rbbt-util 5.5.47 → 5.5.48

checksums.yaml

@@ -1,15 +1,15 @@
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   metadata.gz: !binary |-
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data/lib/rbbt/persist.rb

@@ -129,16 +129,16 @@ module Persist
     when :nil
       nil
     when :boolean
-      Open.write(path, content ? "true" : "false")
+      Misc.sensiblewrite(path, content ? "true" : "false")
     when :fwt
       content.file.seek 0
-      Open.write(path, content.file.read)
+      Misc.sensiblewrite(path, content.file.read)
     when :tsv
-      Open.write(path, content.to_s)
+      Misc.sensiblewrite(path, content.to_s)
     when :annotations
-      Open.write(path, Annotated.tsv(content, :all).to_s)
+      Misc.sensiblewrite(path, Annotated.tsv(content, :all).to_s)
     when :string, :text
-      Open.write(path, content)
+      Misc.sensiblewrite(path, content)
     when :binary
       content.force_encoding("ASCII-8BIT") if content.respond_to? :force_encoding
       f = File.open(path, 'wb')
@@ -147,18 +147,18 @@ module Persist
       content
     when :array
       if content.empty?
-        Open.write(path, "")
+        Misc.sensiblewrite(path, "")
       else
-        Open.write(path, content * "\n" + "\n")
+        Misc.sensiblewrite(path, content * "\n" + "\n")
       end
     when :marshal_tsv
-      Open.write(path, Marshal.dump(content.dup))
+      Misc.sensiblewrite(path, Marshal.dump(content.dup))
     when :marshal
-      Open.write(path, Marshal.dump(content))
+      Misc.sensiblewrite(path, Marshal.dump(content))
     when :yaml
-      Open.write(path, YAML.dump(content))
+      Misc.sensiblewrite(path, YAML.dump(content))
     when :float, :integer, :tsv
-      Open.write(path, content.to_s)
+      Misc.sensiblewrite(path, content.to_s)
     else
       raise "Unknown persistence: #{ type }"
     end

data/lib/rbbt/persist/tsv.rb

@@ -102,7 +102,6 @@ module Persist
           end
         end
 
-
         def write_and_close
           lock_filename = Persist.persistence_path(persistence_path, {:dir => TSV.lock_dir})
           Misc.lock(lock_filename) do
@@ -190,7 +189,9 @@ module Persist
 
              FileUtils.rm path if File.exists? path
 
-             data = open_tokyocabinet(path, true, persist_options[:serializer], persist_options[:engine] || TokyoCabinet::HDB)
+             tmp_path = path + '.persist'
+
+             data = open_tokyocabinet(tmp_path, true, persist_options[:serializer], persist_options[:engine] || TokyoCabinet::HDB)
              data.serializer = :type if TSV === data and data.serializer.nil?
 
              data.close
@@ -210,13 +211,14 @@ module Persist
       end
     rescue Exception
       Log.error "Captured error during persist_tsv. Erasing: #{path}"
-      FileUtils.rm path if path and File.exists? path
+      FileUtils.rm tmp_path if tmp_path and File.exists? tmp_path
       raise $!
     ensure
-      begin
-        data.close if data.respond_to? :close
-      rescue
-        raise $!
+      data.close if data.respond_to? :close
+      if tmp_path 
+        FileUtils.mv tmp_path, path if File.exists? tmp_path and not File.exists? path
+        tsv = TC_CONNECTIONS[path] = TC_CONNECTIONS.delete tmp_path
+        tsv.persistence_path = path
       end
     end
 
@@ -225,4 +227,78 @@ module Persist
 
     data
   end
+
+  def self.get_filename(source)
+    case
+    when Path === source
+      source
+    when (source.respond_to?(:filename) and source.filename)
+      source.filename
+    when source.respond_to?(:cmd)
+      "CMD-#{Misc.digest(source.cmd)}"
+    when TSV === source
+      "TSV[#{Misc.digest Misc.fingerprint(source)}]"
+    end || source.object_id.to_s
+  end
+
+  def self.persist_tsv(source, filename, options = {}, persist_options = {}, &block)
+    persist_options[:prefix] ||= "TSV"
+
+    if data = persist_options[:data]
+      yield data
+      return data 
+    end
+
+    filename ||= get_filename(source)
+
+    path = persistence_path(filename, persist_options, options)
+
+    lock_filename = Persist.persistence_path(path, {:dir => TSV.lock_dir})
+
+    if not persist_options[:persist]
+      data = {}
+
+      yield(data) 
+
+      return data 
+    end
+
+    if is_persisted? path and not persist_options[:update]
+      Log.debug "TSV persistence up-to-date: #{ path }"
+      return open_tokyocabinet(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB) 
+    end
+
+    Misc.lock lock_filename do
+      begin
+        if is_persisted? path 
+          Log.debug "TSV persistence up-to-date: #{ path }"
+          return open_tokyocabinet(path, false, nil, persist_options[:engine] || TokyoCabinet::HDB) 
+        end
+
+        FileUtils.rm path if File.exists? path
+
+        Log.medium "TSV persistence creating: #{ path }"
+
+        tmp_path = path + '.persist'
+
+        data = open_tokyocabinet(tmp_path, true, persist_options[:serializer], persist_options[:engine] || TokyoCabinet::HDB)
+        data.serializer = :type if TSV === data and data.serializer.nil?
+
+        data.write_and_read do
+          yield data
+        end
+
+        FileUtils.mv tmp_path, path if File.exists? tmp_path and not File.exists? path
+        tsv = TC_CONNECTIONS[path] = TC_CONNECTIONS.delete tmp_path
+        tsv.persistence_path = path
+
+        data
+      rescue Exception
+        Log.error "Captured error during persist_tsv. Erasing: #{path}"
+        FileUtils.rm tmp_path if tmp_path and File.exists? tmp_path
+        FileUtils.rm path if path and File.exists? path
+        raise $!
+      end
+    end
+  end
 end

data/lib/rbbt/resource.rb

@@ -63,7 +63,8 @@ module Resource
 
       case response
       when Net::HTTPSuccess then
-        Open.write(final_path, response.body)
+        #Misc.sensiblewrite(final_path, response.body)
+        Misc.sensiblewrite(final_path){ Net::HTTP.get_response(URI(url)).body }
       when Net::HTTPRedirection then
         location = response['location']
         Log.debug("Feching directory from: #{location}. Into: #{final_path}")

data/lib/rbbt/tsv/accessor.rb

@@ -1,7 +1,5 @@
 require 'yaml'
 module TSV
-  #extend ChainMethods
-  #self.chain_prefix = :tsv
 
   TSV_SERIALIZER = YAML
   SERIALIZED_NIL = TSV_SERIALIZER.dump nil

data/lib/rbbt/tsv/index.rb

@@ -126,7 +126,7 @@ module TSV
       data_options = Misc.pull_keys options, :data
       identifiers = TSV.open(file, data_options)
       identifiers.with_monitor :desc => "Creating Index for #{ file }" do
-        identifiers.index(options.merge :persist_data => data, :persist => persist_options[:persist])
+        index = identifiers.index(options.merge :persist_data => data, :persist => persist_options[:persist])
       end
     end
   end
@@ -273,192 +273,5 @@ module TSV
       tsv.range_index(start_field, end_field, options)
     end
   end
-
-
-#  def self.field_matches(tsv, values)
-#    values = [values] if not Array === values
-#    Log.debug "Matcing #{values.length} values to #{tsv.filename}"
-#
-#    if values.flatten.sort[0..9].compact.collect{|n| n.to_i} == (1..10).to_a
-#      return {}
-#    end
-#
-#    key_field = tsv.key_field
-#    fields = tsv.fields
-#
-#    field_values = {}
-#    fields.each{|field|
-#      field_values[field] = []
-#    }
-#
-#    if tsv.type == :double
-#      tsv.through do |key,entry_values|
-#        fields.zip(entry_values).each do |field,entry_field_values|
-#          field_values[field].concat entry_field_values unless entry_field_values.nil?
-#        end
-#      end
-#    else
-#      tsv.through do |key,entry_values|
-#        fields.zip(entry_values).each do |field,entry_field_values|
-#          field_values[field] << entry_field_values
-#        end 
-#      end
-#    end
-#
-#    field_values.each do |field,field_value_list|
-#      field_value_list.replace(values & field_value_list.flatten.uniq)
-#    end
-#
-#    field_values[key_field] = values & tsv.keys
-#
-#    field_values
-#  end
-#
-#  def field_matches(values)
-#    TSV.field_matches(self, values)
-#  end
-#
-#  def guess_field(values)
-#    field_matches(values).sort_by{|field, matches| matches.uniq.length}.last
-#  end
-#
-#  def pos_index(pos_field = nil, options = {})
-#    pos_field ||= "Position"
-#
-#    options = Misc.add_defaults options,
-#      :persistence => true, :persistence_file => nil, :persistence_update => false 
-#
-#    prefix = "Pos[#{pos_field}]"
-#
-#    Persistence.persist(filename, prefix, :fwt, options.merge({
-#      :pos_field => pos_field,
-#      :filters => (self.respond_to?(:filters)? filters.collect{|f| [f.match, f.value]} : [])
-#    })) do |file, options, filename|
-#      pos_field = options[:pos_field]
-#      value_size = 0
-#      index_data = []
-#
-#      through :key, pos_field do |key, values|
-#        value_size = key.length if key.length > value_size
-#
-#        pos = values.first
-#        if Array === pos
-#          pos.each do |p|
-#            index_data << [key, p.to_i]
-#          end
-#        else
-#          index_data << [key, pos.to_i]
-#        end
-#      end
-#
-#      index = FixWidthTable.get(:memory, value_size, false)
-#      index.add_point index_data
-#      index.read
-#      index
-#    end
-#  end
-#
-#  def self.pos_index(file, pos_field = nil, options = {})
-#    options = Misc.add_defaults options,
-#      :persistence => true, :persistence_file => nil, :persistence_update => false, :persistence_source => file, :tsv_serializer => :list,
-#      :data_persistence => false, :data_persistence_file => nil, :data_persistence_update => false, :data_persistence_source => file
-#
-#    #options_data = {
-#    #  :cast               => Misc.process_options(options, :data_cast),
-#    #  :persistence        => Misc.process_options(options, :data_persistence),
-#    #  :monitor            => Misc.process_options(options, :data_monitor),
-#    #  :persistence_file   => Misc.process_options(options, :data_persistence_file),
-#    #  :persistence_update => Misc.process_options(options, :data_persistence_update),
-#    #  :in_situ_persistence => Misc.process_options(options,:data_in_situ_persistence),
-#    #  :persistence_source => Misc.process_options(options, :data_persistence_source),
-#    #  :importtsv => Misc.process_options(options, :data_importtsv),
-#    #}
-#
-#    options_data = Misc.pull_data_keys(options)
-#
-#    prefix = "Pos[#{pos_field}]"
-#
-#    new = Persistence.persist(file, prefix, :fwt, options.merge({:pos_field => pos_field})) do |file, options, filename|
-#      tsv = TSV.new(file, :list, options_data)
-#
-#      if options.include?(:filters) and Array === options[:filters] and not options[:filters].empty?
-#        tsv.filter
-#        options[:filters].each do |match, value, persistence|
-#          tsv.add_filter(match, value, persistence)
-#        end
-#      end
-#
-#      tsv.pos_index options[:pos_field], options.merge(:persistence => false, :persistence_file => nil)
-#    end
-#  end
-#
-#  def range_index(start_field = nil, end_field = nil, options = {})
-#    start_field ||= "Start"
-#    end_field ||= "End"
-#    options = Misc.add_defaults options,
-#      :persistence => true, :persistence_file => nil, :persistence_update => false 
-#
-#    prefix = "Range[#{start_field}-#{end_field}]"
-#
-#    Persistence.persist(filename, prefix, :fwt, options.merge({
-#      :start_field => start_field, :end_field => end_field,
-#      :filters => (self.respond_to?(:filters)? filters.collect{|f| [f.match, f.value]} : [])
-#    })) do |file, options, filename|
-#      start_field, end_field = options.values_at :start_field, :end_field
-#
-#      value_size = 0
-#      index_data = []
-#
-#      through :key, [start_field, end_field] do |key, values|
-#        value_size = key.length if key.length > value_size
-#
-#        start_pos, end_pos = values
-#
-#        if Array === start_pos
-#          start_pos.zip(end_pos).each do |s,e|
-#            index_data << [key, [s.to_i, e.to_i]]
-#          end
-#        else
-#          index_data << [key, [start_pos.to_i, end_pos.to_i]]
-#        end
-#      end
-#
-#      index = FixWidthTable.get(:memory, value_size, true)
-#      index.add_range index_data
-#      index.read
-#      index
-#    end
-#  end
-#
-#  def self.range_index(file, start_field = nil, end_field = nil, options = {})
-#    options = Misc.add_defaults options,
-#      :persistence => true, :persistence_file => nil, :persistence_update => false, :persistence_source => file, :tsv_serializer => :list,
-#      :data_persistence => false, :data_persistence_file => nil, :data_persistence_update => false, :data_persistence_source => file
-#
-#    options_data = {
-#      :persistence        => Misc.process_options(options, :data_persistence),
-#      :persistence_file   => Misc.process_options(options, :data_persistence_file),
-#      :persistence_update => Misc.process_options(options, :data_persistence_update),
-#      :persistence_source => Misc.process_options(options, :data_persistence_source),
-#    }
-#
-#    prefix = "Range[#{start_field}-#{end_field}]"
-#
-#    options_data[:type] = :flat if options[:order] == false
-#
-#    Persistence.persist(file, prefix, :fwt, options.merge({:start_field => start_field, :end_field => end_field})) do |file, options, filename|
-#      tsv = TSV.new(file, :list, options_data)
-#
-#      if options.include?(:filters) and Array === options[:filters] and not options[:filters].empty?
-#        tsv.filter
-#        options[:filters].each do |match, value, persistence|
-#          tsv.add_filter(match, value, persistence)
-#        end
-#      end
-#
-#      tsv.range_index options[:start_field], options[:end_field], options.merge(:persistence => false, :persistence_file => nil)
-#    end
-#  end
-#
 end
 

