rbbt-util 1.2.1 → 2.0.1

data/test/rbbt/util/tsv/test_manipulate.rb

@@ -0,0 +1,226 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/tsv'
+require 'rbbt/util/tsv/manipulate'
+
+class TestTSVManipulate < Test::Unit::TestCase
+
+  def test_indentify_fields
+    content =<<-EOF
+#ID ValueA ValueB Comment
+row1 a b c
+row2 A B C
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s/)
+      assert_equal :key, tsv.identify_field("ID")
+    end
+  end
+
+
+  def test_reorder_simple
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :sep => /\s+/)
+
+      tsv1 = tsv.reorder("ValueA")
+
+      assert_equal "ValueA", tsv1.key_field
+      assert_equal %w(Id ValueB OtherID), tsv1.fields
+      assert_equal ["B"], tsv1["A"]["ValueB"]
+      assert_equal ["b","C"], tsv1["a"]["ValueB"]
+      assert_equal ["b"], tsv1["aa"]["ValueB"]
+
+    end
+  end
+
+  def test_reorder_simple_headerless
+    content =<<-EOF
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :sep => /\s+/)
+
+      tsv1 = tsv.reorder 0 
+
+      assert_nil tsv1.key_field
+      assert_equal ["B"], tsv1["A"][1]
+      assert_equal ["b","C"], tsv1["a"][1]
+      assert_equal ["b"], tsv1["aa"][1]
+      assert_equal ["row1"], tsv1["aa"][0]
+      assert_equal ["row1","row3"], tsv1["a"][0]
+    end
+  end
+
+
+  def test_reorder_remove_field
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :sep => /\s+/)
+
+      tsv1 = tsv.reorder("ValueA", ["ValueB", "Id"])
+
+      assert_equal "ValueA", tsv1.key_field
+      assert_equal %w(ValueB Id), tsv1.fields
+      assert_equal ["B"], tsv1["A"]["ValueB"]
+      assert_equal ["b","C"], tsv1["a"]["ValueB"]
+      assert_equal ["row1"], tsv1["aa"]["Id"]
+      assert_equal ["row1","row3"], tsv1["a"]["Id"]
+    end
+  end
+
+  def test_through
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :sep => /\s+/)
+
+      tsv.through "ValueA" do |key, values|
+        assert(tsv.keys.include? values["Id"].first)
+      end
+    end
+  end
+
+
+  def test_slice
+    content =<<-EOF
+#ID ValueA ValueB Comment
+row1 a b c
+row2 A B C
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s/)
+      assert_equal [["a"],["c"]], tsv.reorder(:key, ["ValueA", "Comment"])["row1"]
+    end
+  end
+
+  def test_sort
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID    Pos
+row1    a|aa|aaa    b    Id1|Id2    2
+row2    A    B    Id3    1
+row3    A|AA|AAA|AAA    B    Id3    3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :sep => /\s+/)
+      assert_equal %w(row1 row2 row3), tsv.sort
+      assert_equal %w(row1 row2 row3), tsv.sort(:key)
+      assert_equal %w(row2 row1 row3), tsv.sort("Pos")
+      assert_equal %w(row3 row2 row1), tsv.sort("ValueA") do |values| values["ValueA"].length end
+    end
+  end
+
+  def test_select
+     content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(filename + '#:sep=/\s+/')
+      assert tsv.type == :double
+      
+      new = tsv.select %w(b Id4)
+      assert_equal %w(row1 row3).sort, new.keys
+
+      new = tsv.select "ValueB" => %w(b Id4)
+      assert_equal %w(row1).sort, new.keys
+
+      new = tsv.select /b|Id4/
+      assert_equal %w(row1 row3).sort, new.keys
+
+      new = tsv.select "ValueB" => /b|Id4/
+      assert_equal %w(row1).sort, new.keys
+
+      tsv = TSV.new(filename + '#:sep=/\s+/#:type=:flat')
+      assert tsv.type != :double
+      
+      new = tsv.select %w(b Id4)
+      assert_equal %w(row1 row3).sort, new.keys.sort
+
+
+      new = tsv.select do |k,v| v["ValueA"].include? "A" end
+      assert_equal %w(row2).sort, new.keys.sort
+    end
+  end
+
+  def test_process
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :sep => /\s+/)
+
+      tsv.process "ValueA" do |field_values,key,values|
+        field_values.collect{|v| "Pref:#{v}"}
+      end
+
+      assert_equal ["Pref:A"], tsv["row2"]["ValueA"]
+    end
+  end
+
+  def test_add_field
+     content =<<-EOF
+#Id    LetterValue:ValueA    LetterValue:ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+ 
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(filename + '#:sep=/\s+/')
+      tsv.add_field "Str length" do |k,v| 
+        (v.flatten * " ").length 
+      end
+
+      assert tsv.fields.include?("Str length")
+    end
+  end
+
+  def test_slice_namespace
+     content =<<-EOF
+#Id    LetterValue:ValueA    LetterValue:ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+ 
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(filename + '#:sep=/\s+/')
+
+      tsv_ns = tsv.slice_namespace "LetterValue"
+      assert_equal %w(LetterValue:ValueA LetterValue:ValueB), tsv_ns.fields
+    end
+ 
+  end
+
+end
+

