rbbt-util 5.14.14 → 5.14.15

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 12a27683f6ea8562a740927dac6dca9e22854834
-  data.tar.gz: 6d69aab1d30fa8d56fc8b579a241779e3d84054c
+  metadata.gz: b4562833949296544e288b767589677cdea4cd54
+  data.tar.gz: 50c2d8f06c365b3334ab046671031b4dadff448f
 SHA512:
-  metadata.gz: 7e33da494e19497c5f1aaaca0a6bd35f32edf91d66dbbc2f6b7cfc9932e381bb4ca08ad703b85d5fde85d5c4cba483a48d2ea287ab5e83c5f4d4a82d4f174833
-  data.tar.gz: 8fafdc22a685ce746ceb13cf10c6162c27afbcc51478c241a2d10402d904655b1c2e348e636758ac29cdcb48a3bf7ce9f3c6f4b50fecb45d895780308b8ff172
+  metadata.gz: 247c31f35e49849089188684402ae360d88800e4d90cdbe897c36a7d666f00360c10e308a2a5626411f7d917595930efa4213c2af20050e7b8ab235fc4b5f349
+  data.tar.gz: 31d136e11cc112d958568a7607fc673876822f8c350ffd326c9b66b58ca55dc6e48659ee1f80ff660527188eb30ba63d0ddfa703c3cef285c865ae8fbf5ff824

data/etc/app.d/base.rb

@@ -19,11 +19,11 @@ helpers Sinatra::RbbtMiscHelpers
 use Rack::Session::Cookie, :key => 'rack.session',
   :path => '/',
   :expire_after => 2592000,
-  :secret => 'StudyExplorer secret!!'
+  :secret => "#{self.to_s} secret!!"
 
 
 #{{{ DIRECTORIES
-local_var = Rbbt.var.find(:current)
+local_var = Rbbt.var#.find(:current)
 set :cache_dir           , local_var.sinatra.cache.find
 set :persist_dir         , local_var.sinatra.cache.persistence.find
 set :persist_options     , {:persist => true, :persist_dir => :persist_dir}

data/etc/app.d/entities.rb

@@ -5,9 +5,9 @@ Rbbt.etc.requires.read.split("\n").each do |file|
 end if Rbbt.etc.requires.exists?
 
 
-Entity.entity_list_cache     = Rbbt.var.find.sinatra.entity_lists
-Entity.entity_map_cache      = Rbbt.var.find.sinatra.entity_maps
-Entity.entity_property_cache = Rbbt.var.find.sinatra.entity_properties
+Entity.entity_list_cache     = Rbbt.var.sinatra.find.entity_lists
+Entity.entity_map_cache      = Rbbt.var.sinatra.find.entity_maps
+Entity.entity_property_cache = Rbbt.var.sinatra.find.entity_properties
 
 Rbbt.etc.entities.read.split("\n").each do |name|
   next if name.empty?
@@ -18,7 +18,7 @@ Rbbt.etc.entities.read.split("\n").each do |name|
   end
 end if Rbbt.etc.entities.exists?
 
-$annotation_repo = Rbbt.var.find.sinatra.annotation_repo.find
+$annotation_repo = Rbbt.var.sinatra.annotation_repo.find
 (Rbbt.etc.persist_properties.yaml || {}).each do |name,list|
   next if name.empty?
   mod = Kernel.const_get name

data/lib/rbbt/association/index.rb

@@ -77,13 +77,18 @@ module Association
       return [] if source.nil? or target.nil?
 
       if source == :all or source == "all"
-        matches = keys
-      else
-        matches = source.uniq.inject([]){|acc,e| 
-          acc.concat(match(e)) 
-        }
+        if target == :all or target == "all"
+          return keys
+        else
+          matches = reverse.subset(target, source)
+          return matches.collect{|m| r = m.partition "~"; r.reverse*"" }
+        end
       end
 
+      matches = source.uniq.inject([]){|acc,e| 
+        acc.concat(match(e)) 
+      }
+
       return matches if target == :all or target == "all"
 
       target_matches = {}

data/lib/rbbt/association/item.rb

@@ -23,6 +23,14 @@ module AssociationItem
     self.clean_annotations.collect{|p| p[/[^~]+/] }
   end
 
+  property :target_entity_type => :both do
+    Entity.formats[target_type].to_s
+  end
+
+  property :source_entity_type => :both do
+    Entity.formats[source_type].to_s
+  end
+
   property :target_type => :both do
     type = reverse ? knowledge_base.source(database) : knowledge_base.target(database)
   end
@@ -69,6 +77,10 @@ module AssociationItem
     self.each do |match|
       tsv[match] = [match.source, match.target].concat match.info.values_at(*info_fields)
     end
+    tsv.entity_options = {:organism => namespace}
+    knowledge_base.entity_options.each do |type,options|
+      tsv.entity_options.merge! options
+    end
     tsv
   end
 

data/lib/rbbt/knowledge_base.rb

@@ -194,7 +194,8 @@ class KnowledgeBase
   end
 
   def annotate(entities, type, database = nil)
-    Misc.prepare_entity(entities, type, entity_options_for(type, database))
+    format = @format[type] || type
+    Misc.prepare_entity(entities, format, entity_options_for(type, database))
   end
 
   #{{{ Identify
@@ -304,7 +305,8 @@ class KnowledgeBase
     repo = get_index name
 
     begin
-      setup(name, repo.subset_entities(entities))
+      s = repo.subset_entities(entities)
+      setup(name, s)
     rescue Exception
       target = entities[:target]
       source = entities[:source]

data/lib/rbbt/persist.rb

@@ -18,7 +18,7 @@ module Persist
     attr_accessor :lock_dir
     
     def lock_dir
-      @lock_dir ||= Rbbt.tmp.persist_locks.find
+      @lock_dir ||= Rbbt.tmp.persist_locks
     end
   end
 

data/lib/rbbt/resource.rb

@@ -174,3 +174,4 @@ source "$INSTALL_HELPER_FILE"
     path
   end
 end
+

data/lib/rbbt/resource/path.rb

@@ -39,9 +39,13 @@ module Path
   end
 
   def glob(pattern = '*')
-    return [] unless self.exists?
-    exp = File.join(self.find, pattern)
-    Dir.glob(exp).collect{|f| Path.setup(f, self.resource, self.pkgdir)}
+    if self.include? "*"
+      Dir.glob(self).collect{|f| Path.setup(f, self.resource, self.pkgdir)}
+    else
+      return [] unless self.exists? 
+      exp = File.join(self.find, pattern)
+      Dir.glob(exp).collect{|f| Path.setup(f, self.resource, self.pkgdir)}
+    end
   end
 
   def [](name, orig = false)
@@ -67,14 +71,16 @@ module Path
     end
   end
 
-  SEARCH_PATHS = {
+  SEARCH_PATHS = IndiferentHash.setup({
     :current => File.join("{PWD}", "{TOPLEVEL}", "{SUBPATH}"),
     :user    => File.join(ENV['HOME'], ".{PKGDIR}", "{TOPLEVEL}", "{SUBPATH}"),
     :global  => File.join('/', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
     :local   => File.join('/usr/local', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
     :lib     => File.join('{LIBDIR}', "{TOPLEVEL}", "{SUBPATH}"),
     :default => :user
-  }
+  })
+
+  STANDARD_SEARCH = %w(current user local global lib cache bulk)
 
   search_path_file = File.join(ENV['HOME'], '.rbbt/etc/search_paths')
   if File.exists?(search_path_file)
@@ -95,7 +101,13 @@ module Path
 
     path = nil
     if where.nil?
-      %w(current user local global lib).each do |w| 
+      STANDARD_SEARCH.each do |w| 
+        w = w.to_sym
+        next unless paths.include? w
+        path = find(w, caller_lib, paths)
+        return path if File.exists? path
+      end
+      (SEARCH_PATHS.keys - STANDARD_SEARCH).each do |w|
         w = w.to_sym
         next unless paths.include? w
         path = find(w, caller_lib, paths)

data/lib/rbbt/resource/util.rb

@@ -31,6 +31,7 @@ end
 module Resource
   def set_software_env(software_dir)
     software_dir.find_all.each do |software_dir|
+      next unless software_dir.exists?
       bin_dir = File.join(software_dir, 'bin')
       opt_dir = File.join(software_dir, 'opt')
 