data/lib/rbbt/tsv/manipulate.rb

@@ -449,18 +449,31 @@ module TSV
 
       when (String === method and method =~ /name:(.*)/)
         name = $1
+        old_unnamed = self.unnamed
+        self.unnamed = false
         if name.strip =~ /^\/(.*)\/$/
           regexp = Regexp.new $1
           through :key, key do |key, values|
-            values = [values] if type == :single
-            new[key] = self[key] if invert ^ (values.flatten.select{|v| v.name =~ regexp}.any?)
+            case type
+            when :single
+              values = values.annotate([values])
+            when :double
+              values = values[0]
+            end
+            new[key] = self[key] if invert ^ (values.select{|v| v.name =~ regexp}.any?)
           end
         else
           through :key, key do |key, values|
-            values = [values] if type == :single
-            new[key] = self[key] if invert ^ (values.flatten.select{|v| v.name == name}.any?)
+            case type
+            when :single
+              values = values.annotate([values])
+            when :double
+              values = values[0]
+            end
+            new[key] = self[key] if invert ^ (values.select{|v| v.name == name}.any?)
           end
         end
+        self.unnamed = old_unnamed
 
       when String === method
         with_unnamed do

data/lib/rbbt/tsv/util.rb

@@ -81,6 +81,29 @@ module TSV
     TSV.identify_field(key_field, fields, field)
   end
 
+  def to_list
+    new = {}
+    case type
+    when :double
+      through do |k,v|
+        new[k] = v.collect{|e| e.first}
+      end
+    when :flat
+      through do |k,v|
+        new[k] = [v.first]
+      end
+    when :single
+      through do |k,v|
+        new[k] = [v]
+      end
+    when :list
+      self
+    end
+    self.annotate(new)
+    new.type = :list
+    new
+  end
+
   def to_double
     new = {}
     case type
@@ -154,6 +177,4 @@ module TSV
     new
   end
 
-
-
 end

data/lib/rbbt/util/misc.rb

@@ -1,6 +1,7 @@
 require 'lockfile'
 require 'net/smtp'
 require 'digest/md5'
+require 'narray'
 require 'cgi'
 
 class Hash
@@ -477,7 +478,6 @@ end
   }
 
   def self.fast_align(reference, sequence)
-    require 'narray'
     init_gap = -1
     gap = -2
     diff = -2
@@ -488,7 +488,6 @@ end
 
     a = NArray.int(cols, rows)
 
-
     for spos in 0..cols-1 do a[spos, 0] = spos * init_gap end
     for rpos in 0..rows-1 do a[0, rpos] = rpos * init_gap end
 
@@ -905,7 +904,8 @@ end
 
     res = nil
 
-    lockfile = Lockfile.new(File.expand_path(file + '.lock'))
+    lock_path = File.expand_path(file + '.lock')
+    lockfile = Lockfile.new(lock_path)
 
     begin
       if File.exists? lockfile and
@@ -917,15 +917,21 @@ end
       end
     rescue
       Log.warn("Error checking lockfile #{lockfile}: #{$!.message}. Removing. Content: #{begin Open.read(lockfile) rescue "Could not open file" end}")
-      FileUtils.rm lockfile if File.exists? lockfile 
+      FileUtils.rm lockfile if File.exists?(lockfile)
     end
 
