rbbt-util 2.1.0 → 3.0.2

data/test/rbbt/util/test_task.rb

@@ -0,0 +1,118 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/util/task'
+
+Task.basedir = Rbbt.tmp.test.taskjobs.find :user
+
+class TestTask < Test::Unit::TestCase
+  def test_task
+    $true
+    task = Task.new(:test_task) do $true = true end
+    job = task.job(:job1)
+    job.start
+
+    assert $true
+  end
+
+  def test_task_fork
+    TmpFile.with_file do |f|
+      task = Task.new(:test_task) do Open.write(f, "Test") end
+      job = task.job(:job1)
+      job.fork
+      job.join
+
+      assert File.exists? f
+    end
+  end
+
+  def test_task_options
+    TmpFile.with_file do |f|
+      task = Task.new(:test_task, nil, :name) do |name| Open.write(f, name) end
+      job = task.job(:job1, :name => "TestName")
+      assert_equal "job1" << "_" << Misc.hash2md5(:name => "TestName"), job.id
+      job.fork
+      job.join
+
+      assert File.exists? f
+      assert_equal "TestName", File.open(f).read
+    end
+  end
+
+  def test_task_result
+    task = Task.new(:test_task, nil, :name) do |name| name end
+    job = task.job(:job1, :name => "TestName")
+    assert_equal "TestName", job.fork.join.load
+  end
+
+  def test_task_info
+    task = Task.new(:test_task, nil, :name) do |name| name end
+    job = task.job(:job1, :name => "TestName")
+    assert_equal "TestName", job.fork.join.info[:options][:name]
+  end
+
+  def test_task_status
+    task = Task.new(:test_task, nil, :name) do |name| 
+      step :one
+      name 
+    end
+    job = task.job(:job1, :name => "TestName")
+    assert_equal "TestName", job.fork.join.info[:options][:name]
+  end
+
+  def test_task_reopen
+    task = Task.new(:test_task, nil, :name) do |name| name end
+    job = task.job(:job1, :name => "TestName")
+    assert_equal "TestName", job.fork.join.info[:options][:name]
+    job = task.job(:job1, :name => "TestName")
+    assert_equal "TestName", job.join.info[:options][:name]
+  end
+
+  def test_marshal_persistence
+    task = Task.new(:test_task, :marshal) do 
+      {:a => :b}
+    end
+    job = task.job(:job1).fork.join
+    assert Hash === job.load
+    assert_equal :b, job.load[:a]
+  end
+
+  def test_yaml_persistence
+    task = Task.new(:test_task, :yaml) do 
+      {:a => :b}
+    end
+    job = task.job(:job1).fork.join
+    assert Hash === job.load
+    assert_equal :b, job.load[:a]
+    assert_equal :b, YAML.load(job.open)[:a]
+  end
+
+  def test_tsv_persistence
+    task = Task.new(:test_task, :tsv) do 
+      tsv = TSV.new({})
+      tsv.key_field = "A"
+      tsv.fields = ["B"]
+      tsv.type = :list
+      tsv["a"] = ["b"]
+      tsv
+    end
+    job = task.job(:job1).fork.join
+    assert TSV === job.load
+    assert_equal "b", job.load["a"]["B"]
+  end
+
+  def test_clean
+    task = Task.new(:test_task, :tsv) do 
+      tsv = TSV.new({})
+      tsv.key_field = "A"
+      tsv.fields = ["B"]
+      tsv.type = :list
+      tsv["a"] = ["b"]
+      tsv
+    end
+    job = task.job(:job1).fork.join
+
+    assert File.exists?(job.path)
+    job.clean
+    assert (not File.exists?(job.path))
+  end
+end
+

data/test/rbbt/util/test_tsv.rb

@@ -178,7 +178,11 @@ row2    A    B
       assert !tsv1.case_insensitive
       assert tsv1.include? "A"
     end
-
+    def test_create_array
+      tsv = TSV.new(%w(a b c))
+      assert_equal %w(a b c).sort, tsv.keys.sort
+      assert_equal [[]] * tsv.keys.length, tsv.values
+    end
   end
 end
 

data/test/rbbt/util/test_workflow.rb

@@ -1,78 +1,93 @@
-require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
-require 'rbbt'
-require 'rbbt/util/tsv'
-require 'rbbt/util/tmpfile'
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
 require 'rbbt/util/workflow'
 
