Rollup before configuration integration

workflow/qhtcp-workflow

@@ -1841,7 +1841,7 @@ wrapper java_extract
 # @exitcode 1 if expected output file does not exist
 java_extract() {
   debug "Running: ${FUNCNAME[0]}"
-  classpath="$APPS_DIR/java/weka-clustering.jar"
+  classpath="$APPS_DIR/java/weka-clustering/weka-clustering.jar"
 
   output_file="${1:-$QHTCP_RESULTS_DIR}/REMcRdy_lm_only.csv-finalTable.csv"
 
@@ -1855,7 +1855,6 @@ java_extract() {
     "${4:-"$APPS_DIR/java/ORF_List_Without_DAmPs.txt"}"
     1
     true
-    true
   )
 
   debug "pushd && ${java_cmd[*]} && popd"
@@ -2269,19 +2268,23 @@ main() {
 
   # Find a scans directory
   # local scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans")
-  local scans_heirarchy=( 
-    "$SCANS_DIR" 
+  local scans_heirarchy=(
     "$SCRIPT_DIR/scans"
     "/mnt/data/scans"
     "$SCRIPT_DIR/templates/scans-demo"
-    "$SCRIPT_DIR/scans" # fallback and create if others not found
   )
   
-  [[ -z $SCANS_DIR ]] && for d in "${scans_heirarchy[@]}"; do
-    if [[ -d $d ]]; then
-      declare -gx SCANS_DIR="$d"
-    fi
-  done
+  # Find an existing scans dir if SCANS_DIR is not set
+  if [[ -z $SCANS_DIR ]]; then
+    for d in "${scans_heirarchy[@]}"; do
+      if [[ -d $d ]]; then
+        declare -gx SCANS_DIR="$d"
+        break
+      fi
+      declare -gx SCANS_DIR="${scans_heirarchy[0]}"
+    done
+  fi
+
   if ! [[ -d $SCANS_DIR ]]; then
     # This is not something we do often, so ask
     if ask "Create the scans directory: $SCANS_DIR?"; then
@@ -2331,11 +2334,6 @@ main() {
   ((DEBUG)) && declare -p
 
   interactive_header "$@"
-
-  # # Prompt user for the PROJECT if we still don't have one
-  # if [[ ${#PROJECTS[@]} -eq 0 ]]; then
-  #   ask_pn && PROJECTS+=("${ADD_PROJECTS[@]}")
-  # fi
   
   for i in "${!PROJECTS[@]}"; do
     if ! sanitize_pn "${PROJECTS[$i]}"; then
@@ -2353,7 +2351,7 @@ main() {
   # Sanitize MODULES
   for i in "${!MODULES[@]}"; do
     if ! [[ " ${ALL_MODULES[*]} " =~ [[:space:]]${MODULES[i]}[[:space:]] ]]; then
-      echo "Module ${MODULES[$i]} not in the module list"
+      echo "Module ${MODULES[$i]} is not available, removing"
       read -r -p "Enter replacement module name: " module
       ! [[ " ${ALL_MODULES[*]} " =~ [[:space:]]${module}[[:space:]] ]] || (echo "RTFM"; return 1)
       MODULES[i]="$module"
@@ -2363,11 +2361,11 @@ main() {
 
   # Sanitize wrappers
   for i in "${!WRAPPERS[@]}"; do
-    if ! [[ " ${ALL_WRAPPERS[*]} " =~ [[:space:]]${WRAPPERS[i]}[[:space:]] ]]; then
-      echo "Wrapper ${WRAPPERS[$i]} not in the module list, removing"
-      unset "WRAPPERS[$i]" "WRAPPERS[$((i+1))]"
+    IFS=',' read -ra args <<< "$wrapper" # load the wrapper and args
+    if ! [[ " ${ALL_WRAPPERS[*]} " =~ [[:space:]]${args[0]}[[:space:]] ]]; then
+      echo "Wrapper ${WRAPPERS[$i]} is not available, removing"
+      unset "WRAPPERS[$i]"
     fi
-    continue 2 # skip the arguments string
   done
 
   # Loop over projects
@@ -2387,8 +2385,8 @@ main() {
     declare -gx GTF_OUT_DIR="$QHTCP_RESULTS_DIR/gtf"
     declare -gx R_LIBS_USER=${R_LIBS_USER:-"$HOME/R/$SCRIPT_NAME"}
     
-    # ((DEBUG)) && declare -p
-
+    # ((DEBUG)) && declare -p # for when the going gets rough
+    debug "Project: $PROJECT_NAME"
     debug "Active modules: ${MODULES[*]}"
     debug "Active wrappers and their args: ${WRAPPERS[*]}"
 
@@ -2401,7 +2399,7 @@ main() {
 
     # Run selected wrappers
     for wrapper in "${WRAPPERS[@]}"; do
-      IFS=',' read -ra args <<< "$wrapper" # load the command args
+      IFS=',' read -ra args <<< "$wrapper" # load the wrapper and args
       if ask "Run ${args[0]} wrapper with args ${args[*]:1}?"; then
         "${args[0]}" "${args[@]:1}" || return 1
       fi
@@ -2415,7 +2413,8 @@ main() {
   unset MODULES WRAPPERS EXCLUDE_MODULES STUDIES SET_STUDIES YES
 }
 
-# (Safe) main loop if we want to rerun automatically
+# During development it's better to just exit
+# (Safer) main loop for automatic rerun
 # if main "$@"; then
 #   for ((i=1; i<2; i++)); do
 #     main &&