Double quote shell variables to prevent globbing and word splitting

1 files changed, 45 insertions, 42 deletions

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 1b933e80..a6ba7241 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -53,25 +53,27 @@
 #   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi"
 
 SCRIPT=$(realpath "$0")
-echo SCRIPT=$SCRIPT
-echo GN2_PROFILE=$GN2_PROFILE
-GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT"))
-GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR)
+echo SCRIPT="${SCRIPT}"
+echo GN2_PROFILE="${GN2_PROFILE}"
+GN2_BASE_DIR=$(dirname "$(dirname "${SCRIPT}")")
+GN2_ID=$(cat /etc/hostname):$(basename "${GN2_BASE_DIR}")
 
-echo GN2_BASE_DIR=$GN2_BASE_DIR
+echo GN2_BASE_DIR="${GN2_BASE_DIR}"
 
 GUIX_SITE=$GN2_BASE_DIR/lib/python3.8/site-packages
-if [ -d $GUIX_SITE ]; then
+if [ -d "${GUIX_SITE}" ]; then
     echo INFO: GN2 is running from GNU Guix
     GN2_BASE_DIR=$GUIX_SITE
-    export GN_VERSION=$GN2_ID:$(cat $GN2_BASE_DIR/etc/VERSION)
+    GN_VERSION="${GN2_ID}:$(cat "${GN2_BASE_DIR}"/etc/VERSION)"
+    export GN_VERSION
 else
     echo INFO: GN2 is running from a source tree
     GIT_HASH=$(git rev-parse HEAD)
     GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
-    export GN_VERSION="${GN2_ID}:$(cat ${GN2_BASE_DIR}/etc/VERSION)-${GIT_BRANCH}-$(echo ${GIT_HASH} | cut -c1-9)"
+    GN_VERSION="${GN2_ID}:$(cat "${GN2_BASE_DIR}"/etc/VERSION)-${GIT_BRANCH}-$(echo "${GIT_HASH}" | cut -c1-9)"
+    export GN_VERSION
 fi
-echo GN_VERSION=$GN_VERSION
+echo GN_VERSION="${GN_VERSION}"
 
 if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
     echo "Can not use $1 switch without default settings file"
@@ -79,12 +81,12 @@ if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
 fi
 
 settings=$1
-if [ -z $settings ]; then
+if [ -z "${settings}" ]; then
     settings=$GN2_BASE_DIR/etc/default_settings.py
 else
     shift
 fi
-settings=$(realpath $settings)
+settings=$(realpath "${settings}")
 
 # ext="${settings##*.}"
 # if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
@@ -93,24 +95,25 @@ settings=$(realpath $settings)
 #     echo $settings
 # fi
 
-if [ ! -e $settings ]; then
+if [ ! -e "${settings}" ]; then
     echo "ERROR: can not locate settings file - pass it in the command line"
     exit 1
 fi
 
 export GN2_SETTINGS=$settings     # Python
-echo GN2_SETTINGS=$settings
+echo GN2_SETTINGS="${settings}"
 
-if [ -z $GN2_PROFILE ] ; then
+if [ -z "${GN2_PROFILE}" ] ; then
     echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!"
-    export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2)))
-    if [ -d $GN2_PROFILE ]; then
+    GN2_PROFILE=$(dirname $(dirname $(which genenetwork2)))
+    export GN2_PROFILE
+    if [ -d "${GN2_PROFILE}" ]; then
         echo "Best guess is $GN2_PROFILE"
     fi
     echo "ERROR: always set GN2_PROFILE"
     exit 1
 fi
-if [ -z $GN2_PROFILE ]; then
+if [ -z "${GN2_PROFILE}" ]; then
     read -p "PRESS [ENTER] TO CONTINUE..."
 else
     export PATH=$GN2_PROFILE/bin:$PATH
@@ -125,21 +128,21 @@ else
     export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2"
     export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
     export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
-    if [ -z $GEMMA_WRAPPER_COMMAND ]; then
+    if [ -z "${GEMMA_WRAPPER_COMMAND}" ]; then
         export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
     fi
     while IFS=":" read -ra PPATH; do
 	for PPART in "${PPATH[@]}"; do
-	    if [ ! -d $PPART ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi
+	    if [ ! -d "${PPART}" ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi
 	done
     done <<< "$PYTHONPATH"
-    if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
+    if [ ! -d "${R_LIBS_SITE}" ] ; then echo "R_LIBS_SITE not valid ${R_LIBS_SITE}" ; exit 1 ; fi
 fi
-if [ -z $PYTHONPATH ] ; then
+if [ -z "${PYTHONPATH}" ] ; then
     echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
     exit 1
 fi
-if [ ! -d $R_LIBS_SITE ] ; then
+if [ ! -d "${R_LIBS_SITE}" ] ; then
     echo "ERROR R_LIBS_SITE has not been set correctly (we only allow one path) - use GN2_PROFILE!"
     echo "Paste into your shell the output of (for example)"
     echo "guix package -p \$GN2_PROFILE --search-paths"
@@ -152,60 +155,60 @@ export PYTHONPATH=$PYTHON_GN_PATH:$GN2_BASE_DIR/wqflask:$GN3_PYTHONPATH:$PYTHONP
 export PYTHONPATH="${GN3_DEV_REPO_PATH:+$GN3_DEV_REPO_PATH:}:${PYTHONPATH}"
 
 # Our UNIX TMPDIR defaults to /tmp - change this on a shared server
-if [ -z $TMPDIR ]; then
+if [ -z "${TMPDIR}" ]; then
     TMPDIR="/tmp"
 fi
 
 # Show environment settings
 set|grep guix
-set|grep $GN2_PROFILE
+set|grep GN2_PROFILE
 set|grep TMPDIR
 
 # Now handle command parameter -c which runs python
 if [ "$1" = '-c' ] ; then
-    cd $GN2_BASE_DIR/wqflask
+    cd "${GN2_BASE_DIR}/wqflask"
     cmd=${2#wqflask/}
-    echo PYTHONPATH=$PYTHONPATH
+    echo PYTHONPATH="${PYTHONPATH}"
     shift ; shift
-    echo RUNNING COMMAND $cmd $*
+    echo "RUNNING COMMAND ${cmd} ${*}"
     python $cmd $*
     exit $?
 fi
 
 # Now handle command parameter -cli which runs in bash
 if [ "$1" = "-cli" ] ; then
-    cd $GN2_BASE_DIR/wqflask
+    cd "${GN2_BASE_DIR}/wqflask"
     cmd=$2
-    echo PYTHONPATH=$PYTHONPATH
+    echo PYTHONPATH="${PYTHONPATH}"
     shift ; shift
-    echo RUNNING COMMAND $cmd $*
+    echo "RUNNING COMMAND ${cmd} ${*}"
     $cmd $*
     exit $?
 fi
 if [ "$1" = '-gunicorn' ] ; then
-    cd $GN2_BASE_DIR/wqflask
+    cd "${GN2_BASE_DIR}/wqflask"
     cmd=$2
-    echo PYTHONPATH=$PYTHONPATH
-    echo RUNNING gunicorn $cmd
+    echo PYTHONPATH="${PYTHONPATH}"
+    echo "RUNNING gunicorn ${cmd}"
     gunicorn $cmd
     exit $?
 fi
 if [ "$1" = '-gunicorn-dev' ] ; then
-    cd $GN2_BASE_DIR/wqflask
-    echo PYTHONPATH=$PYTHONPATH
-    if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
+    cd "${GN2_BASE_DIR}/wqflask"
+    echo PYTHONPATH="${PYTHONPATH}"
+    if [ -z "${SERVER_PORT}" ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
     cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload run_gunicorn:app"
-    echo RUNNING gunicorn $cmd
+    echo "RUNNING gunicorn ${cmd}"
     gunicorn $cmd
     exit $?
 fi
 if [ "$1" = '-gunicorn-prod' ] ; then
-    cd $GN2_BASE_DIR/wqflask
-    echo PYTHONPATH=$PYTHONPATH
-    if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
+    cd "${GN2_BASE_DIR}/wqflask"
+    echo PYTHONPATH="${PYTHONPATH}"
+    if [ -z "${SERVER_PORT}" ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
     PID=$TMPDIR/gunicorn.$USER.pid
     cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID --workers 20 --keep-alive 6000 --max-requests 100 --max-requests-jitter 30 --timeout 1200 wsgi"
-    echo RUNNING gunicorn $cmd
+    echo "RUNNING gunicorn ${cmd}"
     gunicorn $cmd
     exit $?
 fi
@@ -219,6 +222,6 @@ dbfilename gn2.rdb
 # export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
 
 # Start the flask server running GN2
-cd $GN2_BASE_DIR/wqflask
+cd "${GN2_BASE_DIR}/wqflask"
 echo "Starting with $settings"
 python runserver.py