rbbt-util 5.17.21 → 5.17.22

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 557142d92147d54d45af152135df1fe1743002bd
-  data.tar.gz: 5f56410a030766911e3ca59be65a887a84925636
+  metadata.gz: d71a299df6e7ad5194c3eae79edea89ae8e4b274
+  data.tar.gz: dd907c1ed5886f7523e01bd5bd9aade9c75db0dd
 SHA512:
-  metadata.gz: a58ff556d9be4894195d4e317ef7d9f0fb82bca320b7f03804355fb8d7eda0e72307caa50fb432fe1451d4d55ca40d03da5f20d059e105a4cd89044bdbe15ad1
-  data.tar.gz: 79582eaa89d75dccbce3396e71553b4ab3fad049d8787daaa6a6fc93a6fbac0309d0f277639f05faeb6b71ca779d9aeb4d1ec0ad96407ddfd7af30f2ffb06891
+  metadata.gz: dcd03456906cec78394d31424b837e68831201ed9db7a20bf95e6327f1d61b2485b64639d38197a5ebd024a572d103183aa87918a681b44566752620171b2460
+  data.tar.gz: 32e0ee7a9423802af6aaa8f08eb2e9ea841f483d684aee8352e9e2946b4a40b5c04c0f591dbe406e1da25c0bd5b62849ce170fb8dec0d93ad8768904ba18a8a4

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

@@ -374,10 +374,12 @@ module Misc
       parts = []
       lines.each_with_index do |line,i|
         if line.nil?
+          keys[i] = nil
+          parts[i] = []
+        else
           key, *p = line.strip.split(sep, -1) 
           keys[i] = key
           parts[i] = p
-        else
         end
       end
       sizes = parts.collect{|p| p.nil? ? 0 : p.length }

data/test/rbbt/util/misc/test_pipes.rb

@@ -40,7 +40,7 @@ row3 ccc
     s1 = StringIO.new text1
     s2 = StringIO.new text2
     s3 = StringIO.new text3
-    tsv = TSV.open Misc.paste_streams([s1,s2,s3],nil, " "), :sep => " ", :type => :list
+    tsv = TSV.open Misc.paste_streams([s1,s2,s3], nil, " "), :sep => " ", :type => :list
     assert_equal ["A", "B", "C", "a", "b", "c"], tsv["row1"]
     assert_equal ["AA", "BB", "CC", "aa", "bb", "cc"], tsv["row2"]
     assert_equal ["AAA", "BBB", "CCC", "", "", "ccc"], tsv["row3"]

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")
@@ -440,7 +440,7 @@ eum fugiat quo voluptas nulla pariatur?"
     assert_equal "COSMIC", Misc.camel_case("COSMIC")
   end
 
-  def _test_texar
+  def test_texar
     ppp Misc.html_tag('textarea', "hola\nadios\nagain")
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.21
+  version: 5.17.22
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-06 00:00:00.000000000 Z
+date: 2015-05-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake