rbbt-util 3.1.0 → 3.2.0

data/test/rbbt/util/test_tmpfile.rb

@@ -8,7 +8,7 @@ class TestTmpFile < Test::Unit::TestCase
     assert(TmpFile.tmp_file("test") =~ /tmp\/test\d+$/)
   end
 
-  def test_do_tmp_file
+  def _test_do_tmp_file
     content = "Hello World!"
     TmpFile.with_file(content) do |file|
       assert_equal content, File.open(file).read

data/test/rbbt/util/test_tsv.rb

@@ -202,14 +202,20 @@ row2    A    B
         assert TCHash === tsv1.data
         assert !tsv1.case_insensitive
         assert tsv1.include? "A"
+        ddd tsv1.filename
 
         tsv1 = TSV.new(tchash, :key => "ValueA")
         assert TCHash === tsv1.data
         assert !tsv1.case_insensitive
         assert tsv1.include? "A"
+        ddd tsv1.filename
       end
     end
  
   end
+
+  def test_with_hash
+    assert TSV === TSV.new {}, :list
+  end
 end
 

data/test/rbbt/util/test_workflow.rb

@@ -37,7 +37,10 @@ module MathWF2
   task :times => :integer do |times| mult(input, times) end
 
   task_dependencies []
-  task :persist do  task.workflow.methods.include? "local_persist" end
+  task :persist do  
+    task.workflow.methods.include?(:local_persist) or
+    task.workflow.methods.include?("local_persist") 
+  end
 end
 
 
@@ -65,22 +68,22 @@ class TestWorkFlow < Test::Unit::TestCase
  
   def test_math_wf
     job = MathWF.tasks[:times_2].job(:job1, 1)
-    assert_equal 4, job.fork.join.load
+    assert_equal 4, job.recursive_clean.fork.join.load
     job = MathWF.tasks[:times_4].job(:job1, 1)
-    assert_equal 8, job.fork.join.load
+    assert_equal 8, job.recursive_clean.fork.join.load
   end
 
   def test_math_wf2
     job = MathWF2.tasks[:times_2].job(:job1, 1)
-    job.fork.join
+    job.recursive_clean.fork.join
     assert_equal 4, job.load
     job = MathWF2.tasks[:times_4].job(:job1, 1)
-    assert_equal 8, job.fork.join.load
+    assert_equal 8, job.recursive_clean.fork.join.load
   end
 
   def test_math_run
     job = MathWF2.job(:times_2, :job1, 1)
-    job.fork.join
+    job.recursive_clean.fork.join
     assert_equal 4, job.load
   end
 
@@ -88,7 +91,7 @@ class TestWorkFlow < Test::Unit::TestCase
     assert MathWF2.tasks[:times].option_defaults.include? :times
 
     job = MathWF2.job(:times, :job1, 1)
-    job.fork.join
+    job.recursive_clean.fork.join
     assert job.done?
     puts job.messages
     assert File.exists? job.path
@@ -96,7 +99,7 @@ class TestWorkFlow < Test::Unit::TestCase
 
 
     job = MathWF2.job(:times, :job1, 1, :times => 20)
-    job.fork.join
+    job.recursive_clean.fork.join
     assert_equal 40, job.load
   end
 
@@ -112,12 +115,13 @@ class TestWorkFlow < Test::Unit::TestCase
   end
 
   def test_local_persist
+    MathWF2.job(:persist, :persist).clean
     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
+    assert_equal 2, ConWF.run(:times_2, "Test", "one").load
+    assert_equal 4, ConWF.run(:times_2, "Test", "two").load
   end
 
   def test_option_summary

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

@@ -105,5 +105,47 @@ row2 A B C
     end
   end
 
+  def test_namespace
+    content =<<-EOF
+#ID ValueA ValueB Comment
+row1 a b c
+row2 A B C
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s/, :namespace => "TEST")
+
+      assert_equal "TEST", tsv.fields.first.namespace
+      assert_equal "TEST", tsv.key_field.namespace
+    end
+  end
+
+  def test_delete
+    content =<<-EOF
+#ID ValueA ValueB Comment
+row1 a b c
+row2 A B C
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s/)
+      tsv.delete "row1"
+      
+      assert_equal 1, tsv.size
+      assert_equal ["row2"], tsv.keys
+
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s/, :persistence => true)
+      assert_equal 2, tsv.size
+      assert_equal ["row1", "row2"], tsv.keys
+      tsv.write
+      tsv.delete "row1"
+      tsv.read
+
+      assert_equal 1, tsv.size
+      assert_equal ["row2"], tsv.keys
+    end
+  end
+
+
 end
 

