add prediction_feature param

7 files changed, 29 insertions, 15 deletions

diff --git a/report/environment.rb b/report/environment.rb
index 6a449b9..cbed3de 100644
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -27,7 +27,9 @@ load "report/external/mimeparse.rb"
 
 load "lib/prediction_util.rb"
 
-LOGGER = Logger.new(STDOUT)
-LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
+unless(defined? LOGGER)
+  LOGGER = Logger.new(STDOUT)
+  LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
+end
 
 
diff --git a/report/report_application.rb b/report/report_application.rb
index 4cba0ae..83250e8 100644
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -2,7 +2,7 @@ load "report/environment.rb"
 
 def perform
   begin
-    $rep = Reports::ReportService.new(url_for("", :full)) unless $rep
+    $rep = Reports::ReportService.new(url_for("/report", :full)) unless $rep
     yield( $rep )
   rescue Reports::NotFound => ex
     halt 404, ex.message
diff --git a/report/report_format.rb b/report/report_format.rb
index 6d3adcd..d58a1f4 100644
--- a/report/report_format.rb
+++ b/report/report_format.rb
@@ -14,7 +14,7 @@ module Reports::ReportFormat
   RF_HTML = "html"
   RF_PDF = "pdf"
   REPORT_FORMATS = [RF_XML, RF_HTML, RF_PDF]
-  CONTENT_TYPES = {"text/xml"=>RF_XML,"text/html"=>RF_HTML,"application/pdf"=>RF_PDF}
+  CONTENT_TYPES = {"*/xml"=>RF_XML,"*/html"=>RF_HTML,"*/pdf"=>RF_PDF}
   
   # returns report-format, according to header value
   def self.get_format(accept_header_value)
diff --git a/report/report_service.rb b/report/report_service.rb
index 2ff5415..364ac85 100644
--- a/report/report_service.rb
+++ b/report/report_service.rb
@@ -48,12 +48,13 @@ module Reports
       check_report_type(type)
       
       #step 0.5: replace cv-uris with list of validation-uris
-      LOGGER.debug "validation uri list '"+uri_list.inspect+"'"
+      raise Reports::BadRequest.new("validation uri_list missing") unless uri_list
+      LOGGER.debug "validation uri_list: '"+uri_list.inspect+"'"
       uri_list = Reports.validation_access.resolve_cv_uris(uri_list)
   
       # step1: load validations
       validation_set = Reports::ValidationSet.new(uri_list)
-      raise Reports::BadRequest.new("no validations found") unless validation_set and validation_set.size > 0
+      raise Reports::BadRequest.new("cannot get validations from uri_list '"+uri_list.inspect+"'") unless validation_set and validation_set.size > 0
       LOGGER.debug "loaded "+validation_set.size.to_s+" validation/s"
       
       #step 2: create report of type
diff --git a/report/report_test.rb b/report/report_test.rb
index 8822568..9ee9ce5 100644
--- a/report/report_test.rb
+++ b/report/report_test.rb
@@ -148,14 +148,15 @@ class Reports::ReportServiceTest < Test::Unit::TestCase
     val_params = { 
         :dataset_uri => data_uri, 
         :algorithm_uri => ws_class_alg, 
-        :split_ratio=>0.9 }
+        :split_ratio=>0.9,
+        :prediction_feature => "classification",}
     val_params[:feature_service_uri] = ws_feat_alg if ws_feat_alg
     RestClient.post WS_VAL+"/validation/training_test_split", val_params
   end
   
   def create_cross_validation(data_uri, ws_class_alg=WS_CLASS_ALG, ws_feat_alg=WS_FEATURE_ALG)
     puts "cross-validating"
-    ext("curl -X POST -d dataset_uri="+data_uri+" -d algorithm_uri="+ws_class_alg+
+    ext("curl -X POST -d dataset_uri="+data_uri+" -d algorithm_uri="+ws_class_alg+" -d prediction_feature=classification"+
         (ws_feat_alg ? " -d feature_service_uri="+ws_feat_alg : "")+
         " "+WS_VAL+"/crossvalidation",nil)
   end
diff --git a/report/validation_access.rb b/report/validation_access.rb
index 5f04472..ed19c14 100644
--- a/report/validation_access.rb
+++ b/report/validation_access.rb
@@ -16,7 +16,7 @@ class Reports::ValidationAccess
     raise "not implemented"
   end
   
-  def get_predictions( test_dataset_uri, prediction_dataset_uri)
+  def get_predictions( prediction_feature, test_dataset_uri, prediction_dataset_uri)
     raise "not implemented"
   end
   
@@ -52,6 +52,10 @@ class Reports::ValidationDB < Reports::ValidationAccess
       validation.send("#{p.to_s}=".to_sym, v[p])
     end
     
+    model = OpenTox::Model::LazarClassificationModel.new(v[:model_uri])
+    raise "cannot access model '"+v[:model_uri].to_s+"'" unless model
+    validation.prediction_feature = model.get_prediction_feature
+    
     {OpenTox::Validation::VAL_CLASS_PROP => OpenTox::Validation::VAL_CLASS_PROPS}.each do |subset_name,subset_props|
       subset = v[subset_name]
       subset_props.each{ |prop| validation.send("#{prop.to_s}=".to_sym, subset[prop]) } if subset
@@ -68,8 +72,8 @@ class Reports::ValidationDB < Reports::ValidationAccess
     end
   end
 
-  def get_predictions( test_dataset_uri, prediction_dataset_uri)
-    Lib::Predictions.new( test_dataset_uri, prediction_dataset_uri)
+  def get_predictions( prediction_feature, test_dataset_uri, prediction_dataset_uri)
+    Lib::Predictions.new( prediction_feature, test_dataset_uri, prediction_dataset_uri)
   end
 end
 
@@ -107,6 +111,10 @@ class Reports::ValidationWebservice < Reports::ValidationAccess
       validation.send("#{p}=".to_sym, data[p])        
     end
     
+    model = OpenTox::Model::LazarClassificationModel.new(v[:model_uri])
+    raise "cannot access model '"+v[:model_uri].to_s+"'" unless model
+    validation.prediction_feature = model.get_prediction_feature
+    
     {OpenTox::Validation::VAL_CV_PROP => OpenTox::Validation::VAL_CV_PROPS,
      OpenTox::Validation::VAL_CLASS_PROP => OpenTox::Validation::VAL_CLASS_PROPS}.each do |subset_name,subset_props|
       subset = data[subset_name]
@@ -130,8 +138,8 @@ class Reports::ValidationWebservice < Reports::ValidationAccess
     end
   end
 
-  def get_predictions( test_dataset_uri, prediction_dataset_uri)
-    Lib::Predictions.new( test_dataset_uri, prediction_dataset_uri)
+  def get_predictions( prediction_feature, test_dataset_uri, prediction_dataset_uri)
+    Lib::Predictions.new( prediction_feature, test_dataset_uri, prediction_dataset_uri)
   end
 end
 
@@ -197,6 +205,8 @@ class Reports::ValidationMockLayer < Reports::ValidationAccess
     validation.training_dataset_uri = @datasets[@count]
     validation.test_dataset_uri = @datasets[@count]
     
+    validation.prediction_feature = "classification"
+    
     @count += 1
   end
   
@@ -212,7 +222,7 @@ class Reports::ValidationMockLayer < Reports::ValidationAccess
     #validation.CV_dataset_name = @datasets[validation.crossvalidation_id.to_i * NUM_FOLDS]
   end
   
-  def get_predictions(test_dataset_uri, prediction_dataset_uri)
+  def get_predictions( prediction_feature, test_dataset_uri, prediction_dataset_uri)
   
     p = Array.new
     c = Array.new
diff --git a/report/validation_data.rb b/report/validation_data.rb
index 46c5e44..eb609c9 100644
--- a/report/validation_data.rb
+++ b/report/validation_data.rb
@@ -71,7 +71,7 @@ module Reports
         LOGGER.info("no predictions available, prediction_dataset_uri not set")
         return nil
       end
-      @predictions = Reports.validation_access.get_predictions( @test_dataset_uri, @prediction_dataset_uri )
+      @predictions = Reports.validation_access.get_predictions( @prediction_feature, @test_dataset_uri, @prediction_dataset_uri )
     end
     
     # loads all crossvalidation attributes, of the corresponding cv into this object