refactor: detector QA cut code should not be standalone (#306)

Author: c-dilks

bin/qtl-analysis

@@ -267,7 +267,6 @@ inputDir=$(realpath $inputDir)
 [ -z "$outputDir" ] && outputDir=$(realpath $(pwd -P)/outfiles/$dataset) || outputDir=$(realpath $outputDir)
 
 # set subdirectories
-finalDirPreQA=$outputDir/timeline_web_preQA
 finalDir=$outputDir/timeline_web
 logDir=$outputDir/log
 
@@ -279,7 +278,6 @@ $sep
 INPUT_DIR       = $inputDir
 DATASET_NAME    = $dataset
 OUTPUT_DIR      = $outputDir
-FINAL_DIR_PREQA = $finalDirPreQA
 FINAL_DIR       = $finalDir
 LOG_DIR         = $logDir
 PUBLISH_DIR     = $publishDir
@@ -316,9 +314,9 @@ detDirs=(
 
 # cleanup output directories
 if $enableAna; then
-  if [ -d $finalDirPreQA ]; then
-    printWarning "removing output directory $finalDirPreQA"
-    rm -r $finalDirPreQA
+  if [ -d $finalDir ]; then
+    printWarning "removing output directory $finalDir"
+    rm -r $finalDir
   fi
   if [ -d $logDir ]; then
     printWarning "removing log directory $logDir"
@@ -327,7 +325,7 @@ if $enableAna; then
 fi
 
 # make output directories
-mkdir -p $logDir $finalDirPreQA $finalDir
+mkdir -p $logDir $finalDir
 
 
 ##################################################################################
@@ -366,7 +364,7 @@ if $enableAna; then
   }
 
   # change working directory to output directory
-  pushd $finalDirPreQA
+  pushd $finalDir
 
   # make detector subdirectories
   for detDir in ${detDirs[@]}; do
@@ -439,26 +437,6 @@ if $enableAna; then
   popd
 fi
 
-######################################
-# run QA
-######################################
-
-if $enableAna; then
-  # first, copy the timelines to the final timeline directory
-  echo ">>> copy timelines to final directory..."
-  cp -rL $finalDirPreQA/* $finalDir/
-  # then add the QA lines
-  echo ">>> add QA lines..."
-  logFile=$logDir/qa
-  $TIMELINESRC/libexec/run-groovy-timeline.sh $TIMELINESRC/qa-detectors/util/applyBounds.groovy $finalDirPreQA $finalDir > $logFile.out 2> $logFile.err || touch $logFile.fail
-  outputFiles=$(find $finalDir -name "*_QA.hipo")
-  logFile=$logDir/qa_hipo-check
-  if [ -n "$outputFiles" ]; then
-    $TIMELINESRC/libexec/hipo-check.sh $outputFiles > $logFile.out 2> $logFile.err || touch $logFile.fail
-  fi
-fi
-
-
 
 ######################################
 # error checking

doc/dev_notes.md

@@ -28,9 +28,7 @@ flowchart TB
 
     subgraph Step 2: Timeline Analysis
         subgraph "<strong>bin/qtl analysis</strong>"
-            timelineDetectorsPreQA["<strong>Make detector timelines</strong><br/>org.jlab.clas.timeline.analysis.run_analysis"]:::proc
-            outTimelineDetectorsPreQA{{outfiles/$dataset/timeline_web_preQA/$detector/*.hipo}}:::timeline
-            timelineDetectors["<strong>Draw QA lines</strong><br/>qa-detectors/: applyBounds.groovy"]:::proc
+            timelineDetectors["<strong>Make detector timelines</strong><br/>org.jlab.clas.timeline.analysis.run_analysis"]:::proc
             outTimelineDetectors{{outfiles/$dataset/timeline_web/$detector/*.hipo}}:::timeline
             deploy["<strong>Publishing</strong><br/>handled by qtl analysis"]:::proc
         end
@@ -41,7 +39,7 @@ flowchart TB
     end
     timelineDir{{timelines on web server}}:::timeline
 
-    outplots --> timelineDetectorsPreQA --> outTimelineDetectorsPreQA --> timelineDetectors --> outTimelineDetectors
+    outplots --> timelineDetectors --> outTimelineDetectors
     outdat   --> timelinePhysics
     outmon   --> timelinePhysics
     timelinePhysics --> outTimelinePhysics

doc/procedure.md

@@ -80,7 +80,5 @@ qtl analysis -i /path/to/output/files -p some/publish/directory/rga_sp19_v5
 
 > [!NOTE]
 > - detector timeline production is handled by the [`org.jlab.clas.timeline.analysis` package](/src/main/java/org/jlab/clas/timeline/analysis)
-> - QA of detector timelines is handled by the [`qa-detectors/` subdirectory](/qa-detectors);
->   see [its documentation](/qa-detectors/README.md)
 > - physics timeline production and QA are handled by the [`qa-physics/` subdirectory](/qa-physics);
 >   see [their documentation](/qa-physics/README.md)