diff options
| -rw-r--r-- | lib/algorithm.rb | 14 | ||||
| -rw-r--r-- | lib/compound.rb | 8 | ||||
| -rw-r--r-- | lib/dataset.rb | 6 | ||||
| -rw-r--r-- | lib/environment.rb | 95 | ||||
| -rw-r--r-- | lib/model.rb | 8 | ||||
| -rw-r--r-- | lib/opentox-ruby-api-wrapper.rb | 2 | ||||
| -rw-r--r-- | lib/owl.rb | 8 | ||||
| -rw-r--r-- | lib/task.rb | 4 | ||||
| -rw-r--r-- | lib/tasks/opentox.rb | 22 | ||||
| -rw-r--r-- | lib/validation.rb | 2 |
10 files changed, 54 insertions, 115 deletions
diff --git a/lib/algorithm.rb b/lib/algorithm.rb index cc06032..de5902b 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 a293df0..45b96b8 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] diff --git a/lib/dataset.rb b/lib/dataset.rb index af72403..776a55b 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 312eec4..46f8933 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -1,6 +1,6 @@ require 'logger' # set default environment -ENV['RACK_ENV'] = 'test' unless ENV['RACK_ENV'] +ENV['RACK_ENV'] = 'production' unless ENV['RACK_ENV'] # load/setup configuration basedir = File.join(ENV['HOME'], ".opentox") @@ -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 @@ -24,91 +24,30 @@ 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 # load mail settings 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 $sinatra } - -class Sinatra::Base - # overwriting halt to log halts (!= 202) - def halt(*response) - LOGGER.error "halt "+response.first.to_s+" "+(response.size>1 ? response[1].to_s : "") if response and response.first and response.first >= 300 - # orig sinatra code: - response = response.first if response.length == 1 - throw :halt, response - end -end - -# logging -class MyLogger < Logger - - def pwd - path = Dir.pwd.to_s - index = path.rindex(/\//) - return path if index==nil - path[(index+1)..-1] - end - - def trace() - lines = caller(0) - n = 2 - line = lines[n] - - while (line =~ /spork.rb/ or line =~ /as_task/ or line =~ /environment.rb/) - n += 1 - line = lines[n] - end - - index = line.rindex(/\/.*\.rb/) - return line if index==nil - line[index..-1] - end - - def format(msg) - pwd.ljust(18)+" :: "+msg.to_s+" :: "+trace+" :: "+($sinatra ? $sinatra.request.env['REMOTE_ADDR'] : nil).to_s - end - - def debug(msg) - super format(msg) - end - - def info(msg) - super format(msg) - end - - def warn(msg) - super format(msg) - end - - def error(msg) - super format(msg) - end - -end - - logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log" LOGGER = MyLogger.new(logfile,'daily') # daily rotation LOGGER.formatter = Logger::Formatter.new #this is neccessary to restore the formating in case active-record is loaded -if @@config[:logger] and @@config[:logger] == "debug" +if CONFIG[:logger] and CONFIG[:logger] == "debug" LOGGER.level = Logger::DEBUG else LOGGER.level = Logger::WARN @@ -128,18 +67,10 @@ rescue raise "Please edit #{user_file} and restart your application. Create at least one user with password." end -# RDF namespaces -RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' -OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#' -DC = Redland::Namespace.new 'http://purl.org/dc/elements/1.1/' -OT = Redland::Namespace.new 'http://www.opentox.org/api/1.1#' -#OT = Redland::Namespace.new 'http://ortona.informatik.uni-freiburg.de/opentox.owl#' -XML = Redland::Namespace.new 'http://www.w3.org/2001/XMLSchema#' - # Regular expressions for parsing classification data TRUE_REGEXP = /^(true|active|1|1.0)$/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 b6cef46..db9efd4 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 16c23fe..4a6f811 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', 'rest_client_wrapper'].each do |lib| +['owl', 'compound','dataset','algorithm','model','task','validation','utils','authorization','features', 'logger', 'overwrite', 'rest_client_wrapper'].each do |lib| require lib end @@ -1,3 +1,11 @@ +# RDF namespaces +RDF = Redland::Namespace.new 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' +OWL = Redland::Namespace.new 'http://www.w3.org/2002/07/owl#' +DC = Redland::Namespace.new 'http://purl.org/dc/elements/1.1/' +OT = Redland::Namespace.new 'http://www.opentox.org/api/1.1#' +#OT = Redland::Namespace.new 'http://ortona.informatik.uni-freiburg.de/opentox.owl#' +XML = Redland::Namespace.new 'http://www.w3.org/2001/XMLSchema#' + class Redland::Literal def self.create(value, datatype=nil) diff --git a/lib/task.rb b/lib/task.rb index 88bcb71..e1c1cb5 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 7fce35b..6962407 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 bd38488..f1cc987 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] |