I think fixed segmentation fault and also logic to mark job as failur…

…e when there are errors. In addition able to capture partial successful outputs.

instrument_developer_script.rb

@@ -106,7 +106,7 @@ def self.instrument_code orig_r_script
     end
 
     # automatically take care of FOOTER mandatory tag
-    arr_instrumented[arr_instrumented.length] = "\nHTMLEndFile()\nsink()\n\n}, interrupt = function(ex) {\nprint (\"got exception\");\nprint(ex);\n}, error = function(ex) {\nprint (\"got error\");\nprint(ex);\n}, finally = {\n})\n"
+    arr_instrumented[arr_instrumented.length] = "\n}, interrupt = function(ex) {\nprint (\"got exception: Failed Job\");\n returnstatus=\"FAILED JOB, PLEASE CHECK LOG\"; \nHTML(returnstatus, file=crdata_target);\nprint(ex);\n}, error = function(ex) {\nprint (\"got error: Failed Job\");\n returnstatus=\"FAILED JOB, PLEASE CHECK LOG\"; \nHTML(returnstatus, file=crdata_target);\nprint(ex);\n}, finally = {\nHTMLEndFile()\nsink()\n\n})\n"
 
     # now write instrumented array into the original R script
     r_script_file_handle = File.open(orig_r_script, aModeString="w")

job.rb

@@ -26,13 +26,14 @@ class Job
   VALUE_ENUMERATION = "Enumeration"
   VALUE_STRING = "String"
 
-  attr_reader :r_script_filename, :job_id, :curr_uuid, :r_call_interface
+  attr_reader :r_script_filename, :job_id, :curr_uuid, :r_call_interface, :job_status
 
   def initialize(xml_response)
     @r_call_interface = RSRuby.instance
     @r_script_filename = nil
     @job_id = 0
     @curr_uuid = Global.rand_uuid
+    @job_status = Global::SUCCESSFUL_JOB
     # log request
     Global.logger.info(xml_response)
 
@@ -97,9 +98,16 @@ def run
       # to capture HTML output as well as log stuff
       InstrumentDeveloperScript::instrument_code "#{@curr_uuid}.r"
     end
+
+    # assume that job will be successful by default
+    # let the R script will indicate if failure
+    @job_status = Global::SUCCESSFUL_JOB
 
     # run the instrumented script
     @r_call_interface.eval_R("source('#{@curr_uuid}.r')")
+
+    # fetch the r program execution status
+    File.open( Global::JOB_LOG ) {|io| io.grep(/#{Global::FAILED_JOB}/) { |s| @job_status = Global::FAILED_JOB }}
   end
 
   def get_id

processing_node.rb

@@ -58,15 +58,15 @@ def run
           job.store_results_and_logs if !job.nil?
 
           # STEP 8
-          job_completed(job, true) if !job.nil?
+          job_completed(job) if !job.nil?
         rescue => err
           Global.logger.fatal(err)
 
           # STEP 7
           job.store_results_and_logs if !job.nil?
 
           # STEP 8
-          job_completed(job, false) if job.nil?
+          job_completed(job) if job.nil?
           job = nil
         end
       rescue => err2
@@ -79,15 +79,22 @@ def run
 
   def fetch_next_job
     # issue command to fetch next job
-    xml_response = @site['jobs_queues/run_next_job'].put '', {:content_length => '0', :content_type => 'text/xml'}
-    job = Job.new(xml_response)
-
-    job
+    begin
+      xml_response = @site['jobs_queues/run_next_job'].put '', {:content_length => '0', :content_type => 'text/xml'}
+      job = Job.new(xml_response)
+      return job
+    rescue Exception => exception_not_found
+      return_status = exception_not_found.to_s
+      # don't report too much stuff to log, unnecessary logging
+      # ResourceNotFound is reported when there are no new jobs
+      Global.logger.fatal(return_status) if !/ResourceNotFound/.match(return_status)
+      return nil
+    end
   end
 
-  def job_completed(job, successful)
+  def job_completed(job)
     # mark status of the job on server
-    if successful
+    if job.job_status == Global::SUCCESSFUL_JOB
       #success_length = "success=true".length
       #@site["jobs/#{job.get_id}/done.xml?success=true"].put '', {:content_length => '0', :content_type => 'text/plain'}
       Global.logger.info('COMPLETED JOB, MARKING JOB SUCCESSFUL')

testing/test_instrumentation.r

@@ -10,7 +10,6 @@ plot(tmp)
 
 #<crdata_image caption="Second Graph">plot(tmp)
 #</crdata_image>
-
 #<crdata_image caption="Third Graph">plot(tmp)</crdata_image>
 
 #<crdata_image>plot(tmp)</crdata_image>