merged reports into this rep

1 files changed, 230 insertions, 0 deletions

diff --git a/report/validation_access.rb b/report/validation_access.rb
new file mode 100644
index 0000000..b89599c
--- /dev/null
+++ b/report/validation_access.rb
@@ -0,0 +1,230 @@
+
+load "lib/validation_db.rb"
+
+# = Reports::ValidationAccess
+# 
+# service that connects to the validation-service
+#  
+class Reports::ValidationAccess
+
+  # initialize validation object with 
+  def init_validation(validation, uri)
+    raise "not implemented"
+  end
+  
+  def init_cv(validation)
+    raise "not implemented"
+  end
+  
+  def get_predictions( test_dataset_uri, prediction_dataset_uri)
+    raise "not implemented"
+  end
+  
+  def resolve_cv_uris(uri_list)
+    raise "not implemented"
+  end
+end
+
+class Reports::ValidationDB < Reports::ValidationAccess
+  
+  def resolve_cv_uris(uri_list)
+    res = []
+    uri_list.each do |u|
+      if u.to_s =~ /.*\/crossvalidation\/[0-9]+/
+        cv_id = u.split("/")[-1].to_i
+        res += Lib::Validation.all(:crossvalidation_id => cv_id).collect{|v| v.uri.to_s}
+      else
+        res += [u.to_s]
+      end
+    end
+    res
+  end
+  
+  
+  def init_validation(validation, uri)
+  
+    raise Reports::BadRequest.new "not a validation uri: "+uri.to_s unless uri =~ /.*\/validation\/[0-9]+/
+    validation_id = uri.split("/")[-1]
+    v = Lib::Validation.get(validation_id)
+    raise Reports::BadRequest.new "no validation found with id "+validation_id.to_s unless v
+    
+    (OpenTox::Validation::VAL_PROPS + OpenTox::Validation::VAL_CV_PROPS).each do |p|
+      validation.send("#{p.to_s}=".to_sym, v.send("#{p.to_s}"))        
+    end
+    
+    {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
+    end
+  end
+    
+  def init_cv(validation)
+    
+    cv = Lib::Crossvalidation.get(validation.crossvalidation_id)
+    raise Reports::BadRequest.new "no crossvalidation found with id "+validation.crossvalidation_id.to_s unless cv
+    
+    OpenTox::Validation::CROSS_VAL_PROPS.each do |p|
+      validation.send("#{p.to_s}=".to_sym, cv["#{p.to_s}".to_sym])        
+    end
+  end
+
+  def get_predictions( test_dataset_uri, prediction_dataset_uri)
+    Lib::Predictions.new( test_dataset_uri, prediction_dataset_uri)
+  end
+end
+
+
+class Reports::ValidationWebservice < Reports::ValidationAccess
+  
+  def resolve_cv_uris(uri_list)
+    res = []
+    uri_list.each do |u|
+      if u.to_s =~ /.*\/crossvalidation\/.*/
+        uri = u.to_s+"/validations"
+        begin
+          vali_uri_list = RestClient.get uri
+        rescue => ex
+          raise Reports::BadRequest.new "cannot get validations for cv at '"+uri.to_s+"', error msg: "+ex.message
+        end
+        res += vali_uri_list.split("\n")
+      else
+        res += [u.to_s]
+      end
+    end
+    res
+  end
+  
+  
+  def init_validation(validation, uri)
+  
+    begin
+      data = YAML.load(RestClient.get uri)
+    rescue => ex
+      raise Reports::BadRequest.new "cannot get validation at '"+uri.to_s+"', error msg: "+ex.message
+    end
+  
+    OpenTox::Validation::VAL_PROPS.each do |p|
+      validation.send("#{p.to_s}=".to_sym, data[p])        
+    end
+    
+    {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]
+      subset_props.each{ |prop| validation.send("#{prop.to_s}=".to_sym, subset[prop]) } if subset
+    end
+  end
