add subject-id to to-html, minor changes

2 files changed, 71 insertions, 18 deletions

diff --git a/validation/validation_application.rb b/validation/validation_application.rb
index 9b517cf..e07acf0 100755
--- a/validation/validation_application.rb
+++ b/validation/validation_application.rb
@@ -22,7 +22,7 @@ get '/crossvalidation/?' do
       "Use the POST method to perform a crossvalidation."
     post_params = [[:dataset_uri,:algorithm_uri,:prediction_feature,[:num_folds,10],[:random_seed,1],[:stratified,false],[:algorithm_params,""]]]
     content_type "text/html"
-    OpenTox.text_to_html uri_list,related_links,description,post_params
+    OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params
   else
     content_type "text/uri-list"
     uri_list
@@ -101,7 +101,7 @@ get '/crossvalidation/:id' do
     description = 
         "A crossvalidation resource."
     content_type "text/html"
-    OpenTox.text_to_html crossvalidation.to_yaml,related_links,description
+    OpenTox.text_to_html crossvalidation.to_yaml,@subjectid,related_links,description
   when /application\/x-yaml|\*\/\*/
     content_type "application/x-yaml"
     crossvalidation.to_yaml
@@ -139,7 +139,7 @@ get '/crossvalidation/:id/statistics' do
     description = 
        "The averaged statistics for the crossvalidation."
     content_type "text/html"
-    OpenTox.text_to_html v.to_yaml,related_links,description
+    OpenTox.text_to_html v.to_yaml,@subjectid,related_links,description
   else
     content_type "application/x-yaml"
     v.to_yaml
@@ -196,7 +196,7 @@ get '/crossvalidation/:id/predictions' do
     related_links = 
       "All crossvalidations:         "+url_for("/crossvalidation",:full)+"\n"+
       "Correspoding crossvalidation: "+url_for("/crossvalidation/"+params[:id],:full)
-    OpenTox.text_to_html p, related_links, description
+    OpenTox.text_to_html p,@subjectid, related_links, description
   else
     content_type "text/x-yaml"
     p
@@ -226,7 +226,7 @@ get '/?' do
         "A validation web service for the OpenTox project ( http://opentox.org ).\n"+
         "In the root directory (this is where you are now), a list of all validation resources is returned."
     content_type "text/html"
-    OpenTox.text_to_html uri_list,related_links,description
+    OpenTox.text_to_html uri_list,@subjectid,related_links,description
   else
     content_type "text/uri-list"
     uri_list
@@ -274,7 +274,7 @@ get '/test_set_validation' do
         "To perform a test-set-validation use the POST method."
     post_params = [[:model_uri, :test_dataset_uri, [:test_target_dataset_uri,"same-as-test_dataset_uri"], [:prediction_feature, "dependent-variable-of-model"]]]
     content_type "text/html"
-    OpenTox.text_to_html uri_list,related_links,description,post_params
+    OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params
   else
     content_type "text/uri-list"
     uri_list
@@ -323,7 +323,7 @@ get '/training_test_validation' do
                     :prediction_feature, 
                     [:algorithm_params, ""]]]
     content_type "text/html"
-    OpenTox.text_to_html uri_list,related_links,description,post_params
+    OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params
   else
     content_type "text/uri-list"
     uri_list
@@ -371,7 +371,7 @@ get '/bootstrapping' do
                     [:algorithm_params, ""],
                     [:random_seed, 1]]]
     content_type "text/html"
-    OpenTox.text_to_html uri_list,related_links,description,post_params
+    OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params
   else
     content_type "text/uri-list"
     uri_list
@@ -423,7 +423,7 @@ get '/training_test_split' do
                     [:random_seed, 1],
                     [:split_ratio, 0.66]]]
     content_type "text/html"
-    OpenTox.text_to_html uri_list,related_links,description,post_params
+    OpenTox.text_to_html uri_list,@subjectid,related_links,description,post_params
   else
     content_type "text/uri-list"
     uri_list
@@ -502,7 +502,7 @@ get '/:id/predictions' do
     related_links = 
       "All validations:         "+url_for("/",:full)+"\n"+
       "Correspoding validation: "+url_for("/"+params[:id],:full)
-    OpenTox.text_to_html p.to_array.to_yaml, related_links, description
+    OpenTox.text_to_html p.to_array.to_yaml,@subjectid, related_links, description
   else
     content_type "text/x-yaml"
     p.to_array.to_yaml
@@ -548,7 +548,7 @@ get '/:id' do
       "Get validation predictions:      "+url_for("/"+params[:id]+"/predictions",:full)+"\n"+
       "All validations:                 "+url_for("/",:full)+"\n"+
       "All validation reports:          "+url_for("/report/validation",:full)
-    OpenTox.text_to_html validation.to_yaml,related_links,description
+    OpenTox.text_to_html validation.to_yaml,@subjectid,related_links,description
   else #default is yaml 
     content_type "application/x-yaml"
     validation.to_yaml
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index e39dbeb..3f10ca2 100755
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -20,10 +20,10 @@ LOGGER.datetime_format = "%Y-%m-%d %H:%M:%S "
 LOGGER.formatter = Logger::Formatter.new
 
 if AA_SERVER
-  #TEST_USER = "mgtest"
-  #TEST_PW = "mgpasswd"
-  TEST_USER = "guest"
-  TEST_PW = "guest"
+  TEST_USER = "mgtest"
+  TEST_PW = "mgpasswd"
+  #TEST_USER = "guest"
+  #TEST_PW = "guest"
   SUBJECTID = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
   raise "could not log in" unless SUBJECTID
   puts "logged in: "+SUBJECTID.to_s
@@ -60,6 +60,10 @@ class ValidationTest < Test::Unit::TestCase
     begin
       $test_case = self
       
