
+    def cast_values_flat(values)
+      case
+      when Symbol === cast
+        values.collect{|v| v.send(cast)}
+      when Proc === cast
+        values.collect{|v| cast.call v }
+      end
+    end
+
     def cast_values_double(values)
       case
       when Symbol === cast
@@ -408,7 +417,7 @@ module TSV
       when :flat
         @take_all = true if field_positions.nil?
         self.instance_eval do alias get_values get_values_flat end
-        self.instance_eval do alias cast_values cast_values_double end
+        self.instance_eval do alias cast_values cast_values_flat end
         if merge
           if key_position and key_position != 0 and field_positions.nil?
             self.instance_eval do alias add_to_data add_to_data_flat_merge_keys end

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

@@ -35,12 +35,16 @@ module Misc
   end
 
   def self.append_zipped(current, new)
-    current.each do |v|
-      n = new.shift
-      if Array === n
-        v.concat new
-      else
-        v << n
+    if current.empty?
+      current.replace new.collect{|e| [e]}
+    else
+      current.each do |v|
+        n = new.shift
+        if Array === n
+          v.concat new
+        else
+          v << n
+        end
       end
     end
     current

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

@@ -57,7 +57,7 @@ module Misc
         end
         Kernel.exit! 0
       }
-      sin.close #if close
+      sin.close 
       ConcurrentStream.setup sout, :pids => [pid]
     else
       thread = Thread.new(Thread.current) do |parent|
@@ -181,7 +181,6 @@ module Misc
         io.join if io.respond_to? :join
       rescue
         Log.error "Exception consuming stream: #{io.inspect}"
-        ddd caller
         Log.exception $!
         io.abort if io.respond_to? :abort
       end

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

@@ -25,6 +25,10 @@ module SOPT
         value = args.delete_at(i) if value.nil?
         values[input] = value
       else
+        if value.nil? and %w(F false FALSE no).include?(args[i])
+          Log.warn "Boolean values must are best specified as #{current}[=true|false], not #{ current } [true|false]. Token '#{args[i]}' following '#{current}' automatically assigned as value" 
+          value = args.delete_at(i)
+        end
         values[input] = %w(F false FALSE no).include?(value)? false : true
       end
     end

data/lib/rbbt/workflow/examples.rb

@@ -63,6 +63,6 @@ module Workflow
         inputs[input.to_sym]  = file.read.strip
       end
     end
-    Sequence.job(task_name, example, inputs)
+    self.job(task_name, example, inputs)
   end
 end

data/share/rbbt_commands/tsv/info

@@ -15,7 +15,7 @@ Display summary information. Works with Tokyocabinet HDB and BDB as well.
 -tch--tokyocabinet File is a TC HDB
 -tcb--tokyocabinet_bd File is a TC BDB
 -t--type* Type of tsv (single, list, double, flat)
--h--header_hash* Change the character used to mark the header line (defaults to #)
+-hh--header_hash* Change the character used to mark the header line (defaults to #)
 -k--key_field* Change the key field
 -f--fields* Change the fields to load
 -h--help Help

data/share/rbbt_commands/tsv/unzip

@@ -3,7 +3,24 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get("-tch--tokyocabinet:-tcb--tokyocabinet_bd:-f--field Field to append to key:-m--merge Consider multiple values even after unzip")
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Zip fields in a TSV file 
+
+$ rbbt tsv info [options] file.tsv
+
+Display summary information. Works with Tokyocabinet HDB and BDB as well.
+
+-tch--tokyocabinet File is a TC HDB
+-tcb--tokyocabinet_bd File is a TC BDB
+-hh--header_hash* Change the character used to mark the header line (defaults to #)
+-m--merge* Merge lines
+-f--field* Field to unzip
+-h--help Help
+EOF
+
+SOPT.usage if options[:help]
 
 file = ARGV.shift
 
@@ -22,7 +39,7 @@ else
     file = file.dup
     Path.setup(File.expand_path(file))
   end
-  tsv = TSV.open(file, :type => :double)
+  tsv = TSV.open(file, {:type => :double}.merge(options))
 end
 
 puts tsv.unzip(field, merge).to_s

data/share/rbbt_commands/workflow/example

@@ -29,7 +29,7 @@ def run_task(workflow, task, name)
       end
       Process.wait @pid
     end
-    path = Open.read(res) if File.exists? res
+    path = Open.read(res).strip if File.exists? res
   end
   path = "NO RESULT" if path.nil? or path.empty?
 
@@ -51,6 +51,8 @@ task = nil if task == '--'
 name = ARGV.shift if task
 name = nil if name == '--'
 
+orig_name = name
+
 $saved_args = ARGV.dup
 
 workflow = Workflow.require_workflow workflow
@@ -70,8 +72,12 @@ task_result.each do |code,res|
   task, name = code
   path, success = res
   if success
-    puts "#{Log.color :green, "SUCCESS"} #{Log.color :magenta, workflow.to_s}##{Log.color :yellow, task} -- #{Log.color :cyan, name}"
-    puts path
+    if orig_name
+      puts Open.read(path)
+    else
+      puts "#{Log.color :green, "SUCCESS"} #{Log.color :magenta, workflow.to_s}##{Log.color :yellow, task} -- #{Log.color :cyan, name}"
+      puts path
+    end
   else
     puts "#{Log.color :red, "ERROR"} #{Log.color :magenta, workflow.to_s}##{Log.color :yellow, task} -- #{Log.color :cyan, name}"
     puts path

data/share/rbbt_commands/workflow/task

@@ -100,7 +100,7 @@ def fix_options(workflow, task, job_options)
                 end
               end
             when :array
-              if input_options[name] and input_options[name][:stream] and String === value
+              if input_options[name] and input_options[name][:stream] and String === value and Misc.is_filename? value
                 get_value_stream(value)
               else
                 if Array === value
@@ -132,9 +132,11 @@ def fix_options(workflow, task, job_options)
                 when TSV
                   value
                 when '-'
-                  TSV.open(STDIN, :unnamed => true, :sep => $field_separator, :sep2 => $array_separator || "|")
+                  TSV.open(STDIN, :unnamed => true, :sep => $field_separator, :sep2 => ($array_separator || "|"))
+                when (Misc.is_filename?(value) and String)
+                  TSV.open(value, :unnamed => true, :sep => $field_separator, :sep2 => ($array_separator || "|"))
                 else
-                  TSV.open(value, :unnamed => true, :sep => $field_separator, :sep2 => $array_separator || "|")
+                  TSV.open(StringIO.new(value), :unnamed => true, :sep => $field_separator, :sep2 => ($array_separator || "|"))
                 end
               end
             else

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.12.1
+  version: 5.12.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-21 00:00:00.000000000 Z
+date: 2014-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake