Merge branch 'development' of github.com:opentox/opentox-client into development

6 files changed, 15 insertions, 6 deletions

diff --git a/README.markdown b/README.markdown
index f4e20f4..41b7a28 100644
--- a/README.markdown
+++ b/README.markdown
@@ -3,6 +3,11 @@ opentox-ruby-minimal
 
 Thin Ruby wrapper for the [OpenTox](http://www.opentox.org) REST API 
 
+Dependencies
+------------
+
+  libraptor1-dev
+
 Installation
 ------------
 
diff --git a/lib/error.rb b/lib/error.rb
index cc87f47..e12f140 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -45,8 +45,7 @@ module OpenTox
     OpenTox.const_set klass,c
     
     # define global methods for raising errors, eg. bad_request_error
-    Object.send(:define_method, klass.underscore.to_sym) do |message|
-      defined?(@uri) ? uri = @uri : uri=nil
+    Object.send(:define_method, klass.underscore.to_sym) do |message,uri=nil|
       raise c, message, uri
     end
   end
@@ -65,7 +64,6 @@ module OpenTox
   class ErrorReport
     def initialize http_code, error
       @http_code = http_code
-      #@report = report#.to_yaml
       @report = {}
       @report[RDF::OT.actor] = error.uri.to_s
       @report[RDF::OT.message] = error.message.to_s
@@ -95,6 +93,7 @@ module OpenTox
           # TODO: not used for turtle
           # http://rdf.rubyforge.org/RDF/Writer.html#
           writer.prefix :ot, RDF::URI('http://www.opentox.org/api/1.2#')
+          writer.prefix :ot1_1, RDF::URI('http://www.opentox.org/api/1.1#')
           subject = RDF::Node.new
           @report.each do |predicate,object|
             writer << [subject, predicate, object] if object
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
index 8616995..dec3512 100644
--- a/lib/opentox-client.rb
+++ b/lib/opentox-client.rb
@@ -26,6 +26,8 @@ FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-m
 require File.join(File.dirname(__FILE__),"overwrite.rb")
 require File.join(File.dirname(__FILE__),"error.rb")
 require File.join(File.dirname(__FILE__),"rest-client-wrapper.rb") 
+require File.join(File.dirname(__FILE__),"authorization.rb") 
+require File.join(File.dirname(__FILE__),"policy.rb") 
 require File.join(File.dirname(__FILE__),"otlogger.rb") # avoid require conflicts with logger
 require File.join(File.dirname(__FILE__),"opentox.rb")
 require File.join(File.dirname(__FILE__),"task.rb")
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index 97c35aa..e3f72ad 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -64,10 +64,8 @@ module Kernel
       stdout = stdout_stream.read
       stderr = stderr_stream.read
     end
-    raise stderr.strip if !status.success?
+    internal_server_error stdout + stderr if !status.success?
     return stdout
-  rescue Exception 
-    internal_server_error $!
   end
 
   alias_method :system!, :system
diff --git a/lib/task.rb b/lib/task.rb
index 7452012..f19a918 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -15,6 +15,7 @@ module OpenTox
           result_uri = yield 
           task.completed result_uri
         rescue 
+          puts $!.report.to_yaml
           RestClientWrapper.put(File.join(task.uri,'Error'),{:errorReport => $!.report.to_yaml}) if $!.respond_to? :report
           task.kill
         end
diff --git a/opentox-client.gemspec b/opentox-client.gemspec
index 198a6ed..52456a5 100644
--- a/opentox-client.gemspec
+++ b/opentox-client.gemspec
@@ -24,4 +24,8 @@ Gem::Specification.new do |s|
   s.add_runtime_dependency "rdf"
   s.add_runtime_dependency "rdf-raptor"
   s.add_runtime_dependency "open4"
+  
+  # external requirements
+  ["libraptor-dev"].each{|r| s.requirements << r}
+  s.post_install_message = "Please check the version of your libraptor library, if installation of rdf.rb fails"
 end