rbbt-util 5.14.17 → 5.14.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5c5725c2ab4aa762ca676d5d4e18f17dee2e8e92
-  data.tar.gz: 088c84611fccd379434220853ce601256540b9cb
+  metadata.gz: 243728b311e7948c452e6de9e299e5938a3ebd24
+  data.tar.gz: 8eb9ee8a10b1653c79465eab2c68f340a39ecc9f
 SHA512:
-  metadata.gz: 4aa7267702a7587187a85c30fb4bf646efb298ff8d92d2f9aa23daeb58e19ce89dddd470f9d36fcb4258f5bda0e37a6d6bb98327c5308f33b12e79dcaa935e72
-  data.tar.gz: 60796a47e6344334dc576c850df51d405796d8e98f881fcf487f53a23eeaa6db54e0f79207682c28f59b8b694eab063dfbe1395ec114167e3cca9c70b5984116
+  metadata.gz: 46d41fe4394efa9c7ad329e8fa42d0fcd3ea6d2d72cd30a7d2b3f6d7fd8df61565f621ad339abc74d7662a5220df92d2de03beb46f0b5ded72d5a967e532f752
+  data.tar.gz: 20566c536d6b4f4946feedea1e5ad956caf883d8772db394fc8217bbc9eae1bacecb9d5b74fdfde0d45cd94784b82f8ceed01ac3ed286edfa8e35dd3782a12c7

data/etc/app.d/base.rb

@@ -23,17 +23,19 @@ use Rack::Session::Cookie, :key => 'rack.session',
 
 
 #{{{ DIRECTORIES
-global_var = Rbbt.var
-local_var = Rbbt.var.app[$class_name]
+global_var = Rbbt.var.sinatra
+local_var = Rbbt.var.sinatra.app[$class_name]
 
-set :cache_dir           , local_var.sinatra.cache.find
-set :persist_dir         , local_var.sinatra.cache.persistence.find
+set :cache_dir           , local_var.cache
+set :persist_dir         , local_var.cache.persistence
 set :persist_options     , {:persist => true, :persist_dir => :persist_dir}
-set :file_dir            , local_var.sinatra.files.find
-set :permalink_dir       , local_var.sinatra.permalink.find
-set :favourites_dir      , local_var.sinatra.favourites.find
-set :favourite_lists_dir , local_var.sinatra.favourite_lists
-set :favourite_maps_dir  , local_var.sinatra.favourite_maps
+set :file_dir            , local_var.files
+set :permalink_dir       , local_var.permalink
+set :favourites_dir      , local_var.favourites
+set :favourite_lists_dir , local_var.favourite_lists
+set :favourite_maps_dir  , local_var.favourite_maps
+
+#set :finder, nil
 
 #{{{ WORKFLOWS
 

data/etc/app.d/finder.rb

@@ -1,8 +1,8 @@
 #{{{ FINDER
 finder = Finder.new
 if ENV['RBBT_FINDER']
-  finder.add_instance(KEGG.pathways, :grep => '^hsa\|^#', :fields => ["Pathway Name"], :namespace => "Hsa/jun2011", :fix => Proc.new{|l| l.sub(/ - Homo sapiens.*/,'')})
-  finder.add_instance(Organism.lexicon("Hsa/jun2011"), :persist => true, :namespace => "Hsa/jun2011", :grep => '^LRG_', :invert_grep => true)
+  finder.add_instance(KEGG.pathways, :grep => '^hsa\|^#', :fields => ["Pathway Name"], :namespace => Organism.default_code("Hsa"), :fix => Proc.new{|l| l.sub(/ - Homo sapiens.*/,'')})
+  finder.add_instance(Organism.lexicon(Organism.default_code("Hsa")), :persist => true, :namespace => Organism.default_code("Hsa"), :grep => '^LRG_', :invert_grep => true)
 end
 set :finder, finder
 Log.debug("Finder started with: #{finder.instances.length} instances")

data/lib/rbbt/association/index.rb

@@ -16,13 +16,15 @@ module Association
 
     def reverse
       @reverse ||= begin
+                     persistence_path = self.persistence_path
+                     persistence_path = persistence_path.find if Path === persistence_path
                      reverse_filename = persistence_path + '.reverse'
 
                      if File.exists?(reverse_filename)
                        new = Persist.open_tokyocabinet(reverse_filename, false, serializer, TokyoCabinet::BDB)
                        new
                      else
-                       FileUtils.mkdir_p File.basename(reverse_filename) unless File.exists?(File.basename(reverse_filename))
+                       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|

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -336,38 +336,33 @@ module TSV
     begin
       callback, cleanup, join = Misc.process_options options, :callback, :cleanup, :join
 
-      begin
-        q = RbbtProcessQueue.new num, cleanup, join
-        q.callback &callback
-        q.init &block
+      q = RbbtProcessQueue.new num, cleanup, join
+      q.callback &callback
+      q.init &block
 
-        traverse_obj(obj, options) do |*p|
-          q.process *p
-        end
-      rescue Aborted, Errno::EPIPE
-        Log.medium "Aborted"
-      rescue Exception
-        Log.exception $!
-        raise $!
-      ensure
-        q.join
-        q.clean
+      traverse_obj(obj, options) do |*p|
+        q.process *p
       end
+
+      q.join
     rescue Interrupt, Aborted
-      Log.medium{"Aborted traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}: #{$!.backtrace*","}"}
       q.abort
+      Log.medium{"Aborted traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}: #{$!.backtrace*","}"}
       stream = obj_stream(obj)
       stream.abort if stream.respond_to? :abort
       stream = obj_stream(options[:into])
       stream.abort if stream.respond_to? :abort
       raise "Traversal aborted"
     rescue Exception
+      q.abort
       Log.medium "Exception during traversal in CPUs for #{stream_name(obj) || Misc.fingerprint(obj)}: #{$!.message}"
       stream = obj_stream(obj)
       stream.abort if stream.respond_to? :abort
       stream = obj_stream(options[:into])
       stream.abort if stream.respond_to? :abort
       raise $!
+    ensure
+      q.clean
     end
   end
 

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

@@ -111,10 +111,12 @@ class RbbtProcessQueue
 
   def clean
     if (@process_monitor and @process_monitor.alive?) or (@callback_thread and @callback_thread.alive?)
-      self.abort
-    else
+      self.abort 
       self.join
     end
+
+    @queue.clean if @queue
+    @callback_queue.clean if @callback_queue
   end
 
   def abort

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

@@ -10,10 +10,10 @@ class RbbtProcessQueue
       @serializer = serializer || Marshal
                    
 
-      key = "/" << rand(100000000).to_s;
-      @write_sem = key + '.in'
-      @read_sem = key + '.out'
-      Log.low "Creating socket semaphores: #{key}"
+      @key = "/" << rand(1000000000).to_s << '.' << Process.pid.to_s;
+      @write_sem = @key + '.in'
+      @read_sem = @key + '.out'
+      Log.medium "Creating socket semaphores: #{@key}"
       RbbtSemaphore.create_semaphore(@write_sem,1)
       RbbtSemaphore.create_semaphore(@read_sem,1)
     end
@@ -21,7 +21,7 @@ class RbbtProcessQueue
     def clean
       @sread.close unless @sread.closed?
       @swrite.close unless @swrite.closed?
-      Log.low "Destroying socket semaphores"
+      Log.medium "Destroying socket semaphores: #{[@key] * ", "}"
       RbbtSemaphore.delete_semaphore(@write_sem)
       RbbtSemaphore.delete_semaphore(@read_sem)
     end

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

@@ -50,6 +50,16 @@ module Bgzf
                end
   end
 
+  def read_all
+    str = ""
+    while true
+      block = read_block
+      break if block.nil?
+      str << block
+    end
+    str
+  end
+
   def init
     _index
   end
@@ -119,7 +129,9 @@ module Bgzf
     block[offset..-1]
   end
 
-  def read(size)
+  def read(size=nil)
+    return read_all if size.nil?
+
     block = get_block 
     return "" if block.nil? or block.empty?
     len = block.length

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

@@ -286,9 +286,8 @@ module Misc
              end
            end
 
-    #file = caller.first + rand(1000000).to_s if file.nil?
     index = (0..elems.length-1).to_a.collect{|v| v.to_s }
-    TSV.traverse index, :cpus => cpus, :bar => "Bootstrap in #{ cpus } cpus: #{ Misc.fingerprint elems }", :into => Set.new do |pos|
+    TSV.traverse index, :cpus => cpus, :bar => "Bootstrap in #{ cpus } cpus: #{ Misc.fingerprint Annotated.purge(elems) }", :into => Set.new do |pos|
       elem = elems[pos.to_i]
       elems.annotate elem if elems.respond_to? :annotate
       begin

data/lib/rbbt/util/open.rb

@@ -430,6 +430,7 @@ module Open
   def self.write(file, content = nil, options = {})
     options = Misc.add_defaults options, :mode => 'w'
 
+    file = file.find(options[:where]) if Path === file
     mode = Misc.process_options options, :mode
 
     FileUtils.mkdir_p File.dirname(file)

data/share/rbbt_commands/stat/density

@@ -1,7 +1,3 @@
-#!/usr/bin/env ruby
-
-require 'rbbt'
-require 'rbbt/util/simpleopt'
 
 require 'rbbt/util/R'
 

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

@@ -311,8 +311,8 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     head = 2_000
 
     Log.info Log.color :red, "TRAVERSE EXCEPTION"
-    stream = Organism.identifiers("Hsa/jun2011").open 
-    dumper = TSV::Dumper.new Organism.identifiers("Hsa/jun2011").tsv_options
+    stream = Organism.identifiers(Organism.default_code("Hsa")).open 
+    dumper = TSV::Dumper.new Organism.identifiers(Organism.default_code("Hsa")).tsv_options
     dumper.init
 
     assert_raise StopException do
@@ -332,8 +332,8 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     cpus = 2
 
     Log.info Log.color :red, "TRAVERSE EXCEPTION"
-    stream = Organism.identifiers("Hsa/jun2011").open 
-    dumper = TSV::Dumper.new Organism.identifiers("Hsa/jun2011").tsv_options
+    stream = Organism.identifiers(Organism.default_code("Hsa")).open 
+    dumper = TSV::Dumper.new Organism.identifiers(Organism.default_code("Hsa")).tsv_options
     dumper.init
 
     assert_raise ProcessFailed do

data/test/rbbt/util/test_misc.rb

@@ -454,4 +454,14 @@ eum fugiat quo voluptas nulla pariatur?"
     end
     puts `ls -l /proc/#{ Process.pid }/fd`
   end
+
+  def test_bootstrap
+    Misc.bootstrap (0..10).to_a do
+      Misc.bootstrap (0..10).to_a do
+        Misc.bootstrap (0..10).to_a do
+          sleep 0.1
+        end
+      end
+    end
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.17
+  version: 5.14.18
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-20 00:00:00.000000000 Z
+date: 2014-08-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -80,6 +80,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: bio-bgzf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: term-ansicolor
   requirement: !ruby/object:Gem::Requirement