fix create qmrf report, remove not-found-test from unit-test

2 files changed, 55 insertions, 16 deletions

diff --git a/reach_reports/reach_service.rb b/reach_reports/reach_service.rb
index 028a53c..53acb62 100755
--- a/reach_reports/reach_service.rb
+++ b/reach_reports/reach_service.rb
@@ -71,7 +71,7 @@ module ReachReports
     # TODO QSAR_models -> sparql same endpoint     
     r.qsar_identifier.qsar_software << QsarSoftware.new( :url => model.uri, 
       :name => model.metadata[DC.title], :contact => model.metadata[DC.creator] )
-    algorithm = OpenTox::Algorithm::Generic.find(model.metadata[OT.algorithm]) if model.metadata[OT.algorithm]
+    algorithm = OpenTox::Algorithm::Generic.find(model.metadata[OT.algorithm], r.subjectid) if model.metadata[OT.algorithm]
     r.qsar_identifier.qsar_software << QsarSoftware.new( :url => algorithm.uri, :name => algorithm.metadata[DC.title] )
     task.progress(10) if task
 
@@ -108,9 +108,11 @@ module ReachReports
     # TODO app_domain_description, app_domain_method, app_domain_software, applicability_limits
 
     #training_dataset = model.trainingDataset ? OpenTox::Dataset.find(model.trainingDataset+"/metadata") : nil
-    begin
-      training_dataset = model.metadata[OT.trainingDataset] ? OpenTox::Dataset.find(model.metadata[OT.trainingDataset]) : nil
-    rescue
+    if ( OpenTox::Dataset.exist?(model.metadata[OT.trainingDataset]) )
+      training_dataset = OpenTox::Dataset.new( model.metadata[OT.trainingDataset] )
+      training_dataset.load_metadata( r.subjectid )
+    else
+      training_dataset = nil
       LOGGER.warn "build qmrf: training_dataset not found "+model.metadata[OT.trainingDataset].to_s
     end
     task.progress(50) if task
@@ -264,14 +266,13 @@ module ReachReports
         :url => training_dataset.uri} ) if training_dataset
         
     val_datasets.each do |data_uri|
-      begin
-        d = OpenTox::Dataset.find(data_uri) #+"/metadata")
+      if OpenTox::Dataset.exist?(data_uri, r.subjectid)
+        d = OpenTox::Dataset.new(data_uri)
+        d.load_metadata( r.subjectid)
         r.qsar_miscellaneous.attachment_validation_data << AttachmentValidationData.new( 
           { :description => d.title, 
             :filetype => "owl-dl", 
-            :url => data_uri} ) if d
-      rescue
-        LOGGER.warn "could not add dataset: "+data_uri.to_s
+            :url => data_uri} )
       end
     end
     task.progress(90) if task
diff --git a/reach_reports/reach_test.rb b/reach_reports/reach_test.rb
index 7d1569d..47e5158 100755
--- a/reach_reports/reach_test.rb
+++ b/reach_reports/reach_test.rb
@@ -1,3 +1,11 @@
+
+require "rubygems"
+require "sinatra"
+before {
+  request.env['HTTP_HOST']="local-ot/validation"
+  request.env["REQUEST_URI"]=request.env["PATH_INFO"]
+}
+
 require "uri"
 require "yaml"
 ENV['RACK_ENV'] = 'test'
@@ -11,6 +19,19 @@ LOGGER = OTLogger.new(STDOUT)
 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"
+  SUBJECTID = OpenTox::Authorization.authenticate(TEST_USER,TEST_PW)
+  raise "could not log in" unless SUBJECTID
+  puts "logged in: "+SUBJECTID.to_s
+else
+  puts "AA disabled"
+  SUBJECTID = nil
+end
+
 #Rack::Test::DEFAULT_HOST = "local-ot/validation"
 module Sinatra
   module UrlForHelper
@@ -24,8 +45,11 @@ module Sinatra
       "#{BASE}#{url_fragment}"
     end
   end
+  set :raise_errors, false
+  set :show_exceptions, false
 end
 
+
 #DataMapper::Model.raise_on_save_failure = true
 #
 #class TestResourceX
@@ -76,10 +100,12 @@ class ReachTest < Test::Unit::TestCase
 
   def test_it
     
-    delete '/reach_report/QMRF/3'
-    puts last_response.body
+    begin
+    
+   # delete '/reach_report/QMRF/3'
+   # puts last_response.body
     
-    exit
+    #exit
 #    testResource = TestResource.new
 #    
 #    TestResource.info
@@ -120,7 +146,10 @@ class ReachTest < Test::Unit::TestCase
     
     #model_uri = "http://ambit.uni-plovdiv.bg:8080/ambit2/model/173393"
     
-    model_uri = "http://local-ot/majority/class/model/58"
+    #model_uri = "http://local-ot/majority/class/model/58"
+    
+    model_uri = "http://local-ot/model/104"
+    
 #    m = OpenTox::Model::Generic.find(model_uri)
 #    puts m.metadata[OT.algorithm] if m
 #    a = OpenTox::Algorithm::Generic.find(m.metadata[OT.algorithm])
@@ -132,13 +161,15 @@ class ReachTest < Test::Unit::TestCase
     #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 #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
     uri = Lib::TestUtil.wait_for_task(uri)
-    id = uri.split("/")[-1]
-    puts uri
+    if uri
+      id = uri.split("/")[-1]
+      puts uri
+    end
 
 #    id = "8"
 
@@ -164,6 +195,13 @@ class ReachTest < Test::Unit::TestCase
     #File.new("/home/martin/tmp/qmr_rep_del_me.xml","w").puts last_response.body
     #File.new("/home/martin/win/home/qmr_rep_del_me.xml","w").puts last_response.body
     #File.new("/home/martin/info_home/.public_html/qmr_rep_del_me.xml","w").puts last_response.body
+    
+    rescue => ex
+      rep = OpenTox::ErrorReport.create(ex, "")
+      puts rep.to_yaml
+    end
+      
+      
   end
 end