whitelist validation-non-resource-uris, minor fixes

6 files changed, 16 insertions, 6 deletions

diff --git a/application.rb b/application.rb
index cf9621d..319a95d 100755
--- a/application.rb
+++ b/application.rb
@@ -13,6 +13,9 @@ end
 
 require "example.rb"
 
+# this allows GET access to all validation URIS that do NOT end with /<number> or /<number>/
+OpenTox::Authorization.whitelist( /\/[0-9]+(\/?)$/, "GET", true )
+
 get '/examples/?' do
   LOGGER.info "list examples"
   
diff --git a/lib/ot_predictions.rb b/lib/ot_predictions.rb
index c593f55..e28f35b 100755
--- a/lib/ot_predictions.rb
+++ b/lib/ot_predictions.rb
@@ -41,7 +41,7 @@ module Lib
           raise "prediction_feature not found in test_dataset, specify a test_target_dataset\n"+
                 "prediction_feature: '"+prediction_feature.to_s+"'\n"+
                 "test_dataset: '"+test_target_dataset_uri.to_s+"'\n"+
-                "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.index(prediction_feature)==nil
+                "available features are: "+test_target_dataset.features.inspect if test_target_dataset.features.keys.index(prediction_feature)==nil
         else
           test_target_dataset = OpenTox::Dataset.find test_target_dataset_uri,subjectid
           raise "test target datset not found: '"+test_target_dataset_uri.to_s+"'" unless test_target_dataset
diff --git a/report/report_application.rb b/report/report_application.rb
index 9fcf871..8403b4c 100755
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -92,7 +92,7 @@ get '/report/:type/:id' do
   end
 end
 
-OpenTox::Authorization.whitelist( Regexp.new("/report/.*/[0-9]+/.*"),"GET")
+#OpenTox::Authorization.whitelist( Regexp.new("/report/.*/[0-9]+/.*"),"GET")
 
 get '/report/:type/:id/:resource' do
   perform do |rs|
diff --git a/test/test_examples_util.rb b/test/test_examples_util.rb
index 02d5921..c465d94 100755
--- a/test/test_examples_util.rb
+++ b/test/test_examples_util.rb
@@ -66,12 +66,15 @@ module ValidationExamples
     end
     
     def self.validation_get(uri, accept_header='application/rdf+xml')
+      params = {}
+      params[:subjectid] = SUBJECTID if SUBJECTID
       if $test_case
         #puts "getting "+uri+","+accept_header
-        $test_case.get uri,nil,'HTTP_ACCEPT' => accept_header 
+        $test_case.get uri,params,'HTTP_ACCEPT' => accept_header 
         return wait($test_case.last_response.body)
       else
-        return OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],uri),{:accept => accept_header})
+        params[:accept] = accept_header
+        return OpenTox::RestClientWrapper.get(File.join(CONFIG[:services]["opentox-validation"],uri),params)
       end
     end
 
@@ -291,6 +294,7 @@ module ValidationExamples
     def report
       begin
         @report_uri = Util.validation_post '/report/'+report_type,{:validation_uris => @validation_uri}
+        Util.validation_get "/report/"+report_uri.split("/")[-2]+"/"+report_uri.split("/")[-1]
       rescue => ex
         puts "could not create report: "+ex.message
         raise ex
diff --git a/validation/validation_service.rb b/validation/validation_service.rb
index fa638cf..2208116 100755
--- a/validation/validation_service.rb
+++ b/validation/validation_service.rb
@@ -156,6 +156,7 @@ module Validation
         #prediction_dataset_uri = model.predict_dataset(self.test_dataset_uri, OpenTox::SubTask.create(task, 0, 50))
         prediction_dataset_uri = model.run(
           {:dataset_uri => self.test_dataset_uri, :subjectid => self.subjectid},
+          "text/uri-list",
           OpenTox::SubTask.create(task, 0, 50))
       end
 #      self.attributes = { :prediction_dataset_uri => prediction_dataset_uri,
diff --git a/validation/validation_test.rb b/validation/validation_test.rb
index 603b270..c368747 100755
--- a/validation/validation_test.rb
+++ b/validation/validation_test.rb
@@ -140,7 +140,7 @@ class ValidationTest < Test::Unit::TestCase
       
       #puts OpenTox::Authorization.list_policy_uris(SUBJECTID).inspect
 
-      run_test("14a",nil,nil,false) #,{:dataset_uri=>"http://local-ot/dataset/45", :prediction_feature => "http://local-ot/dataset/45/feature/Hamster%20Carcinogenicity"})
+      run_test("15a",nil,nil,false) #,{:dataset_uri=>"http://local-ot/dataset/45", :prediction_feature => "http://local-ot/dataset/45/feature/Hamster%20Carcinogenicity"})
       
       #get "/12123123123123123"
       #get "/chain"
@@ -176,7 +176,7 @@ class ValidationTest < Test::Unit::TestCase
       #do_test_examples_ortona
       
     ensure
-      OpenTox::Authorization.logout(SUBJECTID) if AA_SERVER
+      #OpenTox::Authorization.logout(SUBJECTID) if AA_SERVER
     end
   end
 
@@ -206,10 +206,12 @@ class ValidationTest < Test::Unit::TestCase
           ex.check_requirements
           ex.validate
           LOGGER.debug "validation done '"+ex.validation_uri.to_s+"'"
+          puts ex.validation_uri+"?subjectid="+CGI.escape(SUBJECTID)  if SUBJECTID and !delete
         end
         ex.report_uri = report_uri
         unless ex.report_uri
           ex.report
+          puts ex.report_uri+"?subjectid="+CGI.escape(SUBJECTID)  if SUBJECTID and !delete
         end
         ##ex.verify_yaml
         ##ex.compare_yaml_vs_rdf