rbbt-util 5.13.18 → 5.13.19

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: de34e0b79dc8e1736732e64d42af40d17f2ad53f
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+  data.tar.gz: 034c6c8e537be9f35f8c5630f2dd40810747bdda97126303f7737adc2d7cec2d7e2e19c31568f64caf0bddffaabc6762c32fdbdfaca8bb2eebb05210bf31e891

data/lib/rbbt/persist/tsv/tokyocabinet.rb

@@ -3,7 +3,7 @@ require 'tokyocabinet'
 module Persist
 
   module TCAdapter
-    attr_accessor :persistence_path, :tokyocabinet_class, :closed, :writable
+    attr_accessor :persistence_path, :tokyocabinet_class, :closed, :writable, :mutex
 
     def self.open(path, write, tokyocabinet_class = TokyoCabinet::HDB)
       tokyocabinet_class = TokyoCabinet::HDB if tokyocabinet_class == "HDB"
@@ -23,6 +23,7 @@ module Persist
       database.persistence_path ||= path
       database.tokyocabinet_class = tokyocabinet_class
 
+      database.mutex = Mutex.new
       database
     end
 
@@ -76,6 +77,9 @@ module Persist
       @writable
     end
 
+    def read?
+      ! write?
+    end
     #def each
     #  iterinit
     #  while key = iternext
@@ -102,20 +106,36 @@ module Persist
     def write_and_read
       lock_filename = Persist.persistence_path(persistence_path + '.write', {:dir => TSV.lock_dir})
       Misc.lock(lock_filename) do
-        write if @closed or not write?
-        res = begin
-                yield
-              ensure
-                read
-              end
-        res
+        @mutex.synchronize do
+          write if @closed or not write?
+          res = begin
+                  yield
+                ensure
+                  read
+                end
+          res
+        end
       end
     end
 
     def write_and_close
       lock_filename = Persist.persistence_path(persistence_path + '.write', {:dir => TSV.lock_dir})
       Misc.lock(lock_filename) do
-        write if @closed or not write?
+        @mutex.synchronize do
+          write if @closed or not write?
+          res = begin
+                  yield
+                ensure
+                  close
+                end
+          res
+        end
+      end
+    end
+
+    def read_and_close
+      @mutex.synchronize do
+        read if @closed or not read?
         res = begin
                 yield
               ensure
@@ -125,15 +145,6 @@ module Persist
       end
     end
 
-    def read_and_close
-      read if @closed or write?
-      res = begin
-              yield
-            ensure
-              close
-            end
-      res
-    end
 
     def merge!(hash)
       hash.each do |key,values|

data/lib/rbbt/persist.rb

@@ -289,15 +289,15 @@ module Persist
         res = tee_stream(res, path, type, res.respond_to?(:callback)? res.callback : nil, res.respond_to?(:abort_callback)? res.abort_callback : nil)
         ConcurrentStream.setup res do
           begin
-            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
-          rescue
+            lockfile.unlock #if File.exists? lockfile.path and lockfile.locked?
+          rescue Exception
             Log.medium "Lockfile exception: " << $!.message
           end
         end
         res.abort_callback = Proc.new do
           begin
-            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
-          rescue
+            lockfile.unlock #if File.exists? lockfile.path and lockfile.locked?
+          rescue Exception
             Log.medium "Lockfile exception: " << $!.message
           end
         end
@@ -308,16 +308,16 @@ module Persist
         ConcurrentStream.setup res do
           begin
             stream.callback
-            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
-          rescue
+            lockfile.unlock #if File.exists? lockfile.path and lockfile.locked?
+          rescue Exception
             Log.medium "Lockfile exception: " << $!.message
           end
         end
         res.abort_callback = Proc.new do
           begin
             stream.abort
-            lockfile.unlock if File.exists? lockfile.path and lockfile.locked?
-          rescue
+            lockfile.unlock #if File.exists? lockfile.path and lockfile.locked?
+          rescue Exception
             Log.medium "Lockfile exception: " << $!.message
           end
         end

data/lib/rbbt/util/R.rb

@@ -101,6 +101,7 @@ if (! is.null(data)){ rbbt.tsv.write('#{f}', data); }
       else
         tsv = TSV.open(f, open_options) unless open_options[:ignore_output]
         tsv.key_field = open_options[:key] if open_options.include? :key
+        tsv.namespace ||= self.namespace if self.namespace
         tsv
       end
     end

