From d6482ea41cceaa741dc47192dfea6e5482d17a30 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 7 Mar 2012 13:49:41 +0100
Subject: environment cleanup, turtle error reports

---
 lib/environment.rb | 13 ++++---------
 lib/opentox.rb     | 17 +++++++++--------
 2 files changed, 13 insertions(+), 17 deletions(-)

diff --git a/lib/environment.rb b/lib/environment.rb
index d164925..1af76f8 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -1,5 +1,4 @@
 # set default environment
-
 ENV['RACK_ENV'] = 'production' unless ENV['RACK_ENV']
 
 # load/setup configuration
@@ -12,29 +11,25 @@ LOG_DIR = File.join(basedir, "log")
 
 if File.exist?(config_file)
 	CONFIG = YAML.load_file(config_file)
-  raise "could not load config, config file: "+config_file.to_s unless CONFIG
+  not_found_error "Could not load configuration from \"#{config_file.to_s}\"" unless CONFIG
 else
 	FileUtils.mkdir_p TMP_DIR
 	FileUtils.mkdir_p LOG_DIR
 	FileUtils.mkdir_p config_dir
 	puts "Please edit #{config_file} and restart your application."
-	#exit
+	exit
 end
 
 logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
+$logger = OTLogger.new(logfile) 
 
-$logger = OTLogger.new(logfile) # no rotation
-$logger.formatter = Logger::Formatter.new #this is neccessary to restore the formating in case active-record is loaded
 if CONFIG[:logger] and CONFIG[:logger] == "debug"
 	$logger.level = Logger::DEBUG
 else
 	$logger.level = Logger::WARN 
 end
 
-# Regular expressions for parsing classification data
-TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
-FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
-
+# TODO: move to opentox-client???
 AA_SERVER = CONFIG[:authorization] ? (CONFIG[:authorization][:server] ? CONFIG[:authorization][:server] : nil) : nil
 CONFIG[:authorization][:authenticate_request] = [""] unless CONFIG[:authorization][:authenticate_request]
 CONFIG[:authorization][:authorize_request] =  [""] unless CONFIG[:authorization][:authorize_request]
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 73798ef..16646c1 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -1,18 +1,19 @@
 require 'sinatra/base'
-# Error handling
-# Errors are logged as error and formated according to acccept-header
-# Non OpenTox::Errors (defined in error.rb) are handled as internal error (500), stacktrace is logged
-# IMPT: set sinatra settings :show_exceptions + :raise_errors to false in config.ru, otherwise Rack::Showexceptions takes over
 
 module OpenTox
+  # Base class for OpenTox services
+  # Errors are formated according to acccept-header
+  # Non OpenTox::Errors (defined in error.rb) are handled as internal error (500), stacktrace is logged
   class Service < Sinatra::Base
+
     helpers Sinatra::UrlForHelper
+    # use OpenTox error handling
     set :raise_errors, false
     set :show_exceptions, false
+
     error do
-      #TODO: add actor to error report
-      #actor = "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}"
       error = request.env['sinatra.error']
+      error.report.actor = "#{request.env['rack.url_scheme']}://#{request.env['HTTP_HOST']}#{request.env['REQUEST_URI']}"
       case request.env['HTTP_ACCEPT']
       when 'application/rdf+xml'
         content_type 'application/rdf+xml'
@@ -21,7 +22,7 @@ module OpenTox
       when "text/n3"
         content_type "text/n3"
       else
-        content_type "text/n3"
+        content_type "text/turtle"
       end
       if error.respond_to? :report
         code = error.report.http_code
@@ -33,7 +34,7 @@ module OpenTox
         when "text/n3"
           body = error.report.to_ntriples
         else
-          body = error.report.to_ntriples
+          body = error.report.to_turtle
         end
       else
         content_type "text/plain"
-- 
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