add subject-id to to-html, minor changes

9 files changed, 97 insertions, 41 deletions

diff --git a/application.rb b/application.rb
index c18b05e..f543167 100755
--- a/application.rb
+++ b/application.rb
@@ -19,7 +19,7 @@ get '/examples/?' do
   
   if request.env['HTTP_ACCEPT'] =~ /text\/html/
     content_type "text/html"
-    OpenTox.text_to_html Example.transform_example
+    OpenTox.text_to_html Example.transform_example,@subjectid
   else
     content_type "text/plain"
     Example.transform_example
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index 9b1ee51..116b4db 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -51,7 +51,6 @@ module Lib
                 "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil
         end
         
-        test_dataset.load_all(subjectid)
         @compounds = test_dataset.compounds
         LOGGER.debug "test dataset size: "+@compounds.size.to_s
         raise "test dataset is empty "+test_dataset_uri.to_s unless @compounds.size>0
diff --git a/reach_reports/reach_application.rb b/reach_reports/reach_application.rb
index 293a5ac..fc670fd 100755
--- a/reach_reports/reach_application.rb
+++ b/reach_reports/reach_application.rb
@@ -24,7 +24,7 @@ get '/reach_report' do
       "Validation reporting: "+url_for("/report",:full)
     description = 
         "A list of all suported REACH reporting types."
-    OpenTox.text_to_html uri_list,related_links,description
+    OpenTox.text_to_html uri_list,related_links,description, @subjectid
   else
     content_type "text/uri-list"
     uri_list
@@ -51,7 +51,7 @@ get '/reach_report/:type' do
     when /(?i)QPRF/
       #TODO
     end
-    OpenTox.text_to_html ReachReports.list_reports(type),related_links,description,post_params
+    OpenTox.text_to_html ReachReports.list_reports(type),@subjectid,related_links,description,post_params
   else
     content_type "text/uri-list"
     ReachReports.list_reports(type)
@@ -98,7 +98,7 @@ get '/reach_report/:type/:id' do
         "All "+type+" reports:           "+url_for("/reach_report/"+type,:full)
     description = 
         "A QMRF report."
-    OpenTox.text_to_html rep.to_yaml,related_links,description
+    OpenTox.text_to_html rep.to_yaml,@subjectid,related_links,description
   when /application\/x-yaml|\*\/\*|^$/ # matches 'application/x-yaml', '*/*', ''
     content_type "application/x-yaml"
     rep.to_yaml
diff --git a/reach_reports/reach_test.rb b/reach_reports/reach_test.rb
index 47e5158..87addfa 100755
--- a/reach_reports/reach_test.rb
+++ b/reach_reports/reach_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
@@ -148,7 +148,10 @@ class ReachTest < Test::Unit::TestCase
     
     #model_uri = "http://local-ot/majority/class/model/58"
     
-    model_uri = "http://local-ot/model/104"
+    
+    #model_uri = "http://local-ot/model/104"
+    model_uri = "http://local-ot/majority/class/model/125"
+    
     
 #    m = OpenTox::Model::Generic.find(model_uri)
 #    puts m.metadata[OT.algorithm] if m
@@ -156,12 +159,14 @@ class ReachTest < Test::Unit::TestCase
 #    puts a.metadata.inspect
 #    exit
     
+    puts SUBJECTID
+
 #    model_uri = "http://local-ot/model/1"
     #http://local-ot/majority/class/model/15
     #model_uri = "http://local-ot/majority/class/model/15"
    # model_uri = "http://local-ot/majority/class/model/91"
     #model_uri = "http://apps.ideaconsult.net:8080/ambit2/model/2"
-    post '/reach_report/qmrf', {:model_uri=>model_uri}, {:subjectid => SUBJECTID} #http://local-ot/model/1"
+    post '/reach_report/qmrf',{:model_uri=>model_uri, :subjectid => SUBJECTID} #http://local-ot/model/1"
     ##post '/reach_report/qprf',:compound_uri=>"http://local-ot/compound/XYZ"
     uri = last_response.body
     puts "task: "+uri.to_s
diff --git a/report/report_application.rb b/report/report_application.rb
index ab3d91b..5a47063 100755
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -38,7 +38,7 @@ get '/report/?' do
       description = 
         "A list of all report types."
       content_type "text/html"
-      OpenTox.text_to_html rs.get_report_types,related_links,description
+      OpenTox.text_to_html rs.get_report_types,@subjectid,related_links,description
     else
       content_type "text/uri-list"
       rs.get_report_types
@@ -58,7 +58,7 @@ get '/report/:report_type' do
         "A list of all "+params[:report_type]+" reports. To create a report, use the POST method."
       post_params = [[:validation_uris]]
       content_type "text/html"
-      OpenTox.text_to_html rs.get_all_reports(params[:report_type], params),related_links,description,post_params
+      OpenTox.text_to_html rs.get_all_reports(params[:report_type], params),@subjectid,related_links,description,post_params
     else
       content_type "text/uri-list"
       rs.get_all_reports(params[:report_type], params)
@@ -89,8 +89,6 @@ get '/report/:type/:id' do
       result = body(File.new(report))
     end
   end
-
-  response.set_cookie("subjectid", @subjectid)
 end
 
 #OpenTox::Authorization.whitelist( Regexp.new("/report/.*/[0-9]+/.*"),"GET")
diff --git a/test/test_examples.rb b/test/test_examples.rb
index 53f1f81..503bc13 100755
--- a/test/test_examples.rb
+++ b/test/test_examples.rb
@@ -381,8 +381,9 @@ module ValidationExamples
   
   class AmbitModelValidation < ModelValidation
     def initialize
-      @model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/29139"
-      @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401560"
+      @model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/39319"
+      #@model_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/model/29139"
+      @test_dataset_uri = "https://ambit.uni-plovdiv.bg:8443/ambit2/dataset/R401577?max=3"
     end
   end    
   
diff --git a/test/unit_test.rb b/test/unit_test.rb
index 26fc17e..11b0759 100644
--- a/test/unit_test.rb
+++ b/test/unit_test.rb
@@ -97,7 +97,7 @@ class ValidationTest < Test::Unit::TestCase
   end
     
   def test_crossvalidation_report
-    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/47", @@subjectid)
+    #@@cv = OpenTox::Crossvalidation.find("http://local-ot/validation/crossvalidation/48", @@subjectid)
     
     puts "test_crossvalidation_report"
     assert defined?@@cv,"no crossvalidation defined"
@@ -117,12 +117,12 @@ class ValidationTest < Test::Unit::TestCase
         OpenTox::CrossvalidationReport.find(report.uri)
       end
     end
-    report_uri = OpenTox::CrossvalidationReport.find(report.uri,@@subjectid)
-    assert report_uri.uri?
+    report = OpenTox::CrossvalidationReport.find(report.uri,@@subjectid)
+    assert report.uri.uri?
     report2 = OpenTox::CrossvalidationReport.find_for_crossvalidation(@@cv.uri,@@subjectid)
-    assert_equal report_uri,report2.uri
-    report3 = @@cv.find_or_create_report(@@subjectid)
-    assert_equal report_uri,report3.uri
+    assert_equal report.uri,report2.uri
+    report3_uri = @@cv.find_or_create_report(@@subjectid)
+    assert_equal report.uri,report3_uri
     @report = report2
   end
   
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)