rbbt-util 5.2.4 → 5.3.0

data/share/rbbt_commands/tsv/attach

@@ -0,0 +1,13 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+
+file = ARGV.shift
+identifiers = ARGV.shift
+format = ARGV.shift
+
+
+puts TSV.open(file).attach identifiers, :fields => [format]
+

data/share/rbbt_commands/tsv/change_id

@@ -0,0 +1,15 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+
+file = ARGV.shift
+identifiers = ARGV.shift
+format = ARGV.shift
+
+
+tsv = TSV.open(file).attach identifiers, :fields => [format]
+
+puts tsv.reorder(format, tsv.fields - [format])
+

data/share/rbbt_commands/tsv/info

@@ -16,5 +16,7 @@ header.fields.each_with_index do |f,i|
 end
 puts "Rows: #{`wc -l #{ file }|cut -f 1 -d' '`}"
 puts "First line:"
-puts header.first_line
+parts = []
+header.first_line.split(header.sep).each_with_index{|p,i| parts << "(#{i}) #{p}"}
+puts parts * "\t"
 

data/share/rbbt_commands/workflow/task

@@ -20,6 +20,8 @@ def usage(workflow = nil, task = nil)
     puts workflow.to_s
     puts "=" * workflow.to_s.length
     puts
+    puts workflow.workflow_description
+    puts
     workflow.doc(task)
   end
 
@@ -32,7 +34,7 @@ def SOPT_options(workflow, task)
     short = name.to_s.chars.first
     boolean = workflow.rec_input_types(task.name)[name].to_sym == :boolean
     
-    sopt_options << "-#{short}--#{name}#{boolean ? '' : '*'}"
+    sopt_options << "-#{short}--#{name}*"
   end
 
   sopt_options * ":"
@@ -45,6 +47,8 @@ def fix_options(workflow, task, job_options)
 
   job_options.each do |name, value|
     value = case option_types[name].to_sym
+            when :boolean
+              %w(true TRUE T yes).include? value
             when :float
               value.to_f
             when :integer
@@ -53,7 +57,7 @@ def fix_options(workflow, task, job_options)
               case
               when value == '-'
                 STDIN.read
-              when (String === value and File.exists?(value))
+              when (String === value and File.exists?(value) and not File.directory?(value))
                 Open.read(value)
               else
                 value
@@ -78,18 +82,13 @@ def fix_options(workflow, task, job_options)
                 end
               end
             when :tsv
-              if TSV === value
+              case value
+              when TSV
                 value
+              when '-'
+                TSV.open(STDIN)
               else
-                begin
-                  if value == '-'
-                    TSV.open(STDIN).to_s :sort
-                  else
-                    TSV.new(value).to_s :sort
-                  end
-                rescue
-                  value
-                end
+                TSV.open(value)
               end
             else
               value
@@ -114,7 +113,6 @@ usage if workflow.nil?
 
 task     = ARGV.shift
 
-
 # Set log, fork, clean, recursive_clean and help
 help = !!options.delete(:help)
 do_fork = !!options.delete(:fork)
@@ -136,7 +134,8 @@ if remote_workflows.include? workflow
   workflow = WorkflowRESTClient.new remote_workflows[workflow], workflow
 else
   Workflow.require_workflow workflow
-  workflow = Workflow.workflows.last
+  workflow = Workflow.workflows.select{|mod| Misc.snake_case(mod.to_s) == Misc.snake_case(workflow)}.first
+  workflow = Workflow.workflows.last if workflow.nil?
 end
 
 # Set task
@@ -215,7 +214,7 @@ else
 end
 
 if Step === res
-  puts Open.read(res.path)
+  puts Open.read(res.path) if File.exists? res.path
 else
   puts res
 end

