rbbt-util 5.43.0 → 5.44.1

data/test/rbbt/util/misc/test_multipart_payload.rb

@@ -1,202 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/misc/multipart_payload'
-
-class TestMultipartPayload < Test::Unit::TestCase
-
-  URL='http://localhost:2887/Echo'
-  def _test_post_data_stream
-    content =<<-EOF
-Line 1
-Line 2
-Line 3
-END
-    EOF
-    mutipart =<<-EOF
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input1"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input1<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input2"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input2<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="stream_input"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Line 1
-Line 2
-Line 3
-END
-<>
---Rbbt_Param_Stream--<>
-<>
-    EOF
-    TmpFile.with_file(content) do |tmpfile|
-      inputs = {}
-      stream_input = :stream_input
-      inputs[:input1] = "Input1"
-      inputs[:input2] = "Input2"
-      inputs[:stream_input] = Open.open(tmpfile)
-
-      post_data_stream = RbbtMutiplartPayload.post_data_stream(inputs, stream_input, inputs[stream_input])
-      assert_equal mutipart, post_data_stream.read.gsub(/\r\n/,"<>\n")
-    end
-  end
-
-  def _test_issue
-    content =<<-EOF
-Line 1
-Line 2
-Line 3
-END
-    EOF
-    mutipart =<<-EOF
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input1"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input1<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input2"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input2<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="stream_input"; filename="FILENAME"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Line 1
-Line 2
-Line 3
-END
-<>
---Rbbt_Param_Stream--<>
-<>
-DONE_PARAM_STREAM
-    EOF
-    inputs = {}
-    #mutipart.gsub!('<>',"\r")
-    stream_input = :stream_input
-    inputs[:input1] = "Input1"
-    inputs[:input2] = "Input2"
-    num = 50
-    cpus = 1
-    TmpFile.with_file(content) do |tmpfile|
-      inputs  = inputs.dup
-      inputs[:stream_input] = File.open(tmpfile)
-
-     io = RbbtMutiplartPayload.issue(URL, inputs, stream_input)
-      assert_equal mutipart.sub("FILENAME", tmpfile).force_encoding("ASCII"), io.read.gsub(/\r\n/,"<>\n") 
-    end
-  end
-
-  def _test_issue_multiple
-    content =<<-EOF
-Line 1
-Line 2
-Line 3
-END
-    EOF
-    mutipart =<<-EOF
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input1"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input1<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input2"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input2<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="stream_input"; filename="FILENAME"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Line 1
-Line 2
-Line 3
-END
-<>
---Rbbt_Param_Stream--<>
-<>
-DONE_PARAM_STREAM
-    EOF
-    inputs = {}
-    stream_input = :stream_input
-    inputs[:input1] = "Input1"
-    inputs[:input2] = "Input2"
-    num = 100
-    cpus = 10
-    Misc.bootstrap((0..num-1).to_a, cpus) do  |n|
-      TmpFile.with_file(content) do |tmpfile|
-        inputs  = inputs.dup
-        inputs[:stream_input] = File.open(tmpfile)
-
-        io = RbbtMutiplartPayload.issue(URL, inputs, stream_input)
-        str = io.read
-        assert_equal mutipart.sub("FILENAME", tmpfile).force_encoding("ASCII"), str.gsub(/\r\n/,"<>\n") 
-      end
-    end
-  end
-
-  def _test_raw
-    mutipart =<<-EOF
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input1"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input1<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="input2"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Input2<>
---Rbbt_Param_Stream<>
-Content-Disposition: form-data; name="stream_input"; filename="FILENAME"<>
-Content-Transfer-Encoding: binary<>
-Content-Type: text/plain<>
-<>
-Line 1
-Line 2
-Line 3
-END
-<>
---Rbbt_Param_Stream--<>
-<>
-    EOF
-    mutipart.gsub!('<>',"\r")
-    inputs = {}
-    stream_input = :stream_input
-    inputs[:input1] = "Input1"
-    inputs[:input2] = "Input2"
-    num = 50
-    cpus = 1
-
-    Misc.bootstrap((0..num-1).to_a, cpus) do  |n|
-      puts mutipart
-      TmpFile.with_file(mutipart, false) do |tmpfile|
-        inputs  = inputs.dup
-        inputs[:stream_input] = File.open(tmpfile)
-
-        puts "wget '#{URL}' --post-file #{ tmpfile } -O -"
-        io = CMD.cmd("wget '#{URL}' --post-file #{ tmpfile } -O -", :pipe => true)
-        assert_equal mutipart, io.read
-      end
-    end
-  end
-end
-

