rbbt-util 3.0.3 → 3.1.0

data/test/rbbt/util/test_persistence.rb

@@ -152,5 +152,18 @@ row2   2 4 6 8
     assert_equal "Test", string
   end
 
+  def test_non_blocking
+    $a = TSV.new test_datafile('test.tsv'), :persistence => true, :persistence_dir => Rbbt.tmp.test.persistence
+    $a.data.read
+
+    pid = Process.fork do
+      $b = TSV.new test_datafile('test.tsv'), :persistence => true, :persistence_dir => Rbbt.tmp.test.persistence
+      $b.data.close
+    end
+
+    Process.wait pid
+  end
+
+
 end
 

data/test/rbbt/util/test_tc_hash.rb

@@ -73,13 +73,15 @@ class TestTCHash < Test::Unit::TestCase
       t.close
 
       pid = Process.fork do
-        t2 = TCHash.get f, true, :double
+        t2 = TCHash.get f, false, :double
         assert_equal [["3"],["4","5"]], t2["2"]
+        t2.read
         exit
       end
 
-      t2 = TCHash.get f, true, :double
+      t2 = TCHash.get f, false, :double
       assert_equal [["3"],["4","5"]], t2["2"]
+      t2.read
 
       Process.wait pid
     end

data/test/rbbt/util/test_tsv.rb

@@ -178,11 +178,38 @@ 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
+
+  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
+
+  def test_persistence_data
+     content1 =<<-EOF
+#: :sep=/\\s+/#:case_insensitive=false
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+    EOF
+
+   tsv1 = tsv2 = identifiers = nil
+    TmpFile.with_file(content1) do |filename|
+      TmpFile.with_file do |tchashfile|
+        tchash = TCHash.get(tchashfile, true)
+        tsv1 = TSV.new(File.open(filename), :key => "ValueA", :persistence_data => tchash)
+        assert TCHash === tsv1.data
+        assert !tsv1.case_insensitive
+        assert tsv1.include? "A"
+
+        tsv1 = TSV.new(tchash, :key => "ValueA")
+        assert TCHash === tsv1.data
+        assert !tsv1.case_insensitive
+        assert tsv1.include? "A"
+      end
     end
+ 
   end
 end
 

data/test/rbbt/util/test_workflow.rb

@@ -5,11 +5,11 @@ 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[:add_1].dependencies << tasks[:input]
   self.tasks[:times_2] = Task.new(:times_2, :marshal) do input * 2 end
-  self.tasks[:times_2].dependencies << :add_1
+  self.tasks[:times_2].dependencies << tasks[:add_1]
   self.tasks[:times_4] = Task.new(:times_4, :marshal) do input * 4 end
-  self.tasks[:times_4].dependencies << :add_1
+  self.tasks[:times_4].dependencies << tasks[:add_1]
   self.tasks.each do |name, task| task.workflow = self end
 end
 
@@ -119,5 +119,13 @@ class TestWorkFlow < Test::Unit::TestCase
     assert 2, ConWF.run(:times_2, "Test", "one").load
     assert 4, ConWF.run(:times_2, "Test", "two").load
   end
+
+  def test_option_summary
+   assert MathWF.tasks[:times_2].option_summary.first.first[:name] == :value
+  end
+
+  def test_usage
+    assert  MathWF.tasks[:times_2].usage =~ /^Task:/
+  end
 end
 

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

@@ -350,7 +350,41 @@ row6,dd,dd,ee,,
 
       assert_equal result, Open.read(f)
     end
- 
+  end
+
+  def test_paste
+    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|
+      data1 = TSV.new StringIO.new(file1), :sep => ',', :merge => true
+      data2 = TSV.new StringIO.new(file2), :sep => ',', :merge => true
+      data3 = data1.paste(data2)
+      data3.each do |key, list|
+        list.each do |l| l.replace l.sort_by{|v| v.length}.reverse end
+      end
+
+      assert_equal result, data3.to_s(:sort, true).gsub(/\t/,',')
+    end
   end
 
   def test_merge_rows

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

@@ -50,7 +50,7 @@ row3    A    a|B    Id4
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.new(File.open(filename), :sep => /\s+/, :key => "OtherID", :persistence => true)
-      index = tsv.index(:case_insensitive => false, :order => true)
+      index = tsv.index(:case_insensitive => false, :order => true, :persistence => true)
       assert_equal "Id1", index['a'].first
       assert_equal "Id3", index['A'].first
       assert_equal "OtherID", index.fields.first
@@ -123,9 +123,7 @@ row2    A    B
       values["Range"].last
     end
 
-    ddd tsv.fields
     tsv = tsv.slice ["Start", "End"]
-    ddd tsv.fields
  
     tsv
   end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-util
 version: !ruby/object:Gem::Version 
-  hash: 1
-  prerelease: 
+  hash: 3
+  prerelease: false
   segments: 
   - 3
+  - 1
   - 0
-  - 3
-  version: 3.0.3
+  version: 3.1.0
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-23 00:00:00 +01:00
+date: 2011-04-11 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -109,6 +109,8 @@ executables:
 - tchash.rb
 - workflow.rb
 - rbbt_query.rb
+- rbbt_exec.rb
+- rbbt_Rutil.rb
 extensions: []
 
 extra_rdoc_files: 
@@ -141,9 +143,11 @@ files:
 - lib/rbbt/util/tsv/attach.rb
 - lib/rbbt/util/tsv/index.rb
 - lib/rbbt/util/tsv/manipulate.rb
+- lib/rbbt/util/tsv/misc.rb
 - lib/rbbt/util/tsv/parse.rb
 - lib/rbbt/util/tsv/resource.rb
 - lib/rbbt/util/workflow.rb
+- lib/rbbt/util/workflow/soap.rb
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
 - test/rbbt/util/test_R.rb
@@ -176,6 +180,8 @@ files:
 - bin/tchash.rb
 - bin/workflow.rb
 - bin/rbbt_query.rb
+- bin/rbbt_exec.rb
+- bin/rbbt_Rutil.rb
 has_rdoc: true
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses: []
@@ -206,7 +212,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.4.2
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)