rbbt-util 5.43.0 → 5.44.1

data/test/rbbt/test_tsv.rb

@@ -1,669 +0,0 @@
-require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
-require 'rbbt/tsv'
-require 'rbbt/util/tmpfile'
-require 'test/unit'
-
-class TestTSV < Test::Unit::TestCase
-
-  def test_extend
-    a = {
-      "one" => "1", 
-      "two" => "2"
-    }
-
-    a.extend TSV
-    
-    a.key_field = "Number"
-
-    assert_equal "1", a["one"]
-  end
-  
-  def test_tsv_1
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-      assert_equal ["ValueA", "ValueB", "OtherID"], tsv.fields
-      assert_equal :double, tsv.type
-      assert_equal "Id", tsv.key_field
-
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "Id")
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-      assert_equal ["ValueA", "ValueB", "OtherID"], tsv.fields
-      assert_equal :double, tsv.type
-      assert_equal "Id", tsv.key_field
- 
-    end
-  end
-
-  def test_headerless
-    content =<<-EOF
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-      assert_equal :double, tsv.type
-    end
-  end
-
-  def test_headerless_fields
-    content =<<-EOF
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :fields => [1])
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-      assert_equal :double, tsv.type
-      assert_equal [%w(a aa aaa)], tsv["row1"]
-    end
-  end
-
-  def test_tsv_persistence
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :persist =>  true)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-      assert_equal ["ValueA", "ValueB", "OtherID"], tsv.fields
-      assert_equal :double, tsv.type
-      assert_equal "Id", tsv.key_field
-      assert TokyoCabinet::HDB === tsv
-    end
-  end
-
-  def test_tsv_field_selection
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :type => :single)
-      assert_equal tsv.fields, ["ValueA"]
-    end
-  end
-
-  def test_tsv_field_selection2
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => 0)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "Id")
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-
-      tsv = TSV.open(filename, :sep => /\s+/, :fields => 1)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"].first
-
-      tsv = TSV.open(filename, :sep => /\s+/, :fields => 2)
-      assert_equal ["b"], tsv["row1"].first
-
-      tsv = TSV.open(filename, :sep => /\s+/, :fields => [1,2])
-      assert_equal ["a", "aa", "aaa"], tsv["row1"].first
-      assert_equal ["b"], tsv["row1"].last
-
-      tsv = TSV.open(filename, :sep => /\s+/, :fields => [1,3])
-      assert_equal ["a", "aa", "aaa"], tsv["row1"].first
-      assert_equal ["Id1", "Id2"], tsv["row1"].last
-
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "OtherID")
-      assert_equal ["row1"], tsv["Id1"].first
-      assert_equal tsv["Id2"], tsv["Id1"]
-
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "OtherID", :fields => "Id")
-      assert_equal ["row1"], tsv["Id1"].first
-      assert_equal tsv["Id2"], tsv["Id1"]
-
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "OtherID", :fields => ["ValueA",2])
-      assert_equal ["a", "aa", "aaa"], tsv["Id1"].first
-      assert_equal tsv["Id2"], tsv["Id1"]
-    end
-  end
-
-  def test_tsv_cast
-    content =<<-EOF
-#Id    Value
-row1    1|2|3
-row2    4
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i)
-      assert_equal [1,2,3], tsv["row1"][0]
-      tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_f)
-      assert_equal [1.0,2.0,3.0], tsv["row1"][0]
-    end
-  end
-
-  def test_tsv_single
-    content =<<-EOF
-#Id    Value
-row1    1
-row2    4
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i, :type => :single, :fields => "Value")
-      assert_equal 1, tsv["row1"]
-      tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i, :type => :single, :fields => ["Value"])
-      assert_equal 1, tsv["row1"]
-      tsv = TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value", :fields => ["Id"])
-      assert_equal "row1", tsv["1"]
-    end
-  end
-
-  def test_tsv_single_from_flat
-    content =<<-EOF
-#: :type=:flat
-#Id    Value
-row1    1 2
-row2    4
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value", :fields => ["Id"])
-      assert_equal "row1", tsv["1"]
-    end
-  end
-
-
-  def test_tsv_serializer
-    content =<<-EOF
-#Id    Value
-row1    1
-row2    4
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i, :type => :single, :serializer => :integer)
-      assert_equal 1, tsv["row1"]
-      assert String === tsv.send(:[], "row1", true)
-    end
-  end
-
-  def test_tsv_header_options
-    content =<<-EOF
-#: :sep=/\\s+/
-#Id Value
-1 a
-2 b
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename)
-      assert_equal [["a"]], tsv["1"]
-    end
-  end
-
-  def test_tsv_fastimport
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-row3    AA    B    Id3
-    EOF
-
-    TmpFile.with_file(content.gsub(/ +/,"\t")) do |filename|
-      tsv = TSV.open(filename, :persist => true)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"][0]
-      assert_equal ["ValueA", "ValueB", "OtherID"], tsv.fields
-      assert_equal :double, tsv.type
-      assert_equal "Id", tsv.key_field
-    end
-  end
-
-  def test_header_type
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-1 a
-2 b
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename)
-      assert_equal :single, tsv.type
-      assert_equal "a", tsv["1"]
-    end
- 
-  end
-
-  def test_single_cast
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single#:cast=:to_i
-#Id Value
-a 1
-b 2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename)
-      assert_equal :single, tsv.type
-      assert_equal 1, tsv["a"]
-    end
-  end
-
-  def test_key_field
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-a 1
-b 2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value")
-      assert_equal %w(Id), tsv.fields
-      assert_equal "Value", tsv.key_field
-      assert_equal "a", tsv["1"]
-    end
-  end
-
-  def test_fix
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-a 1
-b 2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :fix => Proc.new{|l| if l =~ /1/;then "a 3" else l end})
-      assert_equal "a", tsv["3"]
-    end
-  end
-
-  def test_select
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-a 1
-b 2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :select => Proc.new{|l| l !~ /1/})
-      assert(! tsv.include?("3"))
-    end
-  end
-
-  def test_grep
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-a 1
-b 2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2")
-      assert(! tsv.include?("3"))
-    end
-  end
-
-  def test_tsv_grep
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-a 1
-b 2
-b 3
-d 22
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :grep => "2")
-      assert(tsv.include?("2"))
-      assert(! tsv.include?("3"))
-    end
-  end
-
-  def test_grep_invert
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-a 1
-b 2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :tsv_grep => "2", :invert_grep => true)
-      assert(! tsv.include?("2"))
-      assert(tsv.include?("1"))
-    end
-  end
-
-  def test_grep_header
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single#:namespace=Test
-#Id Value
-a 7
-a 1
-b 2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :grep => '2')
-      assert(tsv.include?("2"))
-      assert(! tsv.include?("7"))
-    end
-  end
-
-  def test_json
-    content =<<-EOF
-#: :sep=/\\s+/#:type=:single
-#Id Value
-a 1
-b 2
-    EOF
-
-    require 'json'
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2")
-    end
- 
-  end
-
-  def test_flat_no_merge
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :type => :flat, :fields => ["ValueA"])
-      assert_equal ["a", "aa", "aaa"], tsv["row1"]
-      assert_equal ["ValueA"], tsv.fields
-      assert_equal :flat, tsv.type
-      assert_equal "Id", tsv.key_field
-    end
-  end
-
-  def test_flat_merge2
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row1    aaaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :merge => true, :type => :flat, :fields => ["ValueA"])
-      assert_equal ["a", "aa", "aaa", "aaaa"], tsv["row1"]
-    end
-  end
-
-  def test_flat
-    content =<<-EOF
-#Id    ValueA 
-row1   a   aa   aaa
-row2   b  bbb bbbb bb
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :merge => false, :type => :flat)
-      assert_equal ["a", "aa", "aaa"], tsv["row1"]
-    end
-  end
-
-  def test_flat_with_field
-    content =<<-EOF
-#Id    ValueA
-row1   a   aa   aaa
-row2   b  bbb bbbb bb
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :merge => false, :type => :flat, :fields => ["ValueA"])
-      assert_equal ["a", "aa", "aaa"], tsv["row1"]
-    end
-  end
-
-  def test_flat_with_field_header
-    content =<<-EOF
-#: :type=:flat
-#Id    ValueA
-row1   a   aa   aaa
-row2   b  bbb bbbb bb
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :merge => false, :fields => ["ValueA"])
-      assert_equal ["a", "aa", "aaa"], tsv["row1"]
-    end
-  end
-
-  def test_flat_key
-    content =<<-EOF
-#Id    ValueA 
-row1   a   aa   aaa
-row2   b  bbb bbbb bb aa
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :merge => true, :type => :flat, :key_field => "ValueA")
-      assert_equal ["row1"], tsv["a"]
-      assert_equal ["row1", "row2"], tsv["aa"]
-    end
-  end
-
-
-
-  def test_zipped
-    content =<<-EOF
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b|bb|bbb
-row2    a|aa|aaa    c|cc|ccc
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :merge => true, :type => :double, :key_field => "ValueA", :zipped => true)
-      assert_equal [["row1", "row2"], ["b", "c"]], tsv["a"]
-    end
-  end
-
-  def test_named_array_key
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/)
-      assert_equal "row1", tsv["row1"].key
-
-    end
- 
-  end
-
-  def test_unnamed_key
-    content =<<-EOF
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => 1)
-      assert tsv.keys.include? "a"
-    end
- 
-  end
-
-  def test_float_array
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1   0.2   0.3 0
-row2    0.1  4.5 0
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :persist => true, :type => :list, :cast => :to_f)
-      assert_equal [0.2, 0.3, 0], tsv["row1"]
-      assert_equal :float_array, tsv.serializer
-    end
- 
-  end
-
-  def test_flat_field_select
-    content =<<-EOF
-#: :type=:flat
-#Id    Value
-row1   a  aa  aaa
-row2    b  bb bbb
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      assert TSV.open(filename, :sep => /\s+/, :key_field => "Value").include? "aa"
-    end
-  end
-
-  def test_flat2
-    content =<<-EOF
-#: :type=:flat
-#Id    Value
-row1    a|aa|aaa
-row2    A|AA|AAA
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      assert TSV.open(filename, :sep => /\s+/, :type => :flat).include? "row1"
-      assert TSV.open(filename, :sep => /\s+/, :type => :flat)["row1"].include? "a"
-      assert TSV.open(filename, :sep => /\s+/, :type => :flat, :key_field => "Id")["row1"].include? "a"
-      assert TSV.open(filename, :sep => /\s+/, :type => :flat, :key_field => "Id", :fields => ["Value"])["row1"].include? "a"
-    end
-  end
-
-
-  def test_tsv_flat_double
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A    B    Id3
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :type => :flat, :key_field => "ValueA", :fields => ["OtherID"], :merge => true)
-      assert tsv["aaa"].include? "Id1"
-      assert tsv["aaa"].include? "Id2"
-    end
-  end
-
-  def test_flat2single
-    content =<<-EOF
-#: :type=:flat
-#Id    Value
-row1    a aa aaa
-row2    A AA AAA
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      assert TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value").include? "aaa"
-    end
- 
-  end
-
-  def test_shard
-    shard_function = Proc.new do |key|
-      key[-1]
-    end
-    tsv = datafile_test('identifiers').tsv :persist => true, :shard_function => shard_function
-    assert_equal 10000, tsv.keys.length + 2
-  end
-
-  def test_flat_merge
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A|aAa    B    Id3
-row3    AA    BB|BBB    Id3|Id2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "OtherID", :fields => ["ValueA"], :type => :flat, :merge => true)
-      assert_equal %w(A aAa AA).sort, tsv["Id3"].sort 
-      assert_equal %w(a aa aaa AA).sort, tsv["Id2"].sort 
- 
-    end
-  end
-
-  def test_flat_key_field_double
-    content =<<-EOF
-#Id    ValueA 
-row1   a|aa|aaa
-row2   b|bbb|bbbb|bb
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "ValueA", :fields => ["Id"], :type => :flat)
-      assert tsv.include? 'aa'
-    end
-  end
-
-  def test_flat_key_field
-    content =<<-EOF
-#: :type=:flat
-#Id    ValueA 
-row1   a   aa   aaa
-row2   b  bbb bbbb bb
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :sep => /\s+/, :key_field => "ValueA", :fields => ["Id"], :type => :flat)
-      assert tsv.include? 'aa'
-    end
-  end
-
-
-  def test_string_options
-    content =<<-EOF
-#Id    ValueA    ValueB    OtherID
-row1    a|aa|aaa    b    Id1|Id2
-row2    A|aAa    B    Id3
-row3    AA    BB|BBB    Id3|Id2
-    EOF
-
-    TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :flat, 'Id~OtherID#:sep=/\s+/')
-      assert_equal %w(Id1 Id2), tsv["row1"]
- 
-    end
-  end
-
-  def __test_benchmark
-    num = 10_000
-    txt = num.times.inject(nil) do |acc,i|
-      (acc.nil? ? "" : acc << "\n") << (0..10).collect{|v| v == 0 ? i : [v,v] * "|" } * "\t"
-    end 
-
-    txt = StringIO.new(([txt] * (10))*"\n")
-    #Misc.profile do
-    Misc.benchmark(1) do
-      data = TSV.open(txt, type: :double, bar: true, merge: true)
-      assert_equal num, data.size
-    end
-  end
-
-end
-