generated from gCubeCI/Pipeline-Docker-Template
New modality of building the images
This commit is contained in:
parent
fa28a66847
commit
ed286a3f52
GPG Key ID:
147ABE6CEB9E20FF
|
|
@ -1,16 +0,0 @@
|
||||||
#!/bin/bash
|
|
||||||
# shellcheck shell=bash
|
|
||||||
|
|
||||||
if [ -d "/var/run/s6/container_environment" ] ; then
|
|
||||||
## Set our dynamic variables in Renviron.site to be reflected by RStudio Server or Shiny Server
|
|
||||||
exclude_vars="HOME PASSWORD RSTUDIO_VERSION BATCH_USER_CREATION"
|
|
||||||
for file in /var/run/s6/container_environment/*
|
|
||||||
do
|
|
||||||
sed -i "/^${file##*/}=/d" ${R_HOME}/etc/Renviron.site
|
|
||||||
regex="(^| )${file##*/}($| )"
|
|
||||||
[[ ! $exclude_vars =~ $regex ]] && echo "${file##*/}=$(cat $file)" >> ${R_HOME}/etc/Renviron.site || echo "skipping $file"
|
|
||||||
done
|
|
||||||
|
|
||||||
## only file-owner (root) should read container_environment files:
|
|
||||||
chmod 600 /var/run/s6/container_environment/*
|
|
||||||
fi
|
|
||||||
120
02_userconf.sh
120
02_userconf.sh
|
|
@ -1,120 +0,0 @@
|
||||||
#!/usr/bin/with-contenv bash
|
|
||||||
# shellcheck shell=bash
|
|
||||||
|
|
||||||
## Set defaults for environmental variables in case they are undefined
|
|
||||||
DEFAULT_USER=${DEFAULT_USER:-rstudio}
|
|
||||||
USER=${USER:=${DEFAULT_USER}}
|
|
||||||
USERID=${USERID:=1000}
|
|
||||||
GROUPID=${GROUPID:=1000}
|
|
||||||
ROOT=${ROOT:=FALSE}
|
|
||||||
UMASK=${UMASK:=022}
|
|
||||||
LANG=${LANG:=en_US.UTF-8}
|
|
||||||
TZ=${TZ:=Etc/UTC}
|
|
||||||
HOME=/home/${USER}
|
|
||||||
|
|
||||||
bold=$(tput bold)
|
|
||||||
normal=$(tput sgr0)
|
|
||||||
|
|
||||||
if [[ ${DISABLE_AUTH,,} == "true" ]]
|
|
||||||
|
|
||||||
then
|
|
||||||
mv /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
|
|
||||||
echo "USER=$USER" >> /etc/environment
|
|
||||||
fi
|
|
||||||
|
|
||||||
if grep --quiet "auth-none=1" /etc/rstudio/rserver.conf
|
|
||||||
then
|
|
||||||
echo "Skipping authentication as requested"
|
|
||||||
elif [ -z "$PASSWORD" ]
|
|
||||||
then
|
|
||||||
PASSWORD=$(pwgen 16 1)
|
|
||||||
printf "\n\n"
|
|
||||||
tput bold
|
|
||||||
printf "The password is set to \e[31m%s\e[39m\n" "$PASSWORD"
|
|
||||||
printf "If you want to set your own password, set the PASSWORD environment variable. e.g. run with:\n"
|
|
||||||
printf "docker run -e PASSWORD=\e[92m<YOUR_PASS>\e[39m -p 8787:8787 rocker/rstudio\n"
|
|
||||||
tput sgr0
|
|
||||||
printf "\n\n"
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [ "$USERID" -lt 1000 ]
|
|
||||||
# Probably a macOS user, https://github.com/rocker-org/rocker/issues/205
|
|
||||||
then
|
|
||||||
echo "$USERID is less than 1000"
|
|
||||||
check_user_id=$(grep -F "auth-minimum-user-id" /etc/rstudio/rserver.conf)
|
|
||||||
if [[ ! -z $check_user_id ]]
|
|
||||||
then
|
|
||||||
echo "minumum authorised user already exists in /etc/rstudio/rserver.conf: $check_user_id"
|
|
||||||
else
|
|
||||||
echo "setting minumum authorised user to 499"
|
|
||||||
echo auth-minimum-user-id=499 >> /etc/rstudio/rserver.conf
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [ "$USERID" -ne 1000 ]
|
|
||||||
## Configure user with a different USERID if requested.
|
|
||||||
then
|
|
||||||
echo "deleting the default user"
|
|
||||||
userdel $DEFAULT_USER
|
|
||||||
echo "creating new $USER with UID $USERID"
|
|
||||||
useradd -m $USER -u $USERID
|
|
||||||
mkdir -p /home/$USER
|
|
||||||
chown -R $USER /home/$USER
|
|
||||||
usermod -a -G staff $USER
|
|
||||||
elif [ "$USER" != "$DEFAULT_USER" ]
|
|
||||||
then
|
|
||||||
## cannot move home folder when it's a shared volume, have to copy and change permissions instead
|
|
||||||
if ! [ -f /home/$USER/.profile ]
|
|
||||||
then
|
|
||||||
cp -r /home/$DEFAULT_USER/.??* /home/$USER || true
|
|
||||||
fi
|
|
||||||
## RENAME the user
|
|
||||||
usermod -l $USER -d /home/$USER $DEFAULT_USER
|
|
||||||
groupmod -n $USER $DEFAULT_USER
|
|
||||||
usermod -a -G staff $USER
|
|
||||||
chown -R $USER:$USER /home/$USER
|
|
||||||
echo "USER is now $USER"
|
|
||||||
fi
|
|
||||||
|
|
||||||
[ "$USER" != "rstudio" ] && rm -fr /home/rstudio
|
|
||||||
|
|
||||||
if [ "$GROUPID" -ne 1000 ]
|
|
||||||
## Configure the primary GID (whether rstudio or $USER) with a different GROUPID if requested.
|
|
||||||
then
|
|
||||||
echo "Modifying primary group $(id $USER -g -n)"
|
|
||||||
groupmod -g $GROUPID $(id $USER -g -n)
|
|
||||||
echo "Primary group ID is now custom_group $GROUPID"
|
|
||||||
fi
|
|
||||||
|
|
||||||
if [[ ${DISABLE_AUTH,,} != "true" ]]
|
|
||||||
then
|
|
||||||
## Add a password to user
|
|
||||||
echo "$USER:$PASSWORD" | chpasswd
|
|
||||||
fi
|
|
||||||
|
|
||||||
# Use Env flag to know if user should be added to sudoers
|
|
||||||
if [[ ${ROOT,,} == "true" ]]
|
|
||||||
then
|
|
||||||
adduser $USER sudo && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
|
|
||||||
echo "$USER added to sudoers"
|
|
||||||
fi
|
|
||||||
|
|
||||||
## Change Umask value if desired
|
|
||||||
if [ "$UMASK" -ne 022 ]
|
|
||||||
then
|
|
||||||
echo "server-set-umask=false" >> /etc/rstudio/rserver.conf
|
|
||||||
echo "Sys.umask(mode=$UMASK)" >> /home/$USER/.Rprofile
|
|
||||||
fi
|
|
||||||
|
|
||||||
## Next one for timezone setup
|
|
||||||
if [ "$TZ" != "Etc/UTC" ]
|
|
||||||
then
|
|
||||||
ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
|
|
||||||
fi
|
|
||||||
|
|
||||||
## Update Locale if needed
|
|
||||||
if [ "$LANG" != "en_US.UTF-8" ]
|
|
||||||
then
|
|
||||||
/usr/sbin/locale-gen --lang $LANG
|
|
||||||
/usr/sbin/update-locale --reset LANG=$LANG
|
|
||||||
fi
|
|
||||||
|
|
@ -1,11 +0,0 @@
|
||||||
#!/usr/bin/with-contenv bash
|
|
||||||
|
|
||||||
echo "root path: $WWW_ROOT_PATH"
|
|
||||||
|
|
||||||
if [[ ! -z $WWW_ROOT_PATH ]]
|
|
||||||
then
|
|
||||||
echo "Set www-root-path to $WWW_ROOT_PATH"
|
|
||||||
echo "www-root-path=$WWW_ROOT_PATH" >> /etc/rstudio/rserver.conf
|
|
||||||
else
|
|
||||||
echo "Not setting www-root-path"
|
|
||||||
fi
|
|
||||||
|
|
@ -1,5 +0,0 @@
|
||||||
#!/usr/bin/with-contenv bash
|
|
||||||
|
|
||||||
printenv >> /etc/R/Renviron.site
|
|
||||||
|
|
||||||
printenv > /home/$USER/.Renviron
|
|
||||||
|
|
@ -1,13 +0,0 @@
|
||||||
#!/usr/bin/with-contenv bash
|
|
||||||
|
|
||||||
echo "session-timeout-minutes=7200" >> /etc/rstudio/rsession.conf
|
|
||||||
echo "session-disconnected-timeout-minutes=1440" >> /etc/rstudio/rsession.conf
