Some header work

workflow/apps/matlab/easy/DMPexcel2mat.m

@@ -30,7 +30,7 @@ if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
       % This can be silent, not really an error
     end
 
-    for i=1:5 % give users 5 chances to get it right
+
     try
       % For standalone mode
       % GUI input for selecting a MasterPlate Excel file
@@ -53,9 +53,7 @@ if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
       disp('Rerunning directory selection');
       % I don't know what else we'll need to do here
     end
-    end
   else
-    for i=1:5 % give users 5 chances to get it right
     try
       % For standalone mode
       % GUI input for selecting a MasterPlate Excel file
@@ -80,7 +78,6 @@ if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
       % I don't know what else we'll need to do here
     end
   end
-  end
 else
   fprintf('Using MasterPlate file: %s skipping directory selection\n', masterPlateFile);
 end

workflow/apps/matlab/easy/EASYconsole.m

@@ -448,8 +448,7 @@ end
 
 function runResults_DBcombo_Callback(~, ~, ~)
   try
-    DgenResults %similar but semicolons removed to restore so cmdLine display info.
+    DgenResults
-    %Dgen241010qhtcp %par4global -convert 1x1cell of 384cells to be like previous 1x384 cells CFparameter
   catch ME
     fprintf('Error in DgenResults: %s\n', ME.message);
     EASYconsole

workflow/qhtcp-workflow

@@ -299,11 +299,46 @@ print_header() {
 
 	EOF
 
-  cat <<-EOF
+  echo "Using scans directory: $SCANS_DIR"
-		Available modules: ${ALL_MODULES[*]}     
+  echo "Change the SCANS_DIR environment variable to override"
-		Available submodules: ${ALL_SUBMODULES[*]}   
+  echo "Example: SCANS_DIR=/path/to/scans ./qhtcp-workflow"
-	EOF
+  echo ""
+  echo "Using output directory: $OUT_DIR"
+  echo "Change the out_DIR environment variable to override"
+  echo "Example: SCANS_DIR=/path/to/scans OUT_DIR=/path/to/out ./qhtcp-workflow"
+  echo ""
 
+  shopt -s nullglob
+  projects=("$SCANS_DIR"/*/)
+  shopt -u nullglob
+
+  echo "Available Projects:"
+  for i in "${!projects[@]}"; do
+    printf "%d. %s\n" "$((i+1))" "${projects[i]}"
+  done
+
+  echo "Available Modules:"
+  for i in "${!ALL_MODULES[@]}"; do
+    printf "%d. %s\n" "$((i+1))" "${ALL_MODULES[i]}"
+  done
+  echo ""
+  echo "Available Submodules:"
+  for i in "${!ALL_SUBMODULES[@]}"; do
+    printf "%d. %s\n" "$((i+1))" "${ALL_SUBMODULES[i]}"
+  done
+
+  last_index=$(( ${#ALL_MODULES} - 1 ))
+  read -r -p "Enter a comma deliminated list of modules to run: " response1
+  IFS=',' read -ra MODULES <<< "$response1"
+
+  last_index=$(( ${#ALL_SUBMODULES} - 1 ))
+  read -r -p "Enter the item number to select EASY results directory, default ($last_index): " response2
+  IFS=',' read -ra SUBMODULES <<< "$response2"
+
+  # cat <<-EOF
+	# 	Available modules: ${ALL_MODULES[*]}     
+	# 	Available submodules: ${ALL_SUBMODULES[*]}   
+	# EOF
 }
 
 
@@ -618,13 +653,13 @@ easy() {
   script="$EASY_DIR/EASYconsole.m"
 
   # Prompt user for suffix
-  echo "Using default EASY results directory: $EASY_RESULTS_DIR"
+  echo "Using EASY results directory: $EASY_RESULTS_DIR"
-  ((YES)) || read -r -p "Enter a custom suffix and/or hit enter to use the default (no suffix): " EASY_SUFFIX
+  ((YES)) || read -r -p "Enter a custom suffix and/or hit enter to use the default directory (no suffix): " EASY_SUFFIX
   [[ -n $EASY_SUFFIX ]] && EASY_RESULTS_DIR+="_$EASY_SUFFIX"
 
   # This dirname is separate from the project's so multiple EASY results can be generated
   declare -gx EASY_PROJECT_NAME="${EASY_RESULTS_DIR##*/}"
-  debug "EASY results output name: $EASY_PROJECT_NAME"
+  debug "EASY results project name: $EASY_PROJECT_NAME"
 
   # Backup and create EASY results dirs
   [[ -d $EASY_RESULTS_DIR ]] && backup "$EASY_RESULTS_DIR"
@@ -1498,19 +1533,19 @@ documentation() {
 main() {
   debug "Running: ${FUNCNAME[0]}" "$@"
   
-  # Where are we
+  # Some global vars
   SCRIPT=$(realpath -s "${BASH_SOURCE[0]}")
   SCRIPT_DIR=$(dirname "$SCRIPT")
-
-  print_header
-
-  # Global directory variables
-  declare -g TEMPLATES_DIR="$SCRIPT_DIR/templates"
   APPS_DIR="$SCRIPT_DIR/apps"
-  DATE="$(date +%Y%m%d)" # change in EASYconsole.m to match
+  TEMPLATES_DIR="$SCRIPT_DIR/templates"
-  # scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans")
+  PROJECT_USER="$(whoami)"
-  local scans_heirarchy=( "$SCANS_DIR" "./scans" "/mnt/data/scans" "./scans") # TODO change back for production, avoid actual scan dirs during testing
+  DATE="$(date +%Y%m%d)" # change in EASYconsole.m to match 'hardcode'
+
   # Find a scans directory
+  # TODO change back for production, avoid actual scan dirs during testing
+  # local scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans") 
+  local scans_heirarchy=( "$SCANS_DIR" "./scans" "/mnt/data/scans" "./scans")
+  
   [[ -z $SCANS_DIR ]] && for d in "${scans_heirarchy[@]}"; do
     if [[ -d $d ]]; then
       declare -g SCANS_DIR="$d"
@@ -1525,10 +1560,8 @@ main() {
       exit 1;
     fi
   fi
-  echo "Using scans directory: $SCANS_DIR"
-  echo "Change the SCANS environment variable to override"
-  echo "Example: SCANS=/path/to/scans ./qhtcp-workflow"
 
+  # Find an output directory
   local out_heirarchy=("$(dirname "$SCANS_DIR")/out" "$SCRIPT_DIR/out" "/mnt/data/out")
   for d in "${out_heirarchy[@]}"; do
     if [[ -d $d ]]; then
@@ -1545,17 +1578,18 @@ main() {
       debug "mkdir $SCRIPT_DIR/out"
       mkdir "$SCRIPT_DIR/out"
     else
-      err "No output directory, but attempting to continue..."
+      err "No output directory, attempting to continue..."
     fi
   fi
 
   # Set the automatic project directory prefix
-  PROJECT_USER="$(whoami)"
   PROJECT_PREFIX="${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 -a PROJECTS=() # this array will hold all of the projects for this run
 
+  print_header
+
   parse_input "$@" # parse arguments with getopt
 
   # Prompt user for the PROJECT if we still don't have one