Merge remote branch 'mguetlein/development' into development

4 files changed, 15 insertions, 19 deletions

diff --git a/.gitignore b/.gitignore
index a3ee470..e3debba 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 tmp/*
 log/*
 public/*.owl
+*.*~
diff --git a/config.ru b/config.ru
index 67d8493..a1aab0d 100644
--- a/config.ru
+++ b/config.ru
@@ -2,3 +2,5 @@ require 'rubygems'
 require 'opentox-ruby'
 require 'config/config_ru'
 run Sinatra::Application
+set :raise_errors, false
+set :show_exceptions, false
\ No newline at end of file
diff --git a/fminer.rb b/fminer.rb
index 2d0cbb0..5cc83ed 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -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'
diff --git a/lazar.rb b/lazar.rb
index 2a9455a..c8cf6ea 100644
--- a/lazar.rb
+++ b/lazar.rb
@@ -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