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

@@ -20,7 +20,7 @@ class RbbtProcessQueue
     def clean
       @sread.close unless @sread.closed?
       @swrite.close unless @swrite.closed?
-      Log.warn "Destroying socket semaphores: #{key}"
+      Log.warn "Destroying socket semaphores"
       RbbtSemaphore.delete_semaphore(@write_sem)
       RbbtSemaphore.delete_semaphore(@read_sem)
     end

data/lib/rbbt/util/log/progress/report.rb

@@ -34,7 +34,7 @@ module Log
         @history ||= []
       else
         @history << thr
-        @history.shift if @history.length > 10
+        @history.shift if @history.length > 20
       end
 
       @mean_max ||= 0

data/lib/rbbt/util/log.rb

@@ -32,7 +32,9 @@ module Log
   class << self
     attr_accessor :logfile, :severity, :nocolor, :tty_size
   end
+
   self.nocolor = ENV["RBBT_NOCOLOR"] == 'true'
+
   require "highline/system_extensions.rb"
   self.tty_size = HighLine::SystemExtensions.terminal_size.first 
 
@@ -205,7 +207,7 @@ def ppp(message)
   stack = caller
   puts "#{Log.color :cyan, "PRINT:"} " << stack.first
   puts ""
-  puts "=> " << message
+  puts Log.color(:cyan, "=> ") << message
   puts ""
 end
 

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

@@ -1,4 +1,4 @@
-Lockfile.refresh = false if ENV["RBBT_NO_LOCKFILE_REFRESH"] == "true"
+Lockfile.refresh = false #if ENV["RBBT_NO_LOCKFILE_REFRESH"] == "true"
 
 module Misc
 
@@ -23,6 +23,7 @@ module Misc
 
               if hostname == info["host"] and not Misc.pid_exists?(info["pid"])
                 Log.high("Removing lockfile: #{lock_path}. This pid #{Process.pid}. Content: #{info.inspect}")
+
                 FileUtils.rm lock_path
               end
             end
@@ -48,7 +49,10 @@ module Misc
       raise $!
     ensure
       if unlock 
-        lockfile.unlock if lockfile.locked?
+        begin
+          lockfile.unlock #if lockfile.locked?
+        rescue Exception
+        end
       end
     end
 

data/lib/rbbt/util/open.rb

@@ -146,20 +146,21 @@ module Open
   def self.get_stream_from_repo(dir, sub_path)
     repo = get_repo_from_dir(dir)
     repo.read_and_close do
-      StringIO.new repo[sub_path]
+      text = repo[sub_path]
+      text.nil? ? nil : StringIO.new(text)
     end
   end
 
   def self.save_content_in_repo(dir, sub_path, content)
     repo = get_repo_from_dir(dir)
-    repo.write_and_close do
+    repo.write_and_read do
       repo[sub_path] = content
     end
   end
 
   def self.remove_from_repo(dir, sub_path, recursive = false)
     repo = get_repo_from_dir(dir)
-    repo.write_and_close do
+    repo.write_and_read do
       if recursive
         repo.outlist repo.range sub_path, true, sub_path.sub(/.$/,('\1'.ord + 1).chr), false
       else
@@ -171,7 +172,7 @@ module Open
   def self.exists_in_repo(dir, sub_path, content)
     repo = get_repo_from_dir(dir)
     repo.read_and_close do
-      repo.include? sub_path
+      repo.include? sub_path 
     end
   end
 

data/lib/rbbt/util/semaphore.rb

@@ -61,8 +61,12 @@ void post_semaphore(char* name){
   end
 
   def self.with_semaphore(size, file = nil)
-    file = "/" << Misc.digest(rand(1000000000000).to_s) if file.nil?
-    file.gsub!('/', '_')
+    if file.nil?
+      file = "/" << Misc.digest(rand(1000000000000).to_s) if file.nil?
+    else
+      file = file.gsub('/', '_') if file
+    end
+
     begin
       Log.warn "Creating semaphore (#{ size }): #{file}"
       RbbtSemaphore.create_semaphore(file, size)

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

@@ -432,7 +432,7 @@ class Step
   end
 
   def grace
-    until done? or result or streaming? or error? or aborted?
+    until done? or result or error? or aborted? or streaming?
       sleep 1 
     end
     self

data/test/rbbt/util/test_semaphore.rb

@@ -10,7 +10,6 @@ class TestRbbtSemaphore < Test::Unit::TestCase
           100.times do
             RbbtSemaphore.wait_semaphore(s)
             sleep 0.001
-            puts '.'
             RbbtSemaphore.post_semaphore(s)
           end
         end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.18
+  version: 5.13.19
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-22 00:00:00.000000000 Z
+date: 2014-05-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake