rbbt-util 5.14.37 → 5.14.38

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 77b23907cff78c992f6ab59df3960c6971c9d437
-  data.tar.gz: 84e2b4ae253849c8ef098169e731ef783ecaf0bd
+  metadata.gz: d8a0ba5fcb0625780c5a1cca6a17d1c7716533d0
+  data.tar.gz: db0e0a4843e3e8b63e7526ca1c1c6c156ee20f05
 SHA512:
-  metadata.gz: 65b1490c1bfbab80be6acb838ad94c34b0ff331606ce015529076321bdca70ba5c0f30bffebeb731a98474e2c915f969f091bb07ee5d920b9cc5777d548a0c3b
-  data.tar.gz: bea4df8d24aae52b80c67ac8f43365d1974a1b00030882fb73fd9c893c56ec65a9ffb54911c66d1021be13aafbaca1c374a78ff3af8dfb792997a2e5c296162a
+  metadata.gz: 9a4554bce956bd3ae4c4f457cc815d084622bde543504f4105b2b218bb2fb99e1ec33accae814a278b4062d92ad35b30d19e8295ffb9633484ccdb3d89f4a91b
+  data.tar.gz: 3de5de3a7f71fdcbc40f0ca62132e1dbc49dc5924c62101361fbf0f5caf1bdcee797775a5e6d6777871a5b128e1fd74b37eef48e245f12cb8835e7cad968b656

data/lib/rbbt/association/index.rb

@@ -83,9 +83,6 @@ module Association
           end
         end
       end
-
-      data.close
-      data
     end.tap do |data|
       data.read if not Hash === data and data.respond_to? :read
       Association::Index.setup data
@@ -118,8 +115,6 @@ module Association
                        raise "Can only reverse a TokyoCabinet::BDB dataset at the time"
                      end
 
-                     self.read if self.respond_to? :read
-
                      if File.exists?(reverse_filename)
                        new = Persist.open_tokyocabinet(reverse_filename, false, serializer, TokyoCabinet::BDB)
                        new
@@ -127,9 +122,11 @@ module Association
                        FileUtils.mkdir_p File.dirname(reverse_filename) unless File.exists?(File.basename(reverse_filename))
                        new = Persist.open_tokyocabinet(reverse_filename, true, serializer, TokyoCabinet::BDB)
                        new.write
-                       through do |key, value|
-                         new_key = key.split("~").reverse.join("~")
-                         new[new_key] = value
+                       self.with_unnamed do
+                         through do |key, value|
+                           new_key = key.split("~").reverse.join("~")
+                           new[new_key] = value
+                         end
                        end
                        annotate(new)
                        new.key_field = key_field.split("~").values_at(1,0,2).compact * "~"

data/lib/rbbt/tsv/manipulate.rb

@@ -631,6 +631,34 @@ module TSV
     self
   end
 
+  def add_fields(names = [])
+    old_monitor = @monitor
+    @monitor = {:desc => "Adding field #{ names * ", " }"} if TrueClass === monitor
+
+    through do |key, values|
+      new_values = yield(key, values)
+
+      case type
+      when :double
+        new_values = new_values.collect{|v| [v] } if Array === new_values and new_values.first and not Array === new_values.first
+        values += new_values
+      when :list
+        values += new_values
+      end
+
+      self[key] = values
+    end
+    @monitor = old_monitor
+
+    if not fields.nil? and not (names.nil? or names.empty?)
+      new_fields = self.fields + names
+      self.fields = new_fields
+    end
+
+    self
+  end
+
+
   def transpose(key_field="Unkown ID")
     raise "Transposing only works for TSVs of type :list" unless type == :list
     new_fields = keys

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

@@ -276,7 +276,7 @@ module Misc
     end
   end
 
-  def self.bootstrap(elems, num = :current, file = nil, &block)
+  def self.bootstrap(elems, num = :current, file = nil, options = {}, &block)
     num = :current if num.nil?
     cpus = case num
            when :current
@@ -291,8 +291,11 @@ module Misc
              end
            end
 
+
+    options = Misc.add_defaults options, :cpus => cpus, :bar => "Bootstrap in #{ cpus } cpus: #{ Misc.fingerprint Annotated.purge(elems) }", :into => Set.new 
+
     index = (0..elems.length-1).to_a.collect{|v| v.to_s }
-    TSV.traverse index, :cpus => cpus, :bar => "Bootstrap in #{ cpus } cpus: #{ Misc.fingerprint Annotated.purge(elems) }", :into => Set.new do |pos|
+    TSV.traverse index, options do |pos|
       elem = elems[pos.to_i]
       elems.annotate elem if elems.respond_to? :annotate
       begin

data/lib/rbbt/workflow/accessor.rb

@@ -81,7 +81,7 @@ class Step
       end
 
       begin
-        @info_cache = Misc.insist(2, 3, info_file) do
+        @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?
@@ -97,7 +97,7 @@ class Step
     rescue Exception
       Log.debug{"Error loading info file: " + info_file}
       Log.exception $!
-      Open.sensiblewrite(info_file, INFO_SERIALIAZER.dump({:status => :error, :messages => ["Info file lost"]}))
+      Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump({:status => :error, :messages => ["Info file lost"]}))
       raise $!
     end
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.37
+  version: 5.14.38
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-20 00:00:00.000000000 Z
+date: 2014-10-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake