rbbt-util 5.1.0 → 5.2.0

data/test/rbbt/test_resource.rb

@@ -1,4 +1,5 @@
 require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
+require 'rbbt'
 require 'rbbt/resource'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
@@ -41,7 +42,7 @@ class TestTSV < Test::Unit::TestCase
   end
 
 
-  def test_resolve
+  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)
 

data/test/rbbt/test_workflow.rb

@@ -7,6 +7,8 @@ require 'test/unit'
 module TestWF
   extend Workflow
 
+  ddd TestWF.methods.sort
+
   helper :user do
     "User"
   end 
@@ -67,6 +69,7 @@ class TestWorkflow < Test::Unit::TestCase
   def test_helper
     assert_equal "User", TestWF.job(:user, "Default", :number => 3).run
   end
+
   def test_job
     str = "TEST"
     job = TestWF.job(:repeat2, "Default", :number => 3).fork
@@ -110,4 +113,14 @@ class TestWorkflow < Test::Unit::TestCase
     assert_equal ["TEST", "TEST\nTEST", "TEST\nTEST\nTEST\nTEST"], TestWF.job(:double_dep, "foo", :times => 2, :number => 2).run
   end
 
+  def test_object_workflow
+    a = ""
+    a.extend Workflow
+    a.task :foo => :string do
+      "bar"
+    end
+    
+    assert_equal 'bar', a.job(:foo).exec
+  end
+
 end

data/test/rbbt/tsv/test_manipulate.rb

@@ -224,5 +224,23 @@ row3    a
     end
   end
 
+  def test_transpose
+     content =<<-EOF
+#: :type=:list
+#Row   vA   vB   vID
+row1    a    b    Id1
+row2    A    B    Id3
+row3    a    C    Id4
+    EOF
+ 
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+
+      assert_equal %w(vA vB vID),  tsv.transpose("Values").keys
+
+    end
+ 
+  end
+
 
 end

data/test/rbbt/util/test_misc.rb

@@ -199,45 +199,25 @@ class TestMisc < Test::Unit::TestCase
     g = Misc.prepare_entity("TP53", "Gene", :format => "Associated Gene Name", "organism" => "Hsa/jun2011")
   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_collapse_ranges
+    ranges = [(0..100), (50..150), (51..61),(200..250), (300..324),(320..350)]
+    assert_equal [(0..150),(200..250), (300..350)], Misc.collapse_ranges(ranges)
+  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_humanize
+    str1 = "test_string"
+    str2 = "TEST_string"
+    str3 = "test"
+
+    assert_equal "Test string", Misc.humanize(str1)
+    assert_equal "TEST string", Misc.humanize(str2)
+    assert_equal "Test", Misc.humanize(str3)
+  end
 
+  def test_snake_case
+    str1 = "ACRONIMTest"
+    str2 = "ACRONIM_test"
+    assert_equal "ACRONIM_test", Misc.snake_case(str1)
+    assert_equal "ACRONIM_test", Misc.snake_case(str2)
+  end
 end

data/test/rbbt/util/test_tmpfile.rb

@@ -15,6 +15,14 @@ class TestTmpFile < Test::Unit::TestCase
     end
   end
 
+  def test_extension
+    TmpFile.with_file(nil, true, :extension => 'txt') do |file|
+      ddd file
+      assert file =~ /\.txt$/
+    end
+
+  end
+
 end
 
 

data/test/rbbt/workflow/test_soap.rb

@@ -91,6 +91,8 @@ class TestSOAP < Test::Unit::TestCase
   def test_load_job
     str = "TEST"
     id = $driver.repeat2("Default", 3)
+    $driver.clean id
+    id = $driver.repeat2("Default", 3)
     while not $driver.done id
       sleep 1
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.1.0
+  version: 5.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-15 00:00:00.000000000 Z
+date: 2013-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -155,6 +155,22 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: highline
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@cnio.es
 executables:
@@ -165,6 +181,8 @@ executables:
 - rbbt_exec.rb
 - rbbt_Rutil.rb
 - rbbt_monitor.rb
+- rbbt
+- rbbt_dangling_locks.rb
 extensions: []
 extra_rdoc_files:
 - LICENSE
@@ -211,11 +229,20 @@ files:
 - lib/rbbt/workflow.rb
 - lib/rbbt/workflow/accessor.rb
 - lib/rbbt/workflow/annotate.rb
+- lib/rbbt/workflow/definition.rb
 - lib/rbbt/workflow/soap.rb
 - lib/rbbt/workflow/step.rb
 - lib/rbbt/workflow/task.rb
+- lib/rbbt/workflow/usage.rb
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
+- share/rbbt_commands/conf/web_user/add
+- share/rbbt_commands/conf/web_user/list
+- share/rbbt_commands/conf/web_user/remove
+- share/rbbt_commands/workflow/remote/add
+- share/rbbt_commands/workflow/remote/list
+- share/rbbt_commands/workflow/remote/remove
+- share/rbbt_commands/workflow/task
 - README.rdoc
 - test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_index.rb
@@ -252,6 +279,8 @@ files:
 - bin/rbbt_exec.rb
 - bin/rbbt_Rutil.rb
 - bin/rbbt_monitor.rb
+- bin/rbbt
+- bin/rbbt_dangling_locks.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses: []
 post_install_message: