Merge branch 'development' of github.com:opentox/validation into development

8 files changed, 14 insertions, 12 deletions

diff --git a/example.rb b/example.rb
index b0b591e..636579e 100755
--- a/example.rb
+++ b/example.rb
@@ -80,7 +80,7 @@ class Example
       task.progress(10)
       
       log "upload dataset"
-      halt 400,"File not found: "+@@file.path.to_s unless File.exist?(@@file.path)
+      raise OpenTox::BadRequestError.new"File not found: "+@@file.path.to_s unless File.exist?(@@file.path)
       #data = File.read(@@file.path)
       #data_uri = OpenTox::RestClientWrapper.post(CONFIG[:services]["opentox-dataset"],{:content_type => @@file_type},data).chomp("\n")
       dataset = OpenTox::Dataset.create_from_csv_file(@@file.path,nil)
diff --git a/lib/active_record_setup.rb b/lib/active_record_setup.rb
index b43e692..5f081af 100755
--- a/lib/active_record_setup.rb
+++ b/lib/active_record_setup.rb
@@ -34,7 +34,7 @@ class ActiveRecord::Base
             unless self.column_names.include?(key)
               err = "no attribute found: '"+k.to_s+"'"
 #              if $sinatra
-#                $sinatra.halt 400,err
+#                $sinatra.raise OpenTox::BadRequestError.newerr
 #              else
                 raise err
 #              end
@@ -47,4 +47,4 @@ class ActiveRecord::Base
     #puts "params after "+filter_params.inspect
     self.find(:all, :conditions => filter_params)
   end
-end
\ No newline at end of file
+end
diff --git a/reach_reports/reach_application.rb b/reach_reports/reach_application.rb
index aa64ea2..c0e89b5 100755
--- a/reach_reports/reach_application.rb
+++ b/reach_reports/reach_application.rb
@@ -18,14 +18,14 @@ def mysql_lite_retry( n_times=15 )
   end
   yield # try a last time
 end
-  
+
 require 'reach_reports/reach_persistance.rb'
 require 'reach_reports/reach_service.rb'
 
 require "lib/format_util.rb"
 
 def extract_type(params)
-  halt 400, "illegal type, neither QMRF nor QPRF: "+params[:type] unless params[:type] && params[:type] =~ /(?i)Q(M|P)RF/
+  raise OpenTox::BadRequestError.new "illegal type, neither QMRF nor QPRF: "+params[:type] unless params[:type] && params[:type] =~ /(?i)Q(M|P)RF/
   params.delete("type")
 end
 
@@ -100,7 +100,7 @@ get '/reach_report/:type/:id' do
 
   case request.env['HTTP_ACCEPT'].to_s
   when "application/rdf+xml"
-    halt 400, "application/rdf+xml not yet supported"
+    raise OpenTox::BadRequestError.new "application/rdf+xml not yet supported"
     owl = OpenTox::Owl.create(type+"Report",rep.report_uri)
     owl.set_data( rep.get_content.keys_to_rdf_format )
     owl.rdf
@@ -121,7 +121,7 @@ get '/reach_report/:type/:id' do
     content_type "application/x-yaml"
     rep.to_yaml
   else
-    halt 400, "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported, valid Accept-Headers are \"application/rdf+xml\", \"application/x-yaml\", \"application/qmrf-xml\"."
+    raise OpenTox::BadRequestError.new "MIME type '"+request.env['HTTP_ACCEPT'].to_s+"' not supported, valid Accept-Headers are \"application/rdf+xml\", \"application/x-yaml\", \"application/qmrf-xml\"."
   end
 end
 
@@ -132,7 +132,7 @@ post '/reach_report/:type/:id' do
   rep = ReachReports.get_report(type, params[:id])
 
   input = request.env["rack.input"].read
-  halt 400, "no xml data specified" unless input && input.to_s.size>0
+  raise OpenTox::BadRequestError.new "no xml data specified" unless input && input.to_s.size>0
   LOGGER.debug "size of posted data: "+input.to_s.size.to_s
   
   ReachReports::QmrfReport.from_xml(rep,input)
diff --git a/reach_reports/reach_persistance.rb b/reach_reports/reach_persistance.rb
index 147ee84..1226d95 100755
--- a/reach_reports/reach_persistance.rb
+++ b/reach_reports/reach_persistance.rb
@@ -1210,6 +1210,7 @@ module ReachReports
       model.auto_upgrade!
       model.raise_on_save_failure = true
     end
+
   end
   
 end
\ No newline at end of file
diff --git a/reach_reports/reach_service.rb b/reach_reports/reach_service.rb
index 916a7a4..fa4c0d7 100755
--- a/reach_reports/reach_service.rb
+++ b/reach_reports/reach_service.rb
@@ -279,6 +279,7 @@ module ReachReports
       end
     end
     task.progress(90) if task
+
     mysql_lite_retry do 
       r.save
     end
@@ -289,7 +290,7 @@ module ReachReports
 #    
 #    report_content = get_report(type, id).get_content
 #    keys.each do |k|
-#      $sinatra.halt 400, type+" unknown report property '#{key}'" unless report_content.is_a?(Hash) and report_content.has_key?(k)
+#      $sinatra.raise OpenTox::BadRequestError.new type+" unknown report property '#{key}'" unless report_content.is_a?(Hash) and report_content.has_key?(k)
 #      report_content = report_content[k]
 #    end
 #    report_content    
diff --git a/report/report_application.rb b/report/report_application.rb
index f7780c3..8f74bd9 100755
--- a/report/report_application.rb
+++ b/report/report_application.rb
@@ -7,7 +7,7 @@ end
 
 def get_docbook_resource(filepath)
   perform do |rs|
-    halt 404,"not found: "+filepath unless File.exist?(filepath)
+    raise OpenTox::NotFoundError.new"not found: "+filepath unless File.exist?(filepath)
     types = MIME::Types.type_for(filepath)
     content_type(types[0].content_type) if types and types.size>0 and types[0]
     result = body(File.new(filepath))
diff --git a/report/report_persistance.rb b/report/report_persistance.rb
index 78ae47b..e02387f 100755
--- a/report/report_persistance.rb
+++ b/report/report_persistance.rb
@@ -315,7 +315,7 @@ end
 #            unless prop_names.include?(key)
 #              err = "no attribute found: '"+k.to_s+"'"
 #              if $sinatra
-#                $sinatra.halt 400,err
+#                $sinatra.raise OpenTox::BadRequestError.newerr
 #              else
 #                raise err
 #              end
diff --git a/report/statistical_test.rb b/report/statistical_test.rb
index bee6241..9461cac 100644
--- a/report/statistical_test.rb
+++ b/report/statistical_test.rb
@@ -78,7 +78,7 @@ module Reports
     def self.quit_r
       LIB::StatisticalTest.quit_r
     end
-    
+
   end
 
 end