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Export more vars on declare

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Bryan Roessler
2024-07-31 21:48:10 -04:00
parent a78b8e4d96
commit a672b66e1a
1 changed files with 72 additions and 79 deletions
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workflow/qhtcp-workflow
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@@ -587,7 +587,7 @@ easy() {
'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder. 'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder.
EOF EOF
EASY_DIR="$APPS_DIR/matlab/easy" declare -gx EASY_DIR="$APPS_DIR/matlab/easy"
script="$EASY_DIR/EASYconsole.m" script="$EASY_DIR/EASYconsole.m"
# Copy templates # Copy templates
@@ -604,14 +604,12 @@ easy() {
# TODO will need to play with the -sd startup option to see what works (well) # TODO will need to play with the -sd startup option to see what works (well)
# Skip this step altogether in auto mode since it requires graphical interaction # Skip this step altogether in auto mode since it requires graphical interaction
if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then
export PROJECT_SCANS_DIR PROJECT_DATE PROJECT_USER PROJECT # export PROJECT_SCANS_DIR PROJECT_DATE PROJECT_USER PROJECT
export EASY_DIR EASY_NAME EASY_SUFFIX EASY_RESULTS_DIR # export EASY_DIR EASY_NAME EASY_SUFFIX EASY_RESULTS_DIR
export MASTER_PLATE_FILE DRUG_MEDIA_FILE # export MASTER_PLATE_FILE DRUG_MEDIA_FILE
choose_easy_results_dir declare -gx DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT.xls"
declare -gx MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT.xls"
DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT.xls"
MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT.xls"
# Make EASY dirs # Make EASY dirs
debug "mkdir -p $EASY_RESULTS_DIR" debug "mkdir -p $EASY_RESULTS_DIR"
@@ -631,9 +629,6 @@ easy() {
# matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script" # matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
matlab -nosplash -r "run $script" matlab -nosplash -r "run $script"
fi fi
# Use the function return code see if we succeeded
# choose_easy_results_dir || (err "No EASY results found in $PROJECT_SCANS_DIR"; return 1)
} }
@@ -642,18 +637,16 @@ module ezview
# @description TODO WIP # @description TODO WIP
ezview() { ezview() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
export PROJECT_SCANS_DIR PROJECT_DATE PROJECT_USER EZVIEW_DIR
export EASY_RESULTS_DIR
EZVIEW_DIR="$APPS_DIR/matlab/ezview" declare -gx EZVIEW_DIR="$APPS_DIR/matlab/ezview"
script="$EZVIEW_DIR/EZviewGui.m" script="$EZVIEW_DIR/EZviewGui.m"
# Try to load EASY output dir fromENV or easy module if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then
# Then scan for EASY results
[[ -z $EASY_RESULTS_DIR ]] && choose_easy_results_dir
# Make EZview dirs # Make EZview dirs
# Start EZview
matlab -nosplash -r "run $script" matlab -nosplash -r "run $script"
fi
} }
@@ -1397,57 +1390,57 @@ get_studies() {
} }
submodule choose_easy_results_dir # # submodule choose_easy_results_dir #
# @description Chooses an EASY scans directory if the information is undefined # # @description Chooses an EASY scans directory if the information is undefined
# TODO: Standardize EASY output, it's hard to understand # # TODO: Standardize EASY output, it's hard to understand
# TODO eventually we could run this on multiple results dirs simultaneously with some refactoring # # TODO eventually we could run this on multiple results dirs simultaneously with some refactoring
# @exitcode 0 if successfully choose an EASY results dir # # @exitcode 0 if successfully choose an EASY results dir
# @set EASY_RESULTS_DIR string The working EASY output directory # # @set EASY_RESULTS_DIR string The working EASY output directory
choose_easy_results_dir() { # choose_easy_results_dir() {
debug "Running: ${FUNCNAME[0]}" # debug "Running: ${FUNCNAME[0]}"
declare -g EASY_RESULTS_DIR="$QHTCP_PROJECT_DIR/easy"
# Always backup existing output
# This would happen if you ran the same experiment twice in one day, for instance
[[ -d $EASY_RESULTS_DIR ]] && backup "$EASY_RESULTS_DIR"
if [[ ! -d $EASY_RESULTS_DIR ]]; then # # Always backup existing output
debug "mkdir $EASY_RESULTS_DIR" # # This would happen if you ran the same experiment twice in one day, for instance
mkdir "$EASY_RESULTS_DIR" # [[ -d $EASY_RESULTS_DIR ]] && backup "$EASY_RESULTS_DIR"
else
err "Could not create $EASY_RESULTS_DIR"
return 0
fi
# echo "Hit enter to use the default EASY results directory: $default_easy_results_dir" # if [[ ! -d $EASY_RESULTS_DIR ]]; then
# if ! (( YES )); then # debug "mkdir $EASY_RESULTS_DIR"
# read -r -p "Or enter a custom directory name, example: $PROJECT" dirname # mkdir "$EASY_RESULTS_DIR"
# [[ -z $dirname ]] && EASY_RESULTS_DIR="$default_easy_results_dir" && return 0 # else
# fi # err "Could not create $EASY_RESULTS_DIR"
# ((YES)) && return 0 # return 0
# # Let's get a little fancy # fi
# shopt -s nullglob
# declare -la easy_results_dirs=( "$easy_out_dir/"*/ ) # # echo "Hit enter to use the default EASY results directory: $default_easy_results_dir"
# shopt -u nullglob # # if ! (( YES )); then
# # Sort the dirs # # read -r -p "Or enter a custom directory name, example: $PROJECT" dirname
# mapfile -t easy_results_dirs < <(printf '%s\n' "${easy_results_dirs[@]}" | sort) # # [[ -z $dirname ]] && EASY_RESULTS_DIR="$default_easy_results_dir" && return 0
# last_index=$(( ${#easy_results_dirs} - 1 )) # # fi
# ((YES)) && EASY_RESULTS_DIR="${easy_results_dirs[$last_index]}" && return 0 # # ((YES)) && return 0
# echo "Multiple EASY results dirs found in $PROJECT_SCANS_DIR" # # # Let's get a little fancy
# echo "Here is a list: " # # shopt -s nullglob
# for i in "${!easy_results_dirs[@]}"; do # # declare -la easy_results_dirs=( "$easy_out_dir/"*/ )
# printf "%d. %s\n" "$((i+1))" "${easy_results_dirs[i]}" # # shopt -u nullglob
# done # # # Sort the dirs
# printf "%s\n" "${easy_results_dirs[@]}" # # mapfile -t easy_results_dirs < <(printf '%s\n' "${easy_results_dirs[@]}" | sort)
# last_index=$(( ${#easy_results_dirs} - 1 )) # # last_index=$(( ${#easy_results_dirs} - 1 ))
# read -r -p "Enter the item number to select EASY results directory, default ($last_index): " response # # ((YES)) && EASY_RESULTS_DIR="${easy_results_dirs[$last_index]}" && return 0
# [[ -z $response ]] && response=$last_index # # echo "Multiple EASY results dirs found in $PROJECT_SCANS_DIR"
# response=$(( response - 1 )) # bash arrays use zero indexing # # echo "Here is a list: "
# EASY_RESULTS_DIR="${easy_results_dirs[$response]}" # # for i in "${!easy_results_dirs[@]}"; do
# EASY_RESULTS_FILES=("$EASY_RESULTS_DIR/"*"/PrintResults/!!"*) # # printf "%d. %s\n" "$((i+1))" "${easy_results_dirs[i]}"
# [[ ${#easy_results_dirs[@]} -gt 0 ]] # # done
} # # printf "%s\n" "${easy_results_dirs[@]}"
# # last_index=$(( ${#easy_results_dirs} - 1 ))
# # read -r -p "Enter the item number to select EASY results directory, default ($last_index): " response
# # [[ -z $response ]] && response=$last_index
# # response=$(( response - 1 )) # bash arrays use zero indexing
# # EASY_RESULTS_DIR="${easy_results_dirs[$response]}"
# # EASY_RESULTS_FILES=("$EASY_RESULTS_DIR/"*"/PrintResults/!!"*)
# # [[ ${#easy_results_dirs[@]} -gt 0 ]]
# }
submodule documentation submodule documentation
@@ -1575,16 +1568,16 @@ main() {
# Loop over projects # Loop over projects
for PROJECT in "${PROJECTS[@]}"; do for PROJECT in "${PROJECTS[@]}"; do
declare -g PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT" declare -gx PROJECT_SCANS_DIR="$SCANS_DIR/$PROJECT"
declare -g PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723 declare -gx PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
declare -g PROJECT_SUFFIX="${PROJECT#????????_*_}" declare -gx PROJECT_SUFFIX="${PROJECT#????????_*_}"
declare -g PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}" declare -gx PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
declare -g STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt" declare -gx STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
declare -g QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT" declare -gx QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
declare -g QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp" declare -gx QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
declare -g STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp" declare -gx STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
declare -g STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv" declare -gx STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
declare -gx EASY_RESULTS_DIR="$QHTCP_PROJECT_DIR/easy"
if ((DEBUG)); then if ((DEBUG)); then
declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \ declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \
PROJECTS PROJECT \ PROJECTS PROJECT \