From 8fc11578aadcf1e7d152764c926e12e553bd8d65 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 7 Mar 2012 13:28:51 +0000
Subject: fixed stdout, stderr in overwritten backtick operator, error report
 in turtle

---
 lib/error.rb           | 34 ++++++++++++++++++++++++----------
 opentox-client.gemspec |  1 +
 2 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/lib/error.rb b/lib/error.rb
index 90b55e3..b65651f 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -1,12 +1,13 @@
-# adding additional fields to Exception class to format errors according to OT-API
+require 'open4'
 
+# adding additional fields to Exception class to format errors according to OT-API
 class RuntimeError
   attr_accessor :report, :http_code
   def initialize message
     super message
     @http_code ||= 500
     @report = OpenTox::ErrorReport.create self
-    $logger.error "\n"+@report.to_ntriples
+    $logger.error "\n"+@report.to_turtle
   end
 end
 
@@ -99,7 +100,6 @@ module OpenTox
       subject = RDF::Query.execute(@rdf) do
           pattern [:subject, RDF.type, RDF::OT.ErrorReport]
       end.limit(1).select(:subject)
-  })
       @rdf << [subject, RDF::OT.actor, uri]
     end
     
@@ -126,13 +126,27 @@ module OpenTox
 end
 
 # overwrite backtick operator to catch system errors
-class Object
-  def `(code)
-    msg = super("#{code} 2>&1").chomp
-    internal_server_error msg unless $?.to_i == 0
-    msg
-  rescue Errno::ENOENT => e
-    internal_server_error e
+module Kernel
+
+  # Override raises an error if _cmd_ returns a non-zero exit status.
+  # Returns stdout if _cmd_ succeeds.  Note that these are simply concatenated; STDERR is not inline.
+  def ` cmd
+    stdout, stderr = ''
+    status = Open4::popen4(cmd) do |pid, stdin_stream, stdout_stream, stderr_stream|
+      stdout = stdout_stream.read
+      stderr = stderr_stream.read
+    end
+    raise stderr.strip if !status.success?
+    return stdout
+  rescue Exception 
+    internal_server_error "'#{cmd}' failed with: '#{$!.message}'"
+  end
+
+  alias_method :system!, :system
+
+  def system cmd
+    `#{cmd}`
+    return true
   end
 end
 
diff --git a/opentox-client.gemspec b/opentox-client.gemspec
index 7ba3ab0..82a5bef 100644
--- a/opentox-client.gemspec
+++ b/opentox-client.gemspec
@@ -24,4 +24,5 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "rest-client"
   s.add_runtime_dependency "rdf"
   s.add_runtime_dependency "rdf-raptor"
+  s.add_runtime_dependency "open4"
 end
-- 
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