CONFIG reverted to @@config

11 files changed, 110 insertions, 47 deletions

diff --git a/lib/algorithm.rb b/lib/algorithm.rb
index de5902b..cc06032 100644
--- a/lib/algorithm.rb
+++ b/lib/algorithm.rb
@@ -12,7 +12,7 @@ module OpenTox
       end
 
 			def self.uri
-				File.join(CONFIG[:services]["opentox-algorithm"], "fminer")
+				File.join(@@config[:services]["opentox-algorithm"], "fminer")
 			end
     end
 
@@ -21,15 +21,15 @@ module OpenTox
 			def self.create_model(params)
 				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 => "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
+				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 => "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
 			end
 
 			def self.uri
-				File.join(CONFIG[:services]["opentox-algorithm"], "lazar")
+				File.join(@@config[:services]["opentox-algorithm"], "lazar")
 			end
 
     end
diff --git a/lib/compound.rb b/lib/compound.rb
index 45b96b8..9366db4 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -11,19 +11,19 @@ module OpenTox
 		def initialize(params)
 			if params[:smiles]
 				@inchi = smiles2inchi(params[:smiles])
-				@uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(@inchi))
+				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:inchi]
 				@inchi = params[:inchi]
-				@uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(@inchi))
+				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:sdf]
 				@inchi = sdf2inchi(params[:sdf])
-				@uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(@inchi))
+				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:name]
 				# paranoid URI encoding to keep SMILES charges and brackets
 				@inchi = RestClient.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").body.chomp
 				# this was too hard for me to debug and leads to additional errors (ch)
 				#@inchi = RestClientWrapper.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").chomp
-				@uri = File.join(CONFIG[:services]["opentox-compound"],URI.escape(@inchi))
+				@uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi))
 			elsif params[:uri]
 				@uri = params[:uri]
 				case params[:uri]
@@ -56,7 +56,8 @@ module OpenTox
 		end
 
 		def image_uri
-			"#{@@ambit_uri}#{smiles}"
+      File.join @uri, "image"
+			#"#{@@ambit_uri}#{smiles}"
 			#"#{@@cactus_uri}#{@inchi}/image"
 		end
 
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 776a55b..af72403 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -15,8 +15,8 @@ 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/
-        if !CONFIG[:accept_headers]["opentox-dataset"].grep(/yaml/).empty?
+        #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"
@@ -203,7 +203,7 @@ module OpenTox
     
 			@features.uniq!
 			@compounds.uniq!
-        OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip 	
+        OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type =>  "application/x-yaml"},self.to_yaml).strip 	
 		end
 
     def init_dirty_features(owl)
diff --git a/lib/environment.rb b/lib/environment.rb
index 46f8933..917011d 100644
--- a/lib/environment.rb
+++ b/lib/environment.rb
@@ -1,4 +1,4 @@
-require 'logger'
+require "ot-logger"
 # set default environment
 ENV['RACK_ENV'] = 'production' unless ENV['RACK_ENV']
 
@@ -12,8 +12,8 @@ TMP_DIR = File.join(basedir, "tmp")
 LOG_DIR = File.join(basedir, "log")
 
 if File.exist?(config_file)
-	CONFIG = YAML.load_file(config_file)
-  raise "could not load config, config file: "+config_file.to_s unless CONFIG
+	@@config = YAML.load_file(config_file)
+  raise "could not load config, config file: "+config_file.to_s unless @@config
 else
 	FileUtils.mkdir_p TMP_DIR
 	FileUtils.mkdir_p LOG_DIR
@@ -24,20 +24,20 @@ else
 end
 
 # database
-if CONFIG[:database]
+if @@config[:database]
 	['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types', 'dm-migrations' ].each{|lib| require lib }
-	case CONFIG[:database][:adapter]
+	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]})
+				:adapter  => @@config[:database][:adapter],
+				:database => @@config[:database][:database],
+				:username => @@config[:database][:username],
+				:password => @@config[:database][:password],
+				:host     => @@config[:database][:host]})
 	end
 end
 
@@ -47,7 +47,7 @@ load File.join config_dir,"mail.rb" if File.exists?(File.join config_dir,"mail.r
 logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log"
 LOGGER = MyLogger.new(logfile,'daily') # daily rotation
 LOGGER.formatter = Logger::Formatter.new #this is neccessary to restore the formating in case active-record is loaded
-if CONFIG[:logger] and CONFIG[:logger] == "debug"
+if @@config[:logger] and @@config[:logger] == "debug"
 	LOGGER.level = Logger::DEBUG
 else
 	LOGGER.level = Logger::WARN 
@@ -72,5 +72,5 @@ TRUE_REGEXP = /^(true|active|1|1.0)$/i
 FALSE_REGEXP = /^(false|inactive|0|0.0)$/i
 
 # Task durations
-DEFAULT_TASK_MAX_DURATION = CONFIG[:default_task_max_duration]
-EXTERNAL_TASK_MAX_DURATION = CONFIG[:external_task_max_duration]
+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 db9efd4..b6cef46 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -86,8 +86,8 @@ module OpenTox
       
 			def initialize
 				@source = "http://github.com/helma/opentox-model"
-				@algorithm = File.join(CONFIG[:services]["opentox-algorithm"],"lazar")
-				#@independent_variables = File.join(CONFIG[:services]["opentox-algorithm"],"fminer#BBRC_representative")
+				@algorithm = File.join(@@config[:services]["opentox-algorithm"],"lazar")
+				#@independent_variables = File.join(@@config[:services]["opentox-algorithm"],"fminer#BBRC_representative")
 				@features = []
 				@effects = {}
 				@activities = {}
@@ -97,12 +97,12 @@ 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 = RestClient::Resource.new(@@config[:services]["opentox-model"], :user => @@users[:users].keys[0], :password => @@users[:users].values[0])
 			  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")
+				RestClientWrapper.get(@@config[:services]["opentox-model"]).chomp.split("\n")
 			end
 		end
 	end
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb
index 4a6f811..45a3428 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', 'logger', 'overwrite', 'rest_client_wrapper'].each do |lib|
+['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization','features', 'ot-logger', 'overwrite', 'rest_client_wrapper'].each do |lib|
 	require lib
 end
diff --git a/lib/ot-logger.rb b/lib/ot-logger.rb
new file mode 100644
index 0000000..6c35ed2
--- /dev/null
+++ b/lib/ot-logger.rb
@@ -0,0 +1,48 @@
+require 'logger'
+# logging
+class MyLogger < Logger
+  
+  def pwd
+    path = Dir.pwd.to_s
+    index = path.rindex(/\//)
+    return path if index==nil
+    path[(index+1)..-1]
+  end
+  
+  def trace()
+    lines = caller(0)
+    n = 2
+    line = lines[n]
+    
+    while (line =~ /spork.rb/ or line =~ /as_task/ or line =~ /environment.rb/)
+      n += 1
+      line = lines[n]
+    end
+  
+    index = line.rindex(/\/.*\.rb/)
+    return line if index==nil
+    line[index..-1]
+  end
+  
+  def format(msg)
+    pwd.ljust(18)+" :: "+msg.to_s+"           :: "+trace+" :: "+($sinatra ? $sinatra.request.env['REMOTE_ADDR'] : nil).to_s
+  end
+  
+  def debug(msg)
+    super format(msg)
+  end
+  
+  def info(msg)
+    super format(msg)
+  end
+  
+  def warn(msg)
+    super format(msg)
+  end
+
+  def error(msg)
+    super format(msg)
+  end
+
+end
+
diff --git a/lib/overwrite.rb b/lib/overwrite.rb
new file mode 100644
index 0000000..1d0161b
--- /dev/null
+++ b/lib/overwrite.rb
@@ -0,0 +1,14 @@
+# class overwrites aka monkey patches
+# hack: store sinatra in global var to make url_for and halt methods accessible
+before{ $sinatra = self unless $sinatra }
+
+class Sinatra::Base
+  # overwriting halt to log halts (!= 202)
+  def halt(*response)
+    LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response and response.first and response.first >= 300
+    # orig sinatra code:
+    response = response.first if response.length == 1
+    throw :halt, response
+  end
+end
+
diff --git a/lib/task.rb b/lib/task.rb
index e1c1cb5..88bcb71 100644
--- a/lib/task.rb
+++ b/lib/task.rb
@@ -18,7 +18,7 @@ module OpenTox
     
     # create is private now, use OpenTox::Task.as_task
 		def self.create(max_duration)
-      task_uri = RestClientWrapper.post(CONFIG[:services]["opentox-task"], {:max_duration => max_duration}, nil, false).to_s
+      task_uri = RestClientWrapper.post(@@config[:services]["opentox-task"], {:max_duration => max_duration}, nil, false).to_s
 			Task.find(task_uri.chomp)
 		end
 
@@ -94,7 +94,7 @@ module OpenTox
     # waits for a task, unless time exceeds or state is no longer running
 		def wait_for_completion(dur=0.3)
       
-      if (@uri.match(CONFIG[:services]["opentox-task"]))
+      if (@uri.match(@@config[:services]["opentox-task"]))
         due_to_time = Time.parse(@due_to_time)
         running_time = due_to_time - Time.parse(@date)
       else
diff --git a/lib/tasks/opentox.rb b/lib/tasks/opentox.rb
index 6962407..7fce35b 100644
--- a/lib/tasks/opentox.rb
+++ b/lib/tasks/opentox.rb
@@ -6,9 +6,9 @@ namespace :opentox do
 
 		desc "Run opentox services"
 		task :start do
-			CONFIG[:services].each do |service,uri|
-				dir = File.join(CONFIG[:base_dir], service)
-				server = CONFIG[:webserver]
+			@@config[:services].each do |service,uri|
+				dir = File.join(@@config[:base_dir], service)
+				server = @@config[:webserver]
 				case server
 				when /thin|mongrel|webrick/
 					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
@@ -32,9 +32,9 @@ namespace :opentox do
 
 		desc "Stop opentox services"
 		task :stop do
-			server = CONFIG[:webserver]
+			server = @@config[:webserver]
 			if server =~ /thin|mongrel|webrick/
-				CONFIG[:services].each do |service,uri|
+				@@config[:services].each do |service,uri|
 					port = uri.sub(/^.*:/,'').sub(/\/$/,'')
 					pid_file = File.join(TMP_DIR,"#{service}.pid") 
 					begin
@@ -54,8 +54,8 @@ namespace :opentox do
 
 	desc "Run all OpenTox tests"
 	task :test do
-		CONFIG[:services].each do |service,uri|
-			dir = File.join(CONFIG[:base_dir], service)
+		@@config[:services].each do |service,uri|
+			dir = File.join(@@config[:base_dir], service)
 			Dir.chdir dir
 			puts "Running tests in #{dir}"
 			`rake test -t 1>&2`
@@ -67,10 +67,10 @@ end
 desc "Start service in current directory"
 task :start do
 	service = File.basename(Dir.pwd).intern
-	server = CONFIG[:webserver]
+	server = @@config[:webserver]
 	case server 
 		when /thin|mongrel|webrick/
-			port = CONFIG[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
+			port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
 			pid_file = File.join(TMP_DIR,"#{service}.pid") 
 			begin
 				`#{server} --trace --rackup config.ru start -p #{port} -e #{ENV['RACK_ENV']} -P #{pid_file} -d &`
@@ -90,9 +90,9 @@ end
 desc "Stop service in current directory"
 task :stop do
 	service = File.basename(Dir.pwd).intern
-	server = CONFIG[:webserver]
+	server = @@config[:webserver]
 	if server =~ /thin|mongrel|webrick/
-		port = CONFIG[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
+		port = @@config[:services][service].sub(/^.*:/,'').sub(/\/$/,'')
 		pid_file = File.join(TMP_DIR,"#{service}.pid") 
 		begin
 			puts `thin stop -P #{pid_file}` 
diff --git a/lib/validation.rb b/lib/validation.rb
index f1cc987..bd38488 100644
--- a/lib/validation.rb
+++ b/lib/validation.rb
@@ -17,7 +17,7 @@ module OpenTox
 		end
 		
 		def self.crossvalidation(params)
-			params[:uri] = File.join(CONFIG[:services]['opentox-validation'], "crossvalidation")
+			params[:uri] = File.join(@@config[:services]['opentox-validation'], "crossvalidation")
       params[:num_folds] = 10 unless params[:num_folds]
 		 	params[:random_seed] = 2 unless params[:random_seed]
 		 	params[:stratified] = false unless params[:stratified]