rbbt-util 5.21.115 → 5.21.116

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 646ea32ae9ce7ff64c1d2ba88179b9883ca19522
-  data.tar.gz: 7cfc05f02e007ce786ab4e2158fde5c324375ad3
+  metadata.gz: 77c923c4547ab8c088116d35a69d5963d69c9288
+  data.tar.gz: 1d770671abe5b42e35e7466239f3a20d68c54615
 SHA512:
-  metadata.gz: bf93e300a29a6736da94cd6f715e9a17088dfb6d1a5ac4b51315191d00668930ca53bb3cd8fbd162d0591b7f3173da3a5500fff55ca267f1c08702b77193293d
-  data.tar.gz: f143574d50f916ffa09e196335246e89fcdb99ef08ce82e22e17eb271bfefde22ab159f8b4a24befa1fe114911d162c4b39290878c33f5da7c89745773094c23
+  metadata.gz: 435ffaa1be1e204fd0e98c4c7e0f8d3df28dffb79ca1acd0102d32d6078ff2d64d8a27cff3158ec4fd7034b2168b70b44df1cd511be46b582feeb48e95ca08b4
+  data.tar.gz: '08612a841a790fcbd898133e21c47188c905cee765aa8db675464cef651f0c842986249a65192014953451f9fa16cae4c3108360b18f8830c2b7951913b34056'

data/lib/rbbt/tsv/accessor.rb

@@ -692,10 +692,14 @@ Example:
       if merge
         self.through do |key,values|
           field_values = values[field_pos]
-          values.delete_at(field_pos) if delete
+          if delete
+            values = values.dup
+            values.delete_at(field_pos) 
+          end
           next if field_values.nil?
           zipped = Misc.zip_fields(values)
           field_values.zip(zipped).each do |field_value,rest|
+            rest = [nil] * values.length if rest.nil?
             k = [key,field_value]*sep
             if new.include? k
               new[k] = Misc.zip_fields(Misc.zip_fields(new[k]) << rest)
@@ -712,6 +716,7 @@ Example:
           next if field_values.nil?
           zipped = Misc.zip_fields(values)
           field_values.zip(zipped).each do |field_value,rest|
+            rest = [nil] * values.length if rest.nil?
             k = [key,field_value]*sep
             new[k] = rest
           end
@@ -730,7 +735,7 @@ Example:
     new
   end
   
-  def zip(field = 0, merge = false, sep = ":")
+  def zip(merge = false, field = "New Field", sep = ":")
     new = {}
     self.annotate new
 
@@ -740,9 +745,12 @@ Example:
       if merge
         self.through do |key,values|
           new_key, new_value = key.split(sep)
-          new_values = values + [[new_value]]
+          new_values = values + [[new_value] * values.first.length]
           if new.include? new_key
-            new[new_key] = Misc.zip_fields(Misc.zip_fields(new[new_key]) << new_values)
+            current = new[new_key]
+            current.each_with_index do |v,i|
+              v.concat(new_values[i])
+            end
           else
             new[new_key] = new_values
           end
@@ -763,5 +771,13 @@ Example:
 
     new
   end
+
+  def remove_duplicates(pivot = 0)
+    new = self.annotate({})
+    self.through do |k,values|
+      new[k] = Misc.zip_fields(Misc.zip_fields(values).uniq)
+    end
+    new
+  end
 end
 

data/lib/rbbt/util/R.rb

@@ -60,8 +60,13 @@ source('#{UTIL}');
        Open.write(init_file) do |f|
           f.puts "# Loading basic rbbt environment"
           f.puts "library(utils, quietly=TRUE);\n"
+          f.puts "interactive.script.file = '#{init_file}'"
+
           f.puts "source('#{R::UTIL}');\n"
-          f.puts 
+          f.puts "rbbt.require('readr')"
+          f.puts "interactive.script = read_file(interactive.script.file)"
+          f.puts "cat(interactive.script)"
+          f.puts ""
           f.puts script
         end
         CMD.cmd("env R_PROFILE='#{init_file}' xterm \"$R_HOME/bin/R\"")

