task catches and reports errors (some dataset tests still fail)

5 files changed, 19 insertions, 11 deletions

diff --git a/lib/error.rb b/lib/error.rb
index 64cc4eb..6987f35 100644
--- a/lib/error.rb
+++ b/lib/error.rb
@@ -17,16 +17,22 @@ module OpenTox
   class NotFoundError < RuntimeError
     def http_code; 404; end
   end
+  
+  class LockedError < RuntimeError
+    def http_code; 423; end
+  end
 
   class ServiceUnavailableError < RuntimeError
     def http_code; 503; end
   end
   
+  # TODO: add to RestClientCalls
   class RestCallError < RuntimeError
     attr_accessor :rest_params
     def http_code; 502; end
   end
 
+  # TODO: add to Exception class??
   class ErrorReport
     
     # TODO replace params with URIs (errorCause -> OT.errorCause)
@@ -78,11 +84,14 @@ module OpenTox
       c
     end
     
+    # TODO: use rdf.rb
     def to_rdfxml
       s = Serializer::Owl.new
       s.add_resource(CONFIG[:services]["opentox-task"]+"/tmpId/ErrorReport/tmpId", OT.errorReport, rdf_content)
       s.to_rdfxml
     end
+=begin
+=end
   end
 end
 
diff --git a/lib/opentox-client.rb b/lib/opentox-client.rb
index c5c701b..fc6cbd1 100644
--- a/lib/opentox-client.rb
+++ b/lib/opentox-client.rb
@@ -5,9 +5,10 @@ require 'rdf/raptor'
 require "rest-client"
 require 'uri'
 require 'yaml'
+require 'logger'
 require File.join(File.dirname(__FILE__),"error.rb")
-require File.join(File.dirname(__FILE__),"logger.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")
 require File.join(File.dirname(__FILE__),"compound.rb")
-require File.join(File.dirname(__FILE__),"dataset.rb")
+#require File.join(File.dirname(__FILE__),"dataset.rb")
diff --git a/lib/opentox.rb b/lib/opentox.rb
index ab5c95f..01de3e7 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -13,7 +13,8 @@ class String
   def to_object
     # TODO: fix, this is unsafe
     self =~ /dataset/ ? uri = File.join(self.chomp,"metadata") : uri = self.chomp
-    raise "#{uri} is not a valid URI." unless RDF::URI.new(uri).uri? 
+    #raise "#{uri} is not a valid URI." unless RDF::URI.new(uri).uri? 
+    raise "#{uri} is not a valid URI." unless uri.uri? 
     RDF::Reader.open(uri) do |reader|
       reader.each_statement do |statement|
         if statement.predicate == RDF.type and statement.subject == uri
@@ -82,7 +83,10 @@ module OpenTox
     if reload
       @metadata = {}
       begin
-        RDF::Reader.open(@uri) do |reader|
+        #puts self.class
+        #self.kind_of?(OpenTox::Dataset) ? uri = URI.join(@uri,"metadata") : uri = @uri
+        #$logger.debug uri
+        RDF::Reader.open(uri) do |reader|
           reader.each_statement do |statement|
             @metadata[statement.predicate] = statement.object if statement.subject == @uri
           end
@@ -151,9 +155,6 @@ module OpenTox
 
   end
 
-  class FromUri
-  end
-
   # create default classes
   SERVICES.each do |s|
     eval "class #{s}
@@ -162,7 +163,5 @@ module OpenTox
     end"
   end
 
-  private
-
 end
 
diff --git a/lib/logger.rb b/lib/otlogger.rb
index c98f1ca..295d0c1 100644
--- a/lib/logger.rb
+++ b/lib/otlogger.rb
@@ -1,4 +1,3 @@
-require 'logger'
 class OTLogger < Logger
   
   def pwd
diff --git a/lib/task.rb b/lib/task.rb
index 52d4a30..582f592 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -89,7 +89,7 @@ module OpenTox
       end
     rescue
       $logger.error "Unknown #{self.class} method #{method}"
-      super
+      #super
     end
   end