rbbt-util 5.4.1 → 5.5.0

data/test/rbbt/test_workflow.rb

@@ -104,11 +104,13 @@ class TestWorkflow < Test::Unit::TestCase
 
     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
+    assert TestWF.jobs(:repeat2).include?(job1.name)
+    assert TestWF.jobs(:repeat2).include?(job2.name)
+    assert TestWF.jobs(:repeat2).include?(job3.name)
   end
 
   def test_double_dep
-    assert_equal ["TEST", "TEST\nTEST", "TEST\nTEST\nTEST\nTEST"], TestWF.job(:double_dep, "foo", :times => 2, :number => 2).run
+    assert_equal ["TEST", "TEST\nTEST", "TEST\nTEST\nTEST\nTEST"], TestWF.job(:double_dep, "foo", :times => 2, :number => 2).clean.run
   end
 
   def test_object_workflow

data/test/rbbt/tsv/test_change_id.rb

@@ -0,0 +1,43 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/tsv'
+require 'rbbt/tsv/change_id'
+
+class TestTSVChangeID < Test::Unit::TestCase
+
+  FILE1=<<-EOF
+#: :sep=' '
+#A B C
+a b c
+aa bb cc
+  EOF
+
+  FILE2=<<-EOF
+#: :sep=' '
+#X Y Z
+x y z
+xx yy zz
+  EOF
+
+  IDENTIFIERS=<<-EOF
+#: :sep=' '
+#A X
+a x
+aa xx
+  EOF
+
+  def tsv(text, options = {})
+    options = Misc.add_defaults options, :type => :list
+    TSV.open StringIO.new(text), options
+  end
+
+  def setup
+    @f1 = tsv(FILE1)
+    @f2 = tsv(FILE2)
+    @id = tsv(IDENTIFIERS)
+  end
+
+  def test_change_id
+    @f1.identifiers = @id
+    puts @f1.change_key "X"
+  end
+end

data/test/rbbt/tsv/test_index.rb

@@ -6,14 +6,15 @@ class TestTSVManipulate < Test::Unit::TestCase
 
   def load_segment_data(data)
     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
+
     tsv.add_field "End" do |key, values|
       values["Range"].last
     end
 
-    puts tsv.type
     tsv = tsv.slice ["Start", "End"]
  
     tsv

data/test/rbbt/tsv/test_manipulate.rb

@@ -132,6 +132,37 @@ row3    a    C    Id4
     end
   end
 
+  def test_select_invert
+     content =<<-EOF
+#Id    ValueA    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.open(filename, :sep => /\s+/)
+      assert tsv.type == :double
+      
+      new = tsv.select %w(b Id4), true
+      assert_equal %w(row2).sort, new.keys
+
+      new = tsv.select /b|Id4/, true
+      assert_equal %w(row2).sort, new.keys
+      
+      new = tsv.select %w(b Id4)
+      assert_equal %w(row1 row3).sort, new.keys.sort
+
+      new = tsv.select do |k,v| 
+        v["ValueA"].include? "A" 
+      end
+      assert_equal %w(row2).sort, new.keys.sort
+
+      tsv = TSV.open(filename, :sep => /\s+/, :type => :flat)
+      assert tsv.type != :double
+    end
+  end
+
   def test_process
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
@@ -242,5 +273,25 @@ row3    a    C    Id4
  
   end
 
+  def test_through_flat
+     content =<<-EOF
+#: :type=:flat
+#Row   vA
+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+/)
+      tsv.through :key, ["vA"] do |k,v|
+        assert_equal 3, v.length
+      end
+
+
+    end
+ 
+  end
+
 
 end

data/test/rbbt/util/test_misc.rb

@@ -1,6 +1,8 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'rbbt/util/misc'
 require 'test/unit'
+require 'rbbt/tsv'
+require 'rbbt/entity'
 
 class TestMisc < Test::Unit::TestCase
 
@@ -42,6 +44,20 @@ class TestMisc < Test::Unit::TestCase
   def test_intersect_sorted_arrays
     assert_equal [2,4], Misc.intersect_sorted_arrays([1,2,3,4], [2,4])
   end
+
+  def test_sorted_array_matches
+    assert_equal [1,3], Misc.sorted_array_hits(%w(a b c d e), %w(b d))
+  end
+
+  def test_binary_include?
+    a = %w(a b c d e).sort
+    assert Misc.binary_include?(a, "a")
+    assert(!Misc.binary_include?(a, "z"))
+    assert(Misc.binary_include?(a, "b"))
+    assert(Misc.binary_include?(a, "c"))
+    assert(Misc.binary_include?(a, "d"))
+  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]
@@ -127,8 +143,8 @@ class TestMisc < Test::Unit::TestCase
     a = {:a => 1, "b" => 2}
     a.extend IndiferentHash
 
-    assert_equal 1, a["a"]
     assert_equal 1, a[:a]
+    assert_equal 1, a["a"]
     assert_equal 2, a["b"]
     assert_equal 2, a[:b]
   end
@@ -219,4 +235,8 @@ class TestMisc < Test::Unit::TestCase
   def test_correct_vcf_mutations
     assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
   end
+
+  def test_fingerprint
+    puts Misc.fingerprint({:a => 1})
+  end
 end

data/test/test_helper.rb

@@ -11,13 +11,17 @@ class Test::Unit::TestCase
   include FileUtils
 
   def setup
-    Persist.cachedir = Rbbt.tmp.test.persistence.find :user
+    if defined? Persist
+      Persist.cachedir = Rbbt.tmp.test.persistence.find :user
+    end
   end
 
   def teardown
-    FileUtils.rm_rf Path.setup("", 'rbbt').tmp.test.find :user
-    Persist::TC_CONNECTIONS.values.each do |c| c.close end
-    Persist::TC_CONNECTIONS.clear
+    if defined? Persist
+      FileUtils.rm_rf Path.setup("", 'rbbt').tmp.test.find :user
+      Persist::TC_CONNECTIONS.values.each do |c| c.close end
+      Persist::TC_CONNECTIONS.clear
+    end
   end
 
   def datafile_test(file)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.4.1
+  version: 5.5.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-07 00:00:00.000000000 Z
+date: 2013-10-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -24,34 +24,6 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: spreadsheet
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: ruby-prof
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: progress-monitor
   requirement: !ruby/object:Gem::Requirement
@@ -80,48 +52,6 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: narray
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: simplews
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: highline
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: ZenTest
   requirement: !ruby/object:Gem::Requirement
@@ -136,20 +66,6 @@ dependencies:
     - - '='
       - !ruby/object:Gem::Version
         version: '4.3'
-- !ruby/object:Gem::Dependency
-  name: RubyInline
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@cnio.es
 executables:
@@ -174,8 +90,11 @@ files:
 - lib/rbbt/annotations/annotated_array.rb
 - lib/rbbt/annotations/util.rb
 - lib/rbbt/association.rb
+- lib/rbbt/association/index.rb
+- lib/rbbt/association/item.rb
 - lib/rbbt/entity.rb
 - lib/rbbt/fix_width_table.rb
+- lib/rbbt/knowledge_base.rb
 - lib/rbbt/persist.rb
 - lib/rbbt/persist/tsv.rb
 - lib/rbbt/resource.rb
@@ -187,6 +106,7 @@ files:
 - lib/rbbt/tsv/accessor.rb
 - lib/rbbt/tsv/attach.rb
 - lib/rbbt/tsv/attach/util.rb
+- lib/rbbt/tsv/change_id.rb
 - lib/rbbt/tsv/excel.rb
 - lib/rbbt/tsv/filter.rb
 - lib/rbbt/tsv/index.rb
@@ -240,7 +160,9 @@ files:
 - test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_change_id.rb
 - test/rbbt/test_fix_width_table.rb
+- test/rbbt/association/test_index.rb
 - test/rbbt/test_association.rb
 - test/rbbt/test_workflow.rb
 - test/rbbt/workflow/test_step.rb
@@ -251,6 +173,7 @@ files:
 - test/rbbt/test_resource.rb
 - test/rbbt/test_annotations.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_persist.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_tmpfile.rb
@@ -304,7 +227,9 @@ test_files:
 - test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_change_id.rb
 - test/rbbt/test_fix_width_table.rb
+- test/rbbt/association/test_index.rb
 - test/rbbt/test_association.rb
 - test/rbbt/test_workflow.rb
 - test/rbbt/workflow/test_step.rb
@@ -315,6 +240,7 @@ test_files:
 - test/rbbt/test_resource.rb
 - test/rbbt/test_annotations.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_persist.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_tmpfile.rb