From 2e3db6f6532ded28dfada22d4445038b79271814 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 7 Mar 2012 13:51:45 +0100
Subject: actor for error reports, turtle output for error reports

---
 lib/error.rb     | 13 +++++++++++--
 lib/opentox.rb   |  9 +++++++--
 lib/overwrite.rb |  1 +
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/lib/error.rb b/lib/error.rb
index 81ec979..90b55e3 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -93,9 +93,18 @@ module OpenTox
       #report.rdf << [subject, OT.errorCause, error.report] if error.respond_to?(:report) and !error.report.empty?
       report
     end
+
+    def actor=(uri)
+      # TODO: test actor assignement (in opentox-server)
+      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
     
     # define to_ and self.from_ methods for various rdf formats
-    [:rdfxml,:ntriples].each do |format|
+    [:rdfxml,:ntriples,:turtle].each do |format|
 
       define_singleton_method "from_#{format}".to_sym do |rdf|
         report = ErrorReport.new
@@ -116,7 +125,7 @@ module OpenTox
   end
 end
 
-  # overwrite backtick operator to catch system errors
+# overwrite backtick operator to catch system errors
 class Object
   def `(code)
     msg = super("#{code} 2>&1").chomp
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 10c7895..566c458 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -2,10 +2,15 @@
 RDF::OT =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.2#'
 RDF::OT1 =  RDF::Vocabulary.new 'http://www.opentox.org/api/1.1#'
 RDF::OTA =  RDF::Vocabulary.new 'http://www.opentox.org/algorithmTypes.owl#'
+
 SERVICES = ["Compound", "Feature", "Dataset", "Algorithm", "Model", "Validation", "Task", "Investigation"]
 
-# defaults to stderr, may be changed to file output
-$logger = OTLogger.new(STDERR) # no rotation
+# Regular expressions for parsing classification data
+TRUE_REGEXP = /^(true|active|1|1.0|tox|activating|carcinogen|mutagenic)$/i
+FALSE_REGEXP = /^(false|inactive|0|0.0|low tox|deactivating|non-carcinogen|non-mutagenic)$/i
+
+# defaults to stderr, may be changed to file output (e.g in opentox-service)
+$logger = OTLogger.new(STDERR) 
 $logger.level = Logger::DEBUG
 
 module OpenTox
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index e883d45..f0dcda9 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -35,5 +35,6 @@ module URI
   rescue URI::InvalidURIError
     false
   end
+
 end
 
-- 
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