rbbt-util 5.43.0 → 5.44.1

data/test/rbbt/tsv/test_attach.rb

@@ -1,715 +0,0 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/tsv'
-require 'rbbt/tsv/attach'
-require 'rbbt'
-
-class TestAttach < Test::Unit::TestCase
-  def test_attach_same_key
-    content1 =<<-EOF
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#ID    ValueB    OtherID
-row1    b    Id1|Id2
-row3    B    Id3
-    EOF
-
-    tsv1 = tsv2 = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    tsv1.attach_same_key tsv2, "OtherID"
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]
-
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    tsv1.attach_same_key tsv2
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-
-    tsv1 = tsv2 = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :list, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    tsv1.attach_same_key tsv2, "OtherID"
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal "Id1", tsv1["row1"]["OtherID"]
-  end
-
-  def test_attach_source_field
-    content1 =<<-EOF
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#ValueB    OtherID
-b    Id1|Id2
-B    Id3
-    EOF
-
-    tsv1 = tsv2 = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    tsv1.attach_source_key tsv2, "ValueB"
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]
-
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :list, :sep => /\s+/)
-    end
-
-    tsv1.attach_source_key tsv2, "ValueB"
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal "Id1", tsv1["row1"]["OtherID"]
-  end
-
-  def test_attach_index
-    content1 =<<-EOF
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#ValueE    OtherID
-e    Id1|Id2
-E    Id3
-    EOF
-
-    content_index =<<-EOF
-#Id    ValueE
-row1    e
-row2    E
-    EOF
-
-    tsv1 = tsv2 = index = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content_index) do |filename|
-      index = TSV.open(File.open(filename), :flat, :sep => /\s+/)
-    end
-
-    tsv1.attach_index tsv2, index
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]
-
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :list, :sep => /\s+/)
-    end
-
-    tsv1.attach_index tsv2, index
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal "Id1", tsv1["row1"]["OtherID"]
-  end
-
-  def test_attach
-    content1 =<<-EOF
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#Id    ValueB    OtherID
-row1    b    Id1|Id2
-row3    B    Id3
-    EOF
-
-    content3 =<<-EOF
-#ValueB    OtherID
-b    Id1|Id2
-B    Id3
-    EOF
-   tsv1 = tsv2 = tsv3 = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content3) do |filename|
-      tsv3 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    tsv1.attach tsv2, :fields => "OtherID"
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]
-
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    tsv1.attach tsv3
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]
-
-  end
-
-  def test_attach_using_index
-    content1 =<<-EOF
-#: :sep=/\\s+/
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#: :sep=/\\s+/
-#ValueE    OtherID
-e    Id1|Id2
-E    Id3
-    EOF
-
-    content_index =<<-EOF
-#: :sep=/\\s+/
-#Id    ValueE
-row1    e
-row2    E
-    EOF
-
-    Rbbt.claim Rbbt.tmp.test.test1.data, :string, content1
-    Rbbt.claim Rbbt.tmp.test.test2.data, :string, content2
-    Rbbt.claim Rbbt.tmp.test.test2.identifiers, :string, content_index
-
-    tsv1 = tsv2 = nil
-
-    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-
-    tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce.find #.to_s
-
-    tsv1.attach tsv2, :fields => ["OtherID"] #, :persist_input => true
-    
-    assert_equal tsv1.fields, %w(ValueA ValueB OtherID)
-    assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]
-  end
-
-  def test_find_path
-     content1 =<<-EOF
-#: :sep=/\\s+/#:case_insensitive=false
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#: :sep=/\\s+/#:case_insensitive=false
-#OtherID ValueE
-Id1|Id2    e    
-Id3        E    
-    EOF
-
-    content_identifiers =<<-EOF
-#: :sep=/\\s+/#:case_insensitive=false
-#Id    ValueE
-row1    e
-row2    E
-    EOF
-
-    tsv1 = tsv2 = identifiers = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(Path.setup(filename), :key => "Id")
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(Path.setup(filename), :double)
-    end
-
-    TmpFile.with_file(content_identifiers) do |filename|
-      identifiers = TSV.open(Path.setup(filename), :flat, :sep => /\s+/)
-    end
-
-    tsv1.identifiers = identifiers
-
-    tsv1.attach tsv2
- 
-    assert_equal %w(ValueA ValueB ValueE), tsv1.fields
-  end
-
-  def test_merge_different_rows
-    file1 =<<-EOF
-row6 dd dd ee
-row1 a b c
-row2 A B C
-row3 1 2 3
-   EOF
-    file2 =<<-EOF
-row20 rr rr
-row1 d e
-row2 D E
-row4 x y z
-    EOF
-    result =<<-EOF
-row1 a b c d e
-row2 A B C D E
-row20    rr rr
-row3 1 2 3  
-row4    x y z
-row6 dd dd ee  
-    EOF
-
-    TmpFile.with_file do |f|
-      TSV.merge_different_fields(StringIO.new(file1), StringIO.new(file2), f, :sep => " ")
-      assert_equal result, Open.read(f)
-    end
-  end
-
-  def test_merge_different_rows_tsv
-    file1 =<<-EOF
-row6 dd dd ee
-row1 a b c
-row2 A B C
-row3 1 2 3
-   EOF
-    file2 =<<-EOF
-row20 rr rr
-row1 d e
-row2 D E
-row4 x y
-    EOF
-    result =<<-EOF
-row1 a b c d e
-row2 A B C D E
-row20    rr rr
-row3 1 2 3  
-row4    x y
-row6 dd dd ee  
-    EOF
-
-    TmpFile.with_file do |f|
-      tsv1 = TSV.open StringIO.new(file1), :sep => " "
-      tsv2 = TSV.open StringIO.new(file2), :sep => " "
-      tsv_r = tsv1.merge_different_fields tsv2
-      assert_equal result, tsv_r.to_s(tsv_r.keys.sort, true).gsub(/\t/,' ')
-    end
-  end
-
-  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
-row2,A,B,C
-row3,1,2,3
-   EOF
-    file2 =<<-EOF
-#ID,letterD,letterE
-row20,rr,rr
-row1,d,e
-row2,D,E
-row4,x,y
-    EOF
-
-    # 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
-row3,1,2,3,,
-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
-row3,1,2,3,,
-row4,,,,x,y
-row6,dd,dd,ee,,
-    EOF
-
-    TmpFile.with_file do |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
-  end
-
-  def test_merge_different_rows_split_lines_tsv
-    file1 =<<-EOF
-row6,dd,dd,ee
-row1,a,b,c
-row1,aa,bb,cc
-row2,A,B,C
-row3,1,2,3
-   EOF
-    file2 =<<-EOF
-row20,rr,rr
-row1,d,e
-row2,D,E
-row4,x,y
-    EOF
-    result =<<-EOF
-row1,aa|a,bb|b,cc|c,d,e
-row2,A,B,C,D,E
-row20,,,,rr,rr
-row3,1,2,3,,
-row4,,,,x,y
-row6,dd,dd,ee,,
-    EOF
-
-    TmpFile.with_file do |f|
-      data1 = TSV.open StringIO.new(file1), :sep => ',', :merge => true
-      data2 = TSV.open StringIO.new(file2), :sep => ',', :merge => true
-      data3 = data1.merge_different_fields(data2)
-      data3.each do |key, list|
-        list.each do |l| l.replace l.sort_by{|v| v.length}.reverse end
-      end
-
-      assert_equal result, data3.to_s(:sort, true).gsub(/\t/,',')
-    end
-  end
-
-  def test_merge_rows
-    file1 =<<-EOF
-#ID,letterA,letterB,letterC
-row1,a,b,c
-row1,aa,bb,cc
-row2,A,B,C
-row3,1,2,3
-    EOF
-    TmpFile.with_file(file1) do |input|
-      TmpFile.with_file() do |output|
-        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
-
-
-  end
-
-  def test_one2one
-    content1 =<<-EOF
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-row3    A    b|bb
-    EOF
-
-    content2 =<<-EOF
-#ValueB    OtherID
-b    Id1|Id2
-B    Id3
-bb   Id4
-    EOF
-   tsv1 = tsv2 = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    tsv1.attach tsv2, :one2one => true
-
-    assert_equal %w(ValueA ValueB OtherID), tsv1.fields
-    assert_equal %w(Id1 Id4), tsv1["row3"]["OtherID"]
-  end
-
-  def test_attach_flat
-    content1 =<<-EOF
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#ValueA    OtherID
-a    Id1|Id2
-A    Id3
-    EOF
-
-    tsv1 = tsv2 = index = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :flat, :fields => ["ValueA"], :sep => /\s+/)
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => /\s+/)
-    end
-
-    res = tsv1.attach tsv2, :fields => ["OtherID"]
-    assert res["row2"].include? "Id3"
-    assert ! res["row2"].include?("b")
-  end
-
-  def test_attached_parenthesis
-
-    content1 =<<-EOF
-#Id,ValueA,bar (ValueB)
-row1,a|aa|aaa,b
-row2,A,B
-    EOF
-
-    content2 =<<-EOF
-#foo (ValueA),OtherID
-a,Id1|Id2
-A,Id3
-    EOF
-
-    content3 =<<-EOF
-#ValueB,ValueC
-b,c
-B,C
-    EOF
-
-    content4 =<<-EOF
-#foobar (Id),ValueD
-row1,d
-row5,D
-    EOF
-
-    tsv1 = tsv2 = tsv3 = tsv4 = index = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => ',')
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => ',')
-    end
-
-    TmpFile.with_file(content3) do |filename|
-      tsv3 = TSV.open(File.open(filename), :double, :sep => ',')
-    end
-
-    TmpFile.with_file(content4) do |filename|
-      tsv4 = TSV.open(File.open(filename), :double, :sep => ',')
-    end
-
-
-    assert_equal tsv1.attach(tsv2)["row1"]["OtherID"], %w(Id1 Id2)
-    assert_equal tsv1.attach(tsv2)["row2"]["OtherID"], %w(Id3)
-
-    assert_equal tsv1.attach(tsv4)["row1"]["ValueD"], %w(d)
-    assert_equal tsv4.attach(tsv1)["row1"]["bar (ValueB)"], %w(b)
-    assert_equal tsv3.attach(tsv1)["b"]["ValueD"], %w(d)
-  end
-
-  def test_attach_single_nils
-    content1 =<<-EOF
-#Id,ValueA
-row1,
-row2,AA
-    EOF
-    content2 =<<-EOF
-#Id,ValueB
-row1,B
-row2,BB
-    EOF
-    content3 =<<-EOF
-#Id,ValueC
-row1,
-row2,CC
-    EOF
-
-    tsv1 = tsv2 = tsv3 = tsv4 = index = nil
-    TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.open(File.open(filename), :double, :sep => ',', :type => :single)
-      tsv1.keys.each{|k| tsv1[k] = nil if tsv1[k] == ""}
-    end
-
-    TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.open(File.open(filename), :double, :sep => ',', :type => :single)
-      tsv2.keys.each{|k| tsv2[k] = nil if tsv2[k] == ""}
-    end
-
-    TmpFile.with_file(content3) do |filename|
-      tsv3 = TSV.open(File.open(filename), :double, :sep => ',', :type => :single)
-      tsv3.keys.each{|k| tsv3[k] = nil if tsv3[k] == ""}
-    end