-    lockfile.lock do 
-      res = yield file, *args
+    begin
+      lockfile.lock do 
+        res = yield file, *args
+      end
+    rescue Interrupt
+      Log.error "Process #{Process.pid} interrupted while in lock: #{ lock_path }"
+      raise $!
     end
 
     res
   end
+  
 
   LOCK_REPO_SERIALIZER=Marshal
 
@@ -1011,32 +1017,32 @@ end
     end
   end
 
-  def self.sensiblewrite(path, content)
+  def self.sensiblewrite(path, content = nil)
+    return if File.exists? path
     Misc.lock path + '.sensible_write' do
       if not File.exists? path
         begin
           tmp_path = path + '.tmp'
+          content = yield if block_given?
           case
           when String === content
             File.open(tmp_path, 'w') do |f|  f.write content  end
           when (IO === content or StringIO === content)
-            File.open(tmp_path, 'w') do |f|  while l = content.gets; f.write l; end  end
-        else
-          File.open(tmp_path, 'w') do |f|  end
+            File.open(tmp_path, 'w') do |f|  
+              while l = content.gets; f.write l; end  
+            end
+          else
+            File.open(tmp_path, 'w') do |f|  end
+          end
+          FileUtils.mv tmp_path, path
+        rescue Exception
+          FileUtils.rm_f tmp_path if File.exists? tmp_path
+          FileUtils.rm_f path if File.exists? path
+          raise $!
         end
-        FileUtils.mv tmp_path, path
-      rescue Interrupt
-        FileUtils.rm_f tmp_path if File.exists? tmp_path
-        FileUtils.rm_f path if File.exists? path
-        raise "Interrupted (Ctrl-c)"
-      rescue Exception
-        FileUtils.rm_f tmp_path if File.exists? tmp_path
-        FileUtils.rm_f path if File.exists? path
-        raise $!
       end
     end
   end
-  end
 
   def self.add_defaults(options, defaults = {})
     case

data/test/rbbt/association/test_index.rb

@@ -3,11 +3,13 @@ require 'rbbt/workflow'
 require 'rbbt/association'
 require 'rbbt/association/index'
 
+gem 'rbbt-sources'
+Workflow.require_workflow "Genomics"
+require 'rbbt/entity/gene'
+
 class TestAssociationIndex < Test::Unit::TestCase
 
   def setup
-    Workflow.require_workflow "Genomics"
-    require 'rbbt/entity/gene'
   end
 
   def teardown

data/test/rbbt/test_association.rb

@@ -1,13 +1,20 @@
 require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+
 require 'rbbt/workflow'
+require 'rbbt/entity'
+
 require 'rbbt/association'
 require 'rbbt/knowledge_base'
-require 'rbbt/entity'
-require 'rbbt/util/tmpfile'
-require 'test/unit'
 
+gem 'rbbt-sources'
+gem 'rbbt-phgx'
+
+Log.severity=0
 Workflow.require_workflow "Genomics"
 require 'rbbt/entity/gene'
+require 'rbbt/sources/pina'
 
 TEST_ASSOCIATIONS =<<-EOF
 #: :sep=" "#:namespace=Hsa/jan2013
@@ -51,7 +58,6 @@ class TestAssociations < Test::Unit::TestCase
   end
 
   def test_target_open
-    require 'rbbt/sources/pina'
 
     database = Association.open(Pina.protein_protein,{ 
                                 :undirected => false, 

data/test/rbbt/test_knowledge_base.rb

@@ -2,20 +2,25 @@ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '../..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'test/unit'
 require 'rbbt/knowledge_base'
+
+gem 'rbbt-sources'
+gem 'rbbt-phgx'
+gem 'rest-client'
+
 require 'rbbt/sources/pina'
+require 'rbbt/workflow'
+Workflow.require_workflow "Genomics"
+require 'genomics_kb'
 
 class TestKnowledgeBase < Test::Unit::TestCase
   def setup
-    require 'rbbt/workflow'
-    Workflow.require_workflow "Genomics"
-    require 'genomics_kb'
-
-
     KnowledgeBase.knowledge_base_dir = Rbbt.tmp.knowledge_base_test.find
     @kb = Genomics.knowledge_base
   end
 
   def test_register
+    require 'rbbt/sources/pina'
+
     TmpFile.with_file do |dir|
       kb = KnowledgeBase.new dir
 

data/test/rbbt/test_tsv.rb

@@ -173,7 +173,6 @@ row1    1
 row2    4
     EOF
 
-    require 'rbbt/sources/organism'
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i, :type => :single, :fields => "Value")
       assert_equal 1, tsv["row1"]
@@ -192,7 +191,6 @@ row1    1 2
 row2    4
     EOF
 
-    require 'rbbt/sources/organism'
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value", :fields => ["Id"])
       assert_equal "row1", tsv["1"]

data/test/rbbt/tsv/test_attach.rb

@@ -217,9 +217,9 @@ row2    E
     tsv1 = Rbbt.tmp.test.test1.data.tsv :double,  :sep => /\s+/
     tsv2 = Rbbt.tmp.test.test2.data.tsv :double,  :sep => /\s+/
 
-    tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce.find.to_s
+    tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce.find #.to_s
 
-    tsv1.attach tsv2, :fields => ["OtherID"], :persist_input => true
+    tsv1.attach tsv2, :fields => ["OtherID"] #, :persist_input => true
     
     assert_equal tsv1.fields, %w(ValueA ValueB OtherID)
     assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]

data/test/rbbt/tsv/test_filter.rb

@@ -1,4 +1,5 @@
 require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/tsv'
 require 'rbbt/tsv/filter'
 
 class TestTSVFilters < Test::Unit::TestCase
@@ -129,9 +130,10 @@ row2    A    B
       tsv.filter
       tsv.add_filter "field:ValueA", ["A"], Rbbt.tmp.test.Filter.fieldValueA.find(:user)
 
+      puts tsv
       elem = []
       tsv.through do |k,v| elem << k end
-      assert_equal 2, elem.size
+      assert_equal 1, elem.size
     end
   end
 

data/test/rbbt/tsv/test_index.rb

@@ -112,13 +112,13 @@ row3    A    a|B    Id4
   def test_index_static
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b|A    Id1
-row2    A    a|B    Id3
-row3    A    a|B    Id4
+row1    a|aa|aaa    b|B    Id1
+row2    A    bb    Id3
+row3    AA    bb    Id4
     EOF
 
     TmpFile.with_file(content) do |filename|
-      index = TSV.index(filename, :target => "OtherID", :data_sep => /\s+/, :order => true, :persist => false)
+      index = TSV.index(filename, :target => "OtherID", :data_sep => /\s+/, :order => true, :persist => true, :data_persist => true)
       assert_equal "Id1", index['a']
       assert_equal "Id3", index['A']
       assert_equal "OtherID", index.fields.first

data/test/rbbt/util/test_filecache.rb

@@ -1,4 +1,5 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
+require 'rbbt-util'
 require 'rbbt/util/filecache'
 require 'test/unit'
 

data/test/rbbt/workflow/test_step.rb

@@ -41,7 +41,7 @@ class TestStep < Test::Unit::TestCase
       step2 = Step.new tmpfile + 'step2', task2, [], step1
 
       step1.clean
-      step2.run
+      step2.clean.run
       assert_equal "TEST2", Open.read(tmpfile + 'step2')
     end
   end

data/test/test_helper.rb

@@ -1,11 +1,12 @@
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'rbbt'
+
 require 'test/unit'
-require 'rbbt/util/log'
-require 'rbbt/util/tmpfile'
-require 'rbbt/resource/path'
 require 'fileutils'
+require 'rubygems'
+
+require 'rbbt'
+require 'rbbt/resource/path'
 
 class Test::Unit::TestCase
   include FileUtils

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.47
+  version: 5.5.48
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-21 00:00:00.000000000 Z
+date: 2013-11-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -232,7 +232,6 @@ files:
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
 - test/test_helper.rb
-- test/test_rbbt.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
@@ -291,5 +290,4 @@ test_files:
 - test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_R.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/test_rbbt.rb
 - test/test_helper.rb

data/test/test_rbbt.rb

@@ -1,10 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/test_helper')
-require 'rbbt'
-require 'rbbt/util/misc'
-require 'rbbt/util/open'
-
-class TestRbbt < Test::Unit::TestCase
-  def test_true
-    assert true
-  end
-end