-class TestWorkflow < Test::Unit::TestCase
-
-  def workflow
-    TmpFile.with_file do |dir|
-      old_pdw = FileUtils.pwd
-      begin
-        FileUtils.mkdir dir
-        cd dir
-        yield dir
-      ensure
-        cd old_pdw
-      end
-    end
+module MathWF
+  extend WorkFlow
+  self.tasks[:input] = Task.new(:input, :marshal, :value) do |value| value end
+  self.tasks[:add_1] = Task.new(:add_1, :marshal) do input + 1 end
+  self.tasks[:add_1].dependencies << :input
+  self.tasks[:times_2] = Task.new(:times_2, :marshal) do input * 2 end
+  self.tasks[:times_2].dependencies << :add_1
+  self.tasks[:times_4] = Task.new(:times_4, :marshal) do input * 4 end
+  self.tasks[:times_4].dependencies << :add_1
+  self.tasks.each do |name, task| task.workflow = self end
+end
+
+MathWF.basedir  = Rbbt.tmp.test.jobs.mathwf.find :user
+
+module MathWF2
+  def mult(num, t)
+    num * t
   end
 
-  def _test_run
-    workflow do |dir|
-      WorkFlow.run do
-        file :foo do |t|
-          touch t.name
-        end
-      end
-      assert File.exists? File.join(dir, 'foo')
-    end
+  extend WorkFlow
+
+  task_option :value
+  task :input => :integer do |value| value end
+
+  task :add_1 => :integer do input + 1 end
+
+  task :times_2 => :integer do input * 2 end
+
+  task_dependencies :add_1
+  task :times_4 => :integer do input * 4 end
+  
+  task_option :times, "Times to multiply by", :integer, 10
+  task_dependencies :add_1
+  task :times => :integer do |times| mult(input, times) end
+end
+
+MathWF2.jobdir = Rbbt.tmp.test.jobs.mathwf.find :user
+
+class TestWorkFlow < Test::Unit::TestCase
+ 
+  def test_math_wf
+    job = MathWF.tasks[:times_2].job(:job1, :value => 1)
+    assert_equal 4, job.fork.join.load
+    job = MathWF.tasks[:times_4].job(:job1, :value => 1)
+    assert_equal 8, job.fork.join.load
   end
 
-  def _test_step
-    jobid = 'jobid'
-    target_step = 'last'
-    workflow do |dir|
-
-      WorkFlow.run(File.join(target_step, jobid)) do
-        self.extend WorkFlow::Runner
-
-        step :first do 
-          "Test"
-        end
-
-        step :last do 
-          data.reverse
-        end
-      end
-      assert File.exists? File.join(dir, target_step, 'jobid')
-      assert_equal 'tseT', Open.read(File.join(dir, target_step, 'jobid'))
-    end
+  def test_math_wf2
+    job = MathWF2.tasks[:times_2].job(:job1, :value => 1)
+    job.fork.join
+    assert_equal 4, job.load
+    job = MathWF2.tasks[:times_4].job(:job1, :value => 1)
+    assert_equal 8, job.fork.join.load
   end
 
-  def test_input
-    jobid = 'jobid'
-    target_step = 'last'
-    message = "Message"
+  def test_math_run
+    job = MathWF2.job(:times_2, :job1,1)
+    job.fork.join
+    assert_equal 4, job.load
+  end
 
-    workflow do |dir|
+  def test_math_defaults
+    assert MathWF2.tasks[:times].option_defaults.include? :times
 
-      WorkFlow.run(File.join(target_step, jobid), message) do
-        self.extend WorkFlow::Runner
+    job = MathWF2.job(:times, :job1, 1)
+    job.fork.join
+    assert job.done?
+    puts job.messages
+    assert File.exists? job.path
+    assert_equal 20, job.load
 
-        step :first, :marshal do 
-          input
-        end
 
-        step :last do 
-          data.reverse
-        end
-      end
+    job = MathWF2.job(:times, :job1, 1, :times => 20)
+    job.fork.join
+    assert_equal 40, job.load
+  end
 
-      assert File.exists? File.join(dir, target_step, 'jobid')
-      assert_equal message.reverse, Open.read(File.join(dir, target_step, 'jobid'))
-    end
+  def test_recursive_clean
+    job = MathWF2.job(:times, :job1, 1, :times => 20)
+    job.fork.join
+    assert File.exists?(job.path)
+    job.clean
+    assert (not File.exists?(job.path))
+    assert File.exists?(job.dependencies.first.first.path)
+    job.recursive_clean
+    assert (not File.exists?(job.dependencies.first.first.path))
   end
+
 end
 

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

@@ -206,22 +206,21 @@ row1    e
 row2    E
     EOF
 
-    Rbbt.claim "data", StringIO.new(content1), "Test1"
-    Rbbt.claim "data", StringIO.new(content2), "Test2"
-    Rbbt.claim "identifiers", StringIO.new(content_index), "Test2"
+    Rbbt.tmp.test.test1.data.define_as_string content1
+    Rbbt.tmp.test.test2.data.define_as_string content2
+    Rbbt.tmp.test.test2.identifiers.define_as_string content_index
 
     tsv1 = tsv2 = nil
 
-    tsv1 = Rbbt.files.Test1.data.tsv :double,  :sep => /\s+/
-    tsv2 = Rbbt.files.Test2.data.tsv :double,  :sep => /\s+/
+    tsv1 = Rbbt.tmp.test.test1.data.tsv :double,  :sep => /\s+/
+    tsv2 = Rbbt.tmp.test.test2.data.tsv :double,  :sep => /\s+/
 
-    tsv2.identifiers = Rbbt.files.Test2.identifiers.produce
+    tsv2.identifiers = Rbbt.tmp.test.test2.identifiers.produce
 
     tsv1.attach tsv2, "OtherID", :in_namespace => false
 
     assert_equal tsv1.fields,%w(ValueA ValueB OtherID)
     assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"]
-
   end
 
   def test_find_path
@@ -264,5 +263,94 @@ row2    E
  
     assert_equal %w(ValueA ValueB ValueE), tsv1.fields
   end
+
+  def test_paste
+    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.paste(StringIO.new(file1), StringIO.new(file2), f, " ")
+      assert_equal result, Open.read(f)
+    end
+  end
+
+  def test_paste
+    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.new StringIO.new(file1), :sep => " "
+      tsv2 = TSV.new StringIO.new(file2), :sep => " "
+      tsv_r = tsv1.paste tsv2
+      assert_equal result, tsv_r.to_s(tsv_r.keys.sort, true).gsub(/\t/,' ')
+    end
+  end
+
+  def test_paste_merge
+    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|
+      TSV.paste_merge StringIO.new(file1), StringIO.new(file2), f, ','
+
+      assert_equal result, Open.read(f)
+    end
+ 
+  end
 end
 

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

@@ -94,7 +94,6 @@ C    B    Id3
 
     assert_equal "C", tsv1["row2"]["ValueC"].first
     assert %w(c cc ccc).include? tsv1["row1"]["ValueC"].first
-    ddd tsv1
     assert_equal %w(Id1 Id2), tsv1["row1"]["OtherID"].sort
   end
 

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

@@ -222,5 +222,25 @@ row3    a    C    Id4
  
   end
 
+  def test_add_field_double_with_list_result
+     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 "Test" do
+        "test"
+      end
+
+      assert Array === tsv["row1"]["Test"]
+    end
+ 
+  end
+
 end
 

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

@@ -0,0 +1,9 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/tsv/resource'
+
+class TestTSVResource < Test::Unit::TestCase
+  def test_true
+    assert true
+  end
+end
+