data/test/rbbt/util/misc/test_omics.rb

@@ -1,116 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../../test_helper')
-require 'test/unit'
-require 'rbbt/util/misc/omics'
-
-class TestMiscOmics < Test::Unit::TestCase
-
-  def test_translate_dna_mutation_hgvs2rbbt
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.395G>A"), "A"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-124C>T"), "T"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.639+6T>A"), "A"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.3386-2A>G"), "G"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.4090_4091insT"), "+T"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.533_534insGGGG"), "+GGGG"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.4249_4249delC"), "-"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.464-2_465delAGTG"), "----"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.209+1delGTAA"), "----"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.371_397del27"), "---------------------------"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1359+2_1359+11delTTAGAAGAGC"), "----------"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.ins?"), "?(c.ins?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?ins?"), "?(c.?_?ins?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.184_185ins?"), "?(c.184_185ins?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?ins57"), "+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?insCT"), "+CT"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?_?del?"), "?(c.?_?del?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.?"), "?(c.?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(312)?"), "?(c.(312)?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(1669_1671)>?"), "?"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1050-?"), "?(c.1050-?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(1347_1540)?"), "?(c.(1347_1540)?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-?_850+?del"), "?(c.1-?_850+?del)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.2289_?del(7236)"), "?(c.2289_?del(7236))"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.(3916_3927)del?"), "?(c.(3916_3927)del?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1705_?del?"), "?(c.1705_?del?)"
-    assert_equal Misc.translate_dna_mutation_hgvs2rbbt("c.1-?_421+?del"), "?(c.1-?_421+?del)"
-  end
-
-  def test_translate_prot_mutation_hgvs2rbbt
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.Arg2459Gly"), "R2459G"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E255K"), "E255K"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E279Z"), "E279Z"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.R132?"), "R132?"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.*757?"), "*757?"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.A2216>?"), "A2216Indel"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.M552_W557>Z"), "M552Indel"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.T1151_L1152insT"), "T1151Indel"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.N771_P772ins?"), "N771Indel"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.T310_?insKAAQRGA"), "T310Indel"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.D579del"), "D579Indel"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.E746_A750delELREA"), "E746Indel"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.P14fs*?"), "P14Frameshift"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.*588fs?"), "*588Frameshift"
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs*(46_47)"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(A443)fs*?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(574_1542)fs*?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.fs*?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?fs*?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(P1249)fs*?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.WQQSYLD25?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(449_514)?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.0?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?_?ins?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?_?insXXXX"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.(A775)ins?"), nil
-    assert_equal Misc.translate_prot_mutation_hgvs2rbbt("p.?del"), nil
-  end
-
-  def test_index_BED
-    text= ""
-
-    %w(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y MT).each do |chr|
-      %w(1 2 3 4 5 6 7 8).each do |i|
-        start = i.to_i * 100
-        eend = start + 50
-        id = [chr, i] * ":"
-        text << [chr, start.to_s, eend.to_s, id] * "\t" + "\n"
-      end
-    end
-
-    io = Misc.open_pipe do |sin|
-      sin.write text
-    end
-
-    TmpFile.with_file do |dir|
-      index = Misc.index_BED(io, dir)
-      assert_equal ["1:1"], index["1:120:130"]
-      index = Misc.index_BED(io, dir)
-      assert_equal ["2:2"], index["2:220:230"]
-    end
-  end
-
-  def test_sort_genomic_locations
-    mutations =<<-EOF.split("\n").shuffle
-1:100:A
-1:20:A
-1:300:A
-2:100:A
-2:20:A
-2:300:A
-10:100:A
-10:20:A
-10:300:A
-    EOF
-    sorted =  Misc.sort_mutation_stream(StringIO.new(mutations * "\n")).read.split("\n")
-    strict_sorted = Misc.sort_mutation_stream_strict(StringIO.new(mutations * "\n")).read.split("\n")
-
-    assert sorted.index("1:20:A") < sorted.index("1:100:A")
-    assert sorted.index("1:300:A") < sorted.index("10:300:A")
-    assert sorted.index("10:300:A") < sorted.index("2:300:A")
-    assert strict_sorted.index("1:20:A") < strict_sorted.index("1:100:A")
-    assert strict_sorted.index("1:300:A") < strict_sorted.index("10:300:A")
-    assert strict_sorted.index("2:300:A") < strict_sorted.index("10:300:A")
-  end
-end

data/test/rbbt/util/misc/test_pipes.rb

@@ -1,343 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../../test_helper')
-require 'test/unit'
-require 'rbbt/tsv'
-require 'rbbt/util/misc'
-
-class TestMiscPipes < Test::Unit::TestCase
-
-  def test_collapse_stream
-    text=<<-EOF
-row1 A B C
-row1 a b c
-row2 AA BB CC
-row2 aa bb cc
-    EOF
-
-    s = StringIO.new text
-    tsv = TSV.open Misc.collapse_stream(s,nil, " "), :sep => " " 
-    assert_equal ["A", "a"], tsv["row1"][0]
-    assert_equal ["BB", "bb"], tsv["row2"][1]
-  end
-
-  def test_collapse_sum
-    text=<<-EOF
-row1 12
-row1 4
-row2 10
-row2 6
-    EOF
-
-    s = StringIO.new text
-    stream = Misc.collapse_stream(s,nil, " ") do |parts|
-      next nil if parts.empty?
-      parts.first.split("|").collect{|p| p.to_f}.inject(0){|acc,e| acc += e}.to_s
-    end
-    tsv = TSV.open  stream, :sep => " " 
-    ppp tsv.to_s
-  end
-
-  def test_collapse_stream_gap
-    text=<<-EOF
-row2 AA BB 
-row2 aa bb cc
-    EOF
-
-    s = StringIO.new text
-    assert Misc.collapse_stream(s, nil, " ").read =~  /\|cc$/
-    
-    text=<<-EOF
-row2 aa bb cc
-row2 AA BB 
-    EOF
-
-    s = StringIO.new text
-    assert Misc.collapse_stream(s, nil, " ").read =~  /cc\|$/
-
-    text=<<-EOF
-row2 AA BB
-row2 aa bb cc
-    EOF
-
-    s = StringIO.new text
-    assert Misc.collapse_stream(s, nil, " ").read =~  /\|cc$/
-
-  end
-
-
-  def test_paste_stream
-    text1=<<-EOF
-row1 A B C
-row2 AA BB CC
-row3 AAA BBB CCC
-    EOF
-
-    text2=<<-EOF
-row1 a b
-row2 aa bb
-    EOF
-
-    text3=<<-EOF
-row1 c
-row2 cc
-row3 ccc
-    EOF
-
-    s1 = StringIO.new text1
-    s2 = StringIO.new text2
-    s3 = StringIO.new text3
-    tsv = TSV.open Misc.paste_streams([s1,s2,s3], nil, " "), :sep => " ", :type => :list
-    assert_equal ["A", "B", "C", "a", "b", "c"], tsv["row1"]
-    assert_equal ["AA", "BB", "CC", "aa", "bb", "cc"], tsv["row2"]
-    assert_equal ["AAA", "BBB", "CCC", "", "", "ccc"], tsv["row3"]
-  end
-
-  def test_sort_stream
-    text =<<-EOF
-##
-##
-##
-#Row LabelA LabelB LabelC
-row2 AA BB CC
-row3 AAA BBB CCC
-row1 A B C
-    EOF
-    s = StringIO.new text
-    sorted = Misc.sort_stream(s)
-    assert_equal %w(## ## ## #Row row2 row3 row1), text.split("\n").collect{|l| l.split(" ").first}
-    assert_equal %w(## ## ## #Row row1 row2 row3), sorted.read.split("\n").collect{|l| l.split(" ").first}
-  end
-
-  def test_sort_long_stream
-    text =<<-EOF
-##
-##
-##
-#Row LabelA LabelB LabelC
-row2 AA BB CC
-row3 AAA BBB CCC
-row1 A B C
-    EOF
-
-    s = StringIO.new text + (text.split("\n")[-3..-1] * "\n" + "\n") * 10000
-    sorted = Misc.sort_stream(s)
-    assert_equal %w(## ## ## #Row row2 row3 row1), text.split("\n").collect{|l| l.split(" ").first}
-    assert_equal %w(## ## ## #Row row1 row2 row3), sorted.read.split("\n").collect{|l| l.split(" ").first}
-  end
-
-  def test_sort_stream2
-    text =<<-EOF
-##
-##
-##
-#Row LabelA LabelB LabelC
-row2 AA BB CC
-row3 AAA BBB CCC
-row1 A B C
-    EOF
-    s = StringIO.new text
-    sorted = Misc.sort_stream(Misc.sort_stream(s))
-    assert_equal %w(## ## ## #Row row2 row3 row1), text.split("\n").collect{|l| l.split(" ").first}
-    assert_equal %w(## ## ## #Row row1 row2 row3), sorted.read.split("\n").collect{|l| l.split(" ").first}
-  end
-
-  def test_dup_stream
-    text =<<-EOF
-#: :sep=" "
-#Row LabelA LabelB LabelC
-row2 AA BB CC
-row3 AAA BBB CCC
-row1 A B C
-    EOF
-
-    text = text * 10000
-    TmpFile.with_file(text) do |tmp|
-      io = Open.open(tmp)
-      dup = Misc.dup_stream(io)
-      new_text = StringIO.new ""
-      Misc.consume_stream dup, true, new_text
-      Misc.consume_stream io, false
