rbbt-util 3.0.2 → 3.0.3

data/test/rbbt/util/test_misc.rb

@@ -4,19 +4,19 @@ require 'test/unit'
 
 class TestMisc < Test::Unit::TestCase
 
-  def test_pdf2text_example
+  def _test_pdf2text_example
     assert PDF2Text.pdf2text(test_datafile('example.pdf')).read =~ /An Example Paper/i
   end
 
-  def test_pdf2text_EPAR
+  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
+  def _test_pdf2text_wrong
     assert_raise CMD::CMDError do PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB#") end
   end
 
-  def test_string2hash
+  def _test_string2hash
     assert(Misc.string2hash("--user-agent=firefox").include? "--user-agent")
     assert(Misc.string2hash(":true")[:true] == true)
     assert(Misc.string2hash("true")["true"] == true)
@@ -27,17 +27,17 @@ class TestMisc < Test::Unit::TestCase
     assert(Misc.string2hash("a=b#c=d#:h=:j")[:h] == :j)
   end
   
-  def test_named_array
+  def _test_named_array
     a = NamedArray.name([1,2,3,4], %w(a b c d))
     assert_equal(1, a['a'])
   end
 
-  def test_path_relative_to
+  def _test_path_relative_to
     assert_equal "test/foo", Misc.path_relative_to('test/test/foo', 'test')
   end
 
-  def test_chunk
-    test =<<-EOF
+  def _test_chunk
+    _test =<<-EOF
 This is an example file. Entries are separated by Entry
 -- Entry
 1
@@ -52,7 +52,7 @@ This is an example file. Entries are separated by Entry
     assert_equal "1\n2\n3", Misc.chunk(test, /^-- Entry/).first.strip
   end
 
-  def test_hash2string
+  def _test_hash2string
     hash = {}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
 
@@ -73,11 +73,43 @@ This is an example file. Entries are separated by Entry
  
  end
 
-  def test_merge
+  def _test_merge
     a = [[1],[2]]
     a = NamedArray.name a, %w(1 2)
     a.merge [3,4]
     assert_equal [1,3], a[0]
   end
 
+  def _test_indiferent_hash
+    a = {:a => 1, "b" => 2}
+    a.extend IndiferentHash
+
+    assert 1, a["a"]
+    assert 1, a[:a]
+    assert 2, a["b"]
+    assert 2, a[:b]
+  end
+
+  def test_lockfile
+    TmpFile.with_file do |tmpfile|
+      pids = []
+      3.times do |i|
+        pids << Process.fork do 
+          pid = pid.to_s
+          Misc.lock(tmpfile, pid) do |f, val|
+            Open.write(f, val)
+            sleep rand * 2
+            if pid == Open.read(tmpfile)
+              exit(0)
+            else
+              exit(1)
+            end
+          end
+        end
+      end
+      pids.each do |pid| Process.waitpid pid; assert $?.success? end
+    end
+
+  end
+
 end

data/test/rbbt/util/test_task.rb

@@ -27,7 +27,7 @@ class TestTask < Test::Unit::TestCase
   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")
+      job = task.job(:job1, "TestName")
       assert_equal "job1" << "_" << Misc.hash2md5(:name => "TestName"), job.id
       job.fork
       job.join
@@ -39,13 +39,13 @@ class TestTask < Test::Unit::TestCase
 
   def test_task_result
     task = Task.new(:test_task, nil, :name) do |name| name end
-    job = task.job(:job1, :name => "TestName")
+    job = task.job(:job1, "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")
+    job = task.job(:job1, "TestName")
     assert_equal "TestName", job.fork.join.info[:options][:name]
   end
 
@@ -54,15 +54,15 @@ class TestTask < Test::Unit::TestCase
       step :one
       name 
     end
-    job = task.job(:job1, :name => "TestName")
+    job = task.job(:job1, "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")
+    job = task.job(:job1, "TestName")
     assert_equal "TestName", job.fork.join.info[:options][:name]
-    job = task.job(:job1, :name => "TestName")
+    job = task.job(:job1, "TestName")
     assert_equal "TestName", job.join.info[:options][:name]
   end
 
@@ -114,5 +114,6 @@ class TestTask < Test::Unit::TestCase
     job.clean
     assert (not File.exists?(job.path))
   end
+
 end
 

data/test/rbbt/util/test_tc_hash.rb

@@ -61,9 +61,27 @@ class TestTCHash < Test::Unit::TestCase
       t["2"] = [[3],[4,5]]
 
       t = TCHash.get f
-      t.collect do |k,v| 
-       assert_equal [["3"],["4","5"]], t["2"]
+      assert_equal [["3"],["4","5"]], t["2"]
+    end
+  end
+
+  def test_non_blocking
+    TmpFile.with_file do |f|
+      t = TCHash.get f, true, :double
+      t["1"] = [[1],[2]]
+      t["2"] = [[3],[4,5]]
+      t.close
+
+      pid = Process.fork do
+        t2 = TCHash.get f, true, :double
+        assert_equal [["3"],["4","5"]], t2["2"]
+        exit
       end
+
+      t2 = TCHash.get f, true, :double
+      assert_equal [["3"],["4","5"]], t2["2"]
+
+      Process.wait pid
     end
   end
 end

data/test/rbbt/util/test_workflow.rb

@@ -13,7 +13,6 @@ module MathWF
   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)
@@ -22,6 +21,7 @@ module MathWF2
 
   extend WorkFlow
 
+
   task_option :value
   task :input => :integer do |value| value end
 
@@ -35,29 +35,51 @@ module MathWF2
   task_option :times, "Times to multiply by", :integer, 10
   task_dependencies :add_1
   task :times => :integer do |times| mult(input, times) end
+
+  task_dependencies []
+  task :persist do  task.workflow.methods.include? "local_persist" end
+end
+
+
+module ConWF
+  extend WorkFlow
+  task :one => :integer do 1 end
+
+  task_dependencies []
+  task :two => :integer do 2 end
+
+  task_option :init, "Initial value", :string
+  task_dependencies  Proc.new{|jobname,run_options| 
+    ConWF.job(run_options[:init].to_sym, jobname, {})
+  }
+  task :times_2 => :integer do 
+    input * 2
+  end
 end
 
 MathWF2.jobdir = Rbbt.tmp.test.jobs.mathwf.find :user
+MathWF.jobdir  = Rbbt.tmp.test.jobs.mathwf.find :user
+ConWF.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)
+    job = MathWF.tasks[:times_2].job(:job1, 1)
     assert_equal 4, job.fork.join.load
-    job = MathWF.tasks[:times_4].job(:job1, :value => 1)
+    job = MathWF.tasks[:times_4].job(:job1, 1)
     assert_equal 8, job.fork.join.load
   end
 
   def test_math_wf2
-    job = MathWF2.tasks[:times_2].job(:job1, :value => 1)
+    job = MathWF2.tasks[:times_2].job(:job1, 1)
     job.fork.join
     assert_equal 4, job.load
-    job = MathWF2.tasks[:times_4].job(:job1, :value => 1)
+    job = MathWF2.tasks[:times_4].job(:job1, 1)
     assert_equal 8, job.fork.join.load
   end
 
   def test_math_run
-    job = MathWF2.job(:times_2, :job1,1)
+    job = MathWF2.job(:times_2, :job1, 1)
     job.fork.join
     assert_equal 4, job.load
   end
@@ -84,10 +106,18 @@ class TestWorkFlow < Test::Unit::TestCase
     assert File.exists?(job.path)
     job.clean
     assert (not File.exists?(job.path))
-    assert File.exists?(job.dependencies.first.first.path)
+    assert File.exists?(job.previous_jobs.first.path)
     job.recursive_clean
-    assert (not File.exists?(job.dependencies.first.first.path))
+    assert (not File.exists?(job.previous_jobs.first.path))
   end
 
+  def test_local_persist
+    assert MathWF2.run(:persist, :persist).load
+  end
+
+  def test_conditional
+    assert 2, ConWF.run(:times_2, "Test", "one").load
+    assert 4, ConWF.run(:times_2, "Test", "two").load
+  end
 end
 

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

@@ -352,5 +352,22 @@ row6,dd,dd,ee,,
     end
  
   end
+
+  def test_merge_rows
+    file1 =<<-EOF
+row1,a,b,c
+row1,aa,bb,cc
+row2,A,B,C
+row3,1,2,3
+    EOF
+    TmpFile.with_file(file1) do |input|
+      TmpFile.with_file() do |output|
+        TSV.merge_rows Open.open(input), output
+        assert Open.read(output) =~ /a|aa/
+      end
+    end
+
+
+  end
 end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-util
 version: !ruby/object:Gem::Version 
-  hash: 3
+  hash: 1
   prerelease: 
   segments: 
   - 3
   - 0
-  - 2
-  version: 3.0.2
+  - 3
+  version: 3.0.3
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-19 00:00:00 +01:00
+date: 2011-03-23 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -88,6 +88,20 @@ dependencies:
         version: "0"
   type: :runtime
   version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: lockfile
+  prerelease: false
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id006
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@fdi.ucm.es
 executables: 
@@ -119,6 +133,7 @@ files:
 - lib/rbbt/util/simpleDSL.rb
 - lib/rbbt/util/simpleopt.rb
 - lib/rbbt/util/task.rb
+- lib/rbbt/util/task/job.rb
 - lib/rbbt/util/tc_hash.rb
 - lib/rbbt/util/tmpfile.rb
 - lib/rbbt/util/tsv.rb