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

@@ -259,4 +259,30 @@ module Misc
     Log.info "Delta: #{delta.inspect}" 
     res
   end
+
+  def self.time_tick
+    if $_last_time_tick.nil?
+      $_last_time_tick = Time.now
+      puts "Tick started: #{Time.now}"
+    else
+      ellapsed = Time.now - $_last_time_tick
+      puts "Tick ellapsed: #{ellapsed.to_i} s. #{(ellapsed * 1000).to_i - ellapsed.to_i * 1000} ms"
+      $_last_time_tick = Time.now
+    end
+  end
+
+  def self.bootstrap(elems, num = :current, file = nil, &block)
+    cpus = case num
+           when :current
+            4 
+           when Integer
+             if num < 100
+               num
+             else
+               32000 / num
+             end
+           end
+    file = caller.first + rand(1000000).to_s if file.nil?
+    RbbtSemaphore.fork_each_on_semaphore elems, cpus, file, &block
+  end
 end

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

@@ -14,6 +14,11 @@ module IndiferentHash
     new
   end
 
+  def []=(key,value)
+    delete(key)
+    super(key,value)
+  end
+
   def [](key)
     res = super(key) 
     return res unless res.nil?

data/lib/rbbt/util/named_array.rb

@@ -10,6 +10,11 @@ module NamedArray
   attr_accessor :entity_options
   attr_accessor :entity_templates
 
+  def shift
+    fields.shift
+    super
+  end
+
   def entity_templates
     @entity_templates ||= {}
   end

data/lib/rbbt/util/semaphore.rb

@@ -79,34 +79,20 @@ void post_semaphore(char* name){
 
   def self.fork_each_on_semaphore(elems, size, file = nil)
     with_semaphore(size, file) do |file|
-      begin
 
-        pids = elems.collect do |elem| 
-          Process.fork do 
-            begin
-              RbbtSemaphore.synchronize(file) do
-                yield elem
-              end
-            rescue Interrupt
-              Log.warn "Process #{Process.pid} was aborted"
-            end
+      TSV.traverse elems, :cpus => size*2, :bar => "Fork each on semaphore: #{ file }" do |elem|
+        elems.annotate elem if elems.respond_to? :annotate
+        begin
+          RbbtSemaphore.synchronize(file) do
+            yield elem
           end
+        rescue Interrupt
+          Log.warn "Process #{Process.pid} was aborted"
         end
-
-        while pids.any?
-          pid = Process.wait -1
-          pids.delete pid
-        end
-        #pids.each do |pid| Process.waitpid pid end
-        
-      rescue Exception
-        Log.warn "Killing children: #{pids.sort * ", " }"
-        pids.each do |pid| begin Process.kill("INT", pid); rescue; end; end
-        pids.each do |pid| begin RbbtSemaphore.post_semaphore(file); rescue; end; end
-        Log.warn "Ensuring children are dead: #{pids.sort * ", " }"
-        pids.each do |pid| begin Process.waitpid pid; rescue; end; end
       end
+
     end
+    true
   end
 
   def self.thread_each_on_semaphore(elems, size)

data/share/rbbt_commands/app/start

@@ -23,6 +23,7 @@ Misc.in_dir(app_dir) do
   if server == 'unicorn'
     `unicorn -c #{ Rbbt.share['unicorn.rb'].find } '#{config_ru_file}' -p #{options[:port] || "2887"}`
   else
-    Rack::Server.start(options.merge(:config => config_ru_file))
+    options[:config] = config_ru_file
+    Rack::Server.start(options)
   end
 end

data/share/rbbt_commands/tsv/info

@@ -30,7 +30,9 @@ file = STDIN if file == '-'
 
 raise ParameterException, "Please specify the tsv file as argument" if file.nil?
 
-options[:fields] = options[:fields].split(/,\|/) if options[:fields]
+iii options
+options[:fields] = options[:fields].split(/[,\|]/) if options[:fields]
+iii options
 options[:header_hash] = options["header_hash"]
 options[:sep] = options["sep"]
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.14.14
+  version: 5.14.15
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-02 00:00:00.000000000 Z
+date: 2014-08-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake