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Switch from SCANS_DIR to PROJECT_SCANS_DIR to avoid collision

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Bryan Roessler
2024-07-29 12:09:10 -04:00
parent 4a2dbbbcd6
commit f27929eb1f
2 changed files with 25 additions and 25 deletions
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8
workflow/apps/matlab/easy/EASYconsole.m
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@@ -45,15 +45,15 @@ function varargout = EASYconsole(varargin)
scansDir=getenv('PROJECT');
fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
disp('This usually indicates that we are in standalone mode');
elseif exist('SCANS_DIR', 'var') && ~isempty(getenv('SCANS_DIR'))
scansDir=getenv('SCANS_DIR');
fprintf('Using scans directory: %s from environment variable SCANS_DIR\n', scansDir);
elseif exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
scansDir=getenv('PROJECT_SCANS_DIR');
fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
disp('This usually indicates that we are in module mode');
else
% TODO Lots of this is hardcoded logic, this TODO is just a reminder to change this block
% when changing EASY and other variables in the parent script
fprintf('Beginning parent scans directory search\n');
fprintf('This usually indicates that we are in stand-alone mode without PROJECT or SCANS_DIR environment variables\n');
fprintf('This usually indicates that we are in stand-alone mode without PROJECT or PROJECT_SCANS_DIR environment variables\n');
dirsToScan={
fullfile(parentDir,'..', '..', 'scans'),
fullfile(parentDir, '..', '..', 'ExpJobs'),

42
workflow/qhtcp-workflow
View File

@@ -406,10 +406,10 @@ init_project() {
# We handle this in main() and pushd to it
# But do it one more time in case this is run as a module
[[ -d $SCANS_DIR ]] ||
( mkdir -p "$SCANS_DIR" && pushd "$SCANS_DIR" || return 1 )
ask "Initialize a project at $SCANS_DIR?" || return 1
ask "Initialize a project at $PROJECT_SCANS_DIR?" || return 1
[[ -d $PROJECT_SCANS_DIR ]] || (mkdir -p "$PROJECT_SCANS_DIR" || return 1)
# Write skeleton files in csv
# If we have to convert to xlsx later, so be it
@@ -425,7 +425,7 @@ init_project() {
EOF
# TODO here we'll copy scan from robot but for now let's pause and wait for transfer
# TODO here we'll copy scans from robot but for now let's pause and wait for transfer
read -r -p "Hit <Enter> to continue: "
}
@@ -585,25 +585,25 @@ easy() {
# 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
if ! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI."; then
export SCANS_DIR PROJECT_DATE EASY_DIR PROJECT_USER EASY_NAME EASY_SUFFIX EASY_RESULTS_DIR MASTER_PLATE_FILE DRUG_MEDIA_FILE
echo "Hit enter to use the default EASY results directory $SCANS_DIR/Results_${PROJECT_PREFIX}_($PROJECT_SUFFIX)"
export PROJECT_SCANS_DIR PROJECT_DATE EASY_DIR PROJECT_USER EASY_NAME EASY_SUFFIX EASY_RESULTS_DIR MASTER_PLATE_FILE DRUG_MEDIA_FILE
echo "Hit enter to use the default EASY results directory $PROJECT_SCANS_DIR/Results_${PROJECT_PREFIX}_($PROJECT_SUFFIX)"
(( YES )) || read -r -p "Or enter a custom suffix: " suffix
EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${suffix:-$PROJECT_SUFFIX}"
EASY_RESULTS_DIR="$PROJECT_SCANS_DIR/Results_${PROJECT_PREFIX}_${suffix:-$PROJECT_SUFFIX}"
while [[ -d $EASY_RESULTS_DIR ]]; do
count=1
if [[ $count -eq 1 ]] && ask "$EASY_RESULTS_DIR already exists, increment dir name (y) or overwrite (N)?"; then
EASY_SUFFIX="${suffix:-$PROJECT_SUFFIX}.$((count++))"
EASY_RESULTS_DIR="$SCANS_DIR/Results_${PROJECT_PREFIX}_${EASY_SUFFIX}"
EASY_RESULTS_DIR="$PROJECT_SCANS_DIR/Results_${PROJECT_PREFIX}_${EASY_SUFFIX}"
else
EASY_SUFFIX=${suffix:-$PROJECT_SUFFIX}
fi
done
EASY_SUFFIX=${EASY_SUFFIX:-$suffix:-$PROJECT_SUFFIX}
EASY_NAME="${PROJECT_PREFIX}_${EASY_SUFFIX}"
EASY_RESULTS_DIR="$SCANS_DIR/Results_$EASY_NAME"
[[ -d $SCANS_DIR/MasterPlateFiles ]] || mkdir -p "$SCANS_DIR/MasterPlateFiles"
DRUG_MEDIA_FILE="$SCANS_DIR/MasterPlateFiles/DrugMedia_$PROJECT.xls"
MASTER_PLATE_FILE="$SCANS_DIR/MasterPlateFiles/MasterPlate_$PROJECT.xls"
EASY_RESULTS_DIR="$PROJECT_SCANS_DIR/Results_$EASY_NAME"
[[ -d $PROJECT_SCANS_DIR/MasterPlateFiles ]] || mkdir -p "$PROJECT_SCANS_DIR/MasterPlateFiles"
DRUG_MEDIA_FILE="$PROJECT_SCANS_DIR/MasterPlateFiles/DrugMedia_$PROJECT.xls"
MASTER_PLATE_FILE="$PROJECT_SCANS_DIR/MasterPlateFiles/MasterPlate_$PROJECT.xls"
# Make EASY dirs
debug "mkdir -p $EASY_RESULTS_DIR"
@@ -618,12 +618,12 @@ easy() {
# Launch matlab
matlab -nosplash -r "run $script"
# matlab -nosplash -sd "$SCANS_DIR" -r "run $script"
# matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
fi
# Use the function return code see if we succeeded
get_easy_results "$SCANS_DIR" || return 1
get_easy_results "$PROJECT_SCANS_DIR" || return 1
}
@@ -775,7 +775,7 @@ qhtcp() {
unset STUDY_DIR
# Replacing ExpFrontend.m
get_easy_results "$SCANS_DIR" || (err "No EASY results found in $SCANS_DIR"; return 1)
get_easy_results "$PROJECT_SCANS_DIR" || (err "No EASY results found in $PROJECT_SCANS_DIR"; return 1)
# Set the right results directory
# TODO eventually we could run this on multiple results dirs simultaneously with some refactoring
@@ -783,7 +783,7 @@ qhtcp() {
# In automatic mode just choose the first OUT DIR in the list
EASY_RESULT_DIR="${EASY_RESULTS_DIRS[0]}" # TODO right now just choose
else
echo "Multiple EASY results dirs found in $SCANS_DIR"
echo "Multiple EASY results dirs found in $PROJECT_SCANS_DIR"
echo "Here is a list: "
for (( i=0; i<${#EASY_RESULTS_DIRS[@]}; i++ )); do
printf "%d. %s\n" "$((i+1))" "${EASY_RESULTS_DIRS[i]}"
@@ -808,7 +808,7 @@ qhtcp() {
# Trying to match old ExpFrontend formatting
printf "%s\t" \
"${DATE//_/}" "$PROJECT" "$QHTCP_PROJECT_DIR" "Exp$s" \
"$PROJECT_DATE" "$SCANS_DIR" "$EASY_RESULT_DIR" "${f##*/}" \
"$PROJECT_DATE" "$PROJECT_SCANS_DIR" "$EASY_RESULT_DIR" "${f##*/}" \
>> "$STUDIES_ARCHIVE_FILE"
done
done
@@ -1407,8 +1407,8 @@ submodule get_easy_results # lol
# TODO: Standardize EASY output, it's hard to understand
# @exitcode 0 if at least one results directory exists
# @exitcode 1 if no results directories exist
# @set EASY_RESULTS_DIRS array Globbed results files from SCANS_DIR/
# @set EASY_RESULTS_FILES array Globbed results files from SCANS_DIR/
# @set EASY_RESULTS_DIRS array Globbed results files from PROJECT_SCANS_DIR/
# @set EASY_RESULTS_FILES array Globbed results files from PROJECT_SCANS_DIR/
# @arg $1 string Project scans (ExpJobs)
get_easy_results() {
debug "Running: ${FUNCNAME[0]}"
@@ -1534,7 +1534,7 @@ main() {
# Loop over projects
for PROJECT in "${PROJECTS[@]}"; do
SCANS_DIR="$SCANS/$PROJECT"
PROJECT_SCANS_DIR="$SCANS/$PROJECT"
PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
PROJECT_SUFFIX="${PROJECT#????????_*_}"
PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"