rbbt-util 5.16.0 → 5.16.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 689c858bc997cfc925e2be00a3a71a8c1d708e85
+  metadata.gz: 29417065f1fbfa88cb5c271a16378bd256a4c212
+  data.tar.gz: 93e3c4e913359512c90fc5de892a39a0a485a97f
 SHA512:
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+  metadata.gz: 483bcaa453d07b7f7fbb09241dceb3ab8cd8f7b87ff430be52dcaad9998a393b919a82242f6b0eca2005a4a5ad559ce6ac2f73850c765fc22e351a3c8b057b1e
+  data.tar.gz: 4a89efa036fbfadaea7f553d5396469eecd78e7702857f77db829e55249f63511d3b1472afe31e8a2aa0d3e481e9699a6e1936d0e2c4e341ed0eb4dfefed1b6a

data/lib/rbbt/util/log.rb

@@ -70,7 +70,6 @@ module Log
   self.nocolor = ENV["RBBT_NOCOLOR"] == 'true'
 
   self.ignore_stderr do
-    require 'nokogiri'
     self.tty_size = begin
                       require "highline/system_extensions.rb"
                       HighLine::SystemExtensions.terminal_size.first 

data/lib/rbbt/util/semaphore.rb

@@ -6,138 +6,140 @@ rescue Exception
   continue = false
 end
 
-module RbbtSemaphore
-  inline(:C) do |builder|
-    builder.prefix <<-EOF
-#include <unistd.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <semaphore.h>
-#include <time.h>
-#include <assert.h>
-#include <errno.h>
-#include <signal.h>
-#include <fcntl.h>
-    EOF
-
-    builder.c_singleton <<-EOF
-void create_semaphore(char* name, int value){
-  sem_open(name, O_CREAT, S_IRWXU|S_IRWXG|S_IRWXO, value);
-}
-    EOF
-    builder.c_singleton <<-EOF
-void delete_semaphore(char* name){
-  sem_unlink(name);
-}
-    EOF
-
-    builder.c_singleton <<-EOF
-void wait_semaphore(char* name){
-  sem_t* sem;
-  sem = sem_open(name, 0);
-  sem_wait(sem);
-  sem_close(sem);
-}
-    EOF
-
-    builder.c_singleton <<-EOF
-void post_semaphore(char* name){
-  sem_t* sem;
-  sem = sem_open(name, 0);
-  sem_post(sem);
-  sem_close(sem);
-}
-    EOF
-  end
-
-  SEM_MUTEX = Mutex.new
-  def self.synchronize(sem)
-    RbbtSemaphore.wait_semaphore(sem)
-    begin
-      yield
-    ensure
-      RbbtSemaphore.post_semaphore(sem)
+if continue
+  module RbbtSemaphore
+    inline(:C) do |builder|
+      builder.prefix <<-EOF
+  #include <unistd.h>
+  #include <stdio.h>
+  #include <stdlib.h>
+  #include <semaphore.h>
+  #include <time.h>
+  #include <assert.h>
+  #include <errno.h>
+  #include <signal.h>
+  #include <fcntl.h>
+      EOF
+
+      builder.c_singleton <<-EOF
+  void create_semaphore(char* name, int value){
+    sem_open(name, O_CREAT, S_IRWXU|S_IRWXG|S_IRWXO, value);
+  }
+      EOF
+      builder.c_singleton <<-EOF
+  void delete_semaphore(char* name){
+    sem_unlink(name);
+  }
+      EOF
+
+      builder.c_singleton <<-EOF
+  void wait_semaphore(char* name){
+    sem_t* sem;
+    sem = sem_open(name, 0);
+    sem_wait(sem);
+    sem_close(sem);
+  }
+      EOF
+
+      builder.c_singleton <<-EOF
+  void post_semaphore(char* name){
+    sem_t* sem;
+    sem = sem_open(name, 0);
+    sem_post(sem);
+    sem_close(sem);
+  }
+      EOF
     end
-  end
 
-  def self.with_semaphore(size, file = nil)
-    if file.nil?
-      file = "/" << Misc.digest(rand(1000000000000).to_s) if file.nil?
-    else
-      file = file.gsub('/', '_') if file
+    SEM_MUTEX = Mutex.new
+    def self.synchronize(sem)
+      RbbtSemaphore.wait_semaphore(sem)
+      begin
+        yield
+      ensure
+        RbbtSemaphore.post_semaphore(sem)
+      end
     end
 
-    begin
-      Log.low "Creating semaphore (#{ size }): #{file}"
-      RbbtSemaphore.create_semaphore(file, size)
-      yield file
-    ensure
-      Log.low "Removing semaphore #{ file }"
-      RbbtSemaphore.delete_semaphore(file)
+    def self.with_semaphore(size, file = nil)
+      if file.nil?
+        file = "/" << Misc.digest(rand(1000000000000).to_s) if file.nil?
+      else
+        file = file.gsub('/', '_') if file
+      end
+
+      begin
+        Log.low "Creating semaphore (#{ size }): #{file}"
+        RbbtSemaphore.create_semaphore(file, size)
+        yield file
+      ensure
+        Log.low "Removing semaphore #{ file }"
+        RbbtSemaphore.delete_semaphore(file)
+      end
     end
-  end
 
-  def self.fork_each_on_semaphore(elems, size, file = nil)
+    def self.fork_each_on_semaphore(elems, size, file = nil)
 
-    TSV.traverse elems, :cpus => size, :bar => "Fork each on semaphore: #{ Misc.fingerprint elems }", :into => Set.new do |elem|
-      elems.annotate elem if elems.respond_to? :annotate
-      begin
-        yield elem
-      rescue Interrupt
-        Log.warn "Process #{Process.pid} was aborted"
+      TSV.traverse elems, :cpus => size, :bar => "Fork each on semaphore: #{ Misc.fingerprint elems }", :into => Set.new do |elem|
+        elems.annotate elem if elems.respond_to? :annotate
+        begin
+          yield elem
+        rescue Interrupt
+          Log.warn "Process #{Process.pid} was aborted"
+        end
+        nil
       end
       nil
     end
-    nil
-  end
-
-  def self.thread_each_on_semaphore(elems, size)
-    mutex = Mutex.new
-    count = 0
-    cv = ConditionVariable.new
-    wait_mutex = Mutex.new
-
-    begin
-
-      threads = []
-      wait_mutex.synchronize do
-        threads = elems.collect do |elem| 
-          Thread.new(elem) do |elem|
-
-            continue = false
-            mutex.synchronize do
-              while not continue do
-                if count < size 
-                  continue = true
-                  count += 1
+
+    def self.thread_each_on_semaphore(elems, size)
+      mutex = Mutex.new
+      count = 0
+      cv = ConditionVariable.new
+      wait_mutex = Mutex.new
+
+      begin
+
+        threads = []
+        wait_mutex.synchronize do
+          threads = elems.collect do |elem| 
+            Thread.new(elem) do |elem|
+
+              continue = false
+              mutex.synchronize do
+                while not continue do
+                  if count < size 
+                    continue = true
+                    count += 1
+                  end
+                  mutex.sleep 1 unless continue
                 end
-                mutex.sleep 1 unless continue
               end
-            end
 
-            begin
-              yield elem
-            rescue Interrupt
-              Log.error "Thread was aborted while processing: #{Misc.fingerprint elem}"
-              raise $!
-            ensure
-              mutex.synchronize do
-                count -= 1
-                cv.signal if mutex.locked?
+              begin
+                yield elem
+              rescue Interrupt
+                Log.error "Thread was aborted while processing: #{Misc.fingerprint elem}"
+                raise $!
+              ensure
+                mutex.synchronize do
+                  count -= 1
+                  cv.signal if mutex.locked?
+                end
               end
             end
           end
         end
-      end
 
-      threads.each do |thread| 
-        thread.join 
+        threads.each do |thread| 
+          thread.join 
+        end
+      rescue Exception
+        Log.exception $!
+        Log.info "Ensuring threads are dead: #{threads.length}"
+        threads.each do |thread| thread.kill end
       end
-    rescue Exception
-      Log.exception $!
-      Log.info "Ensuring threads are dead: #{threads.length}"
-      threads.each do |thread| thread.kill end
     end
-  end
-end 
+  end 
+end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.16.0
+  version: 5.16.1
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -108,6 +108,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  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'
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@cnio.es
 executables: