rstudio-server.launcher.sh

#! /usr/bin/bash

# @ID@ #
PREFIX=@PREFIX@
CONTAINER=@CONTAINER@

# -------------------------------------------------------------------------

function show_help() {
  echo -e "\n $0 information:\n"

  cat << __EOF

    This is a containerized setup for rstudio-server, allowing you to run
    rstudio on a public server and use it remotely in your web browser.

    To avoid the risk that someone else is using your session, you will be
    asked for your login name and a password. The password is generated
    per session, and is shown in the terminal window when you start the
    server.

    Also please do not forget to stop the server with 'rstudio-server stop'
    when you are done (just closing the browser will _not_ do the job).


  Available commands are:
  -----------------------

     start          that is indeed the default action, you do not
                    need to enter it.

     stop           this will stop your server and free the resources.

     inspect        you can use this to explore the container you are running,
                    probably only useful for trouble shooting.

     force_cleanup  this will kill any running rstudio-server and cleans your
                    session directory, use this when the server or R has crashed
                    and you can not start or reconnect again.
                    A shortcut is to use 'zap'.

     help           shows the page you are reading now (-h, --help also works).

__EOF

}


function apptainer_exec() {

  container="$1"; shift

  # Note for the unwary: USER_SERVER_BASE is _only_ set when the server is started,
  # not when just inspecting!

  # echo \
  apptainer exec \
    -B /usr:/usr \
    -B /pkg:/pkg \
    -B /project:/project \
    -B /scratch:/scratch \
    -B $USER_SERVER_BASE/var/lib:/var/lib \
    -B $USER_SERVER_BASE/var/run:/var/run \
    "$container" $@
}

# -------------------------------------------------------------------------

USER_SERVER_INFO_DIR=$HOME/.rstudio-server-app
FIRST_RUN=
STOP_SERVER=

# Mariux default for TMPDIR is /scratch/local
TMPDIR=${TMPDIR:-/scratch/local}
if [ "$TMPDIR" = "/scratch/local" ]; then
  TMPDIR=/scratch/local2/$USER
fi
mkdir -p $TMPDIR

if [ ! -d $USER_SERVER_INFO_DIR ]; then
  FIRST_RUN=1
fi
mkdir -p $USER_SERVER_INFO_DIR


echo "[$(date +%c)] ${HOSTNAME%%.*} ${1:-START}" >> $USER_SERVER_INFO_DIR/info.log

case $1 in
   force_cleanup|zap)
     killall rserver
     rm -rf $TMPDIR/rstudio-server-app/session_data
     echo -e "\n#  Note: Removed your rservers and/or session data ...\n"
     exit 0
     ;;
   inspect)
     apptainer inspect $PREFIX/libexec/$CONTAINER
     echo -e "\n#  Note: Leave the container with exit / [Ctrl]-[D]\n"
     apptainer_exec $PREFIX/libexec/$CONTAINER /usr/bin/bash
     exit 0
     ;;
   start) # default, so do nothing here
     :
     ;;
   stop)
     STOP_SERVER=1
     ;;
   -h|--help|help)
     show_help
     exit 0
     ;;
esac


if [ -e $TMPDIR/rstudio-server-app/session_data/rss.pid ]; then
  pid=$(cat $TMPDIR/rstudio-server-app/session_data/rss.pid)
  if [ -e /proc/$pid ]; then
    if [ -r /proc/$pid/exe ]; then
      # echo "# $pid present - need to stop the server ..." >&2
      exe=$(readlink /proc/$pid/exe)
      # this is the path inside the container
      if [ "$exe" = "/apps/rstudio-server/bin/rserver" ]; then
        if [ -n "$STOP_SERVER" ]; then
          echo -e "\n   Note: Stopping rstudio-server (pid:$pid) ...\n"
          kill $pid
          exit 0
        else
          echo "#  Note: A rstudio-server is running here already" >&2
        fi
      else
        echo "#  Note: The task '$exe' runs under the expected pid now, and not rstudio-server ..." >&2
        echo "#        Run 'rstudio-server force_cleanup' to remove old session data."
      fi
    else
      echo "#  Note: Process with pid $pid does no longer belong to you ..." >&2
      echo "#        Run 'rstudio-server force_cleanup' to remove old session data."
    fi
    exit 1
  fi
fi

if [ -n "$STOP_SERVER" ]; then
  echo "#  Error: no running server found here." >&2
  exit 1
fi

rm -rf $TMPDIR/rstudio-server-app
mkdir -p -m 0700 $TMPDIR/rstudio-server-app
USER_SERVER_BASE=$TMPDIR/rstudio-server-app/session_data # will be set to 0777 by rstudio-server ...
USER_SERVER_INFO_DIR=$HOME/.rstudio-server-app

SOCKET_NAME_CHECK="$USER_SERVER_BASE/rstudio-rserver/session-server-rpc.socket"
if [ ${#SOCKET_NAME_CHECK} -ge 108 ]; then
  echo "ERROR: Name of rstudio-server socket file will exceed the 108 character limit (man 7 unix)." >&2
  echo "       You probably need to use a shorter TMPDIR ($TMPDIR [${#TMPDIR}])" >&2
  exit 2
fi

# our 'normal' mechanics for the R binary does not work here, let ptype do the job
MAIN_R_PROGRAM=${R_CUSTOM:-/usr/bin/R}
if ! [ -e "$MAIN_R_PROGRAM" ]; then
  MAIN_R_PROGRAM=$(ptype R | awk '{print($3)}')
  if ! [ -e "$MAIN_R_PROGRAM" ]; then
    echo "# Error: Can not find the R executable (tried on '$MAIN_R_PROGRAM')."
    exit 1
  fi
fi

echo -e "\n   R executable set to: $MAIN_R_PROGRAM\n"

# prepare server start ...

# create a one-time password
# 17 chars are a bit unfair if people don't do copy and paste
RSTUDIO_PASSWORD='******************************'
RSTUDIO_PASSWORD=$(openssl rand -base64 12 | colrm 12)

# also make it clickable ...
RSTUDIO_PASSWORD=${RSTUDIO_PASSWORD//[+\/=]/3}

# ... and this is passed to 'auth-pam-helper'
PASSWORD_DIGEST=$(echo $RSTUDIO_PASSWORD | /usr/bin/sha256sum)
PASSWORD_DIGEST=${PASSWORD_DIGEST%% *}

echo -e "\n   Your password for this session is: '$RSTUDIO_PASSWORD'\n"
RSTUDIO_PASSWORD='******************************'
unset RSTUDIO_PASSWORD
export PASSWORD_DIGEST

LOWER_PORT=28787
UPPER_PORT=38787
RSTUDIO_SERVER_PORT=$LOWER_PORT
while :; do
  # is it free?
  ss -ltn | grep -q ":$RSTUDIO_SERVER_PORT " || break
  RSTUDIO_SERVER_PORT=$(( RSTUDIO_SERVER_PORT+1 ))
  if [ "$RSTUDIO_SERVER_PORT" -gt "$UPPER_PORT" ]; then
    RSTUDIO_SERVER_PORT=$LOWER_PORT
  fi
  sleep 0.15
done

echo -e "   Browser address is: http://$HOSTNAME:$RSTUDIO_SERVER_PORT"
echo -e "                   or: http://localhost:8787   (when at home)\n"
echo -e "   Note for home-users:\n"
echo -e "        to tunnel the server connection to port 8787 on your local computer, enter\n"
echo -e "        ssh -L 8787:$HOSTNAME:$RSTUDIO_SERVER_PORT $USER@geniux.molgen.mpg.de\n"

if [ -n "$FIRST_RUN" ]; then
  echo -e " ------------------------------------------------------------------\n"
  echo -e "   Note: First time run of rstudio-server ...\n"
  echo -e "         Please mind to stop the server from the console with\n"
  echo -e "           rstudio-server stop\n"
  echo -e "         when you are done.\n"
  echo -e "   Hit [Enter] to start now, or [Ctrl]-[C] and eventually take a"
  echo -e "   look at the help page with 'rstudio-server help' ...\n"
  echo -e " ------------------------------------------------------------------"
  read junk
fi

# --------------------------------------------- finally start this thing --

mkdir -p $USER_SERVER_BASE/var/lib
mkdir -p $USER_SERVER_BASE/var/run

  apptainer_exec \
    $PREFIX/libexec/$CONTAINER \
    \
      /apps/rstudio-server/bin/rserver \
        --server-working-dir $USER_SERVER_BASE \
        --server-data-dir $USER_SERVER_BASE \
        --database-config-file $USER_SERVER_BASE/dbconf \
        --server-user $USER \
        --www-port $RSTUDIO_SERVER_PORT \
        --www-address $HOSTNAME \
        --rsession-which-r $MAIN_R_PROGRAM \
        --auth-minimum-user-id 100 \
        --auth-none 0 \
        --auth-pam-helper-path $PREFIX/bin/rstudio-server.pam-helper.sh \
        --server-pid-file $USER_SERVER_BASE/rss.pid \
        --server-daemonize 1

sleep 0.3
if [ -e $USER_SERVER_BASE/rss.pid ]; then
  pid=$(cat $USER_SERVER_BASE/rss.pid)
  echo -e "\n   Note: rstudio-server started (pid:$pid) ...\n"
else
  echo "#  Warning: Could not figure out the process id, check if rstudio-server/rserver is running." >&2
fi

# -------------------------------------------------------------------------