opentox-ruby-api-wrapper 1.2.6 → 1.2.7

data/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", "thin", "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", "thin", "emk-sinatra-url-for", "cehoffman-sinatra-respond_to", "dm-more", "dm-core", "sinatra-static-assets", "do_sqlite3", "do_postgres"].each do |dep|
 			gem.add_dependency dep
 		end
 		gem.add_development_dependency "cucumber"

data/VERSION

@@ -1 +1 @@
-1.2.6
+1.2.7

data/lib/algorithm.rb

@@ -39,6 +39,7 @@ module OpenTox
 			end
 			
 			def self.create_model(params)
+				LOGGER.debug params
 				@uri = RestClient.post File.join(@@config[:services]["opentox-algorithm"], "lazar"), :dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")
 			end
 

data/lib/compound.rb

@@ -21,20 +21,20 @@ module OpenTox
 				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
 				@uri = params[:uri]
-				if params[:uri].match(/InChI/) # shortcut for IST services
+				case params[:uri]
+				when /ambit/ # Ambit does not deliver InChIs reliably
+					smiles = RestClient.get @uri, :accept => 'chemical/x-daylight-smiles'
+					@inchi = obconversion(smiles,'smi','inchi')
+				when /InChI/ # shortcut for IST services
 					@inchi = params[:uri].sub(/^.*InChI/, 'InChI')
 				else
 					@inchi = RestClient.get @uri, :accept => 'chemical/x-inchi'
-					# AMBIT does not provide InChIs
-					#smiles = RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output
-					#@inchi = obconversion(smiles,'smi','inchi')
 				end
 			end
 		end
 
 		# Get the (canonical) smiles
 		def smiles
-			#RestClient.get(@uri, :accept => 'chemical/x-daylight-smiles').split(/\s+/).first # fix ambit output
 			obconversion(@inchi,'inchi','can')
 		end
 

data/lib/config/database.rb

@@ -0,0 +1,21 @@
+# database
+if @@config[:database]
+	require 'dm-core'
+	require 'dm-serializer'
+	require 'dm-timestamps'
+	require 'dm-types'
+	case @@config[:database][:adapter]
+	when /sqlite/i
+		db_dir = File.join(ENV['HOME'], ".opentox", "db")
+		FileUtils.mkdir_p db_dir
+		DataMapper::setup(:default, "sqlite3://#{db_dir}/opentox.sqlite3")
+	else
+		DataMapper.setup(:default, { 
+				:adapter  => @@config[:database][:adapter],
+				:database => @@config[:database][:database],
+				:username => @@config[:database][:username],
+				:password => @@config[:database][:password],
+				:host     => @@config[:database][:host]})
+	end
+end
+

data/lib/dataset.rb

@@ -87,7 +87,7 @@ module OpenTox
 		def self.find(uri)
 			dataset = Dataset.new
 			data = `curl "#{uri}"`
-			#data = RestClient.get uri, :accept => 'application/rdf+xml' # unclear why this does not work for complex uris, Dataset.find works from irb
+			#data = RestClient.get(uri, :accept => 'application/rdf+xml') # unclear why this does not work for complex uris, Dataset.find works from irb
 			dataset.rdf = data
 			dataset
 		end

data/lib/environment.rb

@@ -2,7 +2,7 @@ require 'logger'
 # set default environment
 ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV']
 
-# load configuration
+# load/setup configuration
 basedir = File.join(ENV['HOME'], ".opentox")
 config_dir = File.join(basedir, "config")
 config_file = File.join(config_dir, "#{ENV['RACK_ENV']}.yaml")
@@ -19,6 +19,26 @@ else
 	puts "Please edit #{config_file} and restart your application."
 	exit
 end
+
+# database
+if @@config[:database]
+	['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types'].each{|lib| require lib }
+	case @@config[:database][:adapter]
+	when /sqlite/i
+		db_dir = File.join(basedir, "db")
+		FileUtils.mkdir_p db_dir
+		DataMapper::setup(:default, "sqlite3://#{db_dir}/opentox.sqlite3")
+	else
+		DataMapper.setup(:default, { 
+				:adapter  => @@config[:database][:adapter],
+				:database => @@config[:database][:database],
+				:username => @@config[:database][:username],
+				:password => @@config[:database][:password],
+				:host     => @@config[:database][:host]})
+	end
+end
+
+# logging
 logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
 LOGGER = Logger.new(logfile,'daily') # daily rotation
 LOGGER.level = Logger::DEBUG

data/lib/model.rb

@@ -50,6 +50,14 @@ module OpenTox
 				RestClient.post(@@config[:services]["opentox-model"], data, :content_type => "application/x-yaml").to_s
 			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 => "application/x-yaml").to_s
+#			end
+
 			def endpoint
 				YAML.load(RestClient.get(uri))[:endpoint]
 			end

data/lib/task.rb

@@ -10,7 +10,7 @@ module OpenTox
 		end
 
 		def self.create
-			uri = RestClient.post @@config[:services]["opentox-task"], nil
+			uri = RestClient.post @@config[:services]["opentox-task"], {}
 			Task.new(uri)
 		end
 
@@ -26,19 +26,6 @@ module OpenTox
 			task_uris = RestClient.get(@@config[:services]["opentox-task"]).split(/\n/)
 			task_uris.collect{|uri| Task.new(uri)}
 		end
-
-		def started
-			#LOGGER.info File.join(@uri,'started')
-			RestClient.put File.join(@uri,'started'), {}
-		end
-
-		def cancel
-			RestClient.put File.join(@uri,'cancelled'), {}
-		end
-
-		def completed(uri)
-			RestClient.put File.join(@uri,'completed'), :resource => uri
-		end
 		 
 		def created_at
 			RestClient.get File.join(@uri, 'created_at')
@@ -55,6 +42,26 @@ module OpenTox
 		def resource
 			RestClient.get File.join(@uri, 'resource')
 		end
+
+		def started
+			RestClient.put File.join(@uri,'started'), {}
+		end
+
+		def cancel
+			RestClient.put File.join(@uri,'cancelled'), {}
+		end
+
+		def failed
+			RestClient.put File.join(@uri,'failed'), {}
+		end
+
+		def parent=(task)
+			RestClient.put File.join(@uri,'parent'), {:uri => task.uri}
+		end
+
+		def completed(uri)
+			RestClient.put File.join(@uri,'completed'), :resource => uri
+		end
 		 
 		def pid=(pid)
 			RestClient.put File.join(@uri, 'pid'), :pid => pid
@@ -64,8 +71,12 @@ module OpenTox
 			self.status.to_s == 'completed'
 		end
 
+		def failed?
+			self.status.to_s == 'failed'
+		end
+
 		def wait_for_completion
-			until self.completed?
+			until self.completed? or self.failed?
 				sleep 1
 			end
 		end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: opentox-ruby-api-wrapper
 version: !ruby/object:Gem::Version 
-  version: 1.2.6
+  version: 1.2.7
 platform: ruby
 authors: 
 - Christoph Helma
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-01-31 00:00:00 +01:00
+date: 2010-02-08 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -122,6 +122,26 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: "0"
     version: 
+- !ruby/object:Gem::Dependency 
+  name: do_sqlite3
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: do_postgres
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
 - !ruby/object:Gem::Dependency 
   name: cucumber
   type: :development
@@ -151,6 +171,8 @@ files:
 - bin/yaml2owl.rb
 - lib/algorithm.rb
 - lib/compound.rb
+- lib/config/config_ru.rb
+- lib/config/database.rb
 - lib/dataset.rb
 - lib/environment.rb
 - lib/helper.rb
@@ -160,7 +182,6 @@ files:
 - lib/owl.rb
 - lib/spork.rb
 - lib/task.rb
-- lib/tasks/config.rb
 - lib/tasks/opentox.rb
 - lib/templates/config.yaml
 - lib/utils.rb