rbbt-util 1.1.0 → 1.2.1

data/test/rbbt/util/test_rake.rb

@@ -0,0 +1,54 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/util/rake'
+
+class TestRake < Test::Unit::TestCase
+  def test_run
+    rakefile=<<-EOF
+require 'rbbt/util/rake'
+
+file "foo" do |t|
+  Open.write(t.name, 'bar')
+end
+    EOF
+
+    TmpFile.with_file(rakefile) do |f|
+      RakeHelper.run f, :foo
+
+      assert File.exists? "foo"
+      FileUtils.rm "foo"
+    end
+  end
+
+  def test_run_default
+    rakefile=<<-EOF
+require 'rbbt/util/rake'
+
+file "foo" do |t|
+  Open.write(t.name, 'bar')
+end
+    EOF
+
+    TmpFile.with_file(rakefile) do |f|
+      RakeHelper.run f
+
+      assert File.exists? "foo"
+      FileUtils.rm "foo"
+    end
+  end
+
+
+  def test_files
+    rakefile=<<-EOF
+require 'rbbt/util/rake'
+
+file "foo" do |t|
+  Open.write(t.name, 'bar')
+end
+    EOF
+
+    TmpFile.with_file(rakefile) do |f|
+      assert RakeHelper.files(f).include? "foo"
+    end
+  end
+end
+

data/test/rbbt/util/test_tsv.rb

@@ -12,8 +12,8 @@ row2 A B
 
     TmpFile.with_file(content) do |filename|
       data = {}
-      key_field, fields = TSV.parse(data, File.open(filename), :sep => /\s+/, :keep_empty => true)
-      assert_equal ["ValueA", "ValueB", "Comment"], fields
+      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
@@ -27,7 +27,7 @@ row2 A B C
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s/)
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s/)
       assert_equal [["a"],["c"]], tsv.reorder(:main, ["ValueA", "Comment"])["row1"]
     end
   end
@@ -64,9 +64,9 @@ row2    A    B
 
     TmpFile.with_file(content) do |filename|
       data = {}
-      key_field, fields = TSV.parse(data, File.open(filename), :sep => /\s+/)
-      assert_equal "Id", key_field
-      assert_equal ["ValueA", "ValueB"], fields
+      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
@@ -79,7 +79,7 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :large => true)
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s+/, :key => "OtherID", :large => true)
       assert_equal "OtherID", tsv.key_field
       assert_equal ["Id", "ValueA", "ValueB"], tsv.fields
       assert_equal ["a", "aa", "aaa"], tsv["Id2"][1]
@@ -94,7 +94,7 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID")
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID")
       assert_equal "OtherID", tsv.key_field
       assert_equal ["Id", "ValueA", "ValueB"], tsv.fields
       assert_equal ["a", "aa", "aaa"], tsv["Id1"][1]
@@ -111,7 +111,7 @@ row3    a    C    Id4
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.open_file(filename + '#:sep=/\s+/#:native=OtherID')
+      tsv = TSV.open_file(filename + '#:sep=/\s+/#:key=OtherID')
       assert_equal "OtherID", tsv.key_field
       assert_equal ["Id", "ValueA", "ValueB"], tsv.fields
       assert_equal ["a", "aa", "aaa"], tsv["Id1"][1]
@@ -129,9 +129,9 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :extra => 2)
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :others => 2)
       assert_equal ["b"], tsv["Id2"][0]
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :extra => 'ValueB')
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :others => 'ValueB')
       assert_equal ["b"], tsv["Id2"][0]
     end
   end
@@ -144,7 +144,7 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :case_insensitive => true)
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :case_insensitive => true)
       assert_equal "OtherID", tsv.key_field
       assert_equal ["Id", "ValueA", "ValueB"], tsv.fields
       assert_equal ["a", "aa", "aaa"], tsv["id1"][1]
@@ -160,15 +160,16 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(filename, :sep => /\s+/, :native => "OtherID", :persistence => true)
+      tsv = TSV.new(filename, :sep => /\s+/, :key => "OtherID", :persistence => true)
       assert_equal ["Id", "ValueA", "ValueB"], tsv.fields
       tsv['Id4'] = [["row3"],["aA"],["bB","bbBB"]]
       assert_equal ["aA"], tsv["Id4"][1]
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :persistence => true)
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :persistence => true)
       assert_equal ["Id", "ValueA", "ValueB"], tsv.fields
+
       assert_equal ["aA"], tsv["Id4"][1]
       assert_equal [["b"],["B"]], tsv.values_at("Id1", "Id3").collect{|values| values[2]}
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :persistence => true, :flatten => true)
+      tsv = TSV.new(File.open(filename), :flat, :sep => /\s+/, :key => "OtherID", :persistence => false)
       assert(tsv["Id3"].include? "A")
     end
   end
@@ -181,7 +182,7 @@ row2    A    B    Id3
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.new(File.open(filename), :sep => /\s+/)
-      index = tsv.index(:case_insensitive => true, :field => 2)
+      index = tsv.index(:case_insensitive => true, :target => 2)
       assert index["row1"].include? "Id1"
     end
   end
@@ -195,14 +196,14 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :persistence => false)
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :persistence => false)
       index = tsv.index(:case_insensitive => true)
       assert index["row1"].include? "Id1"
       assert_equal "OtherID", index.key_field
     end
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID")
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID")
       index = tsv.index(:case_insensitive => true)
       assert index["row1"].include? "Id1"
       assert_equal "OtherID", index.key_field
@@ -217,7 +218,7 @@ row2    A    a|B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :persistence => true)
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :persistence => true)
       index = tsv.index(:case_insensitive => false, :order => true)
       assert_equal "Id1", index['a'].first
       assert_equal "Id3", index['A'].first
@@ -225,7 +226,7 @@ row2    A    a|B    Id3
     end
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID")
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID")
       index = tsv.index(:case_insensitive => true)
       assert index["row1"].include? "Id1"
       assert_equal "OtherID", index.key_field
@@ -240,7 +241,7 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :persistence => true)
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :persistence => true)
       index = tsv.index(:case_insensitive => true)
       assert index.values_at(*["row1"]).first.include? "Id1"
     end
@@ -254,7 +255,7 @@ row2    A    B    Id3
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.new(File.open(filename), :sep => /\s+/, :native => "OtherID", :case_insensitive => true)
+      tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :case_insensitive => true)
       assert_equal "OtherID", tsv.key_field
       assert_equal ["Id", "ValueA", "ValueB"], tsv.fields
       assert_equal ["a", "aa", "aaa"], tsv["id1"][1]
@@ -273,16 +274,31 @@ row2    A    B    Id3
       require 'rbbt/sources/organism'
       filename = File.join(Organism.datadir('Sce'), 'identifiers')
       missing = true
-      index = TSV.index(filename, :persistence => true, :native => "Associated Gene Name")
+      index = TSV.index(filename, :persistence => true, :key => "Associated Gene Name")
       assert index['1020'].include? 'CDK5'
-      index = TSV.index(filename, :persistence => true, :native => "Associated Gene Name")
+      index = TSV.index(filename, :persistence => true, :key => "Associated Gene Name")
       assert index[[nil,'1020']].include? 'CDK5'
-      index = TSV.index(filename, :persistence => true, :native => "Associated Gene Name")
+      index = TSV.index(filename, :persistence => true, :key => "Associated Gene Name")
       assert index[['MISSING','1020']].include? 'CDK5'
     rescue Exception
     end
   end
 
+  def test_grep
+    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.new(File.open(filename), :sep => /\s+/, :grep => %w(row1))
+      assert tsv.keys.include? "row1"
+      assert( ! tsv.keys.include?("row2"))
+    end
+  end
+
+
 
   def test_sort
     content =<<-EOF
@@ -316,6 +332,27 @@ row2	A	B	Id3
     end
   end
 
+  def test_to_s_ordered
+    content =<<-EOF
+#Id	ValueA	ValueB	OtherID
+row1	a|aa|aaa	b	Id1|Id2
+row2	A	B	Id3
+    EOF
+
+    content2 =<<-EOF
+#Id	ValueA	ValueB	OtherID
+row2	A	B	Id3
+row1	a|aa|aaa	b	Id1|Id2
+    EOF
+
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :sep => /\s+/)
+      assert_equal content, tsv.to_s(%w(row1 row2))
+      assert_not_equal content, tsv.to_s(%w(row2 row1))
+      assert_equal content2, tsv.to_s(%w(row2 row1))
+    end
+  end
 
   def test_smart_merge_single
     content1 =<<-EOF
@@ -332,11 +369,11 @@ C    B    Id3
 
     tsv1 = tsv2 = nil
     TmpFile.with_file(content1) do |filename|
-      tsv1 = TSV.new(File.open(filename), :sep => /\s+/, :unique => true)
+      tsv1 = TSV.new(File.open(filename), :list, :sep => /\s+/)
     end
 
     TmpFile.with_file(content2) do |filename|
-      tsv2 = TSV.new(File.open(filename), :sep => /\s+/, :unique => true)
+      tsv2 = TSV.new(File.open(filename), :list, :sep => /\s+/)
     end
 
     tsv1.smart_merge tsv2, "ValueB"
@@ -490,6 +527,7 @@ B    BB
 
     assert_equal %w(a aa aaa aaaa), tsv1["row1"]["ValueA"]
   end
+
   def test_smart_merge_common_fields
     content1 =<<-EOF
 #Id    ValueA    ValueB
@@ -649,6 +687,20 @@ row3    a    C    Id4
     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.new(File.open(filename), :sep => /\s+/, :fix => proc{|l| l =~ /^row2/? nil : l})
+      assert_equal %w(row1), tsv.keys
+    end
+  end
+
   def test_open_stringoptions
      content =<<-EOF
 #Id    ValueA    ValueB    OtherID
@@ -678,7 +730,7 @@ row3    a    C    Id4
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.new(filename + '#:sep=/\s+/')
-      assert tsv.list
+      assert tsv.type == :double
       
       new = tsv.select %w(b Id4)
       assert_equal %w(row1 row3).sort, new.keys
@@ -692,8 +744,8 @@ row3    a    C    Id4
       new = tsv.select "ValueB" => /b|Id4/
       assert_equal %w(row1).sort, new.keys
 
-      tsv = TSV.new(filename + '#:sep=/\s+/#:unique')
-      assert ! tsv.list
+      tsv = TSV.new(filename + '#:sep=/\s+/#:type=:flat')
+      assert tsv.type != :double
       
       new = tsv.select %w(b Id4)
     end
@@ -727,15 +779,14 @@ row3    a    C    Id4
       tsv.add_field "Str length" do |k,v| 
         (v.flatten * " ").length 
       end
-      
 
       assert tsv.fields.include?("Str length")
     end
  
   end
 
-  def test_tsv_cache
-      content =<<-EOF
+  def test_cast
+     content =<<-EOF
 #Id    LetterValue#ValueA    LetterValue#ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
 row2    A    B    Id3
@@ -743,20 +794,14 @@ row3    a    C    Id4
     EOF
  
     TmpFile.with_file(content) do |filename|
-      tsv = CacheHelper.tsv_cache('test_tsv_cache', filename) do 
-        TSV.new(filename + '#:sep=/\s+/')
-      end
-      tsv
-      
-      tsv1 = CacheHelper.tsv_cache('test_tsv_cache', filename) do 
-        assert false
-      end
+      tsv = TSV.new(filename + '#:sep=/\s+/#:cast="to_sym"')
+      assert tsv['row1']["OtherID"].include?(:Id1)
+      assert ! tsv['row1']["OtherID"].include?("Id1")
 
-      assert_equal tsv.fields, tsv1.fields
-      
-      CacheHelper.clean 'test_tsv_cache'
+      tsv = TSV.new(filename + '#:sep=/\s+/')
+      assert tsv['row1']["OtherID"].include?("Id1")
+      assert ! tsv['row1']["OtherID"].include?(:Id1)
     end
-
- end
+  end
 end
 

data/test/rbbt/util/test_workflow.rb

@@ -1,10 +1,13 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
+require 'rbbt'
 require 'rbbt/util/tsv'
 require 'rbbt/util/tmpfile'
+require 'rbbt/util/workflow'
 
-class TestTSV < Test::Unit::TestCase
+class TestWorkflow < Test::Unit::TestCase
 
-  def test_add_column
+  def test_true
+    assert true
   end
 
 end

data/test/test_helper.rb

@@ -1,8 +1,12 @@
 require 'test/unit'
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rbbt/util/tmpfile'
+require 'rbbt/util/log'
+require 'fileutils'
 
 class Test::Unit::TestCase
+  include FileUtils
   def test_datafile(file)
     File.join(File.dirname(__FILE__), 'data', file)
   end

data/test/test_pkg.rb

@@ -19,16 +19,6 @@ module B
   self.load_cfg(%w(datadir), {"datadir" => "/tmp/B"}.to_yaml)
 end
 
-module DA
-  PKG=A
-  extend DataModule
-end
-
-module DB
-  PKG=B
-  extend DataModule
-end
-
 class TestPKG < Test::Unit::TestCase
   def test_datadir
     assert_equal "/tmp/A", A.datadir

data/test/test_rbbt.rb

@@ -5,54 +5,9 @@ require 'rbbt/util/open'
 
 class TestRbbt < Test::Unit::TestCase
   def test_url
-    Rbbt.add_datafiles :test => ['test', 'http://google.com']
-    assert(Misc.fixutf8(File.open(Rbbt.find_datafile('test')).read) =~ /html/)
-    FileUtils.rm_rf File.dirname(Rbbt.find_datafile('test'))
-  end
-
-  def test_proc
-    Rbbt.add_datafiles :test => ['test', proc{'test'}]
-    assert(Open.read(Rbbt.find_datafile('test')) == 'test')
-    FileUtils.rm_rf File.dirname(Rbbt.find_datafile('test'))
-  end
-
-  def test_Rakefile
-    sharedir = PKGData.sharedir_for_file(__FILE__)
-    
-    FileUtils.rmtree  File.join(Rbbt.datadir, 'rake')
-    FileUtils.mkdir_p File.join(sharedir, 'install', 'rake')
-    File.open(File.join(sharedir, 'install', 'rake', 'Rakefile'), 'w') do |f|
-      f.puts "task :default do File.open('foo', 'w') do |f| f.puts 'bar' end end"
-    end
-
-    Rbbt.add_datafiles :rake => ['', 'rake']
-
-    assert_equal 'bar', Open.read(File.join(Rbbt.datadir, 'rake', 'foo')).chomp
-
-    FileUtils.rmtree  File.join(sharedir, 'install', 'rake')
-    FileUtils.rmtree  File.join(Rbbt.datadir, 'rake')
-  end
-
-  def test_Rakefile_with_file
-    sharedir = PKGData.sharedir_for_file(__FILE__)
-    
-    FileUtils.mkdir_p File.join(sharedir, 'install', 'rake')
-    File.open(File.join(sharedir, 'install', 'rake', 'Rakefile'), 'w') do |f|
-      f.puts "\
-task :default do File.open('foo', 'w') do |f| f.puts 'bar' end end
-task 'file1' do |t| File.open(t.name, 'w') do |f| f.puts 'file 1' end end
-      "
-    end
-
-    Rbbt.add_datafiles 'rake/file1' => ['', 'rake']
-
-    assert(! File.exists?(File.join(Rbbt.datadir, 'rake', 'foo')))
-    assert(File.exists?(File.join(Rbbt.datadir, 'rake', 'file1')))
-    assert_equal('file 1', Open.read(File.join(Rbbt.datadir, 'rake', 'file1')).chomp)
-    assert_equal('file 1', Open.read(Rbbt.find_datafile('rake/file1')).chomp)
-
-    FileUtils.rm_rf  File.join(sharedir, 'install', 'rake')
-    FileUtils.rm_rf  File.join(Rbbt.datadir, 'rake')
+    Rbbt.claim :test_url, 'http://google.com'
+    assert Rbbt.files.test_url.read =~ /html/
+    FileUtils.rm Rbbt.files.test_url
   end
 
   def test_xclip