data/lib/rbbt/util/cmd.rb

@@ -6,6 +6,9 @@ module CMD
   def self.process_cmd_options(options = {})
     string = ""
     options.each do |option, value|
+      raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=]+$/i
+      raise "Invalid option value: #{value.inspect}" if value.to_s.include? "'"
+
       case 
       when value.nil? || FalseClass === value 
         next
@@ -13,9 +16,9 @@ module CMD
         string << "#{option} "
       else
         if option.to_s.chars.to_a.last == "="
-          string << "#{option}#{value} "
+          string << "#{option}'#{value}' "
         else
-          string << "#{option} #{value} "
+          string << "#{option} '#{value}' "
         end
       end
     end
@@ -75,10 +78,8 @@ module CMD
         STDOUT.reopen sout.last
         sout.last.close
 
-
         STDOUT.sync = STDERR.sync = true
 
-
         exec(ENV, cmd)
 
         exit(-1)

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

@@ -175,6 +175,7 @@ module Misc
   end
 
   def self.humanize_list(list)
+    return "" if list.empty?
     if list.length == 1
       list.first
     else

data/lib/rbbt/util/open.rb

@@ -50,7 +50,7 @@ module Open
 
   def self.wget(url, options = {})
     Log.low "WGET:\n -URL: #{ url }\n -OPTIONS: #{options.inspect}"
-    options = Misc.add_defaults options, "--user-agent=" => 'firefox', :pipe => true
+    options = Misc.add_defaults options, "--user-agent=" => 'rbbt', :pipe => true
 
     wait(options[:nice], options[:nice_key]) if options[:nice]
     options.delete(:nice)

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

@@ -123,7 +123,7 @@ class Step
   def updated?
     return true unless done?
 
-    out_of_date.empty?
+    @updated ||= out_of_date.empty?
   end
 
   def kill_children

data/share/Rlib/svg.R

@@ -20,11 +20,11 @@ rbbt.SVG.extract <- function(plot, size=NULL, prefix=NULL, ...){
         resolution = 72 * (size/7)
 
         if (length(plot$theme) == 0) plot <- plot + theme_gdocs();
+        if (length(plot$theme$text) == 0) plot <- plot + theme(text = element_text(size=base.size));
 
         plot$theme$text$size = base.size
 
         print(plot, type='cairo')
-
         mysvg <- grid.export(res=resolution, prefix=prefix, ...)
     }
 

data/share/Rlib/util.R

@@ -615,7 +615,7 @@ rbbt.plot.matrix <- function(x, ...){
 
 # Adapted from: https://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html
 rbbt.plot.venn <- function(data, a, ...) {
-    rbbt.require(VennDiagram)
+    rbbt.require('VennDiagram')
     group.matches <- function(data, fields) {
         sub = data
         for (i in 1:length(fields)) {

data/test/rbbt/tsv/test_accessor.rb

@@ -221,4 +221,34 @@ row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
       assert_equal 6, CMD.cmd('grep -v "#" | cut -f 1', :in => tsv.to_s(nil, false, true)).read.split("\n").length
     end
   end
+
+  def test_remove_duplicates
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|A|a|a    b|B|b|    Id1|Id2|Id1|Id1
+row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      assert_equal %w(a A a), tsv.remove_duplicates["row1"]["ValueA"]
+      assert tsv.remove_duplicates["row1"]["ValueB"].include?("")
+    end
+
+  end
+
+  def test_unzip_zip
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|A|a|a    b|B|b|    Id1|Id2|Id1|Id1
+row2    aa|aa|AA|AA    b1|b2|B1|B2    Id1|Id1|Id2|Id2
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      assert_equal ["b", "b", ""], tsv.unzip("ValueA", true)["row1:a"]["ValueB"]
+      assert_equal ["b", "b", "", "B"].sort, tsv.unzip("ValueA", true).zip(true)["row1"]["ValueB"].sort
+    end
+
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.115
+  version: 5.21.116
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-14 00:00:00.000000000 Z
+date: 2017-12-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake