rbbt-util 5.6.0 → 5.6.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: b772991027bae39d5d75e7d19fdfc628b2a78871
-  data.tar.gz: aed0bd56fbd0178bff6cd37b386390a392a5a7ec
+  metadata.gz: 3656ab04698a077becda559ac837570042688fa8
+  data.tar.gz: f54aa65f719933df04767b54e896c74adb805e34
 SHA512:
-  metadata.gz: 6aeb956836ee4d77b643249dc63c13ba6aed3aa9568b58173eb872c45e384d5202ea8e742c55e775187371f4e5b438198d57f56896e3daad9041158320692677
-  data.tar.gz: eab7947a295e70759b50bf6333c589f7c71aa535d5c5c26f0c848aacb5b9f723505799bb4baec4c16f30b5fe3f9a5ed8715f3f6326612b33b342823622428497
+  metadata.gz: 929e4be6771df3db4f8507a9af317cb9bd841107d4170ec2ff198f1e1ed2aca0762e5b32851b1653336afdae49dc2729b0143fd65938cedd11660db2a5d687fc
+  data.tar.gz: 63ce2e0a7e12c9e6c6204a5d79764e9691ff781ae68e27586b135c524710ce557ce89a958aff4b7c101aa3cfd67897fdcb0ec415b5b09f315dad8a27ce437199

data/lib/rbbt/tsv/accessor.rb

@@ -484,10 +484,8 @@ module TSV
 
     str = ""
 
-    str << "#: " << Misc.hash2string((ENTRIES - ["key_field", "fields"]).collect{|key| [key.to_sym, self.send(key)]}) << "\n" unless no_options
-    if fields
-      str << "#" << key_field << "\t" << fields * "\t" << "\n"
-    end
+    entry_hash = no_options ? {} : (ENTRIES - ["key_field", "fields"]).collect{|key| [key.to_sym, self.send(key)]}
+    str = TSV.header_lines(key_field, fields, entry_hash)
 
     with_unnamed do
       if keys.nil?

data/lib/rbbt/tsv/attach.rb

@@ -3,7 +3,11 @@ require 'rbbt/tsv/attach/util'
 module TSV
 
   # Merge columns from different rows of a file
-  def self.merge_row_fields(input, output, sep = "\t")
+  def self.merge_row_fields(input, output, options = {})
+    options = Misc.add_defaults options, :sep => "\t"
+    key_field, fields = Misc.process_options options, :key_field, :fields
+    sep = options[:sep]
+
     is = case
          when (String === input and not input.index("\n") and input.length < 250 and File.exists?(input))
            CMD.cmd("sort -k1,1 -t'#{sep}' #{ input } | grep -v '^#{sep}' ", :pipe => true)
@@ -12,16 +16,25 @@ module TSV
          else
            input
          end
+
+    if key_field.nil? or fields.nil?
+      parser = TSV::Parser.new(is, options.dup)
+      fields ||= parser.fields
+      key_field ||= parser.key_field
+      line = parser.first_line
+    else
+      line = is.gets
+    end
  
     current_key  = nil
     current_parts = []
 
     done = false
     Open.write(output) do |os|
+      os.puts TSV.header_lines(key_field, fields, options)
 
-      done = is.eof?
-      while not done
-        key, *parts = is.gets.sub("\n",'').split(sep, -1)
+      while line
+        key, *parts = line.sub("\n",'').split(sep, -1)
         current_key ||= key
         case
         when key.nil?
@@ -39,7 +52,7 @@ module TSV
           current_parts = parts
         end
 
-        done = is.eof?
+        line = is.gets
       end
 
       os.puts [current_key, current_parts].flatten * sep unless current_key.nil?
@@ -48,10 +61,14 @@ module TSV
   end
 
   # Merge two files with the same keys and different fields
-  def self.merge_different_fields(file1, file2, output, sep = "\t", monitor = false)
+  def self.merge_different_fields(file1, file2, output, options = {})
+    options = Misc.add_defaults options, :sep => "\t"
+    monitor, key_field, fields = Misc.process_options options, :monitor, :key_field, :fields
+    sep = options[:sep] || "\t"
+
     case
     when (String === file1 and not file1 =~ /\n/ and file1.length < 250 and File.exists?(file1))
-      size = CMD.cmd("wc -l '#{file1}'").read.to_f if monitor
+      size = CMD.cmd("wc -c '#{file1}'").read.to_f if monitor
       file1 = CMD.cmd("sort -k1,1 -t'#{sep}' #{ file1 } | grep -v '^#{sep}' ", :pipe => true)
     when (String === file1 or StringIO === file1)
       size = file1.length if monitor
@@ -80,19 +97,27 @@ module TSV
 
     key1 = key2 = nil
     while key1.nil?
-      while (line1 = file1.gets) =~ /#/; end
+      while (line1 = file1.gets) =~ /^#/
+        key_field1, *fields1 = line1.strip.sub('#','').split(sep)
+      end
       key1, *parts1 = line1.sub("\n",'').split(sep, -1)
       cols1 = parts1.length
     end
 
     while key2.nil?
-      while (line2 = file2.gets) =~ /#/; end
+      while (line2 = file2.gets) =~ /^#/
+        key_field2, *fields2 = line2.strip.sub('#','').split(sep)
+      end
       key2, *parts2 = line2.sub("\n",'').split(sep, -1)
       cols2 = parts2.length
     end
 
     progress_monitor = Progress::Bar.new(size, 0, 100, "Merging fields") if monitor
 
+    entry_hash = options
+    entry_hash.delete :sep if entry_hash[:sep] == "\t"
+    output.puts TSV.header_lines key_field1, fields1 + fields2, entry_hash if key_field1 and fields1 and fields2
+
     key = key1 < key2 ? key1 : key2
     parts = [""] * (cols1 + cols2)
     while not (done1 and done2)
@@ -189,7 +214,7 @@ module TSV
 
   def merge_different_fields(other, options = {})
     TmpFile.with_file do |output|
-      TSV.merge_different_fields(self, other, output, options[:sep] || "\t")
+      TSV.merge_different_fields(self, other, output, options)
       tsv = TSV.open output, options
       tsv.key_field = self.key_field unless self.key_field.nil?
       tsv.fields = self.fields + other.fields unless self.fields.nil? or other.fields.nil?

data/lib/rbbt/tsv/parser.rb

@@ -34,7 +34,7 @@ module TSV
 
       # Process fields line
 
-      if line and Misc.fixutf8(line) =~ /^#{@header_hash}/
+      while line and Misc.fixutf8(line) =~ /^#{@header_hash}/
         line.chomp!
         @fields = line.split(@sep)
         @key_field = @fields.shift

data/lib/rbbt/tsv/util.rb

@@ -1,6 +1,40 @@
 require 'rbbt/resource/path'
 module TSV
 
+  def self.reorder_stream(stream, positions, sep = "\t")
+    Misc.open_pipe do |sin|
+      line = stream.gets
+      while line =~ /^#\:/
+        sin.puts line
+        line = stream.gets
+      end
+      while line  =~ /^#/
+        if Hash === positions
+          new = (0..line.split(sep).length-1).to_a
+          positions.each do |k,v|
+            new[k] = v
+            new[v] = k
+          end
+          positions = new
+        end
+        sin.puts "#" + line.sub!(/^#/,'').strip.split(sep).values_at(*positions).compact * sep
+        line = stream.gets
+      end
+      while line
+        if Hash === positions
+          new = (0..line.split(sep).length-1).to_a
+          positions.each do |k,v|
+            new[k] = v
+            new[v] = k
+          end
+          positions = new
+        end
+        sin.puts line.strip.split(sep).values_at(*positions) * sep
+        line = stream.gets
+      end
+    end
+  end
+
   def self.field_match_counts(file, values, options = {})
     options = Misc.add_defaults options, :persist_prefix => "Field_Matches"
     persist_options = Misc.pull_keys options, :persist
@@ -52,6 +86,7 @@ module TSV
     when String === file
       Open.open(file, open_options)
     when file.respond_to?(:gets)
+      file.rewind if file.respond_to?(:rewind) and file.eof?
       file
     else
       raise "Cannot get stream from: #{file.inspect}"
@@ -76,6 +111,18 @@ module TSV
       Log.medium "Field #{ field } was not found. Options: (#{key_field}), #{fields * ", "}"
     end
   end
+  
+  def self.header_lines(key_field, fields, entry_hash = {})
+    sep = (Hash === entry_hash and entry_hash[:sep]) ? entry_hash[:sep] : "\t"
+
+    str = "" 
+    str << "#: " << Misc.hash2string(entry_hash) << "\n" if entry_hash and entry_hash.any?
+    if fields
+      str << "#" << key_field << sep << fields * sep << "\n"
+    end
+
+    str
+  end
 
   def identify_field(field)
     TSV.identify_field(key_field, fields, field)

data/lib/rbbt/util/filecache.rb

@@ -55,4 +55,36 @@ module FileCache
 
     FileUtils.rm path if File.exist? path
   end
+
+  def self.cache_online_elements(ids, pattern = nil, &block)
+    ids = [ids] unless Array === ids
+
+    result_files = {}
+    missing = []
+    ids.each do |id|
+      filename = pattern ? pattern.sub("{ID}", id.to_s) : id.to_s
+
+      if FileCache.found(filename)
+        result_files[id] = FileCache.path(filename)
+      else
+        missing << id
+      end
+    end
+
+    yield(missing).each do |id, content|
+      filename = pattern ? pattern.sub("{ID}", id.to_s) : id.to_s
+      path = FileCache.path(filename)
+      Open.write(path, content)
+      result_files[id] = content
+    end
+
+    missing.each do |id|
+      filename = pattern ? pattern.sub("{ID}", id.to_s) : id.to_s
+      result = yield id
+      File.open{|f| f.write(path = FileCache.path(filename)) }
+      result_files[id] = path
+    end
+
+    result_files
+  end
 end

data/lib/rbbt/util/log.rb

@@ -76,6 +76,10 @@ module Log
     log(message, ERROR, &block)
   end
 
+  def self.exception(e)
+    error(e.message)
+    error("BACKTRACE:\n" + e.backtrace * "\n") 
+  end
 
   case ENV['RBBT_LOG']
   when 'DEBUG' 

data/lib/rbbt/util/misc.rb

@@ -1318,6 +1318,7 @@ end
   # Divides the array into +num+ chunks of the same size by placing one
   # element in each chunk iteratively.
   def self.divide(array, num)
+    num = 1 if num == 0
     chunks = []
     num.to_i.times do chunks << [] end
     array.each_with_index{|e, i|
@@ -1341,6 +1342,23 @@ end
     chunks
   end
 
+  def self.open_pipe
+    sout, sin = IO.pipe
+    raise "No block given" unless block_given?
+    Thread.new{
+      begin
+        yield sin
+      rescue
+        Log.exception $!
+        raise $!
+      ensure
+        sin.close
+      end
+    }
+    sout
+  end
+
+
   def self.zip_fields(array)
     return [] if array.empty?
     array[0].zip(*array[1..-1])

data/lib/rbbt/util/simpleopt.rb

@@ -28,11 +28,21 @@ module SOPT
     @description ||= "Missing"
   end
 
-
   def self.shortcuts
     @shortcuts ||= []
   end
 
+  def self.delete_inputs(inputs)
+    inputs.each do |input|
+      input = input.to_s
+      self.shortcuts.delete self.input_shortcuts.delete(input)
+      self.inputs.delete input
+      self.input_types.delete input
+      self.input_defaults.delete input
+      self.input_descriptions.delete input
+    end
+  end
+
   def self.all
     @all ||= {}
   end

data/lib/rbbt/workflow.rb

@@ -28,7 +28,7 @@ module Workflow
   def self.load_workflow_file(filename)
     begin
       $LOAD_PATH.unshift(File.join(File.dirname(File.expand_path(filename)), 'lib'))
-      require filename
+      require File.expand_path(filename)
       Log.debug{"Workflow loaded from: #{ filename }"}
       return true
     rescue Exception
@@ -99,6 +99,12 @@ module Workflow
 