data/test/rbbt/util/tsv/test_parse.rb

@@ -0,0 +1,72 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/tsv/parse'
+
+class TestTSVParse < Test::Unit::TestCase
+
+  def test_keep_empty
+    content =<<-EOF
+#Id ValueA ValueB Comment
+row1 a|aa|aaa b c
+row2 A B
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      data = {}
+      data, extra = TSV.parse(File.open(filename), :sep => /\s+/, :keep_empty => true)
+      assert_equal ["ValueA", "ValueB", "Comment"], extra[:fields]
+      assert_equal ["c"], data["row1"][2]
+      assert_equal [""], data["row2"][2]
+    end
+  end
+
+  def test_break_with_fix
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.parse(File.open(filename), :sep => /\s+/, :fix => proc{|l| l =~ /^row2/? nil : l})
+      assert_equal %w(row1), tsv.first.keys
+    end
+  end
+
+  def test_hash
+    content =<<-EOF
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      data = {}
+      data, extra = TSV.parse(File.open(filename), :sep => /\s+/)
+      assert_equal "Id", extra[:key_field]
+      assert_equal ["ValueA", "ValueB"], extra[:fields]
+      assert_equal ["a", "aa", "aaa"], data["row1"][0]
+    end
+  end
+
+  def test_options_line
+    content =<<-EOF
+#: :sep=/\\s+/#:case_insensitive=true
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      data = {}
+      data, extra = TSV.parse(File.open(filename))
+      assert_equal "Id", extra[:key_field]
+      assert_equal true, extra[:case_insensitive]
+      assert_equal ["ValueA", "ValueB"], extra[:fields]
+      assert_equal ["a", "aa", "aaa"], data["row1"][0]
+    end
+  end
+
+
+end
+

data/test/test_helper.rb

@@ -7,6 +7,7 @@ require 'fileutils'
 
 class Test::Unit::TestCase
   include FileUtils
+
   def test_datafile(file)
     File.join(File.dirname(__FILE__), 'data', file)
   end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-util
 version: !ruby/object:Gem::Version 
-  hash: 29
+  hash: 13
   prerelease: 
   segments: 
-  - 1
   - 2
+  - 0
   - 1
-  version: 1.2.1
+  version: 2.0.1
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-01-30 00:00:00 +01:00
+date: 2011-02-09 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -108,9 +108,11 @@ files:
 - lib/rbbt/util/data_module.rb
 - lib/rbbt/util/excel2tsv.rb
 - lib/rbbt/util/filecache.rb
+- lib/rbbt/util/fix_width_table.rb
 - lib/rbbt/util/log.rb
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/open.rb
+- lib/rbbt/util/path.rb
 - lib/rbbt/util/persistence.rb
 - lib/rbbt/util/pkg_config.rb
 - lib/rbbt/util/pkg_data.rb
@@ -121,6 +123,11 @@ files:
 - lib/rbbt/util/tc_hash.rb
 - lib/rbbt/util/tmpfile.rb
 - lib/rbbt/util/tsv.rb
+- lib/rbbt/util/tsv/accessor.rb
+- lib/rbbt/util/tsv/attach.rb
+- lib/rbbt/util/tsv/index.rb
+- lib/rbbt/util/tsv/manipulate.rb
+- lib/rbbt/util/tsv/parse.rb
 - lib/rbbt/util/workflow.rb
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
@@ -130,8 +137,10 @@ files:
 - test/rbbt/util/test_data_module.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_fix_width_table.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_path.rb
 - test/rbbt/util/test_persistence.rb
 - test/rbbt/util/test_pkg_data.rb
 - test/rbbt/util/test_rake.rb
@@ -141,6 +150,11 @@ files:
 - test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_tsv.rb
 - test/rbbt/util/test_workflow.rb
+- test/rbbt/util/tsv/test_accessor.rb
+- test/rbbt/util/tsv/test_attach.rb
+- test/rbbt/util/tsv/test_index.rb
+- test/rbbt/util/tsv/test_manipulate.rb
+- test/rbbt/util/tsv/test_parse.rb
 - test/test_helper.rb
 - test/test_pkg.rb
 - test/test_rbbt.rb
@@ -187,8 +201,10 @@ test_files:
 - test/rbbt/util/test_data_module.rb
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_fix_width_table.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_path.rb
 - test/rbbt/util/test_persistence.rb
 - test/rbbt/util/test_pkg_data.rb
 - test/rbbt/util/test_rake.rb
@@ -198,6 +214,11 @@ test_files:
 - test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_tsv.rb
 - test/rbbt/util/test_workflow.rb
+- test/rbbt/util/tsv/test_accessor.rb
+- test/rbbt/util/tsv/test_attach.rb
+- test/rbbt/util/tsv/test_index.rb
+- test/rbbt/util/tsv/test_manipulate.rb
+- test/rbbt/util/tsv/test_parse.rb
 - test/test_helper.rb
 - test/test_pkg.rb
 - test/test_rbbt.rb