Files to use as a base.

This commit is contained in:
Andrea Dell'Amico 2023-04-10 17:00:40 +02:00
parent c567d47808
commit 734cbe52a0
Signed by: andrea.dellamico
GPG Key ID: 147ABE6CEB9E20FF
5 changed files with 199 additions and 1 deletions

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Dockerfile Normal file
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FROM d4science/r-full:latest
LABEL org.d4science.image.licenses="EUPL-1.2" \
org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/rstudio-base" \
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>"
ENV DEBIAN_FRONTEND=noninteractive
ENV S6_VERSION=v2.1.0.2
ENV RSTUDIO_VERSION=2023.03.0+386
ENV DEFAULT_USER=rstudio
ENV PANDOC_VERSION=default
ENV QUARTO_VERSION=default
ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"
ARG HOME="/home/${NB_USER}"
ENV S6_VERSION=v2.1.0.2
ENV RSTUDIO_VERSION=2022.02.1+461
ENV DEFAULT_USER="jovyan"
ENV USERID="1000"
ENV GROUPID="100"
ENV PATH=/usr/lib/rstudio-server/bin:$PATH
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
RUN /rocker_scripts/install_rstudio.sh
RUN /rocker_scripts/install_pandoc.sh
RUN /rocker_scripts/install_quarto.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
RUN mv -f /etc/rstudio/disable_auth_rserver.conf /etc/rstudio/rserver.conf
RUN echo "USER=$NB_USER" >> /etc/environment
COPY rsession.conf /etc/rstudio/rsession.conf
RUN chmod 0644 /etc/rstudio/rsession.conf
RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
# 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}

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// REMEMBER TO FILL THE environment section with your values.
// the following filed should be filled: imagename, git_url
// REMEMBER to put your Dockerfile in the root folder of your project
// The related jenkinsjob template is here:
pipeline {
agent {
label 'docker'
}
environment {
imagename = "d4science/rstudio-base"
registryCredential = 'e348bfab-5580-4db6-b0e0-d854966bde08'
dockerImage = ''
git_url='https://code-repo.d4science.org/gCubeSystem/rstudio-base.git'
}
stages {
stage('Cloning Git') {
steps {
git([url: git_url, branch: 'master', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
}
}
stage('Building image') {
steps{
script {
dockerImage = docker.build imagename
}
}
}
stage('Deploy Image') {
steps{
script {
docker.withRegistry( '', registryCredential ) {
dockerImage.push("$BUILD_NUMBER")
dockerImage.push('latest')
}
}
}
}
stage('Remove Unused docker image') {
steps{
sh "docker rmi $imagename:$BUILD_NUMBER"
sh "docker rmi $imagename:latest"
}
}
}
// post-build actions
post {
success {
echo 'The docker pipeline worked!'
emailext to: 'jenkinsbuilds@d4science.org',
subject: "[Jenkins DockerPipeline D4S] build ${currentBuild.fullDisplayName} worked",
body: "Build time: ${currentBuild.durationString}. See ${env.BUILD_URL}"
}
failure {
echo 'The docker pipeline has failed'
emailext attachLog: true,
to: 'jenkinsbuilds@d4science.org',
subject: "[Jenkins DockerPipeline D4S] build ${currentBuild.fullDisplayName} failed for image ${imagename}",
body: "Something is wrong with ${env.BUILD_URL}"
}
}
}

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# rstudio-base # rstudio-base
Rstudio image that builds from "r-full" Rstudio image that builds from "r-full"
* One branch for each corresponding *major.minor* `R` version
* Customizations will be done in rstudio-custom-X

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#!/bin/bash
# From https://github.com/jupyter/docker-stacks/blob/main/docker-stacks-foundation/fix-permissions
# set permissions on a directory
# after any installation, if a directory needs to be (human) user-writable,
# run this script on it.
# It will make everything in the directory owned by the group ${NB_GID}
# and writable by that group.
# Deployments that want to set a specific user id can preserve permissions
# by adding the `--group-add users` line to `docker run`.
# uses find to avoid touching files that already have the right permissions,
# which would cause massive image explosion
# right permissions are:
# group=${NB_GID}
# AND permissions include group rwX (directory-execute)
# AND directories have setuid,setgid bits set
set -e
for d in "$@"; do
find "${d}" \
! \( \
-group "${NB_GID}" \
-a -perm -g+rwX \
\) \
-exec chgrp "${NB_GID}" -- {} \+ \
-exec chmod g+rwX -- {} \+
# setuid, setgid *on directories only*
find "${d}" \
\( \
-type d \
-a ! -perm -6000 \
\) \
-exec chmod +6000 -- {} \+
done

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session-timeout-minutes=7200
session-disconnected-timeout-minutes=1440
session-quit-child-processes-on-exit=0
session-default-working-dir=~
session-default-new-project-dir=~
# session-save-action-default=yes
allow-shell=1
#allow-terminal-websockets=1
limit-cpu-time-minutes=0
limit-file-upload-size-mb=0
#limit-xfs-disk-quota=no