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

@@ -0,0 +1,141 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt/util/tsv/filters'
+
+class TestTSVFilters < Test::Unit::TestCase
+  def test_collect
+    content1 =<<-EOF
+#: :sep=/\\s+/#:case_insensitive=false
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+    EOF
+
+    TmpFile.with_file(content1) do |filename|
+      tsv = TSV.new filename
+      tsv.filter
+      tsv.add_filter "field:ValueA", ["A"]
+      assert_equal 1, tsv.collect.size
+    end
+  end
+
+  def test_through
+    content1 =<<-EOF
+#: :sep=/\\s+/#:case_insensitive=false
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+    EOF
+
+    TmpFile.with_file(content1) do |filename|
+      tsv = TSV.new filename
+      tsv.filter
+      tsv.add_filter "field:ValueA", ["A"]
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 1, elem.size
+    end
+  end
+
+  def test_2_filters
+    content1 =<<-EOF
+#: :sep=/\\s+/#:case_insensitive=false
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+row3    A    C
+    EOF
+
+    TmpFile.with_file(content1) do |filename|
+      tsv = TSV.new filename
+      tsv.filter
+      tsv.add_filter "field:ValueA", ["A"]
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 2, elem.size
+
+      tsv.add_filter "field:ValueB", ["C"]
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 1, elem.size
+    end
+  end
+
+  def test_filter_persistence
+    content1 =<<-EOF
+#: :sep=/\\s+/#:case_insensitive=false
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+row3    A    C
+    EOF
+
+    TmpFile.with_file(content1) do |filename|
+      tsv = TSV.new filename
+      tsv.filter
+      tsv.add_filter "field:ValueA", ["A"], Rbbt.tmp.test.Filter.fieldValueA
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 2, elem.size
+
+      tsv.add_filter "field:ValueB", ["C"]
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 1, elem.size
+
+      tsv = TSV.new filename
+      tsv.filter
+      tsv.add_filter "field:ValueA", ["A"], Rbbt.tmp.test.Filter.fieldValueA
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 2, elem.size
+    end
+  end
+
+  def test_filter_persistence_update
+    content1 =<<-EOF
+#: :sep=/\\s+/#:case_insensitive=false
+#Id    ValueA    ValueB
+row1    a|aa|aaa    b
+row2    A    B
+    EOF
+
+    TmpFile.with_file(content1) do |filename|
+      tsv = TSV.new filename
+      tsv.filter
+      tsv.add_filter "field:ValueA", ["A"], Rbbt.tmp.test.Filter.fieldValueA.find(:user)
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 1, elem.size
+
+      tsv["row3"] = [["A"], ["C"]]
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 2, elem.size
+
+      tsv.add_filter "field:ValueB", ["C"]
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 1, elem.size
+
+      tsv = TSV.new filename
+      tsv.filter
+      tsv.add_filter "field:ValueA", ["A"], Rbbt.tmp.test.Filter.fieldValueA.find(:user)
+
+      elem = []
+      tsv.through do |k,v| elem << k end
+      assert_equal 2, elem.size
+    end
+  end
+
+
+
+end
+

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

@@ -153,5 +153,37 @@ g:         ____
     end
   end
 
+  def test_pos_index
+    content =<<-EOF
+#Id	ValueA    ValueB    Pos
+row1    a|aa|aaa    b    0|10
+row2    A    B    30
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s+/)
+      index = tsv.pos_index("Pos", :memory, true)
+      assert_equal ["row1"], index[10]
+    end
+  end
+
+
+  def test_range_index
+    content =<<-EOF
+#Id	ValueA    ValueB    Pos1    Pos2
+row1    a|aa|aaa    b    0|10    10|30
+row2    A    B    30   35
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(File.open(filename), :double, :sep => /\s+/)
+      index = tsv.pos_index("Pos1", :memory, true)
+      assert_equal ["row1"], index[10]
+
+      index = tsv.range_index("Pos1", "Pos2", :memory, true)
+      assert_equal ["row1"], index[20]
+    end
+  end
+
 end
 

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

@@ -242,5 +242,23 @@ row3    a    C    Id4
  
   end
 
+  def test_through_single
+     content =<<-EOF
+#Id    LetterValue
+row1    a1
+row2    A1
+row3    a2
+    EOF
+ 
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.new(filename + '#:sep=/\s+/#:type=:single')
+
+      #TODO: WTF!!!
+      assert_equal "row1", tsv.reorder("LetterValue", :key)[97]
+    end
+ 
+  end
+
+
 end
 

data/test/test_helper.rb

@@ -16,9 +16,11 @@ class Test::Unit::TestCase
 
   def teardown
     FileUtils.rm_rf Rbbt.tmp.test.find :user
+    TCHash::CONNECTIONS.values.each do |c| c.close end
+    TCHash::CONNECTIONS.clear
   end
 
-  def test_datafile(file)
+  def datafile_test(file)
     File.join(File.dirname(__FILE__), 'data', file)
   end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-util
 version: !ruby/object:Gem::Version 
-  hash: 3
-  prerelease: false
+  hash: 15
+  prerelease: 
   segments: 
   - 3
-  - 1
+  - 2
   - 0
-  version: 3.1.0
+  version: 3.2.0
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-11 00:00:00 +02:00
+date: 2011-06-12 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -141,6 +141,7 @@ files:
 - lib/rbbt/util/tsv.rb
 - lib/rbbt/util/tsv/accessor.rb
 - lib/rbbt/util/tsv/attach.rb
+- lib/rbbt/util/tsv/filters.rb
 - lib/rbbt/util/tsv/index.rb
 - lib/rbbt/util/tsv/manipulate.rb
 - lib/rbbt/util/tsv/misc.rb
@@ -150,31 +151,32 @@ files:
 - lib/rbbt/util/workflow/soap.rb
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_bed.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_excel2tsv.rb
+- test/test_helper.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_fix_width_table.rb
-- test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_persistence.rb
-- test/rbbt/util/test_rake.rb
-- test/rbbt/util/test_resource.rb
+- test/rbbt/util/test_tsv.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_tc_hash.rb
 - test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/test_resource.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_task.rb
-- test/rbbt/util/test_tc_hash.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_tsv.rb
+- test/rbbt/util/test_bed.rb
+- test/rbbt/util/test_rake.rb
+- test/rbbt/util/test_persistence.rb
 - test/rbbt/util/test_workflow.rb
+- test/rbbt/util/tsv/test_parse.rb
 - test/rbbt/util/tsv/test_accessor.rb
-- test/rbbt/util/tsv/test_attach.rb
-- test/rbbt/util/tsv/test_index.rb
 - test/rbbt/util/tsv/test_manipulate.rb
-- test/rbbt/util/tsv/test_parse.rb
+- test/rbbt/util/tsv/test_index.rb
+- test/rbbt/util/tsv/test_attach.rb
 - test/rbbt/util/tsv/test_resource.rb
-- test/test_helper.rb
+- test/rbbt/util/tsv/test_filters.rb
+- test/rbbt/util/test_fix_width_table.rb
 - test/test_rbbt.rb
 - bin/tsv.rb
 - bin/tchash.rb
@@ -212,34 +214,35 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files: 
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_bed.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_excel2tsv.rb
+- test/test_helper.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_fix_width_table.rb
-- test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
-- test/rbbt/util/test_persistence.rb
-- test/rbbt/util/test_rake.rb
-- test/rbbt/util/test_resource.rb
+- test/rbbt/util/test_tsv.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_tc_hash.rb
 - test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/test_resource.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_task.rb
-- test/rbbt/util/test_tc_hash.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_tsv.rb
+- test/rbbt/util/test_bed.rb
+- test/rbbt/util/test_rake.rb
+- test/rbbt/util/test_persistence.rb
 - test/rbbt/util/test_workflow.rb
+- test/rbbt/util/tsv/test_parse.rb
 - test/rbbt/util/tsv/test_accessor.rb
-- test/rbbt/util/tsv/test_attach.rb
-- test/rbbt/util/tsv/test_index.rb
 - test/rbbt/util/tsv/test_manipulate.rb
-- test/rbbt/util/tsv/test_parse.rb
+- test/rbbt/util/tsv/test_index.rb
+- test/rbbt/util/tsv/test_attach.rb
 - test/rbbt/util/tsv/test_resource.rb
-- test/test_helper.rb
+- test/rbbt/util/tsv/test_filters.rb
+- test/rbbt/util/test_fix_width_table.rb
 - test/test_rbbt.rb