     # Load locally
 
+    if wf_name =~ /::\w+$/
+      clean_name = wf_name.sub(/::.*/,'')  
+      Log.info{"Looking for '#{wf_name}' in '#{clean_name}'"}
+      wf_name = clean_name
+    end
+
     Log.info{"Loading workflow #{wf_name}"}
     require_local_workflow(wf_name) or 
     require_local_workflow(Misc.snake_case(wf_name)) or 

data/lib/rbbt/workflow/accessor.rb

@@ -184,7 +184,18 @@ class Step
     end
   end
 
-
+  def provenance
+    provenance = {}
+    dependencies.each do |dep|
+      next unless dep.path.exists?
+      if File.exists? dep.info_file
+        provenance[dep.path] = dep.provenance if File.exists? dep.path
+      else
+        provenance[dep.path] = nil
+      end
+    end
+    {:inputs => info[:inputs], :provenance => provenance}
+  end
 end
 
 module Workflow
@@ -264,16 +275,15 @@ module Workflow
     [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_options}
   end
 
-
   def real_dependencies(task, jobname, inputs, dependencies)
     real_dependencies = []
     dependencies.each do |dependency|
-      real_dependencies << case
-      when Step === dependency
+      real_dependencies << case dependency
+      when Step
         dependency
-      when Symbol === dependency
+      when Symbol
         job(dependency, jobname, inputs)
-      when Proc === dependency
+      when Proc
         dependency.call jobname, inputs
       end
     end
@@ -303,7 +313,6 @@ module Workflow
     }
   end
 
-
   def id_for(path)
     if workdir.respond_to? :find
       workdir_find = workdir.find 
@@ -322,4 +331,5 @@ module Workflow
  
     Misc.path_relative_to(workdir_find, File.dirname(path)).sub(/([^\/]+)\/.*/,'\1')
   end
+
 end

data/lib/rbbt/workflow/step.rb

@@ -281,7 +281,11 @@ class Step
   end
 
   def recursive_clean
-    rec_dependencies.each{|step| step.clean }
+    rec_dependencies.each do |step| 
+      if File.exists?(step.info_file) 
+        step.clean 
+      end
+    end
     clean
   end
 

data/share/rbbt_commands/workflow/task

@@ -6,7 +6,7 @@ require 'rbbt/workflow/usage'
 
 YAML::ENGINE.yamler = 'syck' if defined? YAML::ENGINE and YAML::ENGINE.respond_to? :yamler
 
-def usage(workflow = nil, task = nil, error = nil)
+def usage(workflow = nil, task = nil, error = nil, backtrace = nil)
   puts SOPT.doc
   puts "## WORKFLOW"
   puts
@@ -27,7 +27,8 @@ def usage(workflow = nil, task = nil, error = nil)
     workflow.doc(task)
     if error
         puts
-        puts "Error: " << error 
+        puts Term::ANSIColor.red("Error: ") << error
+        puts Term::ANSIColor.red("Backtrace: ") << backtrace * "\n"
     end
   end
 
@@ -112,8 +113,10 @@ options = SOPT.get <<EOF
 -rcl--recursive_clean Clean the last step and its dependencies to recompute the job completely:
 -jn--jobname* Job name to use. The name 'Default' is used by default:
 -pn--printname Print the name of the job and exit without starting it:
+-jf--job_file* Output one of the job produced files:
 -wd--workdir* Change the working directory of the workflow:
 -O--output* Save job result into file:
+--provenance Report the jobs provenance:
 --fork Run job asyncronously:
 EOF
 
@@ -178,13 +181,13 @@ workflow.workdir = Path.setup(File.expand_path(options.delete(:workdir))) if opt
 job = workflow.job(task.name, name, job_options)
 
 # clean job
-if clean and job.done? != false
+if clean 
   job.clean 
   sleep 1
   job = workflow.job(task.name, name, job_options)
 end
 
-if recursive_clean and job.done?
+if recursive_clean 
   job.recursive_clean 
   sleep 1
   job = workflow.job(task.name, name, job_options)
@@ -192,46 +195,59 @@ end
 
