fix: staging of files from exeQAtimelines

qa-physics/exeQAtimelines.sh

@@ -2,7 +2,7 @@
 # after finishing analysis in the `QA` subdirectory, this script will call
 # qaCut.groovy on the results
 
- set -e
+set -e
 
 if [ -z "$TIMELINESRC" ]; then source `dirname $0`/../bin/environ.sh; fi
 
@@ -11,20 +11,23 @@ if [ $# -ne 2 ]; then
 
   - run this script from \`$TIMELINESRC/qa-physics\`
   - [INPUT_DIR] is the location of the output timeline files from Step 2
-    (likely \`outfiles/[DATASET]/timeline_physics_qa\`)
+    (likely \`outfiles/[DATASET]\`)
   - the \`qaTree.json\` file used will be \`QA/qa.[DATASET]/qaTree.json\`
   """ >&2
   exit 101
 fi
 inDir=$1
 dataset=$2
 
-qaDir=$inDir/outmon.qa
+tlDir=$inDir/timeline_physics_qa
+qaDir=$tlDir/outmon.qa
 
 mkdir -p $qaDir
 rm -r $qaDir
 mkdir -p $qaDir
 
+rm -vf $tlDir/outdat/passFractions.dat
+
 # defect bit lists
 # FIXME: violates DRY (maybe use `jq` to parse from a bit definition's JSON file)
 defect_bits_FD=(
@@ -55,18 +58,21 @@ defect_bits_FT=(
 
 for bit in ${defect_bits_FD[@]}; do
   echo "================ FD DEFECT BIT $bit ================"
-  run-groovy $TIMELINE_GROOVY_OPTS qaCut.groovy $inDir $dataset false $bit
-  qa=$(ls -t $inDir/outmon/electron_FD_*QA*.hipo | grep -v epoch | head -n1)
+  run-groovy $TIMELINE_GROOVY_OPTS qaCut.groovy $tlDir $dataset false $bit
+  qa=$(ls -t $tlDir/outmon/electron_FD_*QA*.hipo | grep -v epoch | head -n1)
   mv -v $qa ${qaDir}/$(echo $qa | sed 's/^.*_QA_//g')
 done
 
 for bit in ${defect_bits_FT[@]}; do
   echo "================ FT DEFECT BIT $bit ================"
-  run-groovy $TIMELINE_GROOVY_OPTS qaCut.groovy $inDir $dataset FT $bit
-  qa=$(ls -t $inDir/outmon/electron_FT_*QA*.hipo | grep -v epoch | head -n1)
+  run-groovy $TIMELINE_GROOVY_OPTS qaCut.groovy $tlDir $dataset FT $bit
+  qa=$(ls -t $tlDir/outmon/electron_FT_*QA*.hipo | grep -v epoch | head -n1)
   mv -v $qa ${qaDir}/$(echo $qa | sed 's/^.*_QA_//g')
 done
 
 cp QA/qa.${dataset}/qaTree.json $qaDir
 echo ""
-cat $inDir/outdat/passFractions.dat
+cat $tlDir/outdat/passFractions.dat
+
+echo "================ STAGE TIMELINES ================"
+./stageTimelines.sh $tlDir $inDir/timeline_web

qa-physics/stageTimelines.sh

@@ -46,10 +46,14 @@ extraList=(
   live_time_average
   relative_yield
 )
-for extraFile in ${extraList[@]}; do
-  mv -v $extraFile.hipo phys_qa_extra/
+for hipoFile in $(ls *.hipo); do
+  hipoFilePatt=\\b$(basename $hipoFile .hipo)\\b
+  if [[ ${extraList[@]} =~ $hipoFilePatt ]]; then
+    cp -v $hipoFile phys_qa_extra/
+  else
+    cp -v $hipoFile phys_qa/
+  fi
 done
-mv -v *.hipo phys_qa/
 
 # if QADB timelines were produced, copy them too
 if [ -d $inputDir.qa ]; then