rbbt-util 4.4.0 → 5.0.0

data/test/rbbt/test_tsv.rb

@@ -173,12 +173,33 @@ row1    1
 row2    4
     EOF
 
+    require 'rbbt/sources/organism'
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i, :type => :single, :fields => "Value")
       assert_equal 1, tsv["row1"]
+      tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i, :type => :single, :fields => ["Value"])
+      assert_equal 1, tsv["row1"]
+      tsv = TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value", :fields => ["Id"])
+      assert_equal "row1", tsv["1"]
+    end
+  end
+
+  def test_tsv_single_from_flat
+    content =<<-EOF
+#: :type=:flat
+#Id    Value
+row1    1 2
+row2    4
+    EOF
+
+    require 'rbbt/sources/organism'
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, :type => :single, :key_field => "Value", :fields => ["Id"])
+      assert_equal "row1", tsv["1"]
     end
   end
 
+
   def test_tsv_serializer
     content =<<-EOF
 #Id    Value
@@ -312,6 +333,20 @@ b 2
     end
   end
 
+  def test_grep_invert
+    content =<<-EOF
+#: :sep=/\\s+/#:type=:single
+#Id Value
+a 1
+b 2
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2", :invert_grep => true)
+      assert(! tsv.include?("2"))
+    end
+  end
+
   def test_grep_header
     content =<<-EOF
 #: :sep=/\\s+/#:type=:single#:namespace=Test

data/test/rbbt/tsv/test_accessor.rb

@@ -175,4 +175,13 @@ row3    A|AA|AAA|AAA    B    Id3    3
     end
   end
 
+  def test_chunked_values_at
+    tsv = TSV.setup({})
+    10.times do |i|
+      tsv[i] = i
+    end
+    pos = tsv.chunked_values_at (0..10-1).to_a, 2
+    assert_equal (0..10-1).to_a, pos
+  end
+
 end

data/test/rbbt/util/test_misc.rb

@@ -4,6 +4,10 @@ require 'test/unit'
 
 class TestMisc < Test::Unit::TestCase
 
+  def test_humanize
+    assert_equal "mutation_enrichment", Misc.humanize("MutationEnrichment")
+  end
+
   def test_fixutf8
     string = "abc\xffdef"
     string = string.force_encoding("UTF-8") if string.respond_to? :force_encoding
@@ -182,9 +186,19 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "--------------------------------TYTIDMKTTQNVNGLSML-------------------------", Misc.fast_align(reference, sequence).last
   end
 
-#  def test_divide
-#    assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
-#  end
+  def test_divide
+    assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
+  end
+
+  def test_ordered_divide
+    assert_equal 5, Misc.ordered_divide(%w(1 2 3 4 5 6 7 8 9),2).length
+  end
+
+  def test_setup
+    require 'rbbt/entity/gene'
+    g = Misc.prepare_entity("TP53", "Gene", :format => "Associated Gene Name", "organism" => "Hsa/jun2011")
+  end
+
 #
 #  def test_process_to_hash
 #    list = [1,2,3,4]

data/test/rbbt/util/test_open.rb

@@ -68,6 +68,27 @@ class TestOpen < Test::Unit::TestCase
 
   end
 
+  def test_read_grep_invert
+    content =<<-EOF
+1
+2
+3
+4
+    EOF
+    TmpFile.with_file(content) do |file|
+      sum = 0
+      Open.read(file, :grep => '^1\|3', :invert_grep => true) do |line| sum += line.to_i end
+      assert_equal(2 + 4, sum)
+    end
+
+    TmpFile.with_file(content) do |file|
+      sum = 0
+      Open.read(file, :grep => ["1","3"]) do |line| sum += line.to_i end
+      assert_equal(1 + 3, sum)
+    end
+
+  end
+
 
   def test_gzip
     content =<<-EOF

data/test/rbbt/workflow/test_step.rb

@@ -41,12 +41,52 @@ class TestStep < Test::Unit::TestCase
       step2 = Step.new tmpfile + 'step2', task2, [], step1
 
       step1.clean
-      sleep 1
       step2.run
       assert_equal "TEST2", Open.read(tmpfile + 'step2')
     end
   end
 
+  def test_dependency_log_relay
+    str = "TEST"
+    TmpFile.with_file do |tmpfile|
+      task1  = Task.setup :result_type => nil, :name => :task1 do 
+        log(:starting_task1, "Starting Task1")
+        Open.write(tmpfile, str); 
+      end
+      step1 = Step.new tmpfile + 'step1', task1
+
+      task2  = Task.setup :result_type => :string, :name => :task1 do 
+        Open.read(tmpfile) 
+      end
+      step2 = Step.new tmpfile + 'step2', task2, [], [step1]
+
+      step2.run
+      assert step2.messages.include? "task1>Starting Task1"
+    end
+  end
+
+  def test_log_relay_step
+    str = "TEST"
+    TmpFile.with_file do |tmpfile|
+      task1  = Task.setup :result_type => nil, :name => :task1 do 
+        log(:starting_task1, "Starting Task1")
+        Open.write(tmpfile, str); 
+      end
+      step1 = Step.new tmpfile + 'step1', task1
+
+
+      task2  = Task.setup :result_type => :string, :name => :task1 do 
+        Open.read(tmpfile) 
+      end
+      step2 = Step.new tmpfile + 'step2', task2, [], [step1]
+
+      Step.log_relay_step = step2
+      step2.run
+      assert step2.messages.include? "task1>Starting Task1"
+    end
+  end
+
+
   def test_exec
     TmpFile.with_file do |lock|
       task  = Task.setup do "TEST" end

metadata

@@ -1,163 +1,175 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: rbbt-util
-version: !ruby/object:Gem::Version 
-  hash: 47
+version: !ruby/object:Gem::Version
+  version: 5.0.0
   prerelease: 
-  segments: 
-  - 4
-  - 4
-  - 0
-  version: 4.4.0
 platform: ruby
-authors: 
+authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-07-18 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-12-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: rake
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: spreadsheet
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: spreadsheet
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: ruby-prof
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: ruby-prof
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: tokyocabinet
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: tokyocabinet
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: progress-monitor
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: progress-monitor
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: lockfile
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: lockfile
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: RubyInline
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: RubyInline
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  name: narray
   prerelease: false
-  requirement: &id008 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: narray
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id008
-- !ruby/object:Gem::Dependency 
-  name: simplews
   prerelease: false
-  requirement: &id009 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: simplews
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id009
+  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: 
+executables:
 - tsv.rb
 - tchash.rb
 - run_workflow.rb
 - rbbt_query.rb
 - rbbt_exec.rb
 - rbbt_Rutil.rb
+- rbbt_monitor.rb
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
 - README.rdoc
-files: 
+files:
 - LICENSE
 - lib/rbbt-util.rb
 - lib/rbbt.rb
@@ -237,40 +249,32 @@ files:
 - bin/rbbt_query.rb
 - bin/rbbt_exec.rb
 - bin/rbbt_Rutil.rb
+- bin/rbbt_monitor.rb
 homepage: http://github.com/mikisvaz/rbbt-util
 licenses: []
-
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
-test_files: 
+test_files:
 - test/test_helper.rb
 - test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_filecache.rb