rbbt-util 5.14.38 → 5.14.39

data/lib/rbbt/util/misc/objects.rb

@@ -51,7 +51,7 @@ module Misc
   end
 
   def self.zip_fields(array)
-    return [] if array.empty? or (first = array.first).nil?
+    return [] if array.nil? or array.empty? or (first = array.first).nil?
     max = array.collect{|l| l.length}.max
     rest = array[1..-1].collect{|v|
       v.length == 1 & max > 1 ? v * max : v

data/lib/rbbt/workflow/accessor.rb

@@ -74,29 +74,32 @@ class Step
   def info(check_lock = true)
     return {} if info_file.nil? or not Open.exists? info_file
     begin
-      begin
-        return @info_cache if @info_cache and File.ctime(info_file) < @info_cache_time
-      rescue Exception
-        raise $!
-      end
+      Misc.insist do
+        begin
+          return @info_cache if @info_cache and File.ctime(info_file) < @info_cache_time
+        rescue Exception
+          raise $!
+        end
 
-      begin
-        @info_cache = Misc.insist(3, 1.6, info_file) do
-          Misc.insist(2, 1, info_file) do
-            Misc.insist(3, 0.2, info_file) do
-              raise TryAgain, "Info locked" if check_lock and info_lock.locked?
-              Open.open(info_file) do |file|
-                INFO_SERIALIAZER.load(file) #|| {}
+        begin
+          @info_cache = Misc.insist(3, 1.6, info_file) do
+            Misc.insist(2, 1, info_file) do
+              Misc.insist(3, 0.2, info_file) do
+                raise TryAgain, "Info locked" if check_lock and info_lock.locked?
+                Open.open(info_file) do |file|
+                  INFO_SERIALIAZER.load(file) #|| {}
+                end
               end
             end
           end
+          @info_cache_time = Time.now
+          @info_cache
         end
-        @info_cache_time = Time.now
-        @info_cache
       end
     rescue Exception
       Log.debug{"Error loading info file: " + info_file}
       Log.exception $!
+      Open.rm info_file
       Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump({:status => :error, :messages => ["Info file lost"]}))
       raise $!
     end
@@ -167,7 +170,7 @@ class Step
     end
   end
 
-  def self.log_block(staus, message, path, &block)
+  def self.log_block(status, message, path, &block)
     start = Time.now
     status = status.to_s
     status_color = self.status_color status
@@ -185,7 +188,7 @@ class Step
     eend = Time.now
     Log.info do 
       now = Time.now
-      str = "#{ Log.color :cyan, status.to_s } +#{Log.color :green, "%.1g" % (eend - start)}"
+      str = "#{ Log.color :cyan, status.to_s } +#{Log.color :green, "%.2f" % (eend - start)}"
       str << " -- #{Log.color :blue, path.to_s}" if path
       str << " #{Log.color :yellow, Process.pid}"
       str

data/lib/rbbt/workflow/step/run.rb

@@ -418,6 +418,13 @@ class Step
     end
   end
 
+  def soft_grace
+    until Open.exists? info_file
+      sleep 1 
+    end
+    self
+  end
+
   def grace
     until done? or result or error? or aborted? or streaming? 
       sleep 1 

data/share/rbbt_commands/app/start

@@ -3,9 +3,10 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-f--finder:-R--Rserve_session*"
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-f--finder:-R--Rserve_session*:-ho--host*"
 options[:Port] ||= options[:port]
-
+options[:Host] ||= "0.0.0.0"
+options[:Bind] ||= "0.0.0.0"
 
 app = ARGV.shift
 

data/test/rbbt/knowledge_base/test_entity.rb

@@ -1,4 +1,5 @@
 require File.expand_path(File.dirname(__FILE__) + '../../../test_helper')
+require 'rbbt-util'
 require 'rbbt/util/tmpfile'
 require 'test/unit'
 require 'rbbt/knowledge_base'
@@ -28,7 +29,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
 
   EFFECT_TSV = TSV.open EFFECT, EFFECT_OPTIONS.dup 
 
-  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo2', "Hsa"
+  KNOWLEDGE_BASE = KnowledgeBase.new '/tmp/kb.foo3', "Hsa"
   KNOWLEDGE_BASE.format = {"Gene" => "Associated Gene Name"}
 
   KNOWLEDGE_BASE.register :effects, EFFECT_TSV, EFFECT_OPTIONS.dup

data/test/rbbt/knowledge_base/test_query.rb

@@ -14,7 +14,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
   END
 
   EFFECT_OPTIONS = {
-    :source => "SG=~Associated Gene Name",
+    :source => "SG=~Associated Gene Name=>Ensembl Gene ID",
     :target => "TG=~Associated Gene Name=>Ensembl Gene ID",
     :persist => false,
     :identifiers => datafile_test('identifiers'),
@@ -32,6 +32,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
   def test_subset_all_persist
     Misc.benchmark(1000) do
       assert_equal 6, KNOWLEDGE_BASE.subset(:effects, :all).length
+
       assert_equal 4, KNOWLEDGE_BASE.subset(:effects, :all).target_entity.uniq.length
       assert_equal %w(Effect), KNOWLEDGE_BASE.subset(:effects, :all).info.first.keys 
     end

data/test/rbbt/test_entity.rb

@@ -53,9 +53,8 @@ module ReversableString
     }
   end
 
-  persist :reverse_text_ary_p, :string
+  persist :reverse_text_ary_p, :marshal
   persist :reverse_text_single_p, :memory
-  #persist :_single_reverse_text_single_p, :string
 
   persist :reverse_text_ary_p_array, :array, :dir => TmpFile.tmp_file
 
@@ -64,7 +63,7 @@ end
 
 class TestEntity < Test::Unit::TestCase
 
-  def _test_property_ary
+  def test_property_ary
     a = ["String1", "String2"]
     ReversableString.setup(a)
 
@@ -84,7 +83,7 @@ class TestEntity < Test::Unit::TestCase
     end
   end
 
-  def _test_property_single
+  def test_property_single
     a = ["String1", "String2"]
     ReversableString.setup a
 
@@ -96,7 +95,7 @@ class TestEntity < Test::Unit::TestCase
     assert_equal 3, $count
   end
 
-  def _test_property_ary_p
+  def test_property_ary_p
     a = ["String1", "String2"]
     ReversableString.setup a
 
@@ -104,7 +103,7 @@ class TestEntity < Test::Unit::TestCase
 
     assert_equal "2gnirtS", a.reverse_text_ary_p.last
     assert_equal "2gnirtS", a.collect{|e| e.reverse_text_ary_p }[1]
-    assert_equal 1, $count
+    assert_equal 0, $count
   end
 
   def test_property_single_p
@@ -122,10 +121,10 @@ class TestEntity < Test::Unit::TestCase
     assert_equal "2gnirtS", a.reverse_text_single_p.last
     assert_equal 0, $count
     assert_equal "2gnirtS", a[1].reverse_text_single_p
-    assert_equal 0, $count
+    assert_equal 1, $count
   end
 
-  def _test_property_ary_p_array
+  def test_property_ary_p_array
     a = ["String1", "String2"]
     ReversableString.setup a
 
@@ -134,12 +133,12 @@ class TestEntity < Test::Unit::TestCase
     $count = 0
 
     assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
-    assert_equal 1, $count
+    assert_equal 0, $count
     assert_equal "2gnirtS", a.reverse_text_ary_p_array.last
-    assert_equal 1, $count
+    assert_equal 0, $count
   end
 
-  def _test_unpersist
+  def test_unpersist
     a = ["String1", "String2"]
     ReversableString.setup a
 
@@ -168,14 +167,14 @@ class TestEntity < Test::Unit::TestCase
 
   end
 
-  def _test_persist_annotations
+  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_clean_annotations
+  def test_clean_annotations
 
     string = "test_string"
     ReversableString.setup string

data/test/rbbt/test_knowledge_base.rb

@@ -56,6 +56,18 @@ end
 
 class TestKnowledgeBase < Test::Unit::TestCase
 
+  def test_knowledge_base_reverse
+    organism = Organism.default_code("Hsa")
+    TmpFile.with_file do |tmpdir|
+      kb = KnowledgeBase.new tmpdir, Organism.default_code("Hsa")
+      kb.format = {"Gene" => "Ensembl Gene ID"}
+
+      kb.register :tfacts, TFacts.regulators, :source =>"=~Associated Gene Name"
+
+      kb.get_index(:tfacts).reverse
+    end
+  end
+
   def test_knowledge_base
     organism = Organism.default_code("Hsa")
     TmpFile.with_file do |tmpdir|
@@ -69,7 +81,7 @@ class TestKnowledgeBase < Test::Unit::TestCase
       kb.register :kegg, KEGG.gene_pathway, :source_format => "Ensembl Gene ID"
       assert_match "Ensembl Gene ID", kb.get_database(:kegg).key_field
 
