rbbt-util 5.8.2 → 5.8.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 242874c88c6d442034c3e929a735f9d8b5613f53
-  data.tar.gz: e7b40e285fbc4faf3961fdda643c9278eba21096
+  metadata.gz: 8f878977d61954ff0e75db2c46a479f60cdb9ac0
+  data.tar.gz: 0d525ca80ffcc1bb9ab128968406e399552fa4d5
 SHA512:
-  metadata.gz: 022e09717e9f321571373dcd56e3f1a589fdcf37d731a9db885535964e59f1209c6071017d7efe15a60cdc309538c675d2db9dbf9baae21564c1fc7e071ae13a
-  data.tar.gz: 244ad59bc44e11e54a015efd5ac17f69c496b35051807118ac9b931fb08a3196d47a6030966007dca9d4402e4be6738cbc1f19fd484f8c3a4daa66372bf191fc
+  metadata.gz: a35853cd5698117c360befd9dc876a36b2c590c3eaa171424700bdd1d28ba75106d28badfb0d76534dd975fe0fe50a43cc92794c3be5b44b66077e649296ab0c
+  data.tar.gz: d4522e6efe04efaa658e19bfee22cf15b41dce5a771e2e5be3137a518691b80dbd6aebf0a638696f6f1d632db6bffc97b4ad8e9266d5236d22bb62ed42a1d435

data/lib/rbbt/util/misc.rb

@@ -1479,6 +1479,17 @@ end
     sout
   end
 
+  def self.append_zipped(current, new)
+    current.each do |v|
+      n = new.shift
+      if Array === n
+        v.concat new
+      else
+        v << n
+      end
+    end
+    current
+  end
 
   def self.zip_fields(array)
     return [] if array.empty? or (first = array.first).nil?
@@ -1574,6 +1585,16 @@ module IndiferentHash
     hash.extend IndiferentHash 
   end
 
+  def merge(other)
+    new = self.dup
+    IndiferentHash.setup(new)
+    other.each do |k,value|
+      new.delete k
+      new[k] = value
+    end
+    new
+  end
+
   def [](key)
     res = super(key) 
     return res unless res.nil?

data/share/rbbt_commands/workflow/example

@@ -10,7 +10,7 @@ def run_task(workflow, task, name)
   example_dir = workflow.libdir.examples[task][name].find
   Log.debug "Using #{example_dir}"
 
-  ARGV.replace([workflow.to_s, task, '--load_inputs', example_dir, '--jobname', name,'--O','/dev/null'] + $saved_args)
+  ARGV.replace([workflow.to_s, task, '--load_inputs', example_dir, '--jobname', name,'--pf'] + $saved_args)
 
   @pid = Process.fork{
     load Rbbt.share.rbbt_commands.workflow.task.find

data/share/rbbt_commands/workflow/task

@@ -17,10 +17,10 @@ def load_inputs(dir, task)
       inputs[input.to_sym]  = file
     else
       Log.debug "Loading #{ input } from #{file}"
-      inputs[input.to_sym]  = file.read
+      inputs[input.to_sym]  = file.read.strip
     end
   end
-  inputs
+  IndiferentHash.setup(inputs)
 end
 
 def report_options(options)
@@ -136,6 +136,7 @@ options = SOPT.get <<EOF
 -as--array_separator* Change the character that separates elements of Arrays, ',', '|', or '\\n' by default:
 -jn--jobname* Job name to use. The name 'Default' is used by default:
 -pn--printname Print the name of the job and exit without starting it:
+-pf--printpath Print the path of the job result:
 -cl--clean Clean the last step of the job so that it gets recomputed:
 -rcl--recursive_clean Clean the last step and its dependencies to recompute the job completely:
 --fork Run job asyncronously:
@@ -203,7 +204,7 @@ name = options.delete(:jobname) || "Default"
 # get job args
 sopt_option_string = SOPT_options(workflow, task)
 if options[:load_inputs]
-  job_options = load_inputs(options[:load_inputs], task)
+  job_options = load_inputs(options[:load_inputs], task).merge(SOPT.get(sopt_option_string))
 else
   job_options = SOPT.get sopt_option_string
 end
@@ -282,6 +283,13 @@ begin
   else
     Log.low "Job name: #{job.name}" 
   end
+
+  if options.delete(:printpath)
+    puts job.path
+    exit 0
+  else
+    Log.low "Job name: #{job.name}" 
+  end
 rescue ParameterException
   SOPT.delete_inputs(workflow.rec_inputs(task.name))
   usage(workflow, task, $!)

