improved error handling

5 files changed, 195 insertions, 76 deletions

diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index c795ca8..16c23fe 100644
--- a/lib/opentox-ruby-api-wrapper.rb
+++ b/lib/opentox-ruby-api-wrapper.rb
@@ -8,6 +8,6 @@ rescue LoadError
 	puts "Please install Openbabel with 'rake openbabel:install' in the compound component"
 end
 
-['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization','features'].each do |lib|
+['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization','features', 'rest_client_wrapper'].each do |lib|
 	require lib
 end
diff --git a/lib/owl.rb b/lib/owl.rb
index c410f76..ec8c699 100644
--- a/lib/owl.rb
+++ b/lib/owl.rb
@@ -62,16 +62,25 @@ module OpenTox
 					@model.add @uri, DC[name], args.first
 				else # getter
           #HACK for reading Panteli's models
-          if @uri.to_s =~ /ntua.*model|tu-muenchen.*model/ and !["title", "source", "identifier"].include?(name.to_s)
-            me = @model.subject(RDF['type'],OT['Model'])
-            #puts "going for "+name.to_s
-            return @model.object(me, OT[name.to_s]).uri.to_s
+          if @uri.to_s =~ /194.141.0.136.*model|ambit2.*model|ntua.*model|tu-muenchen.*model/ and !["title", "source", "identifier"].include?(name.to_s)
+            begin
+              me = @model.subject(RDF['type'],OT['Model'])
+              return @model.object(me, OT[name.to_s]).uri.to_s
+            rescue
+              LOGGER.warn "cannot get "+name.to_s+" from model"
+              return nil
+            end
           elsif @uri.to_s =~ /ambit.*task/ and ["hasStatus", "percentageCompleted"].include?(name.to_s)
             me = @model.subject(RDF['type'],OT['Task'])
             return @model.object(me, OT[name.to_s]).literal.value.to_s
           end
           #raise "stop there "+name.to_s
-					@model.object(@uri, DC[name.to_s]).to_s
+					val = @model.object(@uri, DC[name.to_s])
+          if val.is_a?(Redland::Literal)
+            return val.value
+          else
+            return val.to_s
+          end
 				end
 			else
 				raise "Method '#{name.to_s}' not found."
diff --git a/lib/rest_client_wrapper.rb b/lib/rest_client_wrapper.rb
new file mode 100644
index 0000000..1532a79
--- /dev/null
+++ b/lib/rest_client_wrapper.rb
@@ -0,0 +1,155 @@
+module OpenTox
+
+  #PENDING: implement ot error api, move to own file
+  class Error
+    
+    attr_accessor :code, :body, :uri, :payload, :headers
+    
+    def initialize(code, body, uri, payload, headers)
+      self.code = code
+      self.body = body
+      self.uri = uri
+      self.payload = payload
+      self.headers = headers
+    end
+    
+    def self.parse(error_array_string)
+      begin
+        err = YAML.load(error_array_string)
+        if err.is_a?(Array) and err.size>0 and err[0].is_a?(Error)
+          return err
+        else
+          return nil
+        end
+      rescue
+        return nil
+      end
+    end
+    
+  end
+
+  module RestClientWrapper
+    
+    # PENDING: remove as soon as redirect tasks are remove from partner webservices
+    def self.redirect_task( uri )
+     raise "no redirect task uri: "+uri.to_s unless uri.to_s =~ /194.141.0.136|ambit.*task|tu-muenchen.*task/
+     
+     while (uri.to_s =~ /194.141.0.136|ambit.*task|tu-muenchen.*task/) 
+       #HACK handle redirect
+       LOGGER.debug "REDIRECT TASK: "+uri.to_s
+       redirect = ""
+       while (redirect.size == 0)
+         IO.popen("bin/redirect.sh "+uri.to_s) do |f| 
+           while line = f.gets
+             redirect += line.chomp
+           end
+         end
+         raise "TASK ERROR" if $?!=0
+         sleep 0.3
+       end
+       uri = redirect
+       LOGGER.debug "REDIRECT TO: "+uri.to_s
+     end
+     return uri
+    end
+     
+    def self.get(uri, headers=nil, wait_for_task=false, curl_hack=false)
+      execute( "get", uri, nil, headers, wait_for_task, curl_hack )
+    end
+    
+    def self.post(uri, payload=nil, headers=nil, wait_for_task=false, curl_hack=false)
+      execute( "post", uri, payload, headers, wait_for_task, curl_hack )
+    end
+
+    def self.delete(uri, headers=nil, wait_for_task=false, curl_hack=false)
+      execute( "delete", uri, nil, headers, wait_for_task, curl_hack )
+    end
+
+    private
+    def self.execute( rest_call, uri, payload, headers, wait_for_task=false, curl_hack=false )
+      
+      do_halt 400,"uri is null",uri,payload,headers unless uri
+      begin
+        
+        payload.each{ |k,v| payload.delete(k) if v==nil } if payload #remove keys with empty values, as this can cause problems
+        unless curl_hack
+          if payload
+            result = RestClient.send(rest_call, uri, payload, headers)
+          else  
+            result = RestClient.send(rest_call, uri, headers)
+          end
+        else
+         result = ""
+         cmd = " curl -v -X "+rest_call.upcase+" "+payload.collect{|k,v| "-d "+k.to_s+"='"+v.to_s+"' "}.join("")+" "+uri.to_s
+         LOGGER.debug "CURL HACK: "+cmd
+         IO.popen(cmd+" 2> /dev/null") do |f| 
+           while line = f.gets
+             result += line
+           end
+         end
+         result.chomp!("\n")
+         LOGGER.debug "CURL -> "+result.to_s
+         raise "curl call failed "+result if $?!=0
+         #raise "STOP "+result
+      end
+       
+      if wait_for_task
+        if result.to_s =~ /ambit.*task|tu-muenchen.*task/
+          result = redirect_task(result)
+        elsif Utils.task_uri?(result)
+          task = OpenTox::Task.find(result)
+          task.wait_for_completion
+          raise task.description if task.failed?
+          result = task.resource
+        end
+      end
+      return result
+        
+      rescue RestClient::RequestFailed => ex
+        do_halt ex.http_code,ex.http_body,uri,payload,headers
+      rescue RestClient::RequestTimeout => ex
+        do_halt 408,ex.message,uri,payload,headers
+      rescue => ex
+        begin
+          code = ex.http_code
+          msg = ex.http_body
+        rescue
+          code = 500
+          msg = ex.to_s
+        end
+        do_halt code,msg,uri,payload,headers
+      end
+    end
+    
+    def self.do_halt( code, body, uri, payload, headers )
+      
+      #build error
+      causing_errors = Error.parse(body)
+      if causing_errors
+        error = causing_errors + [Error.new(code, "subsequent error", uri, payload, headers)]
+      else
+        error = [Error.new(code, body, uri, payload, headers)]
+      end
+
+#     debug utility: write error to file       
+#      error_dir = "/tmp/ot_errors"
+#      FileUtils.mkdir(error_dir) unless File.exist?(error_dir)
+#      raise "could not create error dir" unless File.exist?(error_dir) and File.directory?(error_dir)
+#      file_name = "error"
+#      time=Time.now.strftime("%m.%d.%Y-%H:%M:%S")
+#      count = 1
+#      count+=1 while File.exist?(File.join(error_dir,file_name+"_"+time+"_"+count.to_s))
+#      File.new(File.join(error_dir,file_name+"_"+time+"_"+count.to_s),"w").puts(body)
+      
+      # return error (by halting, halts should be logged)
+      # PENDING always return yaml for now
+      if defined?(halt)
+        halt(502,error.to_yaml)
+      elsif defined?($sinatra)
+        $sinatra.halt(502,error.to_yaml)
+      else
+        raise error.to_yaml
+      end
+    end
+  end
+end
diff --git a/lib/task.rb b/lib/task.rb
index 75cc2d2..8b1ab5d 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -35,8 +35,12 @@ module OpenTox
 		 
 		def finished_at
 			RestClient.get File.join(@uri, 'finished_at')
-		end
-		 
+	 end
+  
+    def description
+      RestClient.get File.join(@uri, 'description')
+    end
+    
 		def status
 			RestClient.get File.join(@uri, 'status')
 		end
@@ -61,9 +65,10 @@ module OpenTox
 			resource.put :resource => uri
 		end
 
-		def failed
+		def failed(description)
 			resource = RestClient::Resource.new(File.join(@uri,'failed'), :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			resource.put({})
+			resource.put :description => description
+      #resource.put({})
 		end
 
 		def parent=(task)
@@ -92,19 +97,30 @@ module OpenTox
 			end
 	  end
   
-    def self.as_task
+    def self.as_task(parent_task=nil)
+      #return yield
+      
       task = OpenTox::Task.create
+      task.parent = parent_task if parent_task
       LOGGER.debug "Starting task"
       pid = Spork.spork(:logger => LOGGER) do
         task.started
         LOGGER.debug "Task #{task.uri} started #{Time.now}"
         begin
-          result = yield
+          result = catch(:halt) do
+            yield task
+          end
+          if result && result.is_a?(Array) && result.size==2 && result[0]>202
+            # halted while executing task
+            LOGGER.error "task was halted: "+result.inspect
+            task.failed(result[1])
+            throw :halt,result 
+          end
           task.completed(result)
         rescue => ex
-          raise ex
-          LOGGER.error ex.message
-          task.failed
+          #raise ex
+          LOGGER.error "task failed: "+ex.message
+          task.failed(ex.message)
         end
         raise "Invalid task state" unless task.completed? || task.failed?
       end  
@@ -113,15 +129,6 @@ module OpenTox
       task.uri
     end  
   
-    def wait_for_resource
-      wait_for_completion
-      if failed?
-        LOGGER.error "task failed: "+uri.to_s
-        return nil
-      end
-      return resource
-    end
-
 	end
 
 end
diff --git a/lib/utils.rb b/lib/utils.rb
index a31e405..fa61a28 100644
--- a/lib/utils.rb
+++ b/lib/utils.rb
@@ -21,57 +21,5 @@ module OpenTox
         false
       end
     end
-  
-end
-
-
-  module RestClientWrapper
-    
-    def self.get(uri, headers=nil)
-      execute( "get", uri, nil, headers )
-    end
-    
-    def self.post(uri, payload=nil, headers=nil)
-      execute( "post", uri, payload, headers )
-    end
-
-    def self.delete(uri, headers=nil)
-      execute( "delete", uri, nil, headers )
-    end
-
-    private
-    def self.execute( rest_call, uri, payload, headers )
-      
-      do_halt 400,"uri is null",uri,payload,headers unless uri
-      begin
-        if payload
-          RestClient.send(rest_call, uri, payload, headers)
-        else
-          RestClient.send(rest_call, uri, headers)
-        end
-      rescue RestClient::RequestFailed, RestClient::RequestTimeout => ex
-        do_halt 502,ex.message,uri,payload,headers
-      rescue SocketError, RestClient::ResourceNotFound => ex
-        do_halt 400,ex.message,uri,payload,headers
-      rescue Exception => ex
-        do_halt 500,"add error '"+ex.class.to_s+"'' to rescue in OpenTox::RestClientWrapper::execute(), msg: '"+ex.message.to_s+"'",uri,payload,headers
-      end
-    end
-    
-    def self.do_halt(status, msg, uri, payload, headers)
-      
-      message = msg+""
-      message += ", uri: '"+uri.to_s+"'" if uri
-      message += ", payload: '"+payload.inspect+"'" if payload
-      message += ", headers: '"+headers.inspect+"'" if headers
-      
-      if defined?(halt)
-        halt(status,message)
-      elsif defined?($sinatra)
-        $sinatra.halt(status,message)
-      else
-        raise "halt '"+status.to_s+"' '"+message+"'"
-      end
-    end
   end
 end