-
-    assert_equal [nil, "B", nil], tsv1.attach(tsv2, :complete => true).attach(tsv3, :complete => true)["row1"]
-  end
-
-  def test_attach_index_both_non_key
-    content1 =<<-EOF
-#: :sep=/\\s+/
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#: :sep=/\\s+/
-#ValueE    OtherID
-e    Id1|Id2
-E    Id3
-    EOF
-
-    content_index =<<-EOF
-#: :sep=/\\s+/
-#ValueA    OtherID
-a    Id1
-A    Id3
-    EOF
-
-    Rbbt.claim Rbbt.tmp.test.test1.data, :string, content1
-    Rbbt.claim Rbbt.tmp.test.test2.data, :string, content2
-    Rbbt.claim Rbbt.tmp.test.test2.identifiers, :string, content_index
-
-    tsv1 = tsv2 = nil
-
-    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-
-    tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce(true).produce.find #.to_s
-
-    tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
-    assert_equal [["a", "aa", "aaa"], ["b"], ["e"]], tsv1["row1"]
-    
-  end
-
-  def test_attach_both_non_key
-    content1 =<<-EOF
-#: :sep=/\\s+/
-#Id    ValueA    ValueB
-row1    a|aa|aaa    b
-row2    A    B
-    EOF
-
-    content2 =<<-EOF
-#: :sep=/\\s+/
-#ValueE    ValueB
-e    b
-E    B
-    EOF
-    Rbbt.claim Rbbt.tmp.test.test1.data, :string, content1
-    Rbbt.claim Rbbt.tmp.test.test2.data, :string, content2
-
-    tsv1 = tsv2 = nil
-
-    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-
-    tsv1.attach tsv2, :fields => ["ValueE"] #, :persist_input => true
-    assert_equal [["a", "aa", "aaa"], ["b"], ["e"]], tsv1["row1"]
-    
-  end
-
-  def test_attach_complete
-    content1 =<<-EOF
-#: :sep=/\\s+/
-#Id    ValueA
-row1    a|aa|aaa
-row2    A
-    EOF
-
-    content2 =<<-EOF
-#: :sep=/\\s+/
-#Id    ValueB
-row1    b
-row3    C
-    EOF
-    Rbbt.claim Rbbt.tmp.test.test1.data, :string, content1
-    Rbbt.claim Rbbt.tmp.test.test2.data, :string, content2
-
-    tsv1 = tsv2 = nil
-
-    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-
-    tsv1.attach tsv2, :complete => true
-    assert_equal [[], ["C"]], tsv1["row3"]
-
-    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-
-    tsv1.attach tsv2, :complete => ["AA"]
-    assert_equal [["AA"], ["C"]], tsv1["row3"]
-  end
-
-  def test_attach_complete_identifiers
-    content1 =<<-EOF
-#: :sep=/\\s+/
-#Id    ValueA
-row1    a|aa|aaa
-row2    A
-    EOF
-
-    content2 =<<-EOF
-#: :sep=/\\s+/
-#Id2    ValueB
-ROW_1    b
-ROW_2    C
-    EOF
-
-    identifiers =<<-EOF
-#: :sep=/\\s+/
-#Id    Id2
-row1    ROW_1
-row2    ROW_2
-row3    ROW_3
-    EOF
-    Rbbt.claim Rbbt.tmp.test.test1.data, :string, content1
-    Rbbt.claim Rbbt.tmp.test.test2.data, :string, content2
-    Rbbt.claim Rbbt.tmp.test.identifiers.data, :string, identifiers
-
-    tsv1 = tsv2 = nil
-
-    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-    ids = Rbbt.tmp.test.identifiers.data.produce(true).tsv :double,  :sep => /\s+/
-
-    tsv1.identifiers = ids
-
-    tsv1.attach tsv2
-    assert_equal [["A"], ["C"]], tsv1["row2"]
-
-    tsv1 = Rbbt.tmp.test.test1.data.produce(true).tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.tmp.test.test2.data.produce(true).tsv :double,  :sep => /\s+/
-    ids = Rbbt.tmp.test.identifiers.data.produce(true).tsv :double,  :sep => /\s+/
-
-    tsv1.identifiers = ids
-
-    tsv1.attach tsv2, :complete => true
-    assert_equal [["A"], ["C"]], tsv1["row2"]
-  end
-end
-