Modification for new RestClient: body instead of to_s

8 files changed, 78 insertions, 205 deletions

diff --git a/Rakefile b/Rakefile
index 4c9e00a..c00a13f 100644
--- a/Rakefile
+++ b/Rakefile
@@ -10,7 +10,7 @@ begin
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
-		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets"].each do |dep|
+		["sinatra", "rest-client", "rack", "rack-contrib", "rack-flash", "sinatra-url-for", "sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets","tmail"].each do |dep|
 			gem.add_dependency dep
 		end
 		['cucumber','jeweler'].each do |dep|
diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index b573ea3..cc06032 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -22,7 +22,7 @@ module OpenTox
 				LOGGER.debug params
 				LOGGER.debug File.basename(__FILE__) + ": creating model"
 				LOGGER.debug File.join(@@config[:services]["opentox-algorithm"], "lazar")
-        #resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "text/x-yaml")
+        #resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml")
         resource = RestClient::Resource.new(File.join(@@config[:services]["opentox-algorithm"], "lazar"), :user => @@users[:users].keys[0], :password => @@users[:users].values[0], :content_type => "application/x-yaml")
         #@uri = resource.post(:dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).chomp
         @uri = resource.post(:dataset_uri => params[:dataset_uri], :prediction_feature => params[:prediction_feature], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).body.chomp
diff --git a/lib/config/config_ru.rb b/lib/config/config_ru.rb
index 8470f0e..09fba3b 100644
--- a/lib/config/config_ru.rb
+++ b/lib/config/config_ru.rb
@@ -18,8 +18,11 @@ set :raise_errors, true
 end
  
 use Rack::ShowExceptions
-#use Rack::MailExceptions do |mail|
-#		mail.to '...@example.com'
-#		mail.subject '[ERROR] %s'
-#		mail.smtp MAIL
-#end 
+#if MAIL
+#	use Rack::MailExceptions do |mail|
+#			mail.to 'helma@in-silico.ch'
+#			mail.subject '[ERROR] %s'
+#			mail.from "toxcreate@in-silico.ch"
+#			mail.smtp MAIL
+#	end 
+#end
diff --git a/lib/dataset.rb b/lib/dataset.rb
index e21ccce..17f0997 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -15,16 +15,17 @@ module OpenTox
 		def self.find(uri, accept_header=nil) 
     
       unless accept_header
-        if uri.match(@@config[:services]["opentox-dataset"]) || uri=~ /188.40.32.88/ || uri =~ /informatik/
-          accept_header = 'text/x-yaml'
+        #if uri.match(@@config[:services]["opentox-dataset"]) || uri=~ /188.40.32.88/ || uri =~ /informatik/
+        if !@@config[:accept_headers]["opentox-dataset"].grep(/yaml/).empty?
+          accept_header = 'application/x-yaml'
         else
           accept_header = "application/rdf+xml"
         end
       end
       
       case accept_header
-      when "text/x-yaml"
-				d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'text/x-yaml').to_s 
+      when "application/x-yaml"
+				d = YAML.load RestClientWrapper.get(uri.to_s.strip, :accept => 'application/x-yaml').to_s 
         d.uri = uri unless d.uri
 			when "application/rdf+xml"
 				owl = OpenTox::Owl.from_uri(uri.to_s.strip, "Dataset")
@@ -172,122 +173,9 @@ module OpenTox
     
 			@features.uniq!
 			@compounds.uniq!
-      OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "text/x-yaml"},self.to_yaml).strip 	
+      OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip 	
 		end
 
