diff options
| -rw-r--r-- | Rakefile | 34 | ||||
| -rw-r--r-- | VERSION | 2 | ||||
| -rwxr-xr-x | bin/opentox-install-ubuntu.sh | 4 | ||||
| -rw-r--r-- | lib/algorithm.rb | 7 | ||||
| -rw-r--r-- | lib/compound.rb | 4 | ||||
| -rw-r--r-- | lib/config/config_ru.rb | 31 | ||||
| -rw-r--r-- | lib/dataset.rb | 145 | ||||
| -rw-r--r-- | lib/environment.rb | 13 | ||||
| -rw-r--r-- | lib/model.rb | 69 | ||||
| -rw-r--r-- | lib/task.rb | 11 | ||||
| -rw-r--r-- | lib/templates/config.yaml | 74 | ||||
| -rw-r--r-- | lib/validation.rb | 12 | ||||
| -rw-r--r-- | opentox-ruby-api-wrapper.gemspec | 73 |
13 files changed, 227 insertions, 252 deletions
@@ -9,13 +9,33 @@ begin gem.description = %Q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)} 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", "datamapper", "sinatra-static-assets"].each do |dep| - gem.add_dependency dep - end - ['cucumber','jeweler', "thin"].each do |dep| - gem.add_development_dependency dep - end + gem.authors = ["Christoph Helma, Martin Guetlein"] + # dependencies + [ "sinatra", + "emk-sinatra-url-for", + "sinatra-respond_to", + "sinatra-static-assets", + "rest-client", + "rack", + "rack-contrib", + "rack-flash", + "nokogiri", + "rubyzip", + "builder", + "roo", + "spreadsheet", + "google-spreadsheet-ruby", + "tmail" + ].each { |dep| gem.add_dependency dep } + [ "dm-core", + 'dm-serializer', + 'dm-timestamps', + 'dm-types', + 'dm-migrations', + "dm-mysql-adapter" + ].each {|dep| gem.add_dependency dep, ">= 1" } + gem.add_dependency "haml", ">=3" + ['cucumber','jeweler'].each { |dep| gem.add_development_dependency dep } gem.files = FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore'] gem.files.include %w(lib/tasks/owl.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/model.rb, lib/utils.rb, lib/validation.rb, lib/templates/*) # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings @@ -1 +1 @@ -1.4.4.4 +1.5.6 diff --git a/bin/opentox-install-ubuntu.sh b/bin/opentox-install-ubuntu.sh index 75faff7..ae4807d 100755 --- a/bin/opentox-install-ubuntu.sh +++ b/bin/opentox-install-ubuntu.sh @@ -90,9 +90,9 @@ sudo apt-get install postgresql-server-dev-8.4 | tee -a $INSTALLLOG #echo "Installing gems jeweler sinatra emk-sinatra-url-for dm-core cehoffman-sinatra-respond_to rest-client rack-contrib thin cucumber datamapper data_objects do_sqlite3 rinruby" sudo gem install jeweler | tee -a $INSTALLLOG sudo gem install sinatra | tee -a $INSTALLLOG -sudo gem install emk-sinatra-url-for -s http://gems.github.com | tee -a $INSTALLLOG +sudo gem install emk-sinatra-url-for -s http://gems.github.com | tee -a $INSTALLLOG sudo gem install dm-core | tee -a $INSTALLLOG -sudo gem install cehoffman-sinatra-respond_to -s http://gems.github.com | tee -a $INSTALLLOG +sudo gem install sinatra-respond_to | tee -a $INSTALLLOG sudo gem install rest-client | tee -a $INSTALLLOG sudo gem install rack-contrib | tee -a $INSTALLLOG sudo gem install thin | tee -a $INSTALLLOG diff --git a/lib/algorithm.rb b/lib/algorithm.rb index 7a25408..cc06032 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -21,8 +21,11 @@ module OpenTox def self.create_model(params) LOGGER.debug params LOGGER.debug File.basename(__FILE__) + ": creating model" - 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") - @uri = resource.post(:dataset_uri => params[:dataset_uri], :feature_uri => params[:feature_uri], :feature_generation_uri => File.join(@@config[:services]["opentox-algorithm"], "fminer")).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 diff --git a/lib/compound.rb b/lib/compound.rb index cc29fc5..6ab78e0 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -18,7 +18,9 @@ module OpenTox @uri = File.join(@@config[:services]["opentox-compound"],URI.escape(@inchi)) elsif params[:name] # paranoid URI encoding to keep SMILES charges and brackets - @inchi = RestClientWrapper.get("#{@@cactus_uri}#{URI.encode(params[:name], Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))}/stdinchi").chomp + @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)) elsif params[:uri] @uri = params[:uri] diff --git a/lib/config/config_ru.rb b/lib/config/config_ru.rb index 1d32c7e..3d8dce2 100644 --- a/lib/config/config_ru.rb +++ b/lib/config/config_ru.rb @@ -18,3 +18,34 @@ set :raise_errors, true end use Rack::ShowExceptions +if defined?(MAIL) + + # monkeypatch with the original method + # strangely enough my mailserver returns "Connection refused - connect(2)" errors without this patch + module Rack + class MailExceptions + + def send_notification(exception, env) + mail = generate_mail(exception, env) + smtp = config[:smtp] + env['mail.sent'] = true + return if smtp[:server] == 'example.com' + + Net::SMTP.start smtp[:server], smtp[:port], smtp[:domain], smtp[:user_name], smtp[:password], smtp[:authentication] do |server| + mail.to.each do |recipient| + server.send_message mail.to_s, mail.from, recipient + end + end + end + end + end + + + require "socket" + use Rack::MailExceptions do |mail| + mail.to MAIL[:user_name] + mail.subject '[ERROR] %s' + mail.from "#{Socket.gethostname}@#{MAIL[:domain]}" + mail.smtp MAIL + end +end diff --git a/lib/dataset.rb b/lib/dataset.rb index e506305..1254992 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -15,15 +15,16 @@ 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 =~ /in-silico.ch/ - 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") @@ -90,15 +91,16 @@ module OpenTox else return "no classification key" end - else - raise "predicted class value is not a hash\n"+ + elsif v.is_a?(Array) + raise "predicted class value is an array\n"+ "value "+v.to_s+"\n"+ "value-class "+v.class.to_s+"\n"+ "dataset "+@uri.to_s+"\n"+ "compound "+compound.to_s+"\n"+ "feature "+feature.to_s+"\n" + else + return v end - end # returns prediction confidence if available @@ -112,12 +114,14 @@ module OpenTox raise "no confidence key" end else - raise "prediction confidence value is not a hash value\n"+ - "value "+v.to_s+"\n"+ - "value-class "+v.class.to_s+"\n"+ - "dataset "+@uri.to_s+"\n"+ - "compound "+compound.to_s+"\n"+ - "feature "+feature.to_s+"\n" + LOGGER.warn "no confidence for compound: "+compound.to_s+", feature: "+feature.to_s + return 1 +# raise "prediction confidence value is not a hash value\n"+ +# "value "+v.to_s+"\n"+ +# "value-class "+v.class.to_s+"\n"+ +# "dataset "+@uri.to_s+"\n"+ +# "compound "+compound.to_s+"\n"+ +# "feature "+feature.to_s+"\n" end end @@ -172,122 +176,9 @@ module OpenTox @features.uniq! @compounds.uniq! - OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type => "text/x-yaml"},self.to_yaml).strip.to_s - 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 + OpenTox::RestClientWrapper.post(@@config[:services]["opentox-dataset"],{:content_type => "application/x-yaml"},self.to_yaml).strip end -=end - def init_dirty_features(owl) @dirty_features = @features @owl = owl diff --git a/lib/environment.rb b/lib/environment.rb index d24c37d..b53167b 100644 --- a/lib/environment.rb +++ b/lib/environment.rb @@ -25,8 +25,7 @@ end # database if @@config[:database] - #['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types'].each{|lib| require lib } - ['rubygems', 'datamapper'].each{|lib| require lib } + ['dm-core', 'dm-serializer', 'dm-timestamps', 'dm-types', 'dm-migrations' ].each{|lib| require lib } case @@config[:database][:adapter] when /sqlite/i db_dir = File.join(basedir, "db") @@ -42,13 +41,16 @@ if @@config[:database] end end +# 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 } 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.first >= 300 + 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 @@ -105,6 +107,7 @@ end logfile = "#{LOG_DIR}/#{ENV["RACK_ENV"]}.log" LOGGER = MyLogger.new(logfile,'daily') # daily rotation +LOGGER.level = Logger::WARN if ENV["RACK_ENV"] == 'production' #LOGGER = MyLogger.new(STDOUT) #LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S " @@ -136,3 +139,7 @@ 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 3553919..e3ddeb0 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -96,79 +96,12 @@ 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 60c1159..88bcb71 100644 --- a/lib/task.rb +++ b/lib/task.rb @@ -1,8 +1,5 @@ LOGGER.progname = File.expand_path(__FILE__) -DEFAULT_TASK_MAX_DURATION = 10*60*60 -EXTERNAL_TASK_MAX_DURATION = 10*60*60 - $self_task=nil module OpenTox @@ -40,18 +37,14 @@ module OpenTox end def reload - if uri=~ /188.40.32.88/ || uri=~/in-silico.ch/ - result = RestClientWrapper.get(uri, {:accept => 'text/x-yaml'}, false) - else - result = RestClientWrapper.get(uri, {:accept => 'application/rdf+xml'}, false) - end + 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..3b97983 100644 --- a/lib/templates/config.yaml +++ b/lib/templates/config.yaml @@ -1,20 +1,68 @@ # Example configuration for OpenTox, please adjust to your settings # +# Database setup: +# +# Example MySql: +# + :database: + :adapter: mysql + :database: production + :username: root + :password: opentox + :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 -# :webserver: thin -# :services: -# opentox-compound: "http://localhost:4000/" -# opentox-dataset: "http://localhost:4001/" -# opentox-algorithm: "http://localhost:4002/" -# opentox-model: "http://localhost:4003/" -# opentox-task: "http://localhost:4004/" + :base_dir: /home/ist/webservices + :webserver: passenger + :services: + opentox-compound: "http://localhost/compound/" + opentox-dataset: "http://localhost/dataset/" + opentox-algorithm: "http://localhost/algorithm/" + opentox-model: "http://localhost/model/" + opentox-task: "http://localhost/task/" + 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 diff --git a/lib/validation.rb b/lib/validation.rb index 6fd5704..bd38488 100644 --- a/lib/validation.rb +++ b/lib/validation.rb @@ -4,8 +4,16 @@ module OpenTox attr_accessor :uri def initialize(params) - resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]) - @uri = resource.post(params).to_s + #resource = RestClient::Resource.new(params[:uri], :user => @@users[:users].keys[0], :password => @@users[:users].values[0]) + #@uri = resource.post(params).body + #LOGGER.debug "VALIDATION URI: " + @uri.to_s + call = "curl -X POST " + params.each do |k,v| + call += " -d "+k.to_s+"=\""+URI.encode(v.to_s)+"\"" unless k == :uri + end + call += " "+params[:uri] + LOGGER.debug call + @uri = `#{call}` end def self.crossvalidation(params) diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec index 18dc1df..d158479 100644 --- a/opentox-ruby-api-wrapper.gemspec +++ b/opentox-ruby-api-wrapper.gemspec @@ -5,11 +5,11 @@ Gem::Specification.new do |s| s.name = %q{opentox-ruby-api-wrapper} - s.version = "1.4.4.4" + s.version = "1.5.6" s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= - s.authors = ["Christoph Helma"] - s.date = %q{2010-05-28} + s.authors = ["Christoph Helma, Martin Guetlein"] + s.date = %q{2010-06-25} s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)} s.email = %q{helma@in-silico.ch} s.executables = ["yaml2owl.rb", "opentox-install-ubuntu.sh", "opentox-install-debian.sh"] @@ -49,50 +49,89 @@ Gem::Specification.new do |s| s.homepage = %q{http://github.com/helma/opentox-ruby-api-wrapper} s.rdoc_options = ["--charset=UTF-8"] s.require_paths = ["lib"] - s.rubygems_version = %q{1.3.5} + s.rubygems_version = %q{1.3.7} s.summary = %q{Ruby wrapper for the OpenTox REST API} if s.respond_to? :specification_version then current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION s.specification_version = 3 - if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then + if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then s.add_runtime_dependency(%q<sinatra>, [">= 0"]) + s.add_runtime_dependency(%q<emk-sinatra-url-for>, [">= 0"]) + s.add_runtime_dependency(%q<sinatra-respond_to>, [">= 0"]) + s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"]) s.add_runtime_dependency(%q<rest-client>, [">= 0"]) s.add_runtime_dependency(%q<rack>, [">= 0"]) s.add_runtime_dependency(%q<rack-contrib>, [">= 0"]) s.add_runtime_dependency(%q<rack-flash>, [">= 0"]) - s.add_runtime_dependency(%q<emk-sinatra-url-for>, [">= 0"]) - s.add_runtime_dependency(%q<datamapper>, [">= 0"]) - s.add_runtime_dependency(%q<sinatra-static-assets>, [">= 0"]) + s.add_runtime_dependency(%q<nokogiri>, [">= 0"]) + s.add_runtime_dependency(%q<rubyzip>, [">= 0"]) + s.add_runtime_dependency(%q<builder>, [">= 0"]) + s.add_runtime_dependency(%q<roo>, [">= 0"]) + s.add_runtime_dependency(%q<spreadsheet>, [">= 0"]) + s.add_runtime_dependency(%q<google-spreadsheet-ruby>, [">= 0"]) + s.add_runtime_dependency(%q<tmail>, [">= 0"]) + s.add_runtime_dependency(%q<dm-core>, [">= 1"]) + s.add_runtime_dependency(%q<dm-serializer>, [">= 1"]) + s.add_runtime_dependency(%q<dm-timestamps>, [">= 1"]) + s.add_runtime_dependency(%q<dm-types>, [">= 1"]) + s.add_runtime_dependency(%q<dm-migrations>, [">= 1"]) + s.add_runtime_dependency(%q<dm-mysql-adapter>, [">= 1"]) + s.add_runtime_dependency(%q<haml>, [">= 3"]) s.add_development_dependency(%q<cucumber>, [">= 0"]) s.add_development_dependency(%q<jeweler>, [">= 0"]) - s.add_development_dependency(%q<thin>, [">= 0"]) else s.add_dependency(%q<sinatra>, [">= 0"]) + s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"]) + s.add_dependency(%q<sinatra-respond_to>, [">= 0"]) + s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) s.add_dependency(%q<rest-client>, [">= 0"]) s.add_dependency(%q<rack>, [">= 0"]) s.add_dependency(%q<rack-contrib>, [">= 0"]) s.add_dependency(%q<rack-flash>, [">= 0"]) - s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"]) - s.add_dependency(%q<datamapper>, [">= 0"]) - s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) + s.add_dependency(%q<nokogiri>, [">= 0"]) + s.add_dependency(%q<rubyzip>, [">= 0"]) + s.add_dependency(%q<builder>, [">= 0"]) + s.add_dependency(%q<roo>, [">= 0"]) + s.add_dependency(%q<spreadsheet>, [">= 0"]) + s.add_dependency(%q<google-spreadsheet-ruby>, [">= 0"]) + s.add_dependency(%q<tmail>, [">= 0"]) + s.add_dependency(%q<dm-core>, [">= 1"]) + s.add_dependency(%q<dm-serializer>, [">= 1"]) + s.add_dependency(%q<dm-timestamps>, [">= 1"]) + s.add_dependency(%q<dm-types>, [">= 1"]) + s.add_dependency(%q<dm-migrations>, [">= 1"]) + s.add_dependency(%q<dm-mysql-adapter>, [">= 1"]) + s.add_dependency(%q<haml>, [">= 3"]) s.add_dependency(%q<cucumber>, [">= 0"]) s.add_dependency(%q<jeweler>, [">= 0"]) - s.add_dependency(%q<thin>, [">= 0"]) end else s.add_dependency(%q<sinatra>, [">= 0"]) + s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"]) + s.add_dependency(%q<sinatra-respond_to>, [">= 0"]) + s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) s.add_dependency(%q<rest-client>, [">= 0"]) s.add_dependency(%q<rack>, [">= 0"]) s.add_dependency(%q<rack-contrib>, [">= 0"]) s.add_dependency(%q<rack-flash>, [">= 0"]) - s.add_dependency(%q<emk-sinatra-url-for>, [">= 0"]) - s.add_dependency(%q<datamapper>, [">= 0"]) - s.add_dependency(%q<sinatra-static-assets>, [">= 0"]) + s.add_dependency(%q<nokogiri>, [">= 0"]) + s.add_dependency(%q<rubyzip>, [">= 0"]) + s.add_dependency(%q<builder>, [">= 0"]) + s.add_dependency(%q<roo>, [">= 0"]) + s.add_dependency(%q<spreadsheet>, [">= 0"]) + s.add_dependency(%q<google-spreadsheet-ruby>, [">= 0"]) + s.add_dependency(%q<tmail>, [">= 0"]) + s.add_dependency(%q<dm-core>, [">= 1"]) + s.add_dependency(%q<dm-serializer>, [">= 1"]) + s.add_dependency(%q<dm-timestamps>, [">= 1"]) + s.add_dependency(%q<dm-types>, [">= 1"]) + s.add_dependency(%q<dm-migrations>, [">= 1"]) + s.add_dependency(%q<dm-mysql-adapter>, [">= 1"]) + s.add_dependency(%q<haml>, [">= 3"]) s.add_dependency(%q<cucumber>, [">= 0"]) s.add_dependency(%q<jeweler>, [">= 0"]) - s.add_dependency(%q<thin>, [">= 0"]) end end |