diff options
Diffstat (limited to 'lib/opentox-ruby-api-wrapper.rb')
| -rw-r--r-- | lib/opentox-ruby-api-wrapper.rb | 31 |
1 files changed, 16 insertions, 15 deletions
diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb index 4ee6fd3..d74b412 100644 --- a/lib/opentox-ruby-api-wrapper.rb +++ b/lib/opentox-ruby-api-wrapper.rb @@ -1,4 +1,4 @@ -['rubygems', 'rest_client', 'spork', 'environment'].each do |lib| +['rubygems', 'sinatra', 'sinatra/respond_to', 'sinatra/url_for', 'builder', 'rest_client', 'yaml', 'spork', 'environment'].each do |lib| require lib end @@ -9,12 +9,8 @@ module OpenTox # Escape all nonword characters def uri_escape(string) - URI.escape(string, /[^\w]/) - end - - # Returns true if object creation has finished (for asynchronous processes) - def finished? - YAML.load(RestClient.get(@uri))[:finished] + #URI.escape(string, /[^\w]/) + URI.escape(string, /[^#{URI::PATTERN::UNRESERVED}]/) end # Get the object name @@ -36,9 +32,9 @@ module OpenTox if params[:uri] @uri = params[:uri].to_s elsif params[:smiles] - @uri = RestClient.post @services['opentox-compound'] ,:smiles => uri_escape(params[:smiles]) + @uri = RestClient.post @@config[:services]["opentox-compound"] ,:smiles => uri_escape(params[:smiles]) elsif params[:name] - @uri = RestClient.post @services['opentox-compound'] ,:name => uri_escape(params[:name]) + @uri = RestClient.post @@config[:services]["opentox-compound"] ,:name => uri_escape(params[:name]) end end @@ -47,6 +43,11 @@ module OpenTox RestClient.get @uri end + # Get the unique id (URI encoded canonical smiles) + def uid + RestClient.get @uri + '.uid' + end + # Matchs a smarts string def match?(smarts) if RestClient.get(@uri + '/match/' + uri_escape(smarts)) == 'true' @@ -70,7 +71,7 @@ module OpenTox if params[:uri] @uri = params[:uri].to_s else - @uri = @services['opentox-feature']+ uri_escape(params[:name]) + @uri = @@config[:services]["opentox-feature"] + uri_escape(params[:name]) params[:values].each do |k,v| @uri += '/' + k.to_s + '/' + v.to_s end @@ -91,9 +92,9 @@ module OpenTox if params[:uri] @uri = params[:uri].to_s elsif params[:name] and params[:filename] - @uri = `curl -X POST -F file=@#{params[:filename]} -F name="#{params[:name]}" #{@services['opentox-dataset']}` + @uri = `curl -X POST -F file=@#{params[:filename]} -F name="#{params[:name]}" #{@@config[:services]["opentox-dataset"]}` elsif params[:name] - @uri = RestClient.post @services['opentox-dataset'], :name => params[:name] + @uri = RestClient.post @@config[:services]["opentox-dataset"], :name => params[:name] end end @@ -104,7 +105,7 @@ module OpenTox # Get all compounds and features from a dataset, returns a hash with compound_uris as keys and arrays of feature_uris as values def all_compounds_and_features_uris - YAML.load(RestClient.get(@uri + '/compounds/features')) + YAML.load(RestClient.get(@uri + '/compounds/features.yaml')) end # Get all features from a dataset @@ -133,7 +134,7 @@ module OpenTox # Create a new dataset with BBRC features def initialize(training_dataset) - @dataset_uri = RestClient.post @services['opentox-fminer'], :dataset_uri => training_dataset.uri + @dataset_uri = RestClient.post @@config[:services]["opentox-fminer"], :dataset_uri => training_dataset.uri end def dataset @@ -149,7 +150,7 @@ module OpenTox if params[:uri] @uri = params[:uri] elsif params[:dataset_uri] - @uri = RestClient.post @services['opentox-lazar']+ 'models' , :dataset_uri => params[:dataset_uri] + @uri = RestClient.post @@config[:services]["opentox-lazar"] + 'models' , :dataset_uri => params[:dataset_uri] end end |