Add debugging output

workflow/qhtcp-workflow

@@ -1484,7 +1484,7 @@ main() {
   SCRIPT_DIR=$(dirname "$SCRIPT")
 
   # Global directory variables
-  TEMPLATES_DIR="$SCRIPT_DIR/templates"
+  declare -g TEMPLATES_DIR="$SCRIPT_DIR/templates"
   APPS_DIR="$SCRIPT_DIR/apps"
   DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match
   # scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans")
@@ -1492,7 +1492,7 @@ main() {
   # Find a scans directory
   [[ -z $SCANS_DIR ]] && for d in "${scans_heirarchy[@]}"; do
     if [[ -d $d ]]; then
-      SCANS_DIR="$d"
+      declare -g SCANS_DIR="$d"
     fi
   done
   if ! [[ -d $SCANS_DIR ]]; then
@@ -1512,7 +1512,7 @@ main() {
   for d in "${out_heirarchy[@]}"; do
     if [[ -d $d ]]; then
       debug "Using output directory: $d"
-      OUT_DIR="$d"
+      declare -g OUT_DIR="$d"
     fi
   done
 
@@ -1521,7 +1521,7 @@ main() {
   PROJECT_PREFIX="${DATE}_${PROJECT_USER}" # reversed these so easier to sort and parse date
   sanitize_pn() { [[ $1 =~ [0-9][0-9][0-9][0-9][0-9][0-9][0-9][0-9]_.+_.+ ]]; } # sanitizer regex for prefix
   
-  declare -ag PROJECTS=() # this array will hold all of the projects for this run
+  declare -a PROJECTS=() # this array will hold all of the projects for this run
 
   parse_input "$@" # parse arguments with getopt
 
@@ -1566,22 +1566,29 @@ main() {
 
   # Loop over projects
   for PROJECT in "${PROJECTS[@]}"; do
-    declare -g PROJECT
-    PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT"
-    PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
-    PROJECT_SUFFIX="${PROJECT#????????_*_}"
-    PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
-    STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
-    QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
-    QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
-    STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
-    STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
+    declare -g PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT"
+    declare -g PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
+    declare -g PROJECT_SUFFIX="${PROJECT#????????_*_}"
+    declare -g PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
+    declare -g STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
+    declare -g QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
+    declare -g QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
+    declare -g STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
+    declare -g STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
+
+    if ((DEBUG)); then
+      declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \
+      PROJECTS PROJECT \
+      PROJECT_SCANS_DIR PROJECT_DATE PROJECT_SUFFIX \
+      PROJECT_USER STUDIES_ARCHIVE_FILE QHTCP_PROJECT_DIR QHTCP_TEMPLATE_DIR \
+      STUDY_TEMPLATE_DIR STUDY_INFO_FILE
+    fi
+
     # Run selected modules
     for m in "${MODULES[@]}"; do
       ask "Run $m?" && "$m"
     done
   done
-
 }
 
 main "$@"