diff options
author | mguetlein <martin.guetlein@gmail.com> | 2011-01-25 17:00:17 +0100 |
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committer | mguetlein <martin.guetlein@gmail.com> | 2011-01-25 17:00:17 +0100 |
commit | 255f70b3bda4997b37ef3139c527ea9f481665bd (patch) | |
tree | 9c00a5ca761b1984de731c4ed4a6cba4060a08b2 | |
parent | 20d132d6d960f93558ce6e61f6cef8581f4a5e1c (diff) |
merged (BY HAND) michas GET authorization
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | fminer.rb | 23 | ||||
-rw-r--r-- | lazar.rb | 8 |
3 files changed, 13 insertions, 19 deletions
@@ -1,3 +1,4 @@ tmp/* log/* public/*.owl +*.*~ @@ -66,7 +66,7 @@ end # - min_chisq_significance Significance threshold (between 0 and 1) # @return [text/uri-list] Task URI post '/fminer/bbrc/?' do - + # TODO: is this thread safe?? #@@bbrc = Bbrc::Bbrc.new minfreq = 5 unless minfreq = params[:min_frequency] @@ -80,12 +80,12 @@ post '/fminer/bbrc/?' do halt 404, "Please submit a prediction_feature." unless params[:prediction_feature] and !params[:prediction_feature].nil? prediction_feature = params[:prediction_feature] - training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}" + training_dataset = OpenTox::Dataset.find "#{params[:dataset_uri]}", @subjectid halt 404, "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}" unless training_dataset.features and training_dataset.features.include?(params[:prediction_feature]) task = OpenTox::Task.create("Mining BBRC features", url_for('/fminer',:full)) do - feature_dataset = OpenTox::Dataset.new + feature_dataset = OpenTox::Dataset.new(nil, @subjectid) feature_dataset.add_metadata({ DC.title => "BBRC representatives for " + training_dataset.metadata[DC.title].to_s, DC.creator => url_for('/fminer/bbrc',:full), @@ -95,9 +95,7 @@ post '/fminer/bbrc/?' do { DC.title => "prediction_feature", OT.paramValue => params[:prediction_feature] } ] }) - subjectid = params[:subjectid] if params[:subjectid] - subjectid = CGI.unescape(request.env["HTTP_SUBJECTID"]) if !subjectid and request.env["HTTP_SUBJECTID"] - feature_dataset.save(subjectid) + feature_dataset.save(@subjectid) id = 1 # fminer start id is not 0 compounds = [] @@ -204,7 +202,7 @@ post '/fminer/bbrc/?' do ids.each { |id| feature_dataset.add(compounds[id], feature_uri, true)} end end - feature_dataset.save(subjectid) + feature_dataset.save(@subjectid) feature_dataset.uri end response['Content-Type'] = 'text/uri-list' @@ -223,7 +221,6 @@ post '/fminer/bbrc/?' do # - hops Maximum number of hops # @return [text/uri-list] Task URI post '/fminer/last/?' do - #@@last = Last::Last.new minfreq = 5 unless minfreq = params[:min_frequency] @@last.SetMinfreq(minfreq) @@ -235,9 +232,9 @@ post '/fminer/last/?' do halt 404, "Please submit a prediction_feature." unless params[:prediction_feature] and !params[:prediction_feature].nil? prediction_feature = params[:prediction_feature] - training_dataset = OpenTox::Dataset.new "#{params[:dataset_uri]}" + training_dataset = OpenTox::Dataset.new "#{params[:dataset_uri]}", @subjectid - training_dataset.load_all + training_dataset.load_all(@subjectid) halt 404, "No feature #{params[:prediction_feature]} in dataset #{params[:dataset_uri]}" unless training_dataset.features and training_dataset.features.include?(params[:prediction_feature]) task = OpenTox::Task.create("Mining LAST features", url_for('/fminer',:full)) do @@ -252,9 +249,7 @@ post '/fminer/last/?' do { DC.title => "prediction_feature", OT.paramValue => params[:prediction_feature] } ] }) - subjectid = params[:subjectid] if params[:subjectid] - subjectid = CGI.unescape(request.env["HTTP_SUBJECTID"]) if !subjectid and request.env["HTTP_SUBJECTID"] - feature_dataset.save(subjectid) + feature_dataset.save(@subjectid) id = 1 # fminer start id is not 0 compounds = [] @@ -350,7 +345,7 @@ post '/fminer/last/?' do end ids.each { |id| feature_dataset.add(compounds[id], feature_uri, true)} end - feature_dataset.save(subjectid) + feature_dataset.save(@subjectid) feature_dataset.uri end response['Content-Type'] = 'text/uri-list' @@ -33,7 +33,7 @@ post '/lazar/?' do dataset_uri = params[:dataset_uri] halt 404, "Dataset #{dataset_uri} not found." unless training_activities = OpenTox::Dataset.new(dataset_uri) - training_activities.load_all + training_activities.load_all(@subjectid) prediction_feature = params[:prediction_feature] unless prediction_feature # try to read prediction_feature from dataset @@ -50,8 +50,6 @@ post '/lazar/?' do task = OpenTox::Task.create("Create lazar model",url_for('/lazar',:full)) do |task| lazar = OpenTox::Model::Lazar.new - subjectid = params[:subjectid] if params[:subjectid] - subjectid = request.env["HTTP_SUBJECTID"] if !subjectid and request.env["HTTP_SUBJECTID"] lazar.min_sim = params[:min_sim] if params[:min_sim] if params[:feature_dataset_uri] @@ -74,7 +72,7 @@ post '/lazar/?' do training_features = OpenTox::Dataset.new(feature_dataset_uri) end - training_features.load_all + training_features.load_all(@subjectid) halt 404, "Dataset #{feature_dataset_uri} not found." if training_features.nil? # sorted features for index lookups @@ -140,7 +138,7 @@ post '/lazar/?' do {DC.title => "feature_generation_uri", OT.paramValue => feature_generation_uri} ] - model_uri = lazar.save(subjectid) + model_uri = lazar.save(@subjectid) LOGGER.info model_uri + " created #{Time.now}" model_uri end |