Merge branch 'hotfix/qmrf_mysqlite'

5 files changed, 51 insertions, 19 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
 
diff --git a/report/report_content.rb b/report/report_content.rb
index ca04f25..3e3c3d4 100755
--- a/report/report_content.rb
+++ b/report/report_content.rb
@@ -43,7 +43,8 @@ class Reports::ReportContent
     
     section_test = @xml_report.add_section(@current_section, section_title)
     @xml_report.add_paragraph(section_test, section_text) if section_text
-    @xml_report.add_table(section_test, test_attribute.to_s+", significance-level: "+level.to_s, table, true, true)  
+    @xml_report.add_table(section_test, test_attribute.to_s+", significance-level: "+level.to_s, table, true, true)
+    Reports::ReportStatisticalTest.quit_r
   end
   
   def add_predictions( validation_set, 
diff --git a/report/statistical_test.rb b/report/statistical_test.rb
index c37827e..5e5ea3a 100644
--- a/report/statistical_test.rb
+++ b/report/statistical_test.rb
@@ -1,29 +1,35 @@
 #require "rubygems"
 #require "rinruby"
-#R.quit
 
 module LIB
   class StatisticalTest
   
-    @@r = RinRuby.new(true,false)
-    
     # -1 -> array1 < array2
     # 0 -> not difference
     # 1 -> array2 > array1
     #
     def self.pairedTTest(array1, array2, significance_level=0.95)
+    
+      @@r = RinRuby.new(true,false) unless defined?(@@r) and @@r
       @@r.assign "v1",array1
       @@r.assign "v2",array2
       @@r.eval "ttest = t.test(v1,v2,paired=T)"
       t = @@r.pull "ttest$statistic"
       p = @@r.pull "ttest$p.value"
-      #@@r.quit
       if (1-significance_level > p)
         t
       else
         0
       end
     end
+    
+    def self.quit_r
+      begin
+        @@r.quit
+        @@r = nil
+      rescue
+      end
+    end
   end
 end
 
@@ -68,6 +74,11 @@ module Reports
       LOGGER.debug "paired-t-testing "+attribute.to_s+" "+array1.inspect+" vs "+array2.inspect
       LIB::StatisticalTest.pairedTTest(array1, array2, significance_level)
     end
+    
+    def self.quit_r
+      LIB::StatisticalTest.quit_r
+    end
+
   end
 
 end