+    
+  def init_cv(validation)
+    
+    raise "cv-id not set" unless validation.crossvalidation_id
+    
+    cv_uri = validation.uri.split("/")[0..-3].join("/")+"/crossvalidation/"+validation.crossvalidation_id.to_s
+    begin
+      data = YAML.load(RestClient.get cv_uri)
+    rescue => ex
+      raise Reports::BadRequest.new "cannot get crossvalidation at '"+cv_uri.to_s+"', error msg: "+ex.message
+    end
+    
+    OpenTox::Validation::CROSS_VAL_PROPS.each do |p|
+      validation.send("#{p.to_s}=".to_sym, data["#{p.to_s}".to_sym])        
+    end
+  end
+
+  def get_predictions( test_dataset_uri, prediction_dataset_uri)
+    Lib::Predictions.new( test_dataset_uri, prediction_dataset_uri)
+  end
+end
+
+# = Reports::OTMockLayer
+#
+# does not connect to other services, provides randomly generated data
+#
+class Reports::ValidationMockLayer < Reports::ValidationAccess
+  
+  NUM_DATASETS = 1
+  NUM_ALGS = 4
+  NUM_FOLDS = 5
+  NUM_PREDICTIONS = 30
+  ALGS = ["naive-bayes", "c4.5", "svm", "knn", "lazar", "id3"]
+  DATASETS = ["hamster", "mouse" , "rat", "dog", "cat", "horse", "bug", "ant", "butterfly", "rabbit", "donkey", "monkey", "dragonfly", "frog", "dragon", "dinosaur"]
+  FOLDS = [1,2,3,4,5,6,7,8,9,10]
+  
+  def initialize
+    
+    super
+    @algs = []
+    @datasets = []
+    @folds = []
+    sum = NUM_DATASETS*NUM_ALGS*NUM_FOLDS
+    (0..sum-1).each do |i|
+      @folds[i] = FOLDS[i%NUM_FOLDS]
+      @algs[i] = ALGS[(i/NUM_FOLDS)%NUM_ALGS]
+      @datasets[i] = DATASETS[((i/NUM_FOLDS)/NUM_ALGS)%NUM_DATASETS]
+    end
+    @count = 0
+  end
+  
+  def resolve_cv_uris(uri_list)
+    res = []
+    uri_list.each do |u|
+      if u.to_s =~ /.*crossvalidation.*/
+        res += ["validation_x"]*NUM_FOLDS
+      else
+        res += [u.to_s]
+      end
+    end
+    res
+  end
+  
+  def init_validation(validation, uri)
+    
+    validation.model_uri = @algs[@count]
+    validation.test_dataset_uri = @datasets[@count]
+    validation.prediction_dataset_uri = "bla"
+    
+    cv_id = @count/NUM_FOLDS
+    validation.crossvalidation_id = cv_id
+    validation.crossvalidation_fold = @folds[@count]
+    
+    validation.auc = 0.5 + cv_id*0.02 + rand/3.0
+    validation.acc = 0.5 + cv_id*0.02 + rand/3.0
+    validation.tp = 1
+    validation.fp = 1
+    validation.tn = 1
+    validation.fn = 1
+    
+    validation.algorithm_uri = @algs[@count]
+    validation.training_dataset_uri = @datasets[@count]
+    validation.test_dataset_uri = @datasets[@count]
+    
+    @count += 1
+  end
+  
+  def init_cv(validation)
+    
+    raise "cv-id not set" unless validation.crossvalidation_id
+      
+    validation.num_folds = NUM_FOLDS
+    validation.algorithm_uri = @algs[validation.crossvalidation_id.to_i * NUM_FOLDS]
+    validation.dataset_uri = @datasets[validation.crossvalidation_id.to_i * NUM_FOLDS]
+    validation.stratified = true
+    validation.random_seed = 1
+    #validation.CV_dataset_name = @datasets[validation.crossvalidation_id.to_i * NUM_FOLDS]
+  end
+  
+  def get_predictions(test_dataset_uri, prediction_dataset_uri)
+  
+    p = Array.new
+    c = Array.new
+    conf = Array.new
+    u = Array.new
+    (0..NUM_PREDICTIONS).each do |i|
+      p.push rand(2)
+      c.push rand(2)
+      conf.push rand
+      u.push("compound no"+(i+1).to_s)
+    end
+    Lib::MockPredictions.new( p, c, conf, u )
+  end
+
+ end