aboutsummaryrefslogtreecommitdiff
path: root/bin
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2022-01-31 06:46:50 +0300
committerzsloan2022-02-07 22:57:50 -0600
commit04203f785e5a8c86509089bc68340e1e01162ffd (patch)
tree023343e35486fef747e2eec0d3bf7901fd16c3bc /bin
parentb5bf6432dbf3a75e2306c03aced4180b020304c9 (diff)
downloadgenenetwork2-04203f785e5a8c86509089bc68340e1e01162ffd.tar.gz
Double quote shell variables to prevent globbing and word splitting
Diffstat (limited to 'bin')
-rwxr-xr-xbin/genenetwork287
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