fix search via param functionality for validation, add corresponding unit-tests

5 files changed, 97 insertions, 30 deletions

diff --git a/lib/ohm_util.rb b/lib/ohm_util.rb
new file mode 100644
index 0000000..21d7978
--- /dev/null
+++ b/lib/ohm_util.rb
@@ -0,0 +1,39 @@
+
+module Lib
+  module OhmUtil 
+    
+    def self.check_params(model, params)
+      prop_names = model.attributes.collect{|p| p.to_s}
+      params.keys.each do |k|
+        key = k.to_s
+        if (key == "subjectid")
+          params.delete(k)
+        else
+          unless prop_names.include?(key)
+            key = key.from_rdf_format
+            unless prop_names.include?(key)
+              key = key+"_uri"
+              unless prop_names.include?(key)
+                key = key+"s"
+                unless prop_names.include?(key)
+                  raise OpenTox::BadRequestError.new "no attribute found: '"+k.to_s+"'"
+                end
+              end
+            end
+          end
+          params[key.to_sym] = params.delete(k)
+        end
+      end
+      params
+    end
+    
+    def self.find(model, filter_params)
+      if (filter_params.size==0)
+        model.all
+      else
+        model.find(check_params(model,filter_params))
+      end
+    end
+    
+  end 
+end
\ No newline at end of file
diff --git a/report/environment.rb b/report/environment.rb
index aa8ab56..4729dc8 100755
--- a/report/environment.rb
+++ b/report/environment.rb
@@ -12,8 +12,7 @@ module Reports
 end
 
 require "lib/ot_predictions.rb"
-#require "lib/active_record_setup.rb"
-#require "lib/data_mapper_util.rb"
+require "lib/ohm_util.rb"
 
 require "report/plot_factory.rb"
 require "report/xml_report.rb"
diff --git a/report/report_persistance.rb b/report/report_persistance.rb
index 9097fa3..113c81b 100755
--- a/report/report_persistance.rb
+++ b/report/report_persistance.rb
@@ -198,6 +198,8 @@ module Reports
     attribute :algorithm_uris    
     
     index :report_type
+    index :validation_uris
+    index :crossvalidation_uris
     
     attr_accessor :subjectid
     
@@ -250,16 +252,7 @@ module Reports
     
     def list_reports(type, filter_params={})
       LOGGER.debug "find reports for params: "+filter_params.inspect
-      # unfortunately, datamapper does not allow searching in Objects
-      # do filtering for list = Object params manually
-      list_params = {}
-      [:validation_uris, :crossvalidation_uris, :algorithm_uris, :model_uris].each do |l|
-        list_params[l] = filter_params.delete(l) if filter_params.has_key?(l)
-      end
-      reports = ReportData.find( :report_type => type )
-      list_params.each do |k,v|
-        reports = reports.collect{|x| x}.delete_if{ |r| !r.send(k).include?(v) }
-      end
+      reports = Lib::OhmUtil.find( ReportData, filter_params )
       reports.collect{ |r| r.id }
     end
     
diff --git a/test/unit_test.rb b/test/unit_test.rb
index 2462984..5984f42 100644
--- a/test/unit_test.rb
+++ b/test/unit_test.rb
@@ -44,38 +44,55 @@ class ValidationTest < Test::Unit::TestCase
       puts "AA disabled"
       @@subjectid = nil
     end
-    
+
+    @@data = []
     files = { File.new("data/hamster_carcinogenicity.mini.csv") => :crossvalidation,  
               File.new("data/EPAFHM.mini.csv") => :crossvalidation,
               File.new("data/hamster_carcinogenicity.csv") => :validation,
               File.new("data/EPAFHM.csv") => :validation,
 #              File.new("data/StJudes-HepG2-testset_Class.csv") => :crossvalidation
                }
-    @@data = []
     files.each do |file,type|
       @@data << { :type => type,
         :data => ValidationExamples::Util.upload_dataset(file, @@subjectid),
         :feat => ValidationExamples::Util.prediction_feature_for_file(file),
-        :file => file} 
+        :info => file.path, :delete => true} 
     end
+#    @@data << { :type => :crossvalidation,
+#      :data => "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=50",
+#      :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/21573",
+#      :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/9?max=50" }
+#    @@data << { :type => :validation,
+#      :data => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=50",
+#      :feat => "http://apps.ideaconsult.net:8080/ambit2/feature/26221",
+#      :info => "http://apps.ideaconsult.net:8080/ambit2/dataset/272?max=50" } 
   end
   
   def global_teardown
     puts "delete and logout"
-    @@data.each{|data| OpenTox::Dataset.find(data[:data],@@subjectid).delete(@@subjectid)}
+    @@data.each{|data| OpenTox::Dataset.find(data[:data],@@subjectid).delete(@@subjectid) if data[:delete]}
     @@vs.each{|v| v.delete(@@subjectid)} if defined?@@vs
     @@cvs.each{|cv| cv.delete(@@subjectid)} if defined?@@cvs
     @@reports.each{|report| report.delete(@@subjectid)} if defined?@@reports
     @@qmrfReports.each{|qmrfReport| qmrfReport.delete(@@subjectid)} if defined?@@qmrfReports
     OpenTox::Authorization.logout(@@subjectid) if AA_SERVER
   end
+  
+  def test_validation_list
+    puts "test_validation_list"
+    list = OpenTox::Validation.list
+    assert list.is_a?(Array)
+    list.each do |l|
+      assert l.uri?
+    end
+  end
  