-      gene = Gene.setup("TP53", "Associated Gene Name", organism)
+      gene = Gene.setup("TP53", "Associated Gene Name", organism).ensembl
       assert_equal "TP53", gene.name
       assert_equal "ENSG00000141510", gene.ensembl
 

data/test/rbbt/tsv/test_util.rb

@@ -36,4 +36,19 @@ row2    A    B    Id3
       assert_equal({1 => 1}, Marshal.load(Marshal.dump({1 => 1})))
     end
   end
+
+  def test_replicates
+   content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b|bb|bbb    Id1|Id2|Id3
+row2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+
+      assert_equal 4, tsv.unzip_replicates.length
+      assert_equal %w(aa bb Id2), tsv.unzip_replicates["row1(1)"]
+    end
+  end
 end

data/test/rbbt/util/R/test_model.rb

@@ -75,7 +75,7 @@ data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.
     rppa = rppa.slice([antibody,"Compound", "Dose"])
     rppa.rename_field antibody, "RPPA"
 
-    model = R::Model.new "viability", "Effect ~ Dose", "Compound" => :factor
+    model = R::Model.new "viability", "Effect ~ Dose", nil, "Compound" => :factor
 
     model.fit(viability.select("Compound"){|c| ! c.include? "-"}, 'lm')
 
@@ -85,4 +85,28 @@ data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.
 
     R::SVG.ggplotSVG rppa, plot_script, 7, 7, :R_method => :eval 
   end
+
+  def test_fit_fast
+    data = TSV.setup({}, :key_field => "Dose", :fields => ["Response"], :type => :single)
+    10.times do 
+      x = rand(10)
+      y = 10 + 3 * x + rand * 4
+      data[x] = y
+    end
+
+    model = R::Model.new "Test fit 2", "Response ~ Dose", data, :fit => 'lm'
+
+    x = 5
+    y = 10 + 3 * x 
+
+    pred = model.predict x
+    assert pred > y and pred < y + 4
+
+    pred = model.predict [x, 2*x, 3*x]
+    assert pred.first > y and pred.first  < y + 4
+
+
+    pred = model.predict "Dose" => x
+    assert pred > y and pred < y + 4
+  end
 end

data/test/rbbt/util/test_misc.rb

@@ -6,7 +6,7 @@ require 'rbbt/entity'
 
 class TestMisc < Test::Unit::TestCase
 
-  def test_object_delta
+  def _test_object_delta
     a = []
     b = nil
     d = Misc.object_delta(String) do
@@ -16,13 +16,13 @@ class TestMisc < Test::Unit::TestCase
     assert_match /^0\.\d+$/, a.first
   end
 
-  def test_format_seconds
+  def _test_format_seconds
     t = 61.3232
     assert_equal "00:01:01", Misc.format_seconds(t)
     assert_equal "00:01:01.32", Misc.format_seconds(t, true)
   end
 
-  def test_format_paragraph
+  def _test_format_paragraph
     p = <<-EOF
 Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
 incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
@@ -42,7 +42,7 @@ in culpa qui officia deserunt mollit anim id est laborum.
     assert Misc.format_paragraph(p, 70, 10, 5) =~ /\n\s*\* two/sm
   end
 
-  def test_format_dl
+  def _test_format_dl
     p1 = <<-EOF
 Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
 incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
@@ -72,13 +72,13 @@ eum fugiat quo voluptas nulla pariatur?"
     assert Misc.format_definition_list({:paragraph_first => p1, :paragraph_second => p2}) =~ /       /
   end
 
-  def test_parse_cmd_params
+  def _test_parse_cmd_params
     assert_equal ["workflow", "task", "Translation", "translate", "-f", "Associated Gene Name", "-l", "-"],
       Misc.parse_cmd_params("workflow task Translation translate -f 'Associated Gene Name' -l -")
   end
 
 
-  def test_fixutf8
+  def _test_fixutf8
     string = "abc\xffdef"
     string = string.force_encoding("UTF-8") if string.respond_to? :force_encoding
     assert(! string.valid_encoding?) if string.respond_to? :valid_encoding?
@@ -87,37 +87,37 @@ eum fugiat quo voluptas nulla pariatur?"
     assert( Misc.fixutf8(string).valid_encoding) if string.respond_to? :valid_encoding
   end
 
-  def test_colors_for
+  def _test_colors_for
     colors, used = Misc.colors_for([1,2,2,1,2,1,2,2,3,3,2,3,2])
     assert_equal Misc::COLOR_LIST[1], used[2]
   end
 
-  def test_total_length
+  def _test_total_length
     ranges = [(0..100), (50..150), (120..160)]
     ranges = [(0..100), (50..150), (120..160), (51..70)]
     assert_equal 161, Misc.total_length(ranges)
   end
 
-  def test_id_filename?
+  def _test_id_filename?
     TmpFile.with_file("") do |file|
       assert Misc.is_filename?(file)
       assert ! Misc.is_filename?("TEST STRING")
     end
   end
 
-  def test_merge_sorted_arrays
+  def _test_merge_sorted_arrays
     assert_equal [1,2,3,4], Misc.merge_sorted_arrays([1,3], [2,4])
   end
 
-  def test_intersect_sorted_arrays
+  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
+  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?
+  def _test_binary_include?
     a = %w(a b c d e).sort
     assert Misc.binary_include?(a, "a")
     assert(!Misc.binary_include?(a, "z"))
@@ -126,12 +126,12 @@ eum fugiat quo voluptas nulla pariatur?"
     assert(Misc.binary_include?(a, "d"))
   end
 
-  def test_process_to_hash
+  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]
   end
 
-  def test_pipe_fork
+  def _test_pipe_fork
     sout, sin = Misc.pipe
     pid = Process.fork do
       Misc.purge_pipes(sin)
@@ -143,7 +143,7 @@ eum fugiat quo voluptas nulla pariatur?"
     Process.kill :INT, pid
   end
 
-  def test_open_pipe
+  def _test_open_pipe
     t = 5
     stream = Misc.open_pipe do |sin|
       t.times do |i|
@@ -164,7 +164,7 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal (0..t-1).to_a.collect{|i| "LINE #{ i }"}, lines
   end
 
-  def test_open_pipe_fork
+  def _test_open_pipe_fork
     t = 5
     stream = Misc.open_pipe(true) do |sin|
       t.times do |i|
@@ -185,7 +185,7 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal (0..t-1).to_a.collect{|i| "LINE #{ i }"}, lines
   end
 
-  def test_open_pipe_fork_cascade
+  def _test_open_pipe_fork_cascade
     t = 500
     sleep_time = 2.0 / t
     time = Time.now
@@ -221,7 +221,7 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal (0..t-1).to_a.collect{|i| "LINE #{ i }".reverse.downcase}, lines
   end
 
-  def test_tee_stream
+  def _test_tee_stream
     t = 500
     sleep_time = 2.0 / t
     time = Time.now
@@ -271,7 +271,7 @@ eum fugiat quo voluptas nulla pariatur?"
   end
 
 
-  def test_string2hash
+  def _test_string2hash
     assert(Misc.string2hash("--user-agent=firefox").include? "--user-agent")
     assert_equal(true, Misc.string2hash(":true")[:true])
     assert_equal(true, Misc.string2hash("true")["true"])
@@ -282,16 +282,16 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal(:j, Misc.string2hash("a=b#c=d#:h=:j")[:h])
   end
   
-  def test_named_array
+  def _test_named_array
     a = NamedArray.setup([1,2,3,4], %w(a b c d))
     assert_equal(1, a['a'])
   end
 
-  def test_path_relative_to
+  def _test_path_relative_to
     assert_equal "test/foo", Misc.path_relative_to('/test', '/test/test/foo')
   end
 
-  def test_hash2string
+  def _test_hash2string
     hash = {}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
 
@@ -309,14 +309,14 @@ eum fugiat quo voluptas nulla pariatur?"
  
   end
 
-  def test_merge
+  def _test_merge
     a = [[1],[2]]
     a = NamedArray.setup a, %w(1 2)
     a.merge [3,4]
     assert_equal [1,3], a[0]
   end
 
-  def test_indiferent_hash
+  def _test_indiferent_hash
     a = {:a => 1, "b" => 2}
     a.extend IndiferentHash
 
@@ -326,7 +326,7 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal 2, a[:b]
   end
 
-  def test_lockfile
+  def _test_lockfile
 
     TmpFile.with_file do |tmpfile|
       pids = []
@@ -350,7 +350,7 @@ eum fugiat quo voluptas nulla pariatur?"
     end
   end
 
-  def test_positions2hash
+  def _test_positions2hash
     inputs = Misc.positional2hash([:one, :two, :three], 1, :two => 2, :four => 4)
     assert_equal 1, inputs[:one]
     assert_equal 2, inputs[:two]
@@ -358,44 +358,44 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal nil, inputs[:four]
   end
 
-  def test_mean
+  def _test_mean
     assert_equal 2, Misc.mean([1,2,3])
     assert_equal 3, Misc.mean([1,2,3,4,5])
   end
 
-  def test_zip_fields
+  def _test_zip_fields
     current = [[:a,1], [:b,2]]
     assert_equal [[:a, :b],[1,2]], Misc.zip_fields(current)
     assert_equal current, Misc.zip_fields(Misc.zip_fields(current))
   end
 
-  def test_zip_fields_comp
+  def _test_zip_fields_comp
     current = [[:a,1], [:b,2], [:c]]
     assert_equal [[:a, :b, :c],[1,2,nil]], Misc.zip_fields(current)
     assert_equal current, Misc.zip_fields(Misc.zip_fields(current)).collect{|v| v.compact }
   end
 
-  def test_add_zipped
+  def _test_add_zipped
     current = [[:a,1], [:b,2]]
     new = %w(A B)
     Misc.append_zipped current, new
     assert_equal [[:a,1,"A"], [:b,2,"B"]], current
   end
 
-  def test_divide
+  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
+  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_collapse_ranges
+  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)
   end
 
-  def test_humanize
+  def _test_humanize
     str1 = "test_string"
     str2 = "TEST_string"
     str3 = "test"
@@ -407,22 +407,22 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal "mutation_enrichment", Misc.snake_case("MutationEnrichment")
   end
 
-  def test_snake_case
+  def _test_snake_case
     str1 = "ACRONIMTest"
     str2 = "ACRONIM_test"
     assert_equal "ACRONIM_test", Misc.snake_case(str1)
     assert_equal "ACRONIM_test", Misc.snake_case(str2)
   end
 
-  def test_correct_vcf_mutations
+  def _test_correct_vcf_mutations
     assert_equal [737407, ["-----", "-----G", "-----GTTAAT"]], Misc.correct_vcf_mutation(737406, "GTTAAT", "G,GG,GGTTAAT")
   end
 
-  def test_fingerprint
+  def _test_fingerprint
     assert_equal '{a=>1}', Misc.fingerprint({:a => 1})
   end
 
-  def test_tarize
+  def _test_tarize
     path = File.expand_path('/home/mvazquezg/git/rbbt-util/lib')
     stream = Misc.tarize(path)
     TmpFile.with_file do |res|
@@ -432,7 +432,7 @@ eum fugiat quo voluptas nulla pariatur?"
     end
   end
 
-  def test_camel_case
+  def _test_camel_case
     assert_equal "DbSNP", Misc.camel_case("db_SNP")
     assert_equal "D3Js", Misc.camel_case("D3Js")
     assert_equal "Structure", Misc.camel_case("Structure")
@@ -440,6 +440,9 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal "COSMIC", Misc.camel_case("COSMIC")
   end
 
+  def test_texar
+    ppp Misc.html_tag('textarea', "hola\nadios\nagain")
+  end
 
   def __test_lock_fd
     require 'rbbt/workflow'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.38
+  version: 5.14.39
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-21 00:00:00.000000000 Z
+date: 2014-11-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -108,6 +108,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: sass-css-importer
+  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: