Index: trunk/ippTasks/science.cleanup.pro
===================================================================
--- trunk/ippTasks/science.cleanup.pro	(revision 34203)
+++ trunk/ippTasks/science.cleanup.pro	(revision 34775)
@@ -13,4 +13,17 @@
 
 check.globals
+
+# if set tell cleanup script to check for files from all components regardless of the data_state
+$CHECK_ALL_COMPONENTS = 0
+macro set.check.all.components
+    $CHECK_ALL_COMPONENTS = 1
+end
+macro clear.check.all.components
+    $CHECK_ALL_COMPONENTS = 0
+end
+macro get.check.all.components
+    echo CHECK_ALL_COMPONENTS = $CHECK_ALL_COMPONENTS
+end
+
 
 ## chip.cleanup.pro : -*- sh -*-
@@ -130,14 +143,22 @@
     book getword chipPendingCleanup $pageName state -var CLEANUP_MODE
     book getword chipPendingCleanup $pageName chip_id -var CHIP_ID
+    book getword chipPendingCleanup $pageName exp_tag -var EXP_TAG
+    book getword chipPendingCleanup $pageName workdir -var WORKDIR_TEMPLATE
     book getword chipPendingCleanup $pageName dbname -var DBNAME
 
-    # specify choice of local or remote host based on camera and chip (class_id)
+    # specify choice of local or remote host based on camera and chip (in this case FPA)
     set.host.for.camera $CAMERA FPA
+
+    set.workdir.by.camera $CAMERA FPA $WORKDIR_TEMPLATE $default_host WORKDIR
+
+    sprintf LOGFILE "%s/%s/%s.ch.%s.cleanup.log" $WORKDIR $EXP_TAG $EXP_TAG $CHIP_ID
 
     stdout $LOGDIR/chip.cleanup.log
     stderr $LOGDIR/chip.cleanup.log
 
-    # XXX is everything listed here needed?
-    $run = ipp_cleanup.pl --stage chip --stage_id $CHIP_ID --camera $CAMERA --mode $CLEANUP_MODE
+    $run = ipp_cleanup.pl --stage chip --stage_id $CHIP_ID --camera $CAMERA --mode $CLEANUP_MODE --logfile $LOGFILE
+    if ($CHECK_ALL_COMPONENTS)
+        $run = $run --check-all
+    end
     add_standard_args run
 
@@ -282,4 +303,6 @@
     book getword camPendingCleanup $pageName state  -var CLEANUP_MODE
     book getword camPendingCleanup $pageName cam_id -var CAM_ID
+    book getword camPendingCleanup $pageName exp_tag -var EXP_TAG
+    book getword camPendingCleanup $pageName workdir -var WORKDIR_TEMPLATE
     book getword camPendingCleanup $pageName dbname -var DBNAME
 
@@ -287,9 +310,14 @@
     set.host.for.camera $CAMERA FPA
 
+    # set the WORKDIR variable
+    set.workdir.by.camera $CAMERA FPA $WORKDIR_TEMPLATE $default_host WORKDIR
+
+    ## generate LOGFILE specific to this exposure (& cam_id)
+    sprintf LOGFILE "%s/%s/%s.cm.%s.cleanup.log" $WORKDIR $EXP_TAG $EXP_TAG $CAM_ID
+
     stdout $LOGDIR/camera.cleanup.log
     stderr $LOGDIR/camera.cleanup.log
 
-    # XXX is everything listed here needed?
-    $run = ipp_cleanup.pl --stage camera --stage_id $CAM_ID --camera $CAMERA --mode $CLEANUP_MODE
+    $run = ipp_cleanup.pl --stage camera --stage_id $CAM_ID --camera $CAMERA --mode $CLEANUP_MODE --logfile $LOGFILE
     add_standard_args run
 
@@ -591,8 +619,13 @@
     book getword warpPendingCleanup $pageName state -var CLEANUP_MODE
     book getword warpPendingCleanup $pageName warp_id -var WARP_ID
+    book getword warpPendingCleanup $pageName exp_tag -var EXP_TAG
+    book getword warpPendingCleanup $pageName workdir -var WORKDIR_TEMPLATE
     book getword warpPendingCleanup $pageName dbname -var DBNAME
 
     # specify choice of local or remote host based on camera and warp (class_id)
     set.host.for.camera $CAMERA FPA
+    set.workdir.by.camera $CAMERA $WARP_ID $WORKDIR_TEMPLATE $default_host WORKDIR
+
+    sprintf LOGFILE "%s/%s/%s.wrp.%s.cleanup.log" $WORKDIR $EXP_TAG $EXP_TAG $WARP_ID
 
     stdout $LOGDIR/warp.cleanup.log
@@ -600,5 +633,8 @@
 
     # XXX is everything listed here needed?
-    $run = ipp_cleanup.pl --stage warp --stage_id $WARP_ID --camera $CAMERA --mode $CLEANUP_MODE
+    $run = ipp_cleanup.pl --stage warp --stage_id $WARP_ID --camera $CAMERA --mode $CLEANUP_MODE --logfile $LOGFILE
+    if ($CHECK_ALL_COMPONENTS)
+        $run = $run --check-all
+    end
     add_standard_args run
 
@@ -748,8 +784,13 @@
     book getword diffCleanup $pageName state -var CLEANUP_MODE
     book getword diffCleanup $pageName diff_id -var DIFF_ID
+    book getword diffCleanup $pageName tess_id -var TESS_ID
+    book getword diffCleanup $pageName workdir -var WORKDIR_TEMPLATE
     book getword diffCleanup $pageName dbname -var DBNAME
 
     # specify choice of local or remote host based on camera and diff (class_id)
     set.host.for.camera $CAMERA FPA
+    set.workdir.by.camera $CAMERA $DIFF_ID $WORKDIR_TEMPLATE $default_host WORKDIR
+    sprintf LOGFILE "%s/%s/%s.dif.%s.cleanup.log" $WORKDIR $TESS_ID $TESS_ID $DIFF_ID
+
 
     stdout $LOGDIR/diff.cleanup.log
@@ -757,5 +798,8 @@
 
     # XXX is everything listed here needed?
-    $run = ipp_cleanup.pl --stage diff --stage_id $DIFF_ID --camera $CAMERA --mode $CLEANUP_MODE
+    $run = ipp_cleanup.pl --stage diff --stage_id $DIFF_ID --camera $CAMERA --mode $CLEANUP_MODE --logfile $LOGFILE
+    if ($CHECK_ALL_COMPONENTS)
+        $run = $run --check-all
+    end
     add_standard_args run