   def test_training_test_split
     
     @@vs = []
     @@data.each do |data|
       if data[:type]==:validation
-        puts "test_training_test_split "+data[:file].path.to_s
+        puts "test_training_test_split "+data[:info].to_s
         p = { 
           :dataset_uri => data[:data],
           :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
@@ -100,6 +117,11 @@ class ValidationTest < Test::Unit::TestCase
         end
         v = OpenTox::Validation.find(v.uri, @@subjectid)
         assert v.uri.uri?
+        
+        model = v.metadata[OT.model]
+        assert model.uri?
+        v_list = OpenTox::Validation.list( {:model => model} )
+        assert v_list.size==1 and v_list.include?(v.uri)
         @@vs << v
       end
     end
@@ -118,6 +140,8 @@ class ValidationTest < Test::Unit::TestCase
           OpenTox::CrossvalidationReport.create(v.uri)
         end
       end
+      report = OpenTox::ValidationReport.find_for_validation(v.uri,@@subjectid)
+      assert report==nil,"report already exists for validation\nreport: "+(report ? report.uri.to_s : "")+"\nvalidation: "+v.uri.to_s
       report = OpenTox::ValidationReport.create(v.uri,@@subjectid)
       assert report.uri.uri?
       if @@subjectid
@@ -134,7 +158,16 @@ class ValidationTest < Test::Unit::TestCase
       @@reports << report2
     end  
   end
- 
+
+  def test_crossvalidation_list
+    puts "test_crossvalidation_list"
+    list = OpenTox::Crossvalidation.list
+    assert list.is_a?(Array)
+    list.each do |l|
+      assert l.uri?
+    end
+  end
+
   def test_crossvalidation
     
     #assert_rest_call_error OpenTox::NotFoundError do 
@@ -143,7 +176,7 @@ class ValidationTest < Test::Unit::TestCase
     @@cvs = []
     @@data.each do |data|
       if data[:type]==:crossvalidation
-        puts "test_crossvalidation "+data[:file].path.to_s
+        puts "test_crossvalidation "+data[:info].to_s
         p = { 
           :dataset_uri => data[:data],
           :algorithm_uri => File.join(CONFIG[:services]["opentox-algorithm"],"lazar"),
@@ -174,6 +207,16 @@ class ValidationTest < Test::Unit::TestCase
         end
         summary = cv.summary(@@subjectid)
         assert_kind_of Hash,summary
+        
+        algorithm = cv.metadata[OT.algorithm]
+        assert algorithm.uri?
+        cv_list = OpenTox::Crossvalidation.list( {:algorithm => algorithm} )
+        assert cv_list.include?(cv.uri)
+        cv_list.each do |cv_uri|
+          alg = OpenTox::Crossvalidation.find(cv_uri).metadata[OT.algorithm]
+          assert alg==algorithm,"wrong algorithm for filtered crossvalidation, should be: '"+algorithm.to_s+"', is: '"+alg.to_s+"'"
+        end
+        
         @@cvs << cv
       end
     end
@@ -195,6 +238,7 @@ class ValidationTest < Test::Unit::TestCase
           OpenTox::CrossvalidationReport.create(cv.uri)
         end
       end
+      assert OpenTox::ValidationReport.find_for_validation(cv.uri,@@subjectid)==nil
       report = OpenTox::CrossvalidationReport.create(cv.uri,@@subjectid)
       assert report.uri.uri?
       if @@subjectid
diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index 4ef05a9..2bd2fea 100755
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -9,11 +9,7 @@ require 'validation/validation_service.rb'
 
 get '/crossvalidation/?' do
   LOGGER.info "list all crossvalidations"
-  #uri_list = Validation::Crossvalidation.all.collect{ |cv| cv.crossvalidation_uri }.join("\n")+"\n"
-  #uri_list = Lib::DataMapperUtil.all(Validation::Crossvalidation,params).collect{ |cv| cv.crossvalidation_uri }.join("\n")+"\n"
-  uri_list = Validation::Crossvalidation.all.collect{|cv| cv.crossvalidation_uri}.join("\n") + "\n"
-  
-  #uri_list = Validation::Crossvalidation.find_like(params).collect{ |cv| cv.crossvalidation_uri }.join("\n")+"\n"
+  uri_list = Lib::OhmUtil.find( Validation::Crossvalidation, params ).collect{|v| v.crossvalidation_uri}.join("\n") + "\n"
   if request.env['HTTP_ACCEPT'] =~ /text\/html/
     related_links = 
       "Single validations:      "+url_for("/",:full)+"\n"+
@@ -134,7 +130,7 @@ get '/crossvalidation/:id/statistics' do
 #  LOGGER.debug vals.collect{|v| v.validation_uri}.join("\n")
 #  LOGGER.debug vals.size
 #  LOGGER.debug vals.class
-  
+  raise "could not load all validations for crossvalidation" if vals.include?(nil)
   v = Lib::MergeObjects.merge_array_objects( vals )
   v.created_at = nil
   #v.id = nil
@@ -213,11 +209,7 @@ end
 get '/?' do
   
   LOGGER.info "list all validations, params: "+params.inspect
-  #uri_list = Validation::Validation.find_like(params).collect{ |v| v.validation_uri }.join("\n")+"\n"
-  #uri_list = Validation::Validation.all(params).collect{ |v| v.validation_uri }.join("\n")+"\n"
-  #uri_list = Lib::DataMapperUtil.all(Validation::Validation,params).collect{ |v| v.validation_uri }.join("\n")+"\n"
-  uri_list = Validation::Validation.all.collect{|v| v.validation_uri}.join("\n") + "\n"
-  
+  uri_list = Lib::OhmUtil.find( Validation::Validation, params ).collect{|v| v.validation_uri}.join("\n") + "\n"
   if request.env['HTTP_ACCEPT'] =~ /text\/html/
     related_links = 
       "To perform a validation:\n"+