Added logging to help monitor shadow run folderes.

Added runfolder path to some of log messages so that it is
easier to search the logs.

Added comments to the staging monitor scripts to highlight
that the script is likely to discover and process shadow
runfolders.

bin/staging_area_monitor

@@ -55,7 +55,24 @@ sub main {
     while (1) {
 
         _log_noindent($time->());
-
+
+        #######
+        # find_live finds all run folders in 'incoming and 'analysis'.
+        # It can return two run folders for the same run, one in each
+        # of 'incoming and 'analysis'. In this case the  run folder in
+        # incoming is a 'shadow' run folder, which is sometimes created
+        # by the instrument well after the original run.
+        # 
+        # It is also possible for a 'shadow' folder to exist in 'incoming',
+        # while the run folder with the original data is already in 'outgoing'.
+        #
+        # Depending on how much data is present in a 'shadow' run folder,
+        # the staging monitor might attempt to update the trackign database.
+        # Mostly the values will be the same as for teh main run folder.
+        # However, the actual cycle count might be different. Therefore, it is
+        # important never to upload to the database a cycle count that is
+        # lower than the one already stored in the database.
+        #  
         foreach my $run_path ( $monitor->find_live($staging_area) ) {
             _log_noindent("Considering $run_path");
             my $done;

lib/Monitor/RunFolder.pm

@@ -23,7 +23,7 @@ sub update_cycle_count {
   defined $latest_cycle or croak 'Latest cycle count not supplied';
   my $actual_cycle = $self->tracking_run()->actual_cycle_count();
   $actual_cycle ||= 0;
-  if ($latest_cycle > $actual_cycle) {
+  if ($latest_cycle > $actual_cycle) { # A very important condition!
     $self->tracking_run()->update({actual_cycle_count => $latest_cycle});
     return 1;
   }

lib/Monitor/RunFolder/Staging.pm

@@ -368,7 +368,7 @@ sub update_run_from_path { ##### Method to deal with one run folder
     }
 
     if ($folder->is_in_analysis) {
-        _log('Folder is in /analysis/');
+        _log("Folder $run_path is in /analysis/");
 
         if( $run_status eq 'qc complete') {
             _log('Moving run folder to /outgoing/');
@@ -377,7 +377,7 @@ sub update_run_from_path { ##### Method to deal with one run folder
         return; # Nothing else to do for a folder in /analysis/
     }
 
-    _log('Folder is in /incoming/');
+    _log("Folder $run_path is in /incoming/");
 
     # If we don't remember seeing it before, set the folder name and glob;
     # set staging tag, if appropriate, set/fix instrument side, workflow side.
@@ -411,7 +411,7 @@ sub update_run_from_path { ##### Method to deal with one run folder
 
         my $latest_cycle = $folder->get_latest_cycle();
         if ($folder->update_cycle_count($latest_cycle)) {
-            _log("Cycle count updated to $latest_cycle");
+            _log("Cycle count updated to $latest_cycle for $run_path");
         }
 
         if ( $run_status eq 'run pending' )  {