|
|
||||||
echo "session-quit-child-processes-on-exit=0" >> /etc/rstudio/rsession.conf
|
|
||||||
echo "session-default-working-dir=~" >> /etc/rstudio/rsession.conf
|
|
||||||
echo "session-default-new-project-dir=~" >> /etc/rstudio/rsession.conf
|
|
||||||
#echo "session-save-action-default=yes" >> /etc/rstudio/rsession.conf
|
|
||||||
echo "allow-shell=1" >> /etc/rstudio/rsession.conf
|
|
||||||
#echo "allow-terminal-websockets=1" >> /etc/rstudio/rsession.conf
|
|
||||||
echo "limit-cpu-time-minutes=0" >> /etc/rstudio/rsession.conf
|
|
||||||
echo "limit-file-upload-size-mb=0" >> /etc/rstudio/rsession.conf
|
|
||||||
#echo "limit-xfs-disk-quota=no" >> /etc/rstudio/rsession.conf
|
|
||||||
|
|
@ -1,24 +0,0 @@
|
||||||
<?xml version="1.0" encoding="utf-8"?>
|
|
||||||
<configuration scan="true" scanPeriod="60 seconds" debug="false">
|
|
||||||
<appender name="FILE" class="ch.qos.logback.core.rolling.RollingFileAppender">
|
|
||||||
<file>/var/log/workspace-lib/fuse-workspace.log</file>
|
|
||||||
<append>true</append>
|
|
||||||
<encoder>
|
|
||||||
<pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{0}: %msg%n
|
|
||||||
</pattern>
|
|
||||||
</encoder>
|
|
||||||
<rollingPolicy class="ch.qos.logback.core.rolling.TimeBasedRollingPolicy">
|
|
||||||
<fileNamePattern>./var/log/workspace-lib/fuse-workspace.log%d{yyyy-MM-dd}.log</fileNamePattern>
|
|
||||||
<maxHistory>30</maxHistory>
|
|
||||||
<maxFileSize>10MB</maxFileSize>
|
|
||||||
<totalSizeCap>100MB</totalSizeCap>
|
|
||||||
</rollingPolicy>
|
|
||||||
</appender>
|
|
||||||
|
|
||||||
<logger name="org.gcube.data.access.storagehub.fs" level="WARN" />
|
|
||||||
<logger name="org.gcube" level="WARN" />
|
|
||||||
|
|
||||||
<root level="WARN">
|
|
||||||
<appender-ref ref="FILE" />
|
|
||||||
</root>
|
|
||||||
</configuration>
|
|
||||||
|
|
@ -1,64 +0,0 @@
|
||||||
#!/usr/bin/with-contenv bash
|
|
||||||
|
|
||||||
# Functions that decode a JWT token
|
|
||||||
_decode_base64_url() {
|
|
||||||
local len=$((${#1} % 4))
|
|
||||||
local result="$1"
|
|
||||||
if [ $len -eq 2 ]; then result="$1"'=='
|
|
||||||
elif [ $len -eq 3 ]; then result="$1"'='
|
|
||||||
fi
|
|
||||||
echo "$result" | tr '_-' '/+' | base64 -d
|
|
||||||
}
|
|
||||||
|
|
||||||
# $1 => JWT to decode
|
|
||||||
# $2 => either 1 for header or 2 for body (default is 2)
|
|
||||||
decode_jwt() { _decode_base64_url $(echo -n $1 | cut -d "." -f ${2:-2}) | jq .; }
|
|
||||||
|
|
||||||
_workspace_scope="/d4science.research-infrastructures.eu"
|
|
||||||
echo "Manage the user's workspace"
|
|
||||||
workspace_dir='/workspace'
|
|
||||||
workspace_logdir='/var/log/workspace-lib'
|
|
||||||
workspace_libdir='/opt/workspace-lib'
|
|
||||||
workspace_fuse_jar="$workspace_libdir/fuse-workspace.jar"
|
|
||||||
|
|
||||||
[[ ! -d "$workspace_dir" ]] || [[ -z `ls -A "$workspace_dir"` ]] || mv $workspace_dir ${workspace_dir}.old
|
|
||||||
|
|
||||||
mkdir -p $workspace_dir
|
|
||||||
chown ${USER}:${USER} $workspace_dir
|
|
||||||
chown -R ${USER}:${USER} $workspace_logdir
|
|
||||||
chmod 444 $workspace_fuse_jar
|
|
||||||
|
|
||||||
_retval=
|
|
||||||
if [ -d /home/${USER}/workspace ]; then
|
|
||||||
rmdir /home/${USER}/workspace
|
|
||||||
_retval=$?
|
|
||||||
if [ $_retval -ne 0 ]; then
|
|
||||||
echo "The user has a directory named 'workspace' inside their home directory and it is not empty."
|
|
||||||
echo "Not starting the workspace mount"
|
|
||||||
exit $_retval
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
|
|
||||||
echo "Mount the workspace"
|
|
||||||
su - "$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} $workspace_dir" >/dev/null 2>&1 &
|
|
||||||
|
|
||||||
sleep 5
|
|
||||||
_retval=
|
|
||||||
_fuse_process=$(ps auwwx | grep fuse | grep java)
|
|
||||||
_retval=$?
|
|
||||||
if [ $_retval -ne 0 ]; then
|
|
||||||
echo "The mount of the workspace failed"
|
|
||||||
exit 1
|
|
||||||
else
|
|
||||||
pushd /home/${USER}
|
|
||||||
if [ $? -ne 0 ]; then
|
|
||||||
if ! [ -L workspace ]; then
|
|
||||||
su - "$USER" -c "ln -s $workspace_dir /workspace"
|
|
||||||
fi
|
|
||||||
else
|
|
||||||
echo "Cannot cd inside the user's home directory"
|
|
||||||
exit 1
|
|
||||||
fi
|
|
||||||
echo "The workspace has been mounted"
|
|
||||||
exit 0
|
|
||||||
fi
|
|
||||||
89
Dockerfile
89
Dockerfile
|
|
@ -1,93 +1,12 @@
|
||||||
FROM d4science/r-studio-requirement
|
FROM d4science/rstudio-base:2023-03-R4-2
|
||||||
|
|
||||||
LABEL org.d4science.image.licenses="EUPL-1.2" \
|
LABEL org.d4science.image.licenses="EUPL-1.2" \
|
||||||
org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/r-studio-requirement" \
|
org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/r-studio-test" \
|
||||||
org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
|
org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
|
||||||
org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>, Roberto Cirillo <roberto.cirillo@isti.cnr.it>" \
|
org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>, Roberto Cirillo <roberto.cirillo@isti.cnr.it>" \
|
||||||
org.d4science.image.r_version="2022.02.1+461"
|
org.d4science.image.r_version="2022.02.1+461"
|
||||||
|
|
||||||
ARG NB_USER="jovyan"
|
COPY rsession.conf /etc/rstudio/rsession.conf
|
||||||
ARG NB_UID="1000"
|
RUN chmod 0644 /etc/rstudio/rsession.conf
|
||||||
ARG NB_GID="100"
|
|
||||||
ARG HOME="/home/${NB_USER}"
|
|
||||||
ENV S6_VERSION=v2.1.0.2
|
|
||||||
ENV RSTUDIO_VERSION=2022.02.1+461
|
|
||||||
ENV DEFAULT_USER="jovyan"
|
|
||||||
ENV USERID="1000"
|
|
||||||
ENV GROUPID="100"
|
|
||||||
ENV PANDOC_VERSION=default
|
|
||||||
ENV PATH=/usr/lib/rstudio-server/bin:$PATH
|
|
||||||
ENV DEBIAN_FRONTEND=noninteractive
|
|
||||||
ENV R_HOME=/usr/local/lib/R
|
|
||||||
# Configure environment
|
|
||||||
ENV SHELL=/bin/bash \
|
|
||||||
NB_USER="${NB_USER}" \
|
|
||||||
NB_UID=${NB_UID} \
|
|
||||||
NB_GID=${NB_GID} \
|
|
||||||
LC_ALL=en_US.UTF-8 \
|
|
||||||
LANG=en_US.UTF-8 \
|
|
||||||
LANGUAGE=en_US.UTF-8
|
|
||||||
ENV HOME="/home/${NB_USER}"
|
|
||||||
|
|
||||||
RUN apt-get update --yes && \
|
|
||||||
apt-get upgrade --yes && \
|
|
||||||
apt-get install --yes --no-install-recommends \
|
|
||||||
python3 python3-pip \
|
|
||||||
curl
|
|
||||||
RUN /rocker_scripts/install_rstudio.sh
|
|
||||||
|
|
||||||
# This part comes from https://github.com/openanalytics/shinyproxy-rstudio-ide-demo/blob/master/Dockerfile
|
|
||||||
RUN echo "www-frame-origin=same" >> /etc/rstudio/disable_auth_rserver.conf
|
|
||||||
RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
|
|
||||||
|
|
||||||
# ADD 02_userconf.sh /etc/cont-init.d/02_userconf
|
|
||||||
RUN mv -f /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
|
|
||||||
RUN echo "USER=$NB_USER" >> /etc/environment
|
|
||||||
|
|
||||||
# ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path
|
|
||||||
# ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters
|
|
||||||
RUN echo "session-timeout-minutes=7200" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN echo "session-disconnected-timeout-minutes=1440" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN echo "session-quit-child-processes-on-exit=0" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN echo "session-default-working-dir=~" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN echo "session-default-new-project-dir=~" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN #echo "session-save-action-default=yes" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN echo "allow-shell=1" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN #echo "allow-terminal-websockets=1" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN echo "limit-cpu-time-minutes=0" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN echo "limit-file-upload-size-mb=0" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN #echo "limit-xfs-disk-quota=no" >> /etc/rstudio/rsession.conf
|
|
||||||
RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
|
RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
|
||||||
|
|
||||||
# Copy a script that we will use to correct permissions after running certain commands
|
|
||||||
COPY fix-permissions /usr/local/bin/fix-permissions
|
|
||||||
RUN chmod a+rx /usr/local/bin/fix-permissions
|
|
||||||
|
|
||||||
# Create NB_USER with name jovyan user with UID=1000 and in the 'users' group
|
|
||||||
# and make sure these dirs are writable by the `users` group.
|
|
||||||
RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
|
|
||||||
sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && \
|
|
||||||
sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && \
|
|
||||||
userdel -r "${NB_USER}" && \
|
|
||||||
useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && \
|
|
||||||
chmod g+w /etc/passwd && \
|
|
||||||
fix-permissions "${HOME}"
|
|
||||||
|
|
||||||
# Install the jupiterhub proxy
|
|
||||||
RUN pip3 install \
|
|
||||||
jsonschema'[format,format-nongpl]' \
|
|
||||||
jupyterhub \
|
|
||||||
jupyterlab \
|
|
||||||
jupyter-rsession-proxy \
|
|
||||||
jupyter-server-proxy \
|
|
||||||
notebook
|
|
||||||
|
|
||||||
RUN apt-get clean && rm -rf /var/lib/apt/lists/* && \
|
|
||||||
echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
|
|
||||||
locale-gen
|
|
||||||
|
|
||||||
# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
|
|
||||||
# hadolint ignore=SC2016
|
|
||||||
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc
|
|
||||||
|
|
||||||
WORKDIR ${HOME}
|
|
||||||
|
|
|
||||||
12
README.md
12
README.md
|
|
@ -1,12 +1,4 @@
|
||||||
# Pipeline-Docker-Template
|
# Rstudio test image
|
||||||
|
|
||||||
This is a template useful for building docker images and push to dockerhub.
|
This image is built from the rstudio-base image, to test changes to packages and the environment.
|
||||||
There is a jenkinsjob template on our jenkins with the same name.
|
|
||||||
|
|
||||||
|
|
||||||
## USAGE TIPS:
|
|
||||||
|
|
||||||
* REMEMBER TO FILL the jenkinsfile environment section with your values. The following field should be properly filled: imagename, git_url
|
|
||||||
* REMEMBER TO PUT your Dockerfile in the root folder of your new project
|
|
||||||
|
|
||||||
* You can find the related jenkinsjob template here: https://jenkins.d4science.org/job/Pipeline-Docker-Template/
|
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,11 @@
|
||||||
|
session-timeout-minutes=7200
|
||||||
|
session-disconnected-timeout-minutes=1440
|
||||||
|
session-quit-child-processes-on-exit=1
|
||||||
|
session-default-working-dir=~
|
||||||
|
session-default-new-project-dir=~
|
||||||
|
session-save-action-default=no
|
||||||
|
allow-shell=1
|
||||||
|
allow-terminal-websockets=0
|
||||||
|
limit-cpu-time-minutes=0
|
||||||
|
limit-file-upload-size-mb=0
|
||||||
|
limit-xfs-disk-quota=no
|
||||||
Loading…
Reference in New Issue