 # run
 begin
-if do_exec
-  res = job.exec
-  case
-  when Array === res
-    puts res * "\n"
-  when TSV === res
-    puts res
-  when Hash === res
-    puts res.to_yaml
+  if do_exec
+    res = job.exec
+    case
+    when Array === res
+      puts res * "\n"
+    when TSV === res
+      puts res
+    when Hash === res
+      puts res.to_yaml
+    else
+      puts res
+    end
+    exit 0
+  end
+
+  if do_fork
+    job.fork
+    while not job.done?
+      message = job.messages ? job.messages.last : "no message"
+      Log.debug "#{job.status}: #{message}"
+      sleep 2
+    end
+    raise job.messages.last if job.error?
+    res = job.load
   else
-    puts res
+    res = job.run(true)
   end
-  exit 0
-end
 
-if do_fork
-  job.fork
-  while not job.done?
-    message = job.messages ? job.messages.last : "no message"
-    Log.debug "#{job.status}: #{message}"
-    sleep 2
+
+  if options.delete(:provenance)
+    require 'pp'
+    pp job.provenance
+    exit 0
   end
-  raise job.messages.last if job.error?
-  res = job.load
-else
-  res = job.run(true)
-end
 
-if options.delete(:printname)
-  puts job.name
-  exit 0
-else
-  Log.low "Job name: #{job.name}" 
-end
+  if options.delete(:printname)
+    puts job.name
+    exit 0
+  else
+    Log.low "Job name: #{job.name}" 
+  end
 rescue ParameterException
-    usage(workflow, task, $!.message)
+  SOPT.delete_inputs(workflow.rec_inputs(task.name))
+  usage(workflow, task, $!.message, $!.backtrace)
 end
 
 out = options.include?(:output) ? File.open(options[:output], 'wb') : STDOUT
 
+if job_file = options.delete(:job_file)
+  out.puts res.file(job_file).read
+  exit 0
+end
+
 if Step === res
   out.puts Open.read(res.path) if File.exists? res.path
 else

data/test/rbbt/association/test_index.rb

@@ -29,7 +29,7 @@ class TestAssociationIndex < Test::Unit::TestCase
     genes = tp53.pina_interactors.ensembl
     genes << tp53
 
-    Misc.benchmark(10) do
+    Misc.benchmark(100) do
       index.subset_entities("Ensembl Gene ID" => genes).length
     end
 

data/test/rbbt/test_fix_width_table.rb

@@ -76,8 +76,8 @@ g 25
 
   def test_range
     data =<<-EOF
+##012345678901234567890
 #ID:Range
-#:012345678901234567890
 a:   ______
 b: ______
 c:    _______

data/test/rbbt/test_knowledge_base.rb

@@ -55,53 +55,12 @@ class TestKnowledgeBase < Test::Unit::TestCase
     assert @kb.all_databases.include? "pina"
   end
 
-  def test_items
-    tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013").ensembl
-    kb = KnowledgeBase.new Rbbt.tmp.test.kb2, "Hsa/jan2013"
-    kb.index('g2t', Organism.gene_transcripts("Hsa/jan2013"), :target => "Ensembl Transcript ID")
-  end
-
-  def __test_subset
+  def test_subset
     gene = "TP53"
     found = Genomics.knowledge_base.identify :pina, gene
-    p53_interactors = Misc.profile{ Genomics.knowledge_base.children(:pina, found).target_entity }
+    p53_interactors = Genomics.knowledge_base.children(:pina, found).target_entity 
 
-
-    Misc.profile do
-      puts Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).length
-    end
-    ddd 2
-    #assert Genomics.knowledge_base.subset(:pina,{"Gene" => p53_interactors}).target_entities.name.include? "MDM2"
-  end
-
-  def test_benchmark
-    tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013").ensembl
-    kb = KnowledgeBase.new Rbbt.tmp.test.kb2
-    kb.namespace = "Hsa/jan2013"
-
-      require 'rbbt/sources/COSMIC'
-      require 'rbbt/entity/genomic_mutation'
-      mutations = tp53.COSMIC_mutations
-      Misc.benchmark(10) do 
-        name = "mutations"
-        kb.add_index name, "Ensembl Gene ID", "Genomic Mutation", "Change"
-        kb.write name do
-          mutations.each do |gm|
-            kb.add name, tp53, gm, gm.base
-          end
-        end
-      end
-  end
-
-  def test_benchmark2
-    tp53 = Gene.setup("TP53", "Associated Gene Name", "Hsa/jan2013").ensembl
-    kb = KnowledgeBase.new Rbbt.tmp.test.kb2, "Hsa/jan2013"
-    kb.index('g2t', Organism.gene_transcripts("Hsa/jan2013"), :target => "Ensembl Transcript ID")
-    l = nil
-    Misc.benchmark(1000) do
-     l = tp53.transcripts.length
-    end
-    assert l > 0
+    assert Genomics.knowledge_base.subset(:pina, {"Gene" => p53_interactors}).target_entity.name.include? "MDM2"
   end
 
   def test_syndication

data/test/rbbt/tsv/test_accessor.rb

@@ -57,6 +57,7 @@ row2    A    B    Id3
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/)
+      puts tsv.to_s
       assert tsv.to_s =~ /row1\ta|aa|aaa/
       assert tsv.to_s =~ /:type=:double/
     end

data/test/rbbt/tsv/test_attach.rb

@@ -87,7 +87,6 @@ B    Id3
 
     tsv1.attach_source_key tsv2, "ValueB"
 
-
     assert_equal %w(ValueA ValueB OtherID), tsv1.fields
     assert_equal "Id1", tsv1["row1"]["OtherID"]
   end
@@ -290,7 +289,7 @@ row6 dd dd ee
     EOF
 
     TmpFile.with_file do |f|
-      TSV.merge_different_fields(StringIO.new(file1), StringIO.new(file2), f, " ")
+      TSV.merge_different_fields(StringIO.new(file1), StringIO.new(file2), f, :sep => " ")
       assert_equal result, Open.read(f)
     end
   end
@@ -327,6 +326,7 @@ row6 dd dd ee
 
   def test_merge_different_rows_split_lines
     file1 =<<-EOF
+#ID,letterA,letterB,letterC
 row6,dd,dd,ee
 row1,a,b,c
 row1,aa,bb,cc
@@ -334,6 +334,7 @@ row2,A,B,C
 row3,1,2,3
    EOF
     file2 =<<-EOF
+#ID,letterD,letterE
 row20,rr,rr
 row1,d,e
 row2,D,E
@@ -342,6 +343,8 @@ row4,x,y
 
     # Might be slightly different ...
     result1 =<<-EOF
+#: :sep=,
+#ID,letterA,letterB,letterC,letterD,letterE
 row1,aa|a,bb|b,cc|c,d,e
 row2,A,B,C,D,E
 row20,,,,rr,rr
@@ -350,6 +353,8 @@ row4,,,,x,y
 row6,dd,dd,ee,,
     EOF
     result2 =<<-EOF
+#: :sep=,
+#ID,letterA,letterB,letterC,letterD,letterE
 row1,a|aa,b|bb,c|cc,d,e
 row2,A,B,C,D,E
 row20,,,,rr,rr
@@ -359,8 +364,7 @@ row6,dd,dd,ee,,
     EOF
 
     TmpFile.with_file do |f|
-      TSV.merge_different_fields StringIO.new(file1), StringIO.new(file2), f, ','
-
+      TSV.merge_different_fields StringIO.new(file1), StringIO.new(file2), f, :sep => ','
       # ... so check for either
       assert(Open.read(f) == result1 || Open.read(f) == result2)
     end
@@ -403,6 +407,7 @@ row6,dd,dd,ee,,
 
   def test_merge_rows
     file1 =<<-EOF
+#ID,letterA,letterB,letterC
 row1,a,b,c
 row1,aa,bb,cc
 row2,A,B,C
@@ -410,8 +415,9 @@ row3,1,2,3
     EOF
     TmpFile.with_file(file1) do |input|
       TmpFile.with_file() do |output|
-        TSV.merge_row_fields Open.open(input), output
-        assert Open.read(output) =~ /a|aa/
+        TSV.merge_row_fields Open.open(input), output, :sep => ','
+        assert Open.read(output) =~ /^#ID,letterA,letterB,letterC$/
+        assert Open.read(output).index "a|aa"
       end
     end
 

data/test/rbbt/util/test_misc.rb

@@ -6,11 +6,11 @@ require 'rbbt/entity'
 
 class TestMisc < Test::Unit::TestCase
 
-  def _test_humanize
+  def test_humanize
     assert_equal "mutation_enrichment", Misc.humanize("MutationEnrichment")
   end
 