-      new_text.rewind
-      assert_equal text, new_text.read
-    end
-
-
-    TmpFile.with_file(text) do |tmp|
-      io = Open.open(tmp)
-      dup = Misc.dup_stream(io)
-      Misc.consume_stream dup, true
-      assert_equal text, io.read
-    end
-  end
-
-  def test_dup_stream_multiple
-    text =<<-EOF
-row2 AA BB CC
-row3 AAA BBB CCC
-row1 A B C
-    EOF
-
-    text = text * 10000
-    num = 5
-    str_io = StringIO.new
-    strs = []
-    num.times{ strs << StringIO.new }
-    TmpFile.with_file(text) do |tmp|
-      io = Open.open(tmp)
-      copies = Misc.dup_stream_multiple(io, num)
-
-
-      copies.each_with_index do |cio,i|
-        cio.add_callback do 
-          str = strs[i] 
-          str.rewind
-          assert_equal text, str.read
-        end
-        Misc.consume_stream cio, true, strs[i], false
-      end
-
-
-      Misc.consume_stream io, false, str_io, false
-      str_io.rewind
-      assert_equal text, str_io.read
-
-    end
-  end
-
-  def test_remove_lines
-    text1 =<<-EOF
-line1
-line2
-line3
-line4
-    EOF
-    text2 =<<-EOF
-line3
-line1
-    EOF
-
-    TmpFile.with_file(text1) do |file1|
-      TmpFile.with_file(text2) do |file2|
-        assert ! Misc.remove_lines(file1, file2, true).read.split("\n").include?("line1")
-        assert Misc.remove_lines(file1, file2, true).read.split("\n").include?("line2")
-      end
-    end
-  end
-
-
-
-  def test_select_lines
-    text1 =<<-EOF
-line1
-line2
-line3
-line4
-    EOF
-    text2 =<<-EOF
-line3
-line1
-line5
-    EOF
-
-    TmpFile.with_file(text1) do |file1|
-      TmpFile.with_file(text2) do |file2|
-        assert Misc.select_lines(file1, file2, true).read.split("\n").include?("line1")
-        assert ! Misc.select_lines(file1, file2, true).read.split("\n").include?("line2")
-      end
-    end
-  end
-
-  def test_consume_into_string_io
-    text =<<-EOF
-line1
-line2
-line3
-line4
-    EOF
-
-    TmpFile.with_file(text) do |file|
-      out = StringIO.new
-      io = Open.open(file)
-      Misc.consume_stream(io, false, out, false)
-      out.rewind
-      assert_equal text, out.read
-    end
-  end
-
-  def test_monitor
-    text =<<-EOF
-line1
-line2
-line3
-line4
-    EOF
-
-    TmpFile.with_file(text) do |file|
-      io = Open.open(file)
-      lines = Set.new
-      io2 = Misc.line_monitor_stream io do |line|
-        lines << line
-      end
-      Misc.consume_stream(io2, false)
-      assert_equal text, lines.to_a * ""
-    end
-  end
-
-  def test_sort
-    assert_raise RbbtException do
-      io = Misc.open_pipe do |sin|
-        sin.puts "#START"
-        20.times do
-          sin.puts rand(1000).to_s
-          sleep 0.1
-        end
-        raise RbbtException
-      end
-
-      sio = Misc.sort_stream(io)
-      begin
-        Misc.consume_stream(sio, false, STDOUT)
-      rescue
-        raise $!
-      end
-    end
-  end
-
-  def test_gz_pipe
-    text =<<-EOF
-line1
-line2
-line3
-line4
-    EOF
-
-    TmpFile.with_file nil, :extension => 'txt.gz' do |file|
-      sout = Misc.open_gz_pipe do |sin|
-        text.split("\n").each do |line|
-          sin.puts line
-        end
-      end
-
-      Open.mkdir File.basename(file)
-      thr1 = Misc.consume_stream(sout, true, file)
-      thr1.join
-      assert Open.gzip?(file)
-      assert_equal text, Open.read(file)
-    end
-  end
-
-  def test_open_pipe_error
-    sout = Misc.open_pipe do |sin|
-      10.times do |i|
-        sin.puts "line #{i}"
-      end
-      raise
-    end
-
-    TmpFile.with_file do |tmp|
-      #Misc.consume_stream(sout, false, tmp)
-      assert_raise do
-        Open.write(tmp, sout)
-      end
-    end
-  end
-end

data/test/rbbt/util/misc/test_serialize.rb

@@ -1,24 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/misc/serialize'
-
-class TestClass < Test::Unit::TestCase
-  def test_load_yaml
-    yaml_txt=<<-EOF
----
-a: b
-    EOF
-    yaml_sio = StringIO.new yaml_txt
-
-    assert_equal "b", Misc.load_yaml(yaml_txt)["a"]
-    assert_equal "b", Misc.load_yaml(yaml_sio)["a"]
-
-    TmpFile.with_file yaml_txt do |yaml_file|
-      assert_equal "b", Misc.load_yaml(yaml_file)["a"]
-      Open.open(yaml_file) do |yaml_io|
-        assert_equal "b", Misc.load_yaml(yaml_io)["a"]
-      end
-    end
-
-  end
-end
-

data/test/rbbt/util/python/test_util.rb

@@ -1,25 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
-require 'rbbt/util/python'
-require 'rbbt/util/python/util'
-
-class TestPythonUtil < Test::Unit::TestCase
-
-  def test_tuple
-    tsv = TSV.setup([], :key_field => "Key", :fields => %w(Value1 Value2), :type => :list)
-    tsv["k1"] = %w(V1_1 V2_1)
-    tsv["k2"] = %w(V1_2 V2_2)
-    df = RbbtPython.tsv2df(tsv)
-    new_tsv = RbbtPython.df2tsv(df)
-    assert_equal tsv, new_tsv
-  end
-
-  def test_numpy
-    ra = RbbtPython.run :numpy, :as => :np do
-      na = np.array([[[1,2,3], [4,5,6]]])
-      RbbtPython.numpy2ruby na
-    end
-    assert_equal 6, ra[0][1][2]
-  end
-
-end
-