rbbt-util 5.15.1 → 5.15.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a156a4d881f09ce0cbd2a74e878f682a294d2355
-  data.tar.gz: 5b85742823494158cbd422ae05eb49f1f9662cc1
+  metadata.gz: 018bba9e3d9b7f80d23369d9534036edee4ead06
+  data.tar.gz: 04bf22adf2e811413c22885bc8178be8cd497902
 SHA512:
-  metadata.gz: 5209b9ac5483a28bd744902435b3c194cad41814a7825b48302de178bbc84ed327069c266004db203befc403e3fb0ecebda6b4e96ea4dc3f5b580f64a8d8fb9e
-  data.tar.gz: e5ca07ed990db5ea1e4b4f5de902ea3c00e2d99960eb843b98306ea15550aa6e8e0e67893ba770bc0bcedc8b1b5e6f1e21829ea5e85595c935d18633edb633ee
+  metadata.gz: a164aec636a2c50eabc7801dd500d8ab38585da8b14abb59e4e9af7830a3754348aabe498c006910f03ad7a970e6118048b51b687fcfb8ac8cf85415641c447a
+  data.tar.gz: a6e0d2485331aa9ff75237e4d1b03a6b7fefa1a1cceb32b9dac44512f7c11c99e4d1078115df4b5340dcec6e035c3bdc4fb5f5a5e6075e501f8ee9d0ac681596

data/etc/app.d/grid_system.rb

@@ -1,4 +1,4 @@
 #require 'zen-grids'
 require 'compass'
 require 'compass-susy'
-require 'font-awesome-sass'
+require 'toolkit'

data/etc/app.d/resources.rb

@@ -1,16 +1,18 @@
 
 EntityRESTHelpers.entity_resources.unshift Rbbt.www.views.find if Rbbt.www.views.exists?
 RbbtRESTHelpers.template_resources.unshift Rbbt.www.views.find if Rbbt.www.views.exists?
-
-#load Rbbt.etc['app.d']['foundation.rb'].find if Rbbt.etc['app.d']['foundation.rb'].exists?
+  
 load Rbbt.etc['app.d']['grid_system.rb'].find if Rbbt.etc['app.d']['grid_system.rb'].exists?
 
 require 'sass-css-importer'
 
+Sinatra::RbbtRESTMain.add_resource_path(Path.setup(ENV["RBBT_VIEWS_DIR"])) if ENV["RBBT_VIEWS_DIR"] and not ENV["RBBT_VIEWS_DIR"].empty?
+
 Compass::Frameworks::ALL.each do |importer|
   next unless importer.respond_to? :path
   path = importer.stylesheets_directory
   RbbtRESTHelpers.add_sass_load_path path
 end
+
 RbbtRESTHelpers.add_sass_load_path './www/views/compass'
 

data/lib/rbbt/annotations/util.rb

@@ -25,8 +25,12 @@ module Annotated
     entity_id = info.delete(:entity_id) || info.delete("entity_id")
 
     annotation_types.each do |mod|
-      mod = Misc.string2const(mod) if String === mod
-      object.extend mod unless mod === object
+      begin
+        mod = Misc.string2const(mod) if String === mod
+        object.extend mod unless mod === object
+      rescue Exception
+        Log.warn "Exception loading annotation into object: #{$!.message}"
+      end
     end
 
     object.instance_variable_set(:@annotation_values, info) 

data/lib/rbbt/association/index.rb

@@ -68,6 +68,7 @@ module Association
             annotations.each do |target, info|
               next if target.nil? or target.empty?
               key = [source, target] * "~"
+
               if data[key].nil? or info.nil?
                 data[key] = info
               else
@@ -75,12 +76,22 @@ module Association
                 info = old_info.zip(info).collect{|p| p * ";;" }
                 data[key] = info
               end
-              if undirected
-                reverse_key = [target,source] * "~"
-                data[reverse_key] = info unless data.include? reverse_key
-              end
             end
           end
+
+          if undirected
+            new_data = {}
+
+            data.through do |key,values|
+              reverse_key = key.split("~").reverse * "~"
+              new_data[reverse_key] = values
+            end 
+
+            new_data.each do |key,values|
+              data[key] = values
+            end
+          end
+
         end
       end
     end.tap do |data|
@@ -219,7 +230,7 @@ module Association
 
       matches.each{|code| 
         s,sep,t = code.partition "~"
-        next if undirected and t > s 
+        next if undirected and t > s and source.include? t
         target_matches[t] ||= []
         target_matches[t] << code
       }

data/lib/rbbt/association/util.rb

@@ -124,11 +124,11 @@ module Association
                  all_fields.first
                end
 
-
       field_headers << header
     end
 
     field_pos = info_fields.collect{|f| raise "Field #{f} not found. Options: #{all_fields * ", "}" unless all_fields.include?(f); f == :key ? 0 : all_fields.index(f);  }
+    field_pos.delete source_pos
 
     source_format = specs[:source][2]
     target_format = specs[:target][2]

data/lib/rbbt/entity.rb

@@ -8,7 +8,59 @@ module Entity
   class << self
     attr_accessor :formats, :entity_property_cache
   end
-  self.formats = {}
+  FORMATS = begin
+              hash = {}
+              class << hash
+                alias orig_include? include?
+
+                attr_accessor :find_cache
+
+                def find(value)
+                  self.find_cache ||= {}
+                  if self.find_cache.include? value
+                    self.find_cache[value]
+                  else
+                    self.find_cache[value] = begin
+                                               if orig_include? value
+                                                 self.find_cache[value] = value
+                                               else
+                                                 found = nil
+                                                 each do |k,v|
+                                                   if value =~ /\b#{Regexp.quote k}$/
+                                                     found = k
+                                                     break
+                                                   end
+                                                 end
+                                                 found
+                                               end
+                                             end
+                  end
+                end
+
+                def [](value)
+                  res = super
+                  return res if res
+                  key = find(value)
+                  key ? super(key) : nil
+                end
+
+                def []=(key,value)
+                  self.find_cache = nil
+                  super
+                end
+
+                def include?(value)
+                  find(value) != nil
+                end
+              end
+
+              hash
+            end
+
+  def self.formats
+    FORMATS
+  end
+
   dir = (defined?(Rbbt)? Rbbt.var.entity_property : 'var/entity_property')
   self.entity_property_cache = dir
 

data/lib/rbbt/entity/identifiers.rb

@@ -25,12 +25,15 @@ module Entity
         def identifier_files 
           files = identity_type.identifier_files.dup
           files.collect!{|f| f.annotate f.gsub(/\bNAMESPACE\b/, organism) } if annotations.include? :organism and self.organism
+          if files.select{|f| f =~ /\bNAMESPACE\b/ }.any?
+            Log.warn "Rejecting some identifier files for lack of 'organism': " << files.select{|f| f =~ /\bNAMESPACE\b/ } * ", "
+          end
           files.reject!{|f| f =~ /\bNAMESPACE\b/ } 
           files
         end
 
         def identifier_index(format = nil, source = nil)
-          Persist.memory("Entity index #{identity_type}: #{format} (from #{source || "All"})", :format => format, :source => source) do
+          Persist.memory("Entity index #{identity_type}: #{format} (from #{source || "All"})", :format => format, :source => source, :update => true) do
             source ||= self.respond_to?(:format)? self.format : nil
 
             index = TSV.translation_index(identifier_files, format, source, :persist => true)

data/lib/rbbt/tsv.rb

@@ -60,6 +60,7 @@ module TSV
     unnamed = Misc.process_options options, :unnamed
     entity_options = Misc.process_options options, :entity_options
 
+
     Log.debug "TSV open: #{ filename } - #{Misc.fingerprint options }.#{unnamed ? " [unnamed]" : "[not unnamed]"}"
 
     data = nil
@@ -72,10 +73,12 @@ module TSV
           data.serializer = serializer
         end
 
+        tsv_grep = Misc.process_options options, :tsv_grep
+        tsv_grep ||= Misc.process_options options, :grep
         open_options = Misc.pull_keys options, :open
 
         stream = get_stream source, options.merge(open_options)
-        parse stream, data, options
+        parse stream, data, options.merge(:tsv_grep => tsv_grep)
 
         data.filename = filename.to_s unless filename.nil?
 

data/lib/rbbt/tsv/accessor.rb

@@ -646,35 +646,7 @@ Example:
     new
   end
 
-  def unzip(field = 0, merge = false)
-    new = {}
-    field_pos = self.identify_field field
-
-    self.through do |key,values|
-      field_values = values.delete_at field_pos
-      zipped = values.zip_fields
-      field_values.zip(zipped).each do |value, *rest|
-        k = [key,value]*":"
-        if merge and new.include? k
-          new[k] = Misc.zip_fields(rest)
-        else
-          new[k] = Misc.zip_fields(rest)
-        end
-      end
-    end
-
-    self.annotate new
-    new.type = :list
-
-    new.key_field = [self.key_field, self.fields[field_pos]] * ":"
-    new_fields = self.fields.dup
-    new_fields.delete_at field_pos
-    new.fields = new_fields
-
-    new
-  end
-
-  def unzip(field = 0, merge = false)
+  def unzip(field = 0, merge = false, sep = ":")
     new = {}
     self.annotate new
 
@@ -686,7 +658,7 @@ Example:
           next if field_values.nil?
           zipped = Misc.zip_fields(values)
           field_values.zip(zipped).each do |field_value,rest|
-            k = [key,field_value]*":"
+            k = [key,field_value]*sep
             if new.include? k
               new[k] = Misc.zip_fields(Misc.zip_fields(new[k]) << rest)
             else
@@ -701,7 +673,7 @@ Example:
           next if field_values.nil?
           zipped = Misc.zip_fields(values)
           field_values.zip(zipped).each do |field_value,rest|
-            k = [key,field_value]*":"
+            k = [key,field_value]*sep
             new[k] = rest
           end
         end

data/lib/rbbt/tsv/change_id.rb

@@ -89,7 +89,11 @@ module TSV
   def self.translation_index(files, target = nil, source = nil, options = {})
     return nil if source == target
     options = Misc.add_defaults options.dup, :persist => true
+
+    target = Entity.formats.find(target) if Entity.formats.find(target)
+    source = Entity.formats.find(source) if Entity.formats.find(source)
     fields = (source and not source.empty?) ? [source] : nil
+
     files.each do |file|
       if TSV === file
         all_fields = file.all_fields
@@ -126,6 +130,7 @@ module TSV
 
           index = Persist.persist_tsv(nil, Misc.fingerprint(files), {:files => files, :source => source, :target => target}, :prefix => "Translation index", :persist => options[:persist]) do |data|
 
+            iii options.merge(:target => common_field, :fields => fields)
             index = TSV === file ? 
               file.index(options.merge(:target => common_field, :fields => fields)) :
               TSV.index(file, options.merge(:target => common_field, :fields => fields))

data/lib/rbbt/tsv/excel.rb

@@ -85,6 +85,21 @@ module TSV
         end
       end
 
+      cells = cells.collect do |v| 
+        case v
+        when Float
+          v.to_s.sub(/e(-?\d+)$/,'E\1')
+        when String
+          if v =~ /^-?[\d\.]+e(-?\d+)$/
+            v.sub(/e(-?\d+)$/,'E\1') 
+          else
+            v
+          end
+        else
+          v
+        end
+      end
+
       sheet1.row(i).concat cells
       i += 1
     end

data/lib/rbbt/tsv/index.rb

@@ -16,7 +16,7 @@ module TSV
     persist_options = Misc.pull_keys options, :persist
     persist_options[:prefix] ||= "Index[#{options[:target] || :key}]"
 
-    Log.debug "Index: #{ filename } - #{options.inspect}"
+    Log.debug "Index: #{ filename } - #{Misc.fingerprint options}"
     Persist.persist_tsv self, filename, options, persist_options do |new|
       with_unnamed do
         target, fields, index_type, order = Misc.process_options options, :target, :fields, :type, :order
@@ -116,7 +116,7 @@ module TSV
           end
         end
 
-        TSV.setup(new, :type => index_type, :filename => filename, :fields => [new_key_field], :key_field => new_fields * ", ")
+        TSV.setup(new, :type => index_type, :filename => filename, :fields => [new_key_field], :key_field => new_fields * ", ", :namespace => namespace)
       end
     end
   end
@@ -125,12 +125,12 @@ module TSV
     persist_options = Misc.pull_keys options, :persist
     persist_options[:prefix] ||= "StaticIndex[#{options[:target] || :key}]"
      
-    Log.debug "Static Index: #{ file } - #{options.inspect}"
+    Log.debug "Static Index: #{ file } - #{Misc.fingerprint options}"
     Persist.persist_tsv nil, file, options, persist_options do |data|
       data_options = Misc.pull_keys options, :data
       identifiers = TSV.open(file, data_options)
       identifiers.with_monitor :desc => "Creating Index for #{ file }" do
-        index = identifiers.index(options.merge :persist_data => data, :persist => persist_options[:persist])
+        identifiers.index(options.merge :persist_data => data, :persist => persist_options[:persist])
       end
     end
   end

data/lib/rbbt/tsv/parser.rb

@@ -383,6 +383,7 @@ module TSV
     def initialize(stream = nil, options = {})
       @header_hash = Misc.process_options(options, :header_hash) || "#"
       @sep = Misc.process_options(options, :sep) || "\t"
+      @tsv_grep = Misc.process_options(options, :tsv_grep) 
       stream = TSV.get_stream stream
       @stream = stream
 
@@ -414,6 +415,8 @@ module TSV
       fix_fields(options)
 
       @type = @type.strip.to_sym if String === @type
+      #@type ||= :double if merge == true
+
       case @type
       when :double 
         self.instance_eval do alias get_values get_values_double end
@@ -502,18 +505,24 @@ module TSV
       raise "No block given in TSV::Parser#traverse" unless block_given?
 
       stream = @stream
-      # get parser
 
-      # grep
-      #if grep and false
-      #  stream.rewind if stream.eof?
-      #  stream = Open.grep(stream, grep, invert_grep)
-      #  self.first_line = stream.gets
-      #end
 
       # first line
       line = self.rescue_first_line
 
+      if @tsv_grep
+
+        stream = Open.grep(stream, @tsv_grep, invert_grep)
+        stream.no_fail = true
+        begin
+          match = Open.grep(StringIO.new(line), @tsv_grep, invert_grep).read
+          line = stream.gets if match.empty?
+        rescue Exception
+          Log.exception $!
+          line = stream.gets 
+        end
+      end
+
       progress_monitor, monitor = monitor, nil if Log::ProgressBar === monitor
       # setup monitor
       if monitor and (stream.respond_to?(:size) or (stream.respond_to?(:stat) and stream.stat.respond_to? :size)) and stream.respond_to?(:pos)

data/lib/rbbt/tsv/util.rb

@@ -152,7 +152,7 @@ module TSV
       pos = fields.index field
       return pos if pos
       return identify_field(key_field, fields, field.to_i) if field =~ /^\d+$/
-      raise "Field #{ field } was not found. Options: #{fields * ", "}" if pos.nil?
+      raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
     else
       raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
     end

data/lib/rbbt/util/R.rb

@@ -4,8 +4,9 @@ require 'rbbt/util/R/eval'
 
 module R
 
-  LIB_DIR = File.join(File.expand_path(File.dirname(__FILE__)),'../../../share/Rlib')
+  LIB_DIR = Path.setup(File.join(File.expand_path(File.dirname(__FILE__)),'../../../share/Rlib'))
   UTIL    = File.join(LIB_DIR, 'util.R')
+  PLOT    = File.join(LIB_DIR, 'plot.R')
 
   def self.run(command, options = {})
     cmd =<<-EOF
@@ -127,10 +128,11 @@ module TSV
     open_options, source = source, nil if Hash === source
 
     source ||= Misc.process_options open_options, :source
-    source = [source] if String === source
+    source = [source] unless Array === source 
 
     require_sources  = source.collect{|source|
-      "source('#{source}');"
+      source = R::LIB_DIR["plot.R"] if source == :plot
+      "source('#{source}')"
     } * ";\n" if Array === source and source.any?
 
     script = require_sources + "\n\n" + script if require_sources

data/lib/rbbt/util/R/model.rb

@@ -18,11 +18,14 @@ module R
   class Model
     R_METHOD = :eval
 
-    attr_accessor :name, :formula
+    attr_accessor :name, :formula, :model_file
     def initialize(name, formula, data = nil, options = {})
       @name = name
       @formula = formula
       @options = options || {}
+      @model_file = options[:model_file] if options[:model_file]
+      @model_file ||= Misc.sanitize_filename(File.join(options[:model_dir], name)) if options[:model_dir]
+
       if data and not model_file.exists?
         method = Misc.process_options options, :fit
         fit(data, method || "lm", options)

data/lib/rbbt/util/colorize.rb

@@ -15,12 +15,13 @@ module Colorize
     start_color = Color.new from_name(start)
     end_color = Color.new from_name(eend)
 
-    array = array.collect{|v| v.to_f}
+    array = array.collect{|v| n = v.to_f; n = n > 100 ? 100 : n; n < 0.001 ? 0.001 : n}
     max = array.max
     min = array.min
     range = max - min
     array.collect do |v|
-      start_color.blend end_color, (v - min) / range
+      ratio = (v-min) / range
+      start_color.blend end_color, ratio
     end
   end
 

data/lib/rbbt/util/concurrency/processes/socket.rb

@@ -89,7 +89,9 @@ class RbbtProcessQueue
     
     def push(obj)
       RbbtSemaphore.synchronize(@write_sem) do
+        multiple = MultipleResult === obj
         obj = Annotated.purge(obj)
+        obj.extend MultipleResult if multiple
         self.dump(obj, @swrite)
       end
     end

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

@@ -7,11 +7,11 @@ module Misc
 
     dup_array = options.delete :dup_array
 
-    if Entity === field or (Entity.respond_to?(:formats) and Entity.formats.include? field)
+    if Entity === field or (Entity.respond_to?(:formats) and (_format = Entity.formats.find(field)))
       params = options.dup
 
       params[:format] ||= params.delete "format"
-      params.merge!(:format => field) unless params.include?(:format) and not ((f = params[:format]).nil? or (String === f and f.empty?))
+      params.merge!(:format => _format) unless _format.nil? or (params.include?(:format) and not ((f = params[:format]).nil? or (String === f and f.empty?)))
 
       mod = Entity === field ? field : Entity.formats[field]
       entity = mod.setup(

data/share/Rlib/plot.R

@@ -0,0 +1,40 @@
+library(ggplot2)
+
+geom_entity <- function (real.geom = NULL, mapping = NULL, data = NULL, stat = "identity",
+                          position = "identity", ...) {
+    rg <- real.geom(mapping = mapping, data = data, stat = stat, 
+                    position = position, ...)
+
+    rg$geom <- proto(rg$geom, { 
+        draw <- function(., data, ...) {
+            grobs <- list()
+
+            for (i in 1:nrow(data)) {
+                grob <- .super$draw(., data[i,], ...) 
+                if (is.null(data$entity.type)) 
+                    grobs[[i]] <- garnishGrob(grob, `data-entity`=data[i,]$entity)
+                else
+                    grobs[[i]] <- garnishGrob(grob, `data-entity`=data[i,]$entity, `data-entity-type`=data[i,]$entity.type)
+            }
+
+            ggplot2:::ggname("geom_entity", gTree(children = do.call("gList", grobs)))
+        }
+
+        draw_groups <- function(., data, ...) {
+            grobs <- list()
+
+            for (i in 1:nrow(data)) {
+                grob <- .super$draw_groups(., data[i,], ...) 
+                if (is.null(data$entity.type)) 
+                    grobs[[i]] <- garnishGrob(grob, `data-entity`=data[i,]$entity)
+                else
+                    grobs[[i]] <- garnishGrob(grob, `data-entity`=data[i,]$entity, `data-entity-type`=data[i,]$entity.type)
+            }
+
+            ggplot2:::ggname("geom_entity", gTree(children = do.call("gList", grobs)))
+        }
+    })
+
+    rg
+}
+

data/share/rbbt_commands/app/start

@@ -3,7 +3,7 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-f--finder:-R--Rserve_session*:-ho--host*"
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-f--finder:-R--Rserve_session*:-ho--host*:--views*"
 options[:Port] ||= options[:port]
 options[:Host] ||= "0.0.0.0"
 options[:Bind] ||= "0.0.0.0"
@@ -21,6 +21,7 @@ Misc.in_dir(app_dir) do
   require 'rack'
   ENV["RBBT_FINDER"] = "true" if options.include?(:finder)
   ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
+  ENV["RBBT_VIEWS_DIR"] = options[:views] if options.include?(:views)
 
   config_ru_file = File.exists?('./config.ru') ? './config.ru' : Rbbt.share['config.ru'].find
 

data/share/rbbt_commands/tsv/unzip

@@ -8,7 +8,7 @@ $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_c
 options = SOPT.setup <<EOF
 Zip fields in a TSV file 
 
-$ rbbt tsv info [options] file.tsv
+$ rbbt tsv unzip [options] file.tsv
 
 Display summary information. Works with Tokyocabinet HDB and BDB as well.
 

data/share/rbbt_commands/workflow/example

@@ -36,7 +36,7 @@ def run_task(workflow, task, name)
       end
     end
     sleep 0.5
-    path = Open.read(res).strip if File.exists? res
+    path = Open.read(res).strip.split("\n").last if File.exists? res
   end
   path = "NO RESULT" if path.nil? or path.empty?
 

data/share/rbbt_commands/workflow/server

@@ -13,7 +13,7 @@ require 'rbbt/rest/file_server'
 require 'rbbt/rest/knowledge_base'
 require 'rbbt/rest/helpers'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder"
+options = SOPT.get "-e--environment*:-p--port*:-s--server*:-b--bind*:-e--environment*:-R--RServe_session*:--finder:--views*"
 
 workflow = ARGV.first
 
@@ -31,6 +31,8 @@ load Rbbt.etc['app.d/init.rb'].find
 app = class WorkflowRest < Sinatra::Base; self end
 
 app.register Sinatra::RbbtRESTWorkflow
+app.register Sinatra::RbbtRESTKnowledgeBase
+
 app.get '/' do
   redirect to(File.join('/', wf.to_s))
 end
@@ -43,7 +45,12 @@ app.class_eval do
   eval Rbbt.etc['app.d/finder.rb'].read
 end
 
-WorkflowRest.add_workflow wf, true
+WorkflowRest.add_workflow wf, :all
+
+if options[:views] and not options[:views].empty?
+  Sinatra::RbbtRESTMain.add_resource_path(Path.setup(options[:views]), true)
+end
+
 
 WorkflowRest.port = options[:port] || 4567
 WorkflowRest.bind = options[:bind] || "0.0.0.0"

data/test/rbbt/association/test_database.rb

@@ -58,4 +58,7 @@ TP53 NFKB1|GLI1 activation|activation true|true
     assert_equal [["Bilateria"], ["Euteleostomi"], ["Duplicate"]], tsv["ENSG00000000003"]
   end
 
+  def test_gene_ages
+    assert Association.database('/home/mvazquezg/git/workflows/genomics/share/gene_ages', :source => "FamilyAge", :merge => true, :target => "Ensembl Gene ID", :persist => false).values.first.length > 1
+  end
 end

data/test/rbbt/test_tsv.rb

@@ -308,6 +308,22 @@ b 2
     end
   end
 
+  def test_tsv_grep
+    content =<<-EOF
+#: :sep=/\\s+/#:type=:single
+#Id Value
+a 1
+b 2
+b 3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :key_field => "Value", :tsv_grep => "2")
+      assert(tsv.include?("2"))
+      assert(! tsv.include?("3"))
+    end
+  end
+
   def test_grep_invert
     content =<<-EOF
 #: :sep=/\\s+/#:type=:single
@@ -317,8 +333,9 @@ b 2
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2", :invert_grep => true)
+      tsv = TSV.open(filename, :key_field => "Value", :tsv_grep => "2", :invert_grep => true)
       assert(! tsv.include?("2"))
+      assert(tsv.include?("1"))
     end
   end
 
@@ -326,6 +343,7 @@ b 2
     content =<<-EOF
 #: :sep=/\\s+/#:type=:single#:namespace=Test
 #Id Value
+a 7
 a 1
 b 2
     EOF
@@ -334,6 +352,7 @@ b 2
       tsv = TSV.open(filename, :key_field => "Value", :grep => "#\\|2")
       assert(! tsv.include?("1"))
       assert(tsv.include?("2"))
+      assert(! tsv.include?("7"))
     end
   end
 
@@ -533,4 +552,8 @@ row2    A AA AAA
     tsv = datafile_test('identifiers').tsv :persist => true, :shard_function => shard_function
     assert_equal 10000, tsv.keys.length + 2
   end
+
+  def test_merge_key_field
+    assert TSV.open('/home/mvazquezg/git/workflows/genomics/share/gene_ages', :key_field => "FamilyAge", :merge => true,  :persist => false, :zipped => true, :type => :double).values.first.length > 1
+  end
 end

data/test/rbbt/tsv/parallel/test_traverse.rb

@@ -394,10 +394,14 @@ class TestTSVParallelThrough < Test::Unit::TestCase
   def test_store_multiple
     size = 1000
     array = (1..size).to_a.collect{|n| n.to_s}
-    stream = TSV.traverse array, :bar => {:max => size, :desc => "Array"}, :cpus => 5, :into => :stream do |e|
-      sleep 0.01
-      [e,e+".alt"].extend MultipleResult
+
+    stream = TSV.traverse array, :bar => {:max => size, :desc => "Multiple into stream"}, :cpus => 2, :into => :stream do |e|
+      sleep 0.001
+      res = [e,e+".alt"]
+      res.extend MultipleResult
+      res
     end
+
     assert_equal size*2, stream.read.split("\n").length
   end
 end

data/test/rbbt/tsv/test_manipulate.rb

@@ -13,12 +13,14 @@ rowa    a|aa    b|BB  C|CC
 
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(File.open(filename), :sep => /\s+/, :type => :double)
+      Log.tsv tsv
+      Log.tsv tsv.reorder("ValueA", nil, :zipped => true)
       assert_equal ["A", "AA", "a", "aa"].sort, tsv.reorder("ValueA", nil, :zipped => true).keys.sort
     end
   end
 
 
-  def test_through
+  def _test_through
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -37,7 +39,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_reorder_simple
+  def _test_reorder_simple
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -59,7 +61,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_reorder_remove_field
+  def _test_reorder_remove_field
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -81,7 +83,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_slice
+  def _test_slice
     content =<<-EOF
 #ID ValueA ValueB Comment
 row1 a b c
@@ -94,7 +96,7 @@ row2 A B C
     end
   end
 
-  def test_select
+  def _test_select
      content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -132,7 +134,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_select_invert
+  def _test_select_invert
      content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -163,7 +165,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_process
+  def _test_process
     content =<<-EOF
 #Id    ValueA    ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -182,7 +184,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_add_field
+  def _test_add_field
      content =<<-EOF
 #Id    LetterValue:ValueA    LetterValue:ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -200,7 +202,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_add_field_double_with_list_result
+  def _test_add_field_double_with_list_result
      content =<<-EOF
 #Id    LetterValue:ValueA    LetterValue:ValueB    OtherID
 row1    a|aa|aaa    b    Id1|Id2
@@ -219,7 +221,7 @@ row3    a    C    Id4
     end
   end
 
-  def test_through_headless
+  def _test_through_headless
      content =<<-EOF
 row1    a|aa|aaa    b    Id1|Id2
 row2    A    B    Id3
@@ -229,17 +231,17 @@ row3    a    C    Id4
     TmpFile.with_file(content) do |filename|
       tsv = TSV.open(filename, :sep => /\s+/)
 
-      test = false
+      _test = false
       tsv.through do
-        test = true
+        _test = true
       end
-      assert test
+      assert _test
 
     end
  
   end
 
-  def test_reorder_flat
+  def _test_reorder_flat
     content =<<-EOF
 #Id    ValueA    
 row1    a aa aaa
@@ -255,7 +257,7 @@ row3    a
     end
   end
 
-  def test_transpose
+  def _test_transpose
      content =<<-EOF
 #: :type=:list
 #Row   vA   vB   vID
@@ -273,7 +275,7 @@ row3    a    C    Id4
  
   end
 
-  def test_through_flat
+  def _test_through_flat
      content =<<-EOF
 #: :type=:flat
 #Row   vA

data/test/rbbt/util/test_misc.rb

@@ -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
 
@@ -454,4 +454,8 @@ eum fugiat quo voluptas nulla pariatur?"
     puts `ls -l /proc/#{ Process.pid }/fd`
   end
 
+  def test_snake_case
+    ppp Misc.snake_case("KinaseSARfari")
+  end
+
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.15.1
+  version: 5.15.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-11-21 00:00:00.000000000 Z
+date: 2015-01-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -268,6 +268,7 @@ files:
 - lib/rbbt/workflow/step/run.rb
 - lib/rbbt/workflow/task.rb
 - lib/rbbt/workflow/usage.rb
+- share/Rlib/plot.R
 - share/Rlib/util.R
 - share/config.ru
 - share/install/software/lib/install_helpers