rbbt-util 3.2.1 → 4.0.0

data/test/rbbt/{util/test_fix_width_table.rb → test_fix_width_table.rb}

@@ -1,11 +1,11 @@
-require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
-require 'rbbt/util/fix_width_table'
-require 'rbbt/util/tsv'
+require File.join(File.expand_path(File.dirname(__FILE__)), '../', 'test_helper.rb')
+require 'rbbt/fix_width_table'
+require 'rbbt/tsv'
+require 'rbbt/tsv/manipulate'
 
 class TestFixWidthTable < Test::Unit::TestCase
   def load_data(data)
-    Log.debug("Data:\n#{Open.read(data)}")
-    tsv = TSV.new(data, :list, :sep=>":", :cast => proc{|e| e =~ /(\s*)(_*)/; ($1.length..($1.length + $2.length - 1))})
+    tsv = TSV.open(data, :list, :sep=>":", :cast => proc{|e| e =~ /(\s*)(_*)/; ($1.length..($1.length + $2.length - 1))})
     tsv.add_field "Start" do |key, values|
       values["Range"].first
     end
@@ -50,7 +50,7 @@ class TestFixWidthTable < Test::Unit::TestCase
 
   def test_point
     data =<<-EOF
-#: :sep=/\\s+/#:type=:single#:cast=to_i
+#: :sep=/\\s+/#:type=:single#:cast=:to_i
 #ID Pos
 a 1
 b 10
@@ -61,8 +61,7 @@ f 11
 g 25
     EOF
     TmpFile.with_file(data) do |datafile|
-      tsv = TSV.new datafile
-      ddd tsv
+      tsv = TSV.open datafile
       TmpFile.with_file do |filename|
         f = FixWidthTable.new filename, 100, false
         f.add_point tsv
@@ -88,7 +87,7 @@ f:             ___
 g:         ____
     EOF
     TmpFile.with_file(data) do |datafile|
-      tsv = TSV.new load_data(datafile)
+      tsv = load_data(datafile)
       TmpFile.with_file do |filename|
         f = FixWidthTable.new filename, 100, true
         f.add_range tsv

data/test/rbbt/test_resource.rb

@@ -0,0 +1,66 @@
+require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
+require 'rbbt/resource'
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+
+module TestResource
+  extend Resource
+
+  claim tmp.test.google, :url, "http://google.com"
+  claim tmp.test.string, :string, "TEST"
+  claim tmp.test.proc, :proc do
+    "PROC TEST"
+  end
+
+  claim tmp.test.rakefiles.foo , :string , <<-EOF
+file 'foo' do |t|
+  Open.write(t.name, "TEST")
+end
+  EOF
+
+  claim tmp.test.work.footest, :rake, tmp.test.rakefiles.foo
+end
+
+class TestTSV < Test::Unit::TestCase
+
+  def test_rake
+    TestResource.tmp.test.work.footest.foo.read == "TEST"
+    assert TestResource.tmp.test.work.footest.foo.read == "TEST"
+  end
+
+  def test_proc
+    assert TestResource.tmp.test.proc.read == "PROC TEST"
+  end
+
+  def test_string
+    assert TestResource.tmp.test.string.read == "TEST"
+  end
+
+  def test_url
+    assert TestResource[].tmp.test.google.read =~ /google/
+  end
+
+
+  def test_resolve
+    assert_equal File.join(ENV['HOME'], '.rbbt/etc/foo'), Path.setup('etc/foo').find(:user)
+    assert_equal File.join(ENV['HOME'], '.phgx/etc/foo'), Path.setup('etc/foo', 'phgx').find(:user)
+
+    assert_equal File.join('/', 'etc/rbbt/foo'), Path.setup('etc/foo').find(:global)
+    assert_equal File.join('/', 'etc/phgx/foo'), Path.setup('etc/foo', 'phgx').find(:global)
+
+    assert_equal File.join('/usr/local', 'etc/rbbt/foo'), Path.setup('etc/foo').find(:local)
+    assert_equal File.join('/usr/local', 'etc/phgx/foo'), Path.setup('etc/foo', 'phgx').find(:local)
+
+    assert_equal File.expand_path(File.join(File.dirname(File.expand_path(__FILE__)), '../../', 'etc/foo')), Path.setup('etc/foo').find(:lib)
+    assert_equal File.expand_path(File.join(File.dirname(File.expand_path(__FILE__)), '../../', 'etc/foo')), Path.setup('etc/foo').find(:lib)
+
+    assert_equal File.join(ENV['HOME'], '.rbbt/etc/foo'), Path.setup('etc/foo').find()
+    assert_equal File.join(ENV['HOME'], '.phgx/etc/foo'), Path.setup('etc/foo', 'phgx').find()
+  end
+
+  def test_libdir
+    assert File.exists? TestResource[].share.lib.R["util.R"].find :lib
+    assert File.exists? TestResource[].share.lib.R["util.R"].find 
+  end
+
+end