-=begin
-		# create/add to entry from uris or Redland::Resources
-		def add(compound,feature,value)
-			compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
-			feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
-			data_entry = @model.subject OT['compound'], compound
-			if data_entry.nil?
-				data_entry = @model.create_resource
-				dataset = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add dataset, OT['dataEntry'], data_entry
-				@model.add data_entry, RDF['type'], OT["DataEntry"]
-				@model.add data_entry, OT['compound'], compound
-			end
-			values = @model.create_resource
-			@model.add data_entry, OT['values'], values
-			@model.add values, RDF['type'], OT['FeatureValue']
-			@model.add values, OT['feature'], feature
-			@model.add values, OT['value'], value.to_s
-		end
-
-		def add_tuple(compound,tuple)
-			compound = self.find_or_create_compound compound unless compound.class == Redland::Resource
-			data_entry = @model.subject OT['compound'], compound
-			if data_entry.nil?
-				data_entry = @model.create_resource
-				dataset = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add dataset, OT['dataEntry'], data_entry
-				@model.add data_entry, RDF['type'], OT["DataEntry"]
-				@model.add data_entry, OT['compound'], compound
-			end
-			@model.add data_entry, OT['values'], tuple
-		end
-
-		def create_tuple(feature,t)
-			feature = self.find_or_create_feature feature unless feature.class == Redland::Resource
-			tuple = @model.create_resource
-			@model.add tuple, RDF['type'], OT["Tuple"]
-			@model.add tuple, OT['feature'], feature
-			t.each do |name,value|
-				f = self.find_or_create_feature name unless name.class == Redland::Resource
-				complex_value = @model.create_resource
-				feature = self.find_or_create_feature(name) 
-				@model.add tuple, OT['complexValue'], complex_value
-				@model.add complex_value, RDF['type'], OT["FeatureValue"]
-				@model.add complex_value, OT['feature'], f
-				@model.add complex_value, OT['value'], value.to_s
-      end
-  	
-			tuple
-		end
-
-		# find or create a new compound and return the resource
-		def find_or_create_compound(uri)
-			compound = @model.subject(DC["identifier"], uri)
-			if compound.nil?
-				compound = @model.create_resource(uri)
-				@model.add compound, RDF['type'], OT["Compound"]
-				@model.add compound, DC["identifier"], uri
-			end
-			compound
-		end
-
-		# find or create a new feature and return the resource
-		def find_or_create_feature(uri)
-			feature = @model.subject(DC["identifier"], uri)
-			if feature.nil?
-				feature = @model.create_resource(uri)
-				@model.add feature, RDF['type'], OT["Feature"]
-				@model.add feature, DC["identifier"], uri
-				@model.add feature, DC["title"], File.basename(uri).split(/#/)[1]
-				@model.add feature, DC['source'], uri
-			end
-			feature
-		end
-
-		def self.create(data, content_type = 'application/rdf+xml')
-      resource = RestClient::Resource.new(@@config[:services]["opentox-dataset"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])		  
-		  uri = resource.post data, :content_type => content_type
-			dataset = Dataset.new
-			dataset.read uri.chomp.to_s
-			dataset
-		end
-
-		def features
-			features = []
-			@model.subjects(RDF['type'], OT["Feature"]).each do |feature_node|
-				features << @model.object(feature_node,  DC["identifier"])#
-			end
-			features
-		end
-
-		def compounds
-			compounds = []
-			@model.subjects(RDF['type'], OT["Compound"]).each do |compound_node|
-				compounds << @model.object(compound_node,  DC["identifier"]).to_s
-			end
-			compounds
-		end
-
-		# Delete a dataset
-		def delete
-  		resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-      resource.delete
-    end
-
-		def to_owl
-		end
-
-		def from_owl
-		end
-
-=end
-
     def init_dirty_features(owl)
       @dirty_features = @features
       @owl = owl
diff --git a/lib/environment.rb b/lib/environment.rb
index 44efd6e..c112669 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -40,8 +40,8 @@ if @@config[:database]
 	end
 end
 
-# mail
-#load File.join config_dir,"mail.rb"
+# mail for error messages
+load File.join config_dir,"mail.rb" if File.exists?(File.join config_dir,"mail.rb")
 
 # hack: store sinatra in global var to make url_for and halt methods accessible
 before {$sinatra = self unless $sinatra}
@@ -136,3 +136,7 @@ XML = Redland::Namespace.new 'http://www.w3.org/2001/XMLSchema#'
 # Regular expressions for parsing classification data
 TRUE_REGEXP = /^(true|active|$1^)/
 FALSE_REGEXP = /^(false|inactive|$0^)/
+
+# Task durations
+DEFAULT_TASK_MAX_DURATION = @@config[:default_task_max_duration]
+EXTERNAL_TASK_MAX_DURATION = @@config[:external_task_max_duration]
diff --git a/lib/model.rb b/lib/model.rb
index 74bb598..3fb713f 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -102,79 +102,12 @@ module OpenTox
 			def save
 				@features.uniq!
 			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			  resource.post(self.to_yaml, :content_type => "text/x-yaml").chomp.to_s
+			  resource.post(self.to_yaml, :content_type => "application/x-yaml").chomp.to_s
 			end
 
 			def self.find_all
 				RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
 			end
-=begin
-			
-			# Predict a compound
-			def predict(compound)
-				# nicht absichern??
-				resource = RestClient::Resource.new(@uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-				resource.post(:compound_uri => compound.uri)
-			end
-
-			def self.base_uri
-				File.join @@config[:services]["opentox-model"],'lazar'
-			end
-
-			def self.create(data)
-			  resource = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-			  resource.post(data, :content_type => "text/x-yaml").chomp.to_s
-			end
-
-			def delete
-			  resource = RestClient::Resource.new(self.uri, :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
-				resource.delete
-				#RestClient.delete @uri if @uri
-				#RestClient.delete model.task_uri if model.task_uri
-			end
-
-#			def self.create(task)
-#				@uri = RestClient.post(@@config[:services]["opentox-model"], :task_uri => task.uri)
-#			end
-
-#			def yaml=(data)
-#				RestClient.put(@@uri, data, :content_type => "text/x-yaml").to_s
-#			end
-
-			def endpoint
-				YAML.load(RestClient.get(uri))[:endpoint]
-			end
-
-			def algorithm=(algorithm)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['algorithm'], Redland::Uri.new(algorithm) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(algorithm), RDF['type'], OT['Algorithm']
-			end
-
-			def trainingDataset=(trainingDataset)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-        @model.add me, OT['trainingDataset'], Redland::Uri.new(trainingDataset) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(trainingDataset), RDF['type'], OT['Dataset']
-			end
-
-			def dependentVariables=(dependentVariables)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['dependentVariables'], Redland::Uri.new(dependentVariables) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(dependentVariables), RDF['type'], OT['Feature']
-			end
-
-			def independentVariables=(independentVariables)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['independentVariables'], Redland::Uri.new(independentVariables) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(independentVariables), RDF['type'], OT['Feature']
-			end
-
-			def predictedVariables=(predictedVariables)
-				me = @model.subject(RDF['type'],OT[self.owl_class])
-				@model.add me, OT['predictedVariables'], Redland::Uri.new(predictedVariables) # untyped individual comes from this line, why??
-				@model.add Redland::Uri.new(predictedVariables), RDF['type'], OT['Feature']
-			end
-=end
 		end
 	end
 end
diff --git a/lib/task.rb b/lib/task.rb
index 8f87f45..66d39f4 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -1,8 +1,5 @@
 LOGGER.progname = File.expand_path(__FILE__)
 
-DEFAULT_TASK_MAX_DURATION = 3600
-EXTERNAL_TASK_MAX_DURATION = 1200
-
 $self_task=nil
 
 module OpenTox
@@ -40,14 +37,14 @@ module OpenTox
     end
     
     def reload
-      result = RestClientWrapper.get(uri, {:accept => 'application/rdf+xml'}, false)#'text/x-yaml'})
+      result = RestClientWrapper.get(uri, {:accept => 'application/rdf+xml'}, false)#'application/x-yaml'})
       @http_code = result.code
       reload_from_data(result, result.content_type, uri)
     end
     
     def reload_from_data( data, content_type, base_uri )
       case content_type
-      when /text\/x-yaml/
+      when /yaml/
         task =  YAML.load data
         TASK_ATTRIBS.each do |a|
           raise "task yaml data invalid, key missing: "+a.to_s unless task.has_key?(a)
diff --git a/lib/templates/config.yaml b/lib/templates/config.yaml
index ad7c4ab..e8084bd 100644
--- a/lib/templates/config.yaml
+++ b/lib/templates/config.yaml
@@ -1,13 +1,25 @@
 # Example configuration for OpenTox, please adjust to your settings
 # 
+# Database setup:
+#
+# Example MySql:
+#
+# :database: 
+#   :adapter:  mysql
+#   :database: production
+#   :username: production
+#   :password: your_password
+#   :host:     localhost
+#
 # Example 1: Using external test services
 #
 # :services:
-#  opentox-compound:      "http://webservices.in-silico.ch/test/compound/"
-#  opentox-dataset:       "http://webservices.in-silico.ch/test/dataset/"
-#  opentox-algorithm:     "http://webservices.in-silico.ch/test/algorithm/"
-#  opentox-model:         "http://webservices.in-silico.ch/test/model/"
-#  opentox-task:         "http://webservices.in-silico.ch/test/task/"
+#  opentox-compound:      "http://webservices.in-silico.ch/compound/"
+#  opentox-dataset:       "http://webservices.in-silico.ch/dataset/"
+#  opentox-algorithm:     "http://webservices.in-silico.ch/algorithm/"
+#  opentox-model:         "http://webservices.in-silico.ch/model/"
+#  opentox-task:          "http://webservices.in-silico.ch/task/"
+#  opentox-validation:    "http://opentox.informatik.uni-freiburg.de/validation/"
 #
 # Example 2: Using local services
 # :base_dir: /home/ch/webservices
@@ -18,3 +30,39 @@
 #   opentox-algorithm:     "http://localhost:4002/"
 #   opentox-model:         "http://localhost:4003/"
 #   opentox-task:          "http://localhost:4004/"
+#   opentox-validation:    "http://opentox.informatik.uni-freiburg.de/validation/"
+#
+# Accept headers:
+#
+# :accept_headers:
+#   opentox-compound:      
+#     - "chemical/x-daylight-smiles"
+#     - "chemical/x-inchi"
+#     - "chemical/x-mdl-sdfile"
+#     - "image/gif"
+#     - "text/plain"
+#   opentox-dataset:       
+#     - "application/x-yaml"
+#     - "text/x-yaml"
+#     - "application/rdf+xml"
+#   opentox-algorithm:     
+#     - "application/x-yaml"
+#     - "text/x-yaml"
+#     - "application/rdf+xml"
+#   opentox-model:         
+#     - "application/x-yaml"
+#     - "text/x-yaml"
+#     - "application/rdf+xml"
+#   opentox-task:          
+#     - "application/x-yaml"
+#     - "text/x-yaml"
+#     - "application/rdf+xml"
+#   opentox-validation:    
+#     - "application/x-yaml"
+#     - "text/x-yaml"
+#     - "application/rdf+xml"
+
+# Timeouts:
+# 
+# :default_task_max_duration: 3600
+# :external_task_max_duration: 3600