data/test/rbbt/util/test_misc.rb

@@ -6,12 +6,12 @@ require 'rbbt/entity'
 
 class TestMisc < Test::Unit::TestCase
 
-  def _test_parse_cmd_params
+  def test_parse_cmd_params
     ddd 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?
@@ -20,37 +20,37 @@ class TestMisc < Test::Unit::TestCase
     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"))
@@ -59,24 +59,24 @@ class TestMisc < Test::Unit::TestCase
     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_pdf2text_example
+#  def test_pdf2text_example
 #    assert PDF2Text.pdf2text(datafile_test('example.pdf')).read =~ /An Example Paper/i
 #  end
 #
-#  def _test_pdf2text_EPAR
+#  def test_pdf2text_EPAR
 #    assert PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Scientific_Discussion/human/000402/WC500033103.pdf").read =~ /Tamiflu/i
 #  end
 #
-#  def _test_pdf2text_wrong
+#  def test_pdf2text_wrong
 #    assert_raise CMD::CMDError do PDF2Text.pdf2text("http://www.ema.europa.eu/docs/en_GB#").read end
 #  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"])
@@ -87,7 +87,7 @@ class TestMisc < Test::Unit::TestCase
     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
@@ -102,8 +102,8 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
-#  def _test_chunk
-#    _test =<<-EOF
+#  def test_chunk
+#    test =<<-EOF
 #This is an example file. Entries are separated by Entry
 #-- Entry
 #1
@@ -118,7 +118,7 @@ class TestMisc < Test::Unit::TestCase
 #    assert_equal "1\n2\n3", Misc.chunk(test, /^-- Entry/).first.strip
 #  end
 
-  def _test_hash2string
+  def test_hash2string
     hash = {}
     assert_equal hash, Misc.string2hash(Misc.hash2string(hash))
 
@@ -136,14 +136,14 @@ class TestMisc < Test::Unit::TestCase
  
   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
 
@@ -153,7 +153,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal 2, a[:b]
   end
 
-  def _test_lockfile
+  def test_lockfile
 
     TmpFile.with_file do |tmpfile|
       pids = []
@@ -177,7 +177,7 @@ class TestMisc < Test::Unit::TestCase
     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]
@@ -185,41 +185,42 @@ class TestMisc < Test::Unit::TestCase
     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_sd
-    assert_equal Math.sqrt(2), Misc.sd([1,3])
+  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_align_small
-    reference = "AABCDEBD"
-    sequence  = "ABCD"
-    assert_equal '-ABCD---', Misc.fast_align(reference, sequence).last
+  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_align_real
-    reference = "SGNECNKAIDGNKDTFWHTFYGANGDPKPPPHTYTIDMKTTQNVNGLSMLPRQDGNQNGWIGRHEVYLSSDGTNW"
-    sequence  = "TYTIDMKTTQNVNGLSML"
-    assert_equal "--------------------------------TYTIDMKTTQNVNGLSML-------------------------", Misc.fast_align(reference, sequence).last
+  def __test_sd
+    assert_equal Math.sqrt(2), Misc.sd([1,3])
   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"
@@ -231,22 +232,22 @@ class TestMisc < Test::Unit::TestCase
     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|
@@ -256,7 +257,7 @@ class TestMisc < Test::Unit::TestCase
     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")
@@ -264,7 +265,7 @@ class TestMisc < Test::Unit::TestCase
     assert_equal "COSMIC", Misc.camel_case("COSMIC")
   end
 
-  def _test_pipe
+  def test_pipe
     t = 5
     stream = Misc.open_pipe do |sin|
       t.times do |i|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.8.2
+  version: 5.8.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-12 00:00:00.000000000 Z
+date: 2014-03-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake