diff options
Diffstat (limited to 'lib/dataset.rb')
| -rw-r--r-- | lib/dataset.rb | 54 |
1 files changed, 33 insertions, 21 deletions
diff --git a/lib/dataset.rb b/lib/dataset.rb index ca82f11..f6d0dd7 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -4,7 +4,7 @@ module OpenTox # set: dataset uris # key: /dataset/:dataset/compounds # set: compound uris - # key: /dataset/:dataset/compound/:inchi/:feature_type + # key: /dataset/:dataset/compound/:inchi # set: feature uris class Dataset < OpenTox @@ -19,31 +19,32 @@ module OpenTox end def self.find(params) - if params[:name] - uri = RestClient.get File.join(@@config[:services]["opentox-dataset"], params[:name]) - elsif params[:uri] - uri = params[:uri] - end - if RestClient.get uri - Dataset.new(uri) - else + begin + if params[:name] + uri = File.join(@@config[:services]["opentox-dataset"], URI.encode(params[:name])) + elsif params[:uri] + uri = params[:uri] + end + RestClient.get uri # check if the resource is available + Dataset.new(uri) if uri + rescue nil end end + def self.find_or_create(params) + self.create(params) unless self.find(params) + end + def import(params) if params[:csv] # RestClient seems not to work for file uploads - `curl -X POST -F "file=@#{params[:csv]};type=text/csv" -F compound_format=#{params[:compound_format]} -F feature_type=#{params[:feature_type]} #{@uri + '/import'}` + `curl -X POST -F "file=@#{params[:csv]};type=text/csv" -F compound_format=#{params[:compound_format]} #{@uri + '/import'}` end end - def add_features(features,feature_type) - #puts @uri - #puts feature_type - #puts features.to_yaml - HTTPClient.post @uri, {:feature_type => feature_type, :features => features.to_yaml} - #`curl -X POST -F feature_type="#{feature_type}" -F features="#{features.to_yaml}" #{@uri}` + def add(features) + HTTPClient.post @uri, {:features => features.to_yaml} end # Get all compounds from a dataset @@ -56,14 +57,17 @@ module OpenTox end # Get all features for a compound - def feature_uris(compound,feature_type) - #puts File.join(@uri, 'compound', compound.inchi, feature_type) - RestClient.get(File.join(@uri, 'compound', compound.inchi, feature_type)).split("\n") + def feature_uris(compound) + RestClient.get(File.join(@uri, 'compound', compound.inchi)).split("\n") end # Get all features for a compound - def features(compound,feature_type) - feature_uris(compound,feature_type).collect{|uri| Feature.new(:uri => uri)} + def features(compound) + feature_uris(compound).collect{|uri| Feature.new(:uri => uri)} + end + + def all_features + RestClient.get(File.join(@uri, 'features')).split("\n") end # Delete a dataset @@ -71,6 +75,14 @@ module OpenTox RestClient.delete @uri end + def tanimoto(dataset) + RestClient.get(File.join(@uri,'tanimoto',dataset.path)) + end + + def weighted_tanimoto(dataset) + RestClient.get(File.join(@uri,'weighted_tanimoto',dataset.path)) + end + end end |