rbbt-util 3.2.1 → 4.0.0

data/test/rbbt/util/test_R.rb

@@ -7,7 +7,7 @@ class TestR < Test::Unit::TestCase
   end
 
   def test_tsv_R
-    tsv = TSV.new({:a => 1, :b => 2})
+    tsv = TSV.setup({:a => 1, :b => 2})
     tsv2 = tsv.R <<-EOF
 data = data + 1
     EOF

data/test/rbbt/util/test_chain_methods.rb

@@ -0,0 +1,22 @@
+require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
+require 'rbbt/util/chain_methods'
+require 'test/unit'
+
+module TestChainedModule
+  extend ChainMethods
+
+  def test_chain_get_brackets(value)
+    self.test_chain_clean_get_brackets(value).reverse
+  end
+
+  self.chain_prefix = :test_chain
+end
+
+class TestChaimMethods < Test::Unit::TestCase
+  def test_chained_reverse_get
+    a = ["test", "TEST"]
+    TestChainedModule.setup_chain(a)
+    assert_equal "test".reverse, a[0]
+    assert_equal "TEST".reverse, a[1]
+  end
+end

data/test/rbbt/util/test_filecache.rb

@@ -1,5 +1,4 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
-require 'rbbt-util'
 require 'rbbt/util/filecache'
 require 'test/unit'
 

data/test/rbbt/util/test_misc.rb

@@ -4,53 +4,72 @@ require 'test/unit'
 
 class TestMisc < Test::Unit::TestCase
 
-  def test_pdf2text_example
-    assert PDF2Text.pdf2text(datafile_test('example.pdf')).read =~ /An Example Paper/i
+  def test_id_filename?
+    TmpFile.with_file("") do |file|
+      assert Misc.is_filename?(file)
+      assert ! Misc.is_filename?("TEST STRING")
+    end
   end
 
-  def test_pdf2text_EPAR
-    assert PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Scientific_Discussion/human/000402/WC500033103.pdf").read =~ /Tamiflu/i
+  def test_merge_sorted_arrays
+    assert_equal [1,2,3,4], Misc.merge_sorted_arrays([1,3], [2,4])
   end
 
-  def test_pdf2text_wrong
-    assert_raise CMD::CMDError do PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB#").read end
+  def test_intersect_sorted_arrays
+    assert_equal [2,4], Misc.intersect_sorted_arrays([1,2,3,4], [2,4])
   end
+  def test_process_to_hash
+    list = [1,2,3,4]
+    assert_equal 4, Misc.process_to_hash(list){|l| l.collect{|e| e * 2}}[2]
+  end
+
+#  def test_pdf2text_example
+#    assert PDF2Text.pdf2text(datafile_test('example.pdf')).read =~ /An Example Paper/i
+#  end
+#
+#  def test_pdf2text_EPAR
+#    assert PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Scientific_Discussion/human/000402/WC500033103.pdf").read =~ /Tamiflu/i
+#  end
+#
+#  def test_pdf2text_wrong
+#    assert_raise CMD::CMDError do PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB#").read end
+#  end
 
   def test_string2hash
     assert(Misc.string2hash("--user-agent=firefox").include? "--user-agent")
-    assert(Misc.string2hash(":true")[:true] == true)
-    assert(Misc.string2hash("true")["true"] == true)
-    assert(Misc.string2hash("a=1")["a"] == 1)
-    assert(Misc.string2hash("a=b")["a"] == 'b')
-    assert(Misc.string2hash("a=b#c=d#:h=j")["c"] == 'd')
-    assert(Misc.string2hash("a=b#c=d#:h=j")[:h] == 'j')
-    assert(Misc.string2hash("a=b#c=d#:h=:j")[:h] == :j)
+    assert_equal(true, Misc.string2hash(":true")[:true])
+    assert_equal(true, Misc.string2hash("true")["true"])
+    assert_equal(1, Misc.string2hash("a=1")["a"])
+    assert_equal('b', Misc.string2hash("a=b")["a"])
+    assert_equal('d', Misc.string2hash("a=b#c=d#:h=j")["c"])
+    assert_equal('j', Misc.string2hash("a=b#c=d#:h=j")[:h])
+    assert_equal(:j, Misc.string2hash("a=b#c=d#:h=:j")[:h])
   end
   
   def test_named_array
-    a = NamedArray.name([1,2,3,4], %w(a b c d))
+    a = NamedArray.setup([1,2,3,4], %w(a b c d))
     assert_equal(1, a['a'])
   end
 
-  def test_path_relative_to
-    assert_equal "test/foo", Misc.path_relative_to('test/test/foo', 'test')
-  end
-
-  def test_chunk
-    test =<<-EOF
-This is an example file. Entries are separated by Entry
--- Entry
-1
-2
-3
--- Entry
-4
-5
-6
-    EOF
-
-    assert_equal "1\n2\n3", Misc.chunk(test, /^-- Entry/).first.strip
-  end
+#  def test_path_relative_to
+#    assert_equal "test/foo", Misc.path_relative_to('test/test/foo', 'test')
+#  end
+
+#  def test_chunk
+#    test =<<-EOF
+#This is an example file. Entries are separated by Entry
+#-- Entry
+#1
+#2
+#3
+#-- Entry
+#4
+#5
+#6
+#    EOF
+#
+#    assert_equal "1\n2\n3", Misc.chunk(test, /^-- Entry/).first.strip
+#  end
 
   def test_hash2string
     hash = {}
@@ -71,11 +90,11 @@ This is an example file. Entries are separated by Entry
     hash = {:a => /test/}
     assert_equal({}, Misc.string2hash(Misc.hash2string(hash)))
  
- end
+  end
 
   def test_merge
     a = [[1],[2]]
-    a = NamedArray.name a, %w(1 2)
+    a = NamedArray.setup a, %w(1 2)
     a.merge [3,4]
     assert_equal [1,3], a[0]
   end
@@ -112,51 +131,50 @@ This is an example file. Entries are separated by Entry
       end
       pids.each do |pid| Process.waitpid pid; assert $?.success? end
     end
-
-  end
-
-  def test_divide
-    assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
-  end
-
-  def test_process_to_hash
-    list = [1,2,3,4]
-    assert_equal 4, Misc.process_to_hash(list){|l| l.collect{|e| e * 2}}[2]
-  end
-
-  def test_add_method
-    a = "Test"
-    Misc.add_method a, :invert do self.reverse end
-    assert_equal "Test".reverse, a.invert
   end
 
-  def test_redefine_method
-    a = "Test"
-    worked = false
-    Misc.redefine_method a, :reverse, :old_reverse do worked = true; self.old_reverse end
-    assert_equal "Test".reverse, a.reverse
-    assert worked
-  end
-
-  def test_merge_sorted_arrays
-    assert_equal [1,2,3,4], Misc.merge_sorted_arrays([1,3], [2,4])
-  end
-
-  def test_intersect_sorted_arrays
-    assert_equal [2,4], Misc.intersect_sorted_arrays([1,2,3,4], [2,4])
-  end
-
-
-  def test_in_dir
-    TmpFile.with_file do |dir|
-      FileUtils.mkdir_p dir
-      Open.write(File.join(dir, 'test_file_in_dir'), 'test_file_in_dir')
-      Misc.in_dir(dir) do
-        assert Dir.glob("*").include? 'test_file_in_dir'
-      end
-      assert Dir.glob(File.join(dir, "*")).include?(File.join(dir, 'test_file_in_dir'))
-      assert(! Dir.glob("*").include?('test_file_in_dir'))
-    end
-  end
+#  def test_divide
+#    assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
+#  end
+#
+#  def test_process_to_hash
+#    list = [1,2,3,4]
+#    assert_equal 4, Misc.process_to_hash(list){|l| l.collect{|e| e * 2}}[2]
+#  end
+
+#  def test_add_method
+#    a = "Test"
+#    Misc.add_method a, :invert do self.reverse end
+#    assert_equal "Test".reverse, a.invert
+#  end
+#
+#  def test_redefine_method
+#    a = "Test"
+#    worked = false
+#    Misc.redefine_method a, :reverse, :old_reverse do worked = true; self.old_reverse end
+#    assert_equal "Test".reverse, a.reverse
+#    assert worked
+#  end
+#
+#  def test_merge_sorted_arrays
+#    assert_equal [1,2,3,4], Misc.merge_sorted_arrays([1,3], [2,4])
+#  end
+#
+#  def test_intersect_sorted_arrays
+#    assert_equal [2,4], Misc.intersect_sorted_arrays([1,2,3,4], [2,4])
+#  end
+#
+#
+#  def test_in_dir
+#    TmpFile.with_file do |dir|
+#      FileUtils.mkdir_p dir
+#      Open.write(File.join(dir, 'test_file_in_dir'), 'test_file_in_dir')
+#      Misc.in_dir(dir) do
+#        assert Dir.glob("*").include? 'test_file_in_dir'
+#      end
+#      assert Dir.glob(File.join(dir, "*")).include?(File.join(dir, 'test_file_in_dir'))
+#      assert(! Dir.glob("*").include?('test_file_in_dir'))
+#    end
+#  end
 
 end

data/test/rbbt/util/test_open.rb

@@ -70,6 +70,7 @@ class TestOpen < Test::Unit::TestCase
 
   end
 
+
   def test_gzip
     content =<<-EOF
 1

data/test/rbbt/util/test_tmpfile.rb

@@ -8,7 +8,7 @@ class TestTmpFile < Test::Unit::TestCase
     assert(TmpFile.tmp_file("test") =~ /tmp\/test\d+$/)
   end
 
-  def _test_do_tmp_file
+  def test_do_tmp_file
     content = "Hello World!"
     TmpFile.with_file(content) do |file|
       assert_equal content, File.open(file).read

data/test/rbbt/workflow/test_soap.rb

@@ -0,0 +1,103 @@
+require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
+require 'rbbt/workflow'
+require 'rbbt/workflow/soap'
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+
+module TestSOAPWF
+  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
+
+  export_synchronous :double
+  export_asynchronous :repeat2
+end
+
+TestSOAPWF.workdir = Rbbt.tmp.test.workflow
+
+class TestSOAP < Test::Unit::TestCase
+
+  def setup
+    port= 77177
+    $server = WorkflowSOAP.new TestSOAPWF, "Test WF", 'localhost', port
+    Thread.new do
+      $server.start
+    end
+    Open.write(Rbbt.tmp.test.wsdl.TestWS.find(:user), $server.wsdl)
+
+    $driver = SimpleWS.get_driver('http://localhost:' + port.to_s, "TestSOAPWF")
+  end
+
+  def teardown
+    $server.shutdown
+    FileUtils.rm_rf(Rbbt.tmp.test.wsdl.TestWS.find(:user))
+  end
+
+  def test_wsdl
+    assert $server.wsdl =~ /jobid/
+  end
+
+  def test_check_status
+    str = "TEST"
+    job = TestSOAPWF.job(:repeat2, nil, :number => 3)
+    id = TestSOAPWF.id_for job.path
+    job.run
+    assert $driver.done id
+  end
+
+  def test_launch_job
+    str = "TEST"
+    id = $driver.repeat2("Default", 3)
+    while not $driver.done id
+      sleep 1
+    end
+    assert $driver.status(id) == "done"
+  end
+
+  def test_load_job
+    str = "TEST"
+    id = $driver.repeat2("Default", 3)
+    while not $driver.done id
+      sleep 1
+    end
+    assert_equal ["TEST"] * 6 * "\n", $driver.load_string(id)
+  end
+
+  def test_synchronous
+    assert_equal 6, $driver.double(3)
+  end
+end

data/test/rbbt/workflow/test_step.rb

@@ -0,0 +1,142 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/workflow/task'
+require 'rbbt/workflow/step'
+require 'rbbt'
+
+class TestStrp < Test::Unit::TestCase
+
+  def test_step
+    task  = Task.setup do "TEST" end
+    task2  = Task.setup do raise "Persistence ignored" end
+    TmpFile.with_file do |tmp|
+      step = Step.new tmp, task
+      assert_equal "TEST", step.run
+      assert File.exists? tmp
+      step = Step.new tmp, task2
+      assert_equal "TEST", step.run
+    end
+  end
+
+  def test_dependency
+    str = "TEST"
+    str2 = "TEST2"
+    TmpFile.with_file do |tmpfile|
+
+      task1  = Task.setup :result_type => nil do 
+        Open.write(tmpfile, str); 
+      end
+      step1 = Step.new tmpfile + 'step1', task1
+
+      task2  = Task.setup :result_type => :string do 
+        Open.read(tmpfile) 
+      end
+      step2 = Step.new tmpfile + 'step2', task2, [], [step1]
+
+      step2.run
+      assert_equal "TEST", Open.read(tmpfile + 'step2')
+
+      task2  = Task.setup :result_type => :string do 
+        str2 
+      end
+      step2 = Step.new tmpfile + 'step2', task2, [], step1
+
+      step1.clean
+      sleep 1
+      step2.run
+      assert_equal "TEST2", Open.read(tmpfile + 'step2')
+    end
+  end
+
+  def test_exec
+    TmpFile.with_file do |lock|
+      task  = Task.setup do "TEST" end
+      TmpFile.with_file do |tmp|
+        step = Step.new tmp, task
+        assert_equal "TEST", step.exec
+      end
+    end
+  end
+
+
+  def test_fork
+    TmpFile.with_file do |lock|
+      task  = Task.setup do while not File.exists?(lock) do sleep 1; end; "TEST" end
+      TmpFile.with_file do |tmp|
+        step = Step.new tmp, task
+        job = step.fork
+        assert !job.done?
+        assert_raise RuntimeError do step.fork end
+        sleep 1
+        Open.write(lock, "open")
+        assert_equal "TEST", job.join.load
+        assert job.done?
+      end
+    end
+  end
+
+  def test_abort
+    TmpFile.with_file do |lock|
+      task  = Task.setup do while not File.exists?(lock) do sleep 1; end; "TEST" end
+      TmpFile.with_file do |tmp|
+        step = Step.new tmp, task
+        job = step.fork
+        assert !job.done?
+        assert_raise RuntimeError do step.fork end
+        sleep 1
+        while not job.abort do sleep 1 end
+        Open.write(lock, "open")
+        job.join
+        assert job.error?
+      end
+    end
+  end
+
+  def test_files
+    TmpFile.with_file do |lock|
+      task  = Task.setup do 
+        Open.write(file("test"),"TEST")
+      end
+      TmpFile.with_file do |tmp|
+        step = Step.new tmp, task
+        job = step.fork
+        while not job.done? do sleep 1 end
+        assert_equal "TEST", Open.read(job.file("test"))
+      end
+    end
+  end
+
+  def test_messages
+    TmpFile.with_file do |lock|
+      task  = Task.setup do 
+        message "WRITE"
+        Open.write(file("test"),"TEST")
+      end
+      TmpFile.with_file do |tmp|
+        step = Step.new tmp, task
+        job = step.fork
+        while not job.done? do sleep 1 end
+        assert_equal "TEST", Open.read(job.file("test"))
+        assert_equal "WRITE", job.messages.last
+      end
+    end
+  end
+
+  def test_subdir
+    TmpFile.with_file do |lock|
+      task  = Task.setup do 
+        message "WRITE"
+        Open.write(file("test"),"TEST")
+      end
+
+      TmpFile.with_file do |tmp|
+        step = Step.new File.join(tmp, 'subdir1', 'subdir2'), task
+        job = step.fork
+        while not job.done? do sleep 1 end
+        assert_equal "TEST", Open.read(job.file("test"))
+        assert_equal "WRITE", job.messages.last
+      end
+    end
+  end
+
+
+end