hotfix qmrf sqlite

3 files changed, 34 insertions, 14 deletions

diff --git a/reach_reports/reach_application.rb b/reach_reports/reach_application.rb
index cd0695c..9b45e8b 100755
--- a/reach_reports/reach_application.rb
+++ b/reach_reports/reach_application.rb
@@ -5,6 +5,20 @@ end
 
 QMRF_EDITOR_URI = "http://ortona.informatik.uni-freiburg.de/qmrfedit2/OT_QMRFEditor.jnlp"
 
+# hack for as long as mysql lite is used
+def mysql_lite_retry( n_times=15 )
+  n_times.times do 
+    begin
+      yield
+      return
+    rescue => ex
+      LOGGER.warn "datamapper error, wait and retry : "+ex.message
+      sleep(1+rand(3)) # wait 1-3 seconds
+    end
+  end
+  yield # try a last time
+end
+
 require 'reach_reports/reach_persistance.rb'
 require 'reach_reports/reach_service.rb'
 
diff --git a/reach_reports/reach_persistance.rb b/reach_reports/reach_persistance.rb
index b90778b..2dd687a 100755
--- a/reach_reports/reach_persistance.rb
+++ b/reach_reports/reach_persistance.rb
@@ -1202,11 +1202,13 @@ module ReachReports
 #    end
 #  end
 
-  [ QsarSoftware, QsarIdentifier, QmrfAuthor, ModelAuthor, Reference, QsarGeneralInformation, ModelEndpoint, QsarEndpoint, AlgorithmExplicit, 
-    AlgorithmsDescriptor, DescriptorsGenerationSoftware, QsarAlgorithm, AppDomainSoftware, QsarApplicabilityDomain, TrainingSetData, 
-    QsarRobustness, ValidationSetData, QsarPredictivity, QsarInterpretation, Bibliography, AttachmentTrainingData, AttachmentValidationData, 
-    AttachmentDocument, QsarMiscellaneous, QmrfSummary, QmrfReport ].each do |model|
-    model.auto_upgrade!
-    model.raise_on_save_failure = true
+  mysql_lite_retry do
+    [ QsarSoftware, QsarIdentifier, QmrfAuthor, ModelAuthor, Reference, QsarGeneralInformation, ModelEndpoint, QsarEndpoint, AlgorithmExplicit, 
+      AlgorithmsDescriptor, DescriptorsGenerationSoftware, QsarAlgorithm, AppDomainSoftware, QsarApplicabilityDomain, TrainingSetData, 
+      QsarRobustness, ValidationSetData, QsarPredictivity, QsarInterpretation, Bibliography, AttachmentTrainingData, AttachmentValidationData, 
+      AttachmentDocument, QsarMiscellaneous, QmrfSummary, QmrfReport ].each do |model|
+      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 0cf4172..1ec48e8 100755
--- a/reach_reports/reach_service.rb
+++ b/reach_reports/reach_service.rb
@@ -277,7 +277,9 @@ module ReachReports
     end
     task.progress(90) if task
     
-    r.save
+    mysql_lite_retry do 
+      r.save
+    end
     task.progress(100) if task
   end
   
@@ -292,14 +294,16 @@ module ReachReports
 #  end
   
   def self.get_report(type, id)
-    
-    case type
-    when /(?i)QMRF/
-      report = ReachReports::QmrfReport.get(id)
-    when /(?i)QPRF/
-      report = ReachReports::QprfReport.get(id)
+    report = nil
+    mysql_lite_retry(3) do
+      case type
+      when /(?i)QMRF/
+        report = ReachReports::QmrfReport.get(id)
+      when /(?i)QPRF/
+        report = ReachReports::QprfReport.get(id)
+      end
+      raise OpenTox::NotFoundError.new type+" report with id '#{id}' not found." unless report
     end
-    raise OpenTox::NotFoundError.new type+" report with id '#{id}' not found." unless report
     return report
   end