-  def _test_fixutf8
+  def test_fixutf8
     string = "abc\xffdef"
     string = string.force_encoding("UTF-8") if string.respond_to? :force_encoding
     assert(! string.valid_encoding?) if string.respond_to? :valid_encoding?
@@ -19,37 +19,37 @@ class TestMisc < Test::Unit::TestCase
     assert( Misc.fixutf8(string).valid_encoding) if string.respond_to? :valid_encoding
   end
 
-  def _test_colors_for
+  def test_colors_for
     colors, used = Misc.colors_for([1,2,2,1,2,1,2,2,3,3,2,3,2])
     assert_equal Misc::COLOR_LIST[1], used[2]
   end
 
-  def _test_total_length
+  def test_total_length
     ranges = [(0..100), (50..150), (120..160)]
     ranges = [(0..100), (50..150), (120..160), (51..70)]
     assert_equal 161, Misc.total_length(ranges)
   end
 
-  def _test_id_filename?
+  def test_id_filename?
     TmpFile.with_file("") do |file|
       assert Misc.is_filename?(file)
       assert ! Misc.is_filename?("TEST STRING")
     end
   end
 
-  def _test_merge_sorted_arrays
+  def test_merge_sorted_arrays
     assert_equal [1,2,3,4], Misc.merge_sorted_arrays([1,3], [2,4])
   end
 
-  def _test_intersect_sorted_arrays
+  def test_intersect_sorted_arrays
     assert_equal [2,4], Misc.intersect_sorted_arrays([1,2,3,4], [2,4])
   end
 
-  def _test_sorted_array_matches
+  def test_sorted_array_matches
     assert_equal [1,3], Misc.sorted_array_hits(%w(a b c d e), %w(b d))
   end
 
-  def _test_binary_include?
+  def test_binary_include?
     a = %w(a b c d e).sort
     assert Misc.binary_include?(a, "a")
     assert(!Misc.binary_include?(a, "z"))
@@ -58,24 +58,24 @@ class TestMisc < Test::Unit::TestCase
     assert(Misc.binary_include?(a, "d"))
   end
 
-  def _test_process_to_hash
+  def test_process_to_hash
     list = [1,2,3,4]
     assert_equal 4, Misc.process_to_hash(list){|l| l.collect{|e| e * 2}}[2]
   end
 
-#  def _test_pdf2text_example
+#  def test_pdf2text_example
 #    assert PDF2Text.pdf2text(datafile_test('example.pdf')).read =~ /An Example Paper/i
 #  end
 #
-#  def _test_pdf2text_EPAR
+#  def test_pdf2text_EPAR
 #    assert PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Scientific_Discussion/human/000402/WC500033103.pdf").read =~ /Tamiflu/i
 #  end
 #
-#  def _test_pdf2text_wrong
+#  def test_pdf2text_wrong
 #    assert_raise CMD::CMDError do PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB#").read end
 #  end
 
-  def _test_string2hash
+  def test_string2hash
     assert(Misc.string2hash("--user-agent=firefox").include? "--user-agent")
     assert_equal(true, Misc.string2hash(":true")[:true])
     assert_equal(true, Misc.string2hash("true")["true"])
@@ -93,17 +93,17 @@ class TestMisc < Test::Unit::TestCase
     end
   end
   
-  def _test_named_array
+  def test_named_array
     a = NamedArray.setup([1,2,3,4], %w(a b c d))
     assert_equal(1, a['a'])
   end
 
-#  def _test_path_relative_to
+#  def test_path_relative_to
 #    assert_equal "test/foo", Misc.path_relative_to('test/test/foo', 'test')
 #  end
 
-#  def _test_chunk
-#    _test =<<-EOF
+#  def test_chunk
+#    test =<<-EOF
 #This is an example file. Entries are separated by Entry
 #-- Entry
 #1
@@ -118,7 +118,7 @@ class TestMisc < Test::Unit::TestCase
 #    assert_equal "1\n2\n3", Misc.chunk(test, /^-- Entry/).first.strip
 #  end
 
-  def _test_hash2string
+  def test_hash2string
     hash = {}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
 
@@ -136,14 +136,14 @@ class TestMisc < Test::Unit::TestCase
  
   end
 
-  def _test_merge
+  def test_merge
     a = [[1],[2]]
     a = NamedArray.setup a, %w(1 2)
     a.merge [3,4]
     assert_equal [1,3], a[0]
   end
 
-  def _test_indiferent_hash
+  def test_indiferent_hash
     a = {:a => 1, "b" => 2}
     a.extend IndiferentHash
 
@@ -153,7 +153,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal 2, a[:b]
   end
 
-  def _test_lockfile
+  def test_lockfile
 
     TmpFile.with_file do |tmpfile|
       pids = []
@@ -177,7 +177,7 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
-  def _test_positions2hash
+  def test_positions2hash
     inputs = Misc.positional2hash([:one, :two, :three], 1, :two => 2, :four => 4)
     assert_equal 1, inputs[:one]
     assert_equal 2, inputs[:two]
@@ -185,7 +185,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal nil, inputs[:four]
   end
 
-  def _test_mean
+  def test_mean
     assert_equal 2, Misc.mean([1,2,3])
     assert_equal 3, Misc.mean([1,2,3,4,5])
   end
@@ -194,32 +194,32 @@ class TestMisc < Test::Unit::TestCase
     assert_equal Math.sqrt(2), Misc.sd([1,3])
   end
 
-  def _test_align_small
+  def test_align_small
     reference = "AABCDEBD"
     sequence  = "ABCD"
     assert_equal '-ABCD---', Misc.fast_align(reference, sequence).last
   end
 
-  def _test_align_real
+  def test_align_real
     reference = "SGNECNKAIDGNKDTFWHTFYGANGDPKPPPHTYTIDMKTTQNVNGLSMLPRQDGNQNGWIGRHEVYLSSDGTNW"
     sequence  = "TYTIDMKTTQNVNGLSML"
     assert_equal "--------------------------------TYTIDMKTTQNVNGLSML-------------------------", Misc.fast_align(reference, sequence).last
   end
 
-  def _test_divide
+  def test_divide
     assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end
 
-  def _test_ordered_divide
+  def test_ordered_divide
     assert_equal 5, Misc.ordered_divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end
 
-  def _test_collapse_ranges
+  def test_collapse_ranges
     ranges = [(0..100), (50..150), (51..61),(200..250), (300..324),(320..350)]
     assert_equal [(0..150),(200..250), (300..350)], Misc.collapse_ranges(ranges)
   end
 
-  def _test_humanize
+  def test_humanize
     str1 = "test_string"
     str2 = "TEST_string"
     str3 = "test"
@@ -229,18 +229,18 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "Test", Misc.humanize(str3)
   end
 
-  def _test_snake_case
+  def test_snake_case
     str1 = "ACRONIMTest"
     str2 = "ACRONIM_test"
     assert_equal "ACRONIM_test", Misc.snake_case(str1)
     assert_equal "ACRONIM_test", Misc.snake_case(str2)
   end
 
-  def _test_correct_vcf_mutations
+  def test_correct_vcf_mutations
     assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
   end
 
-  def _test_fingerprint
+  def test_fingerprint
     puts Misc.fingerprint({:a => 1})
   end
 
@@ -253,4 +253,26 @@ class TestMisc < Test::Unit::TestCase
       end
     end
   end
+
+  def test_pipe
+    t = 5
+    stream = Misc.open_pipe do |sin|
+      t.times do |i|
+        puts "Calculating line #{ i }"
+        sleep 0.5
+        sin.puts "LINE #{ i }"
+      end
+    end
+
+    time = Time.now
+    lines = []
+    while line = stream.gets
+      lines << line.strip
+    end
+    time_spent = Time.new - time
+
+    assert time_spent >= t * 0.5
+    assert time_spent <= (t+1) * 0.5
+    assert_equal (0..t-1).to_a.collect{|i| "LINE #{ i }"}, lines
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.0
+  version: 5.6.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-10 00:00:00.000000000 Z
+date: 2014-02-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake