generated from gCubeCI/Pipeline-Docker-Template
Rstudio in a d4science environment.
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147ABE6CEB9E20FF
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#!/usr/bin/with-contenv bash
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# shellcheck shell=bash
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## Set our dynamic variables in Renviron.site to be reflected by RStudio Server or Shiny Server
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exclude_vars="HOME PASSWORD RSTUDIO_VERSION BATCH_USER_CREATION"
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for file in /var/run/s6/container_environment/*
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do
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sed -i "/^${file##*/}=/d" ${R_HOME}/etc/Renviron.site
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regex="(^| )${file##*/}($| )"
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[[ ! $exclude_vars =~ $regex ]] && echo "${file##*/}=$(cat $file)" >> ${R_HOME}/etc/Renviron.site || echo "skipping $file"
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done
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## only file-owner (root) should read container_environment files:
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chmod 600 /var/run/s6/container_environment/*
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#!/usr/bin/with-contenv bash
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# shellcheck shell=bash
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## Set defaults for environmental variables in case they are undefined
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DEFAULT_USER=${DEFAULT_USER:-rstudio}
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USER=${USER:=${DEFAULT_USER}}
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USERID=${USERID:=1000}
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GROUPID=${GROUPID:=1000}
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ROOT=${ROOT:=FALSE}
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UMASK=${UMASK:=022}
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LANG=${LANG:=en_US.UTF-8}
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TZ=${TZ:=Etc/UTC}
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HOME=/home/${USER}
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bold=$(tput bold)
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normal=$(tput sgr0)
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if [[ ${DISABLE_AUTH,,} == "true" ]]
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then
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mv /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
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echo "USER=$USER" >> /etc/environment
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fi
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if grep --quiet "auth-none=1" /etc/rstudio/rserver.conf
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then
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echo "Skipping authentication as requested"
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elif [ -z "$PASSWORD" ]
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then
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PASSWORD=$(pwgen 16 1)
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printf "\n\n"
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tput bold
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printf "The password is set to \e[31m%s\e[39m\n" "$PASSWORD"
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printf "If you want to set your own password, set the PASSWORD environment variable. e.g. run with:\n"
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printf "docker run -e PASSWORD=\e[92m<YOUR_PASS>\e[39m -p 8787:8787 rocker/rstudio\n"
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tput sgr0
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printf "\n\n"
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fi
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if [ "$USERID" -lt 1000 ]
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# Probably a macOS user, https://github.com/rocker-org/rocker/issues/205
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then
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echo "$USERID is less than 1000"
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check_user_id=$(grep -F "auth-minimum-user-id" /etc/rstudio/rserver.conf)
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if [[ ! -z $check_user_id ]]
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then
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echo "minumum authorised user already exists in /etc/rstudio/rserver.conf: $check_user_id"
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else
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echo "setting minumum authorised user to 499"
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echo auth-minimum-user-id=499 >> /etc/rstudio/rserver.conf
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fi
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fi
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if [ "$USERID" -ne 1000 ]
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## Configure user with a different USERID if requested.
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then
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echo "deleting the default user"
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userdel $DEFAULT_USER
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echo "creating new $USER with UID $USERID"
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useradd -m $USER -u $USERID
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mkdir -p /home/$USER
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chown -R $USER /home/$USER
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usermod -a -G staff $USER
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elif [ "$USER" != "$DEFAULT_USER" ]
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then
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## cannot move home folder when it's a shared volume, have to copy and change permissions instead
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cp -r /home/$DEFAULT_USER/.??* /home/$USER || true
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## RENAME the user
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usermod -l $USER -d /home/$USER $DEFAULT_USER
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groupmod -n $USER $DEFAULT_USER
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usermod -a -G staff $USER
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chown -R $USER:$USER /home/$USER
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echo "USER is now $USER"
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fi
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[ "$USER" != "rstudio" ] && rm -fr /home/rstudio
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if [ "$GROUPID" -ne 1000 ]
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## Configure the primary GID (whether rstudio or $USER) with a different GROUPID if requested.
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then
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echo "Modifying primary group $(id $USER -g -n)"
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groupmod -g $GROUPID $(id $USER -g -n)
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echo "Primary group ID is now custom_group $GROUPID"
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fi
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if [[ ${DISABLE_AUTH,,} != "true" ]]
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then
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## Add a password to user
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echo "$USER:$PASSWORD" | chpasswd
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fi
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# Use Env flag to know if user should be added to sudoers
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if [[ ${ROOT,,} == "true" ]]
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then
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adduser $USER sudo && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
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echo "$USER added to sudoers"
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fi
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## Change Umask value if desired
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if [ "$UMASK" -ne 022 ]
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then
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echo "server-set-umask=false" >> /etc/rstudio/rserver.conf
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echo "Sys.umask(mode=$UMASK)" >> /home/$USER/.Rprofile
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fi
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## Next one for timezone setup
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if [ "$TZ" != "Etc/UTC" ]
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then
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ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
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fi
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## Update Locale if needed
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if [ "$LANG" != "en_US.UTF-8" ]
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then
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/usr/sbin/locale-gen --lang $LANG
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/usr/sbin/update-locale --reset LANG=$LANG
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fi
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#!/usr/bin/with-contenv bash
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echo "root path: $WWW_ROOT_PATH"
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if [[ ! -z $WWW_ROOT_PATH ]]
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then
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echo "Set www-root-path to $WWW_ROOT_PATH"
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echo "www-root-path=$WWW_ROOT_PATH" >> /etc/rstudio/rserver.conf
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else
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echo "Not setting www-root-path"
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fi
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#!/usr/bin/with-contenv bash
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printenv >> /etc/R/Renviron.site
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printenv > /home/$USER/.Renviron
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#!/usr/bin/with-contenv bash
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echo "session-timeout-minutes=7200" >> /etc/rstudio/rsession.conf
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echo "session-disconnected-timeout-minutes=1440" >> /etc/rstudio/rsession.conf
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echo "session-quit-child-processes-on-exit=0" >> /etc/rstudio/rsession.conf
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#echo "session-default-working-dir=~" >> /etc/rstudio/rsession.conf
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#echo "session-default-new-project-dir=~" >> /etc/rstudio/rsession.conf
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#echo "session-save-action-default=yes" >> /etc/rstudio/rsession.conf
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echo "allow-shell=0" >> /etc/rstudio/rsession.conf
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#echo "allow-terminal-websockets=1" >> /etc/rstudio/rsession.conf
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echo "limit-cpu-time-minutes=0" >> /etc/rstudio/rsession.conf
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echo "limit-file-upload-size-mb=0" >> /etc/rstudio/rsession.conf
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#echo "limit-xfs-disk-quota=no" >> /etc/rstudio/rsession.conf
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<?xml version="1.0" encoding="utf-8"?>
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<configuration scan="true" scanPeriod="60 seconds" debug="false">
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<appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
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<file>/var/log/workspace-lib/fuse-workspace.log</file>
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<append>true</append>
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<encoder>
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<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{0}: %msg%n
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</pattern>
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</encoder>
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<rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
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<fileNamePattern>./var/log/workspace-lib/fuse-workspace.log%d{yyyy-MM-dd}.log</fileNamePattern>
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<maxHistory>30</maxHistory>
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<maxFileSize>10MB</maxFileSize>
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<totalSizeCap>100MB</totalSizeCap>
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</rollingPolicy>
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</appender>
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<logger name="org.gcube.data.access.storagehub.fs" level="WARN" />
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<logger name="org.gcube" level="WARN" />
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<root level="WARN">
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<appender-ref ref="FILE" />
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</root>
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</configuration>
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#!/usr/bin/with-contenv bash
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# Functions that decode a JWT token
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_decode_base64_url() {
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local len=$((${#1} % 4))
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local result="$1"
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if [ $len -eq 2 ]; then result="$1"'=='
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elif [ $len -eq 3 ]; then result="$1"'='
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fi
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echo "$result" | tr '_-' '/+' | base64 -d
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}
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# $1 => JWT to decode
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# $2 => either 1 for header or 2 for body (default is 2)
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decode_jwt() { _decode_base64_url $(echo -n $1 | cut -d "." -f ${2:-2}) | jq .; }
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_workspace_scope="/d4science.research-infrastructures.eu"
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echo "Manage the user's workspace"
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workspace_dir='/workspace'
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workspace_logdir='/var/log/workspace-lib'
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workspace_libdir='/opt/workspace-lib'
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workspace_fuse_jar="$workspace_libdir/fuse-workspace.jar"
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[[ ! -d "$workspace_dir" ]] || [[ -z `ls -A "$workspace_dir"` ]] || mv $workspace_dir ${workspace_dir}.old
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mkdir -p $workspace_dir
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chown ${USER}:${USER} $workspace_dir
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chown -R ${USER}:${USER} $workspace_logdir
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chmod 444 $workspace_fuse_jar
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_retval=
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if [ -d /home/${USER}/workspace ]; then
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rmdir /home/${USER}/workspace
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_retval=$?
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if [ $_retval -ne 0 ]; then
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echo "The user has a directory named 'workspace' inside their home directory and it is not empty."
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echo "Not starting the workspace mount"
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exit $_retval
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fi
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fi
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echo "Mount the workspace"
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su - "$USER" -c "/usr/bin/java -cp .:${workspace_dir}:${workspace_logdir}/ -Dlogback.configurationFile=${workspace_logdir}/logback.xml -jar $workspace_fuse_jar $SHINYPROXY_OIDC_ACCESS_TOKEN ${_workspace_scope} $workspace_dir" >/dev/null 2>&1 &
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_retval=
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_fuse_process=$(ps auwwx | grep fuse | grep java)
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_retval=$?
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if [ $_retval -ne 0 ]; then
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echo "The mount of the workspace failed"
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exit 1
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fi
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ln -sf $workspace_dir /home/${USER}/workspace
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exit 0
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FROM d4science/r-studio-requirement
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LABEL org.d4science.image.licenses="EUPL-1.2" \
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org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/r-studio-requirement" \
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org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
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org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>, Roberto Cirillo <roberto.cirillo@isti.cnr.it>" \
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org.d4science.image.r_version="2022.02.1+461"
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ENV S6_VERSION=v2.1.0.2
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ENV RSTUDIO_VERSION=2022.02.1+461
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ENV DEFAULT_USER=rstudio
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ENV PANDOC_VERSION=default
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ENV PATH=/usr/lib/rstudio-server/bin:$PATH
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RUN /rocker_scripts/install_rstudio.sh
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# This part comes from https://github.com/openanalytics/shinyproxy-rstudio-ide-demo/blob/master/Dockerfile
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RUN echo "www-frame-origin=same" >> /etc/rstudio/disable_auth_rserver.conf
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RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
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ADD 01_set_env.sh /etc/cont-init.d/01_set_env
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ADD 02_userconf.sh /etc/cont-init.d/02_userconf
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ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path
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# By default RStudio does not give access to all enviornment variables defined in the container (e.g. using ShinyProxy).
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# Uncomment the next line, to change this behavior.
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#ADD 04_copy_env.sh /etc/cont-init.d/04_copy_env
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ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters
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# Prepare the workspace environment
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RUN mkdir -p /opt/workspace-lib
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RUN mkdir /var/log/workspace-lib
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ADD https://maven.d4science.org/nexus/content/repositories/gcube-snapshots/org/gcube/data-access/sh-fuse-integration/2.0.0-SNAPSHOT/sh-fuse-integration-2.0.0-20211005.090627-1-jar-with-dependencies.jar /opt/workspace-lib/fuse-workspace.jar
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ADD 06_workspace_mount.sh /etc/cont-init.d/06_workspace_mount
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ADD 06-fuse-logback.xml /opt/workspace-lib/logback.xml
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EXPOSE 8787
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CMD ["/init"]
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