+#    prediction_feature = "https://ambit.uni-plovdiv.bg:8443/ambit2/feature/26221"
+#    puts OpenTox::Feature.find(prediction_feature).domain.inspect
+#      exit
+
 #      begin
 #        #OpenTox::RestClientWrapper.get "http://local-ot/validation/runtime-error",{:accept => "application/rdf+xml"}
 #        puts OpenTox::RestClientWrapper.post "http://opentox.ntua.gr:4000/model/0d8a9a27-3481-4450-bca1-d420a791de9d",
@@ -151,12 +155,61 @@ class ValidationTest < Test::Unit::TestCase
 #      val = wait_for_task(uri)
 #      puts val
 #      get "/"+val.split("/")[-1]
-      
+
+#     post "/validate_datasets",{
+#         :test_dataset_uri=>"http://opentox.informatik.uni-freiburg.de/dataset/409",
+#         :prediction_dataset_uri=>"http://opentox.informatik.uni-freiburg.de/dataset/410",
+#         :test_target_dataset_uri=>"https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560",
+#         :prediction_feature=>"https://ambit.uni-plovdiv.bg:8443/ambit2/feature/22190",
+#         :predicted_feature=>"https://ambit.uni-plovdiv.bg:8443/ambit2/feature/218304",
+#         :regression=>"true",
+#         :subjectid=>SUBJECTID}
+#         #:model_uri=>"http://local-ot/model/31"}
+#        #:regression=>"true"}
+#  #       :classification=>"true"}
+#      uri = last_response.body
+#      val = wait_for_task(uri)
+#      puts val
+#      #get "/"+val.split("/")[-1]
+     
+     
+
+     #ambit_service = "https://ambit.uni-plovdiv.bg:8443/ambit2"
+      #https%3A%2F%2Fambit.uni-plovdiv.bg%3A8443%2Fambit2
+
+#     post "/validate_datasets",{
+#         :test_dataset_uri=>ambit_service+"/dataset/R401577?max=50",
+#         :prediction_dataset_uri=>ambit_service+"/dataset/R401577?max=50&feature_uris[]="+CGI.escape(ambit_service)+"%2Fmodel%2F35194%2Fpredicted",
+#         #:test_target_dataset_uri=>ambit_service+"/dataset/R401560",
+#         :prediction_feature=>ambit_service+"/feature/26221",
+#         :predicted_feature=>ambit_service+"/feature/218699",
+#         :classification=>"true",
+#         :subjectid=>SUBJECTID}
+#         #:model_uri=>"http://local-ot/model/31"}
+#        #:regression=>"true"}
+#  #       :classification=>"true"}
+#      uri = last_response.body
+#      val = wait_for_task(uri)
+#      puts val
+#      #get "/"+val.split("/")[-1]
+
+
 #      d = OpenTox::Dataset.find("https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R545",SUBJECTID)
 #      puts d.compounds.inspect
 #      exit
+
+#      f = File.new("data/ambit-dataset.rdf")
+#      d = ValidationExamples::Util.upload_dataset(f, SUBJECTID)
+#      puts d
+      
+#      d = OpenTox::Dataset.find("https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560",SUBJECTID)
+#      #puts d.compounds.to_yaml
+#      #puts d.features.keys.to_yaml
+#      puts d.to_yaml
+#      d2 = d.split(d.compounds[0..5], d.features.keys[0..1], {}, SUBJECTID)
+#      puts d2.to_yaml
       
-      run_test("21a")#,:validation_uri=>"http://local-ot/validation/253") #,"http://local-ot/validation/28")#,"http://local-ot/validation/394");
+      run_test("1b")#,:validation_uri=>"http://local-ot/validation/253") #,"http://local-ot/validation/28")#,"http://local-ot/validation/394");
       
       #run_test("3b",:validation_uri=>"http://local-ot/validation/crossvalidation/45") #,{:dataset_uri => "http://local-ot/dataset/773", :prediction_feature => "http://local-ot/dataset/773/feature/Hamster%20Carcinogenicity"})
       
@@ -175,7 +228,7 @@ class ValidationTest < Test::Unit::TestCase
       
       #puts OpenTox::Authorization.list_policy_uris(SUBJECTID).inspect
 
-#      run_test("16b") #,{:dataset_uri => "http://local-ot/dataset/313", :prediction_feature => "http://local-ot/dataset/313/feature/repdose_classification"})
+      #run_test("19d") #,{:dataset_uri => "http://local-ot/dataset/313", :prediction_feature => "http://local-ot/dataset/313/feature/repdose_classification"})
       
 #      model = OpenTox::Model::Generic.find("http://local-ot/majority/class/model/58")
 #      OpenTox::QMRFReport.create(model)