data/test/rbbt/test_tsv.rb

@@ -0,0 +1,332 @@
+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
+    
+    assert a.methods.include? "key_field="
+
+    a.key_field = "Number"
+
+    assert_equal "1", a["one"]
+  end
+   
+  def test_tsv
+    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
+#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+/, :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_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
+
+      FileUtils.rm 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+/, :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"]
+    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.tsv_clean_get_brackets("row1")
+    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
+    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_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
+
+end

data/test/rbbt/test_workflow.rb

@@ -0,0 +1,102 @@
+require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
+require 'rbbt/workflow'
+require 'rbbt/workflow/soap'
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+
+module TestWF
+  extend Workflow
+
+  str = "TEST"
+  task :str => :string do
+    str
+  end
+
+  dep :str
+  task :reverse => :string do
+    step(:str).load.reverse
+  end
+
+  dep :str
+  task :downcase => :string do
+    step(:str).load.downcase
+  end
+
+  dep :str
+  input :times, :integer, "Times to repeat"
+  task :repeat => :string do |times|
+    [step(:str).load] * times * "\n"
+  end
+
+  input :number, :float, "Number to doble"
+  def self.double(number)
+    2 * number
+  end
+  task :double => :float
+
+  desc <<-EOT
+Returns numer * 2 lines containing TEST
+  EOT
+  dep :str
+  dep :double
+  task :repeat2 => :string do 
+    [step(:str).load] * step(:double).load * "\n"
+  end
+
+  dep :str, :repeat, :repeat2
+  task :double_dep => :array do
+   [] << step(:str).load << step(:repeat).load << step(:repeat2).load
+  end
+
+  export_synchronous :double
+  export_asynchronous :repeat2
+end
+
+TestWF.workdir = Rbbt.tmp.test.workflow
+
+class TestWorkflow < Test::Unit::TestCase
+
+  def test_job
+    str = "TEST"
+    job = TestWF.job(:repeat2, "Default", :number => 3).fork
+    while not job.done?
+      sleep 1
+    end
+
+    raise job.messages.last if job.error?
+
+    assert_equal ["TEST"] * 6 * "\n", job.load
+  end
+
+  def test_with_subdir
+    str = "TEST"
+    job = TestWF.job(:repeat2, "Default", :number => 3).fork
+    while not job.done?
+      sleep 1
+    end
+
+    raise job.messages.last if job.error?
+
+    assert_equal ["TEST"] * 6 * "\n", job.load
+  end
+
+  def test_search
+    str = "TEST"
+    job1 = TestWF.job(:repeat2, "subdir/Default", :number => 3).fork
+    job2 = TestWF.job(:repeat2, "subdir/Other", :number => 3).fork
+    job3 = TestWF.job(:repeat2, "Default", :number => 3).fork
+
+    while not job1.done? and not job2.done? and not job3.done?
+      sleep 1
+    end
+
+    assert_equal [job1.name, job2.name].sort, TestWF.jobs(:repeat2, "subdir/").sort
+    assert_equal [job1.name].sort, TestWF.jobs(:repeat2, "subdir/Default")
+    assert_equal [job1.name, job2.name, job3.name].sort, TestWF.jobs(:repeat2).sort
+  end
+
+  def test_double_dep
+    assert_equal ["TEST", "TEST\nTEST", "TEST\nTEST\nTEST\nTEST"], TestWF.job(:double_dep, "foo", :times => 2, :number => 2).run
+  end
+
+end