data/test/rbbt/test_entity.rb

@@ -0,0 +1,221 @@
+require File.expand_path(File.dirname(__FILE__) + '/../test_helper')
+require 'rbbt'
+require 'rbbt/entity'
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+
+class TestA
+  attr_accessor :foo, :bar
+  def initialize(foo, bar)
+    @foo = foo
+    @bar = bar
+  end
+end
+
+module ReversableString
+  extend Entity
+
+  self.annotation :foo, :bar
+
+  property :reverse_text_ary => :array do
+    $count += 1
+    self.collect{|s| s.reverse}
+  end
+ 
+  property :reverse_text_single => :single do
+    $count += 1
+    self.reverse
+  end
+
+  property :reverse_text_ary_p => :array do
+    $count += 1
+    self.collect{|s| s.reverse}
+  end
+ 
+  property :reverse_text_single_p => :single do
+    $count += 1
+    self.reverse
+  end
+
+  property :reverse_text_ary_p_array => :array do
+    $count += 1
+    self.collect{|s| s.reverse}
+  end
+
+  property :random => :single do
+    rand
+  end
+
+  property :annotation_list => :single do
+    self.chars.to_a.collect{|c| 
+      ReversableString.setup(c)
+    }
+  end
+ 
+  persist :reverse_text_ary_p
+  persist :reverse_text_ary_p
+  persist :reverse_text_ary_p
+  persist :reverse_text_single_p
+
+  persist :reverse_text_ary_p_array, :array, :dir => TmpFile.tmp_file
+
+  persist :annotation_list, :annotations, :dir => TmpFile.tmp_file
+end
+
+class TestEntity < Test::Unit::TestCase
+
+  def test_property_ary
+    a = ["String1", "String2"]
+    ReversableString.setup(a)
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_ary.last
+    assert_equal 1, $count
+    a._ary_property_cache.clear
+    assert_equal "2gnirtS", a[1].reverse_text_ary
+    assert_equal 2, $count
+    a._ary_property_cache.clear
+
+    $count = 0
+    a.each do |string|
+      string.reverse_text_ary
+      assert_equal 1, $count
+    end
+  end
+
+  def test_property_single
+    a = ["String1", "String2"]
+    ReversableString.setup a
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_single.last
+    assert_equal 2, $count
+    assert_equal "2gnirtS", a[1].reverse_text_single
+    assert_equal 3, $count
+  end
+
+  def test_property_ary_p
+    a = ["String1", "String2"]
+    ReversableString.setup a
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_ary_p.last
+    assert_equal "2gnirtS", a[1].reverse_text_ary_p
+    assert_equal 1, $count
+  end
+
+  def test_property_single_p
+    a = ["String1", "String2"]
+    ReversableString.setup a
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_single_p.last
+    assert_equal 2, $count
+    assert_equal "2gnirtS", a[1].reverse_text_single_p
+    assert_equal 2, $count
+  end
+
+  def test_property_ary_p_array
+    a = ["String1", "String2"]
+    ReversableString.setup a
+
+    $count = 0
+
+    assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
+    assert_equal 1, $count
+    assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
+    assert_equal 1, $count
+  end
+
+  def test_unpersist
+    a = ["String1", "String2"]
+    ReversableString.setup a
+
+    # Before persist
+    assert(! ReversableString.persisted?(:random))
+
+    r1 = a.random
+    r2 = a.random
+    assert_not_equal r1, r2
+
+    # After persist
+    ReversableString.persist :random
+    assert(ReversableString.persisted?(:random))
+
+    r1 = a.random
+    r2 = a.random
+    assert_equal r1, r2
+
+    # After unpersist
+    ReversableString.unpersist :random
+    assert(! ReversableString.persisted?(:random))
+
+    r1 = a.random
+    r2 = a.random
+    assert_not_equal r1, r2
+
+  end
+
+  def test_persist_annotations
+    string = 'aaabbbccc'
+    ReversableString.setup(string)
+    assert_equal string.length, string.annotation_list.length
+    assert_equal string.length, string.annotation_list.length
+  end
+
+  def __test_performance
+    require 'rbbt/entity/gene'
+    Misc.profile(:min_percent => 2) do
+      1000.times do
+        TestA.new "foo", "bar"
+      end
+    end
+
+    Misc.profile(:min_percent => 2) do
+      1000.times do
+        Gene.setup_positional("", "foo", "bar")
+      end
+    end
+
+    Misc.benchmark(100000) do
+      Gene.setup("", :foo => "foo", :bar => "bar")
+    end
+
+    Misc.benchmark(100000) do
+      TestA.new "foo", "bar"
+    end
+  end
+
+  def __test_clean_annotations
+    Workflow.require_workflow "StudyExplorer"
+
+    s = Study.setup("CLL")
+    mutations = s.cohort.metagenotype
+
+    mis = mutations.mutated_isoforms.compact.flatten
+
+    Misc.profile(:min_percent => 1) do
+      mis.each{|m| m}
+    end
+
+
+    Misc.benchmark(10) do
+      mis.each{|m| m}
+    end
+
+    Misc.benchmark(10) do
+      mis.clean_annotations.each{|m| m}
+    end
+
+    m = mutations.first
+
+    assert_equal m.split(":")[1], m.position.to_s
+    assert_raise NoMethodError do 
+      m.clean_annotations.position
+    end
+  end
+end

data/test/rbbt/test_tsv.rb

@@ -210,7 +210,7 @@ row2    4
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/, :cast => :to_i, :type => :single, :serializer => :integer)
       assert_equal 1, tsv["row1"]
-      assert String === tsv.tsv_clean_get_brackets("row1")
+      assert String === tsv.send(:[], "row1", true)
     end
   end
 
@@ -233,6 +233,7 @@ row2    4
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
 row2    A    B    Id3
+row3    AA    B    Id3
     EOF
 
     TmpFile.with_file(content.gsub(/ +/,"\t")) do |filename|

data/test/rbbt/test_workflow.rb

@@ -7,8 +7,6 @@ require 'test/unit'
 module TestWF
   extend Workflow
 
-  ddd TestWF.methods.sort
-
   helper :user do
     "User"
   end 

data/test/rbbt/tsv/test_accessor.rb

@@ -116,10 +116,10 @@ row2 A b C
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :double, :sep => /\s/)
-      assert_equal %w(row2 row1), tsv.sort{|a,b|
+      assert_equal %w(row2 row1), tsv.tsv_sort{|a,b|
         a[1]["ValueA"] <=> b[1]["ValueA"]
       }.collect{|k,v| k}
-      assert_equal %w(row1 row2), tsv.sort{|a,b|
+      assert_equal %w(row1 row2), tsv.tsv_sort{|a,b|
         a[1]["ValueB"] <=> b[1]["ValueB"]
       }.collect{|k,v| k}
     end

data/test/rbbt/util/test_R.rb

@@ -2,16 +2,23 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helpe
 require 'rbbt/util/R'
 
 class TestR < Test::Unit::TestCase
-  def test_sum
+  def _test_sum
     assert_equal "6", R.run('cat(3+3)').read.split(/\n/).last
   end
 
-  def test_tsv_R
+  def _test_tsv_R
     tsv = TSV.setup({:a => 1, :b => 2})
     tsv2 = tsv.R <<-EOF
 data = data + 1
     EOF
     assert_equal "2", tsv2["a"].first
   end
+
+  def test_format_tsv
+    tsv = TSV.setup({"a" => [1], "b" => [2]}, :type => :list, :key_field => "Letter", :fields => ["Number"])
+    puts tsv.transpose "Field"
+    tsv.unnamed = true
+    puts R.ruby2R tsv
+  end
 end
 

data/test/rbbt/util/test_colorize.rb

@@ -0,0 +1,12 @@
+require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
+require 'rbbt/util/colorize'
+require 'test/unit'
+
+class TestColorize < Test::Unit::TestCase
+  def test_color_array
+    a = [:red, :red, :blue, :blue, :yellow]
+    a = (0..16).to_a
+
+    ddd Colorize.distinct(a)
+  end
+end

data/test/rbbt/util/test_misc.rb

@@ -194,11 +194,6 @@ class TestMisc < Test::Unit::TestCase
     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_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)

data/test/rbbt/util/test_open.rb

@@ -103,6 +103,37 @@ class TestOpen < Test::Unit::TestCase
       FileUtils.rm file + '.gz'
     end
   end
+
+  def test_repo_dir
+    file1 = "TEST"
+    file2 = "TEST" * 1000
+    TmpFile.with_file do |tmpdir|
+      tmpdir = "/home/mvazquezg/tmp/repo_dir"
+      normal = File.join(tmpdir, 'normal')
+      repo = File.join(tmpdir, 'repo')
+
+      Open.repository_dirs.push(repo)
+
+      Misc.benchmark(100) do
+        filename = "file" << (rand * 100).to_i.to_s
+        Open.write(File.join(normal, filename), file2)
+        100.times do 
+          Open.read(File.join(normal,  filename))
+        end
+      end
+
+
+      Misc.benchmark(100) do
+        filename = "file" << (rand * 100).to_i.to_s
+        Open.write(File.join(repo, filename), file2)
+        100.times do 
+          Open.read(File.join(repo, filename))
+        end
+      end
+
+
+    end
+  end
   
 end