genenetwork2

#! /bin/bash
#
# This is the startup script for GN2. It sets the environment variables to pick
# up a Guix profile and allows for overriding parameters.
#
# Typical usage
#
#   env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 ~/my_settings.py
#
# Where GN2_PROFILE points to the GNU Guix profile used for deployment.
#
# This will run the GN2 server (with default settings if none
# supplied). Typically you need a GNU Guix profile which is set with
# an environment variable (this profile is dictated by the
# installation path of genenetwork). Say your profile is in
# ~/opt/gn-latest-guix
#
#   env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2
#
# You can pass in your own settings file, e.g.
#
#   env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ~/my_settings.py
#
# To run a maintenance python script with settings (instead of the
# webserver) run from the base-dir with settings file and add that
# script with a -c switch, e.g.
#
#   env GN2_PROFILE=/usr/local/guix-profiles/gn-latest-20190905 TMPDIR=/export/local/home/zas1024/gn2-zach/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/local/home/zas1024/gn2-zach/genotype_files SQL_URI=mysql://webqtlout:webqtlout@lily.uthsc.edu/db_webqtl ./bin/genenetwork2 ./gn2/default_settings.py -c ./maintenance/gen_select_dataset.py
#
# To run any script in the environment
#
#   env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./gn2/default_settings.py -cli echo "HELLO WORLD"
#
# To get a python REPL(!)
#
#   env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./gn2/default_settings.py -cli python
#
# For development you may want to run
#
#   env GN2_PROFILE=~/opt/gn-latest WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2
#
# For staging and production we use gunicorn. Run with something like
# (note you have to provide the server port). Provide a settings file!
#
#   env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./gn2/default_settings.py -gunicorn-prod
#
# For development use
#
#   env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./gn2/default_settings.py -gunicorn-dev
#
# For extra flexibility you can also provide gunicorn parameters yourself with something like
#
#   env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./gn2/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 GN2_BASE_DIR="${GN2_BASE_DIR}"

GUIX_SITE=$GN2_BASE_DIR/lib/python3.8/site-packages
if [ -d "${GUIX_SITE}" ]; then
    echo INFO: GN2 is running from GNU Guix
    GN2_BASE_DIR=$GUIX_SITE
else
    echo INFO: GN2 is running from a source tree
    GIT_HASH=$(git rev-parse HEAD)
    GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
fi

if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then
    echo "Can not use $1 switch without default settings file"
    exit 1
fi

settings=$1
if [ -z "${settings}" ]; then
    settings=$GN2_BASE_DIR/gn2/default_settings.py
else
    shift
fi
settings=$(realpath "${settings}")

# ext="${settings##*.}"
# if [ "$ext" = "json" -o "$ext" = "JSON" ]; then
#     overrides=$settings
# else
#     echo $settings
# fi

if [ ! -e "${settings}" ]; then
    echo "ERROR: can not locate settings file - pass it in the command line"
    exit 1
fi

# If $GN2_SETTINGS is set, use that, otherwise use default provided at invocation
export GN2_SETTINGS=${GN2_SETTINGS:-$settings}
echo GN2_SETTINGS="${settings}"

if [ -z "${GN2_PROFILE}" ] ; then
    echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!"
    GN2_PROFILE=$(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
    read -p "PRESS [ENTER] TO CONTINUE..."
else
    export PATH=$GN2_PROFILE/bin:$PATH
    export PYTHONPATH="$GN2_PROFILE/lib/python3.10/site-packages" # never inject another PYTHONPATH!!
    export R_LIBS_SITE=$GN2_PROFILE/site-library
    export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
    export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
    export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
    export XDG_DATA_DIRS="$GN2_PROFILE/share"
    export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules"
    export LC_ALL=C # FIXME
    export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2"
    export PLINK_COMMAND="$GN2_PROFILE/bin/plink2"
    export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
    if [ -z "${GEMMA_WRAPPER_COMMAND}" ]; then
        export GEMMA_WRAPPER_COMMAND="$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 $PYTHONPATH" ; exit 1 ; fi
	done
    done <<< "$PYTHONPATH"
    if [ ! -d "${R_LIBS_SITE}" ] ; then echo "R_LIBS_SITE not valid ${R_LIBS_SITE}" ; exit 1 ; fi
fi
if [ -z "${PYTHONPATH}" ] ; then
    echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
    exit 1
fi
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"
    exit 1
fi

# We may change this one:
export PYTHONPATH="${PYTHON_GN_PATH:+$PYTHON_GN_PATH:}$GN2_BASE_DIR/wqflask:${GN3_PYTHONPATH:+$GN3_PYTHONPATH:}$PYTHONPATH"

# Our UNIX TMPDIR defaults to /tmp - change this on a shared server
if [ -z "${TMPDIR}" ]; then
    TMPDIR="/tmp"
fi

# Show environment settings
set|grep guix
set|grep GN2_PROFILE
set|grep TMPDIR

# Now handle command parameter -c which runs python
if [ "$1" = '-c' ] ; then
    echo PYTHONPATH="${PYTHONPATH}"
    shift
    echo "RUNNING COMMAND python ${*}"
    python $*
    exit $?
fi

# Now handle command parameter -cli which runs in bash
if [ "$1" = "-cli" ] ; then
    cmd=$2
    echo PYTHONPATH="${PYTHONPATH}"
    shift ; shift
    echo "RUNNING COMMAND ${cmd} ${*}"
    $cmd $*
    exit $?
fi
if [ "$1" = '-gunicorn' ] ; then
    cmd=$2
    echo PYTHONPATH="${PYTHONPATH}"
    echo "RUNNING gunicorn ${cmd}"
    gunicorn $cmd
    exit $?
fi
if [ "$1" = '-gunicorn-dev' ] ; then
    echo PYTHONPATH="${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 gn2.run_gunicorn:app"
    echo "RUNNING gunicorn ${cmd}"
    gunicorn $cmd
    exit $?
fi
if [ "$1" = '-gunicorn-prod' ] ; then
    echo PYTHONPATH="${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 gn2.wsgi"
    echo "RUNNING gunicorn ${cmd}"
    gunicorn $cmd
    exit $?
fi

if [ -z "$NO_REDIS" ] ; then
    echo "Starting the redis server:"
    echo -n "dir $TMPDIR
dbfilename gn2.rdb
" | redis-server - &
fi

# Overrides for packages that are not yet public (currently r-auwerx)
# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib



if [ "$1" = "--with-pdb" ] ; then
    cmd=$2
    echo PYTHONPATH="${PYTHONPATH}"
    shift ; shift
    echo "RUNNING COMMAND python3 -m gn2.runserver.py"
    python3 -m pdb runserver.py
    exit $?
fi

# Start the flask server running GN2
echo "Starting with $settings"
python -m gn2.runserver