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Add debugging output

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Bryan Roessler
2024-07-31 16:10:15 -04:00
parent 124c7696ba
commit b2f1d72a51
1 changed files with 22 additions and 15 deletions
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workflow/qhtcp-workflow
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@@ -1484,7 +1484,7 @@ main() {
SCRIPT_DIR=$(dirname "$SCRIPT") SCRIPT_DIR=$(dirname "$SCRIPT")
# Global directory variables # Global directory variables
TEMPLATES_DIR="$SCRIPT_DIR/templates" declare -g TEMPLATES_DIR="$SCRIPT_DIR/templates"
APPS_DIR="$SCRIPT_DIR/apps" APPS_DIR="$SCRIPT_DIR/apps"
DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match
# scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans") # scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans")
@@ -1492,7 +1492,7 @@ main() {
# Find a scans directory # Find a scans directory
[[ -z $SCANS_DIR ]] && for d in "${scans_heirarchy[@]}"; do [[ -z $SCANS_DIR ]] && for d in "${scans_heirarchy[@]}"; do
if [[ -d $d ]]; then if [[ -d $d ]]; then
SCANS_DIR="$d" declare -g SCANS_DIR="$d"
fi fi
done done
if ! [[ -d $SCANS_DIR ]]; then if ! [[ -d $SCANS_DIR ]]; then
@@ -1512,7 +1512,7 @@ main() {
for d in "${out_heirarchy[@]}"; do for d in "${out_heirarchy[@]}"; do
if [[ -d $d ]]; then if [[ -d $d ]]; then
debug "Using output directory: $d" debug "Using output directory: $d"
OUT_DIR="$d" declare -g OUT_DIR="$d"
fi fi
done done
@@ -1521,7 +1521,7 @@ main() {
PROJECT_PREFIX="${DATE}_${PROJECT_USER}" # reversed these so easier to sort and parse date PROJECT_PREFIX="${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 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 parse_input "$@" # parse arguments with getopt
@@ -1566,22 +1566,29 @@ main() {
# Loop over projects # Loop over projects
for PROJECT in "${PROJECTS[@]}"; do for PROJECT in "${PROJECTS[@]}"; do
declare -g PROJECT declare -g PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT"
PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT" declare -g PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723 declare -g PROJECT_SUFFIX="${PROJECT#????????_*_}"
PROJECT_SUFFIX="${PROJECT#????????_*_}" declare -g PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}" declare -g STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt" declare -g QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT" declare -g QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp" declare -g STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp" declare -g STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
if ((DEBUG)); then
declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \
PROJECTS PROJECT \
PROJECT_SCANS_DIR PROJECT_DATE PROJECT_SUFFIX \
PROJECT_USER STUDIES_ARCHIVE_FILE QHTCP_PROJECT_DIR QHTCP_TEMPLATE_DIR \
STUDY_TEMPLATE_DIR STUDY_INFO_FILE
fi
# Run selected modules # Run selected modules
for m in "${MODULES[@]}"; do for m in "${MODULES[@]}"; do
ask "Run $m?" && "$m" ask "Run $m?" && "$m"
done done
done done
} }
main "$@" main "$@"