From 65294a8a270bef802dd702038198f854f5cfc864 Mon Sep 17 00:00:00 2001
From: Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>
Date: Tue, 11 Apr 2023 16:02:34 +0200
Subject: [PATCH] First set of files.

---
 Dockerfile      | 11 +++++++++
 Jenkinsfile     | 66 +++++++++++++++++++++++++++++++++++++++++++++++++
 README.md       |  5 +++-
 fix-permissions | 36 +++++++++++++++++++++++++++
 rsession.conf   | 11 +++++++++
 5 files changed, 128 insertions(+), 1 deletion(-)
 create mode 100644 Dockerfile
 create mode 100644 Jenkinsfile
 create mode 100644 fix-permissions
 create mode 100644 rsession.conf

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..49411e1
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,11 @@
+FROM d4science/rstudio-base:2023-03-R4-2
+
+LABEL org.d4science.image.licenses="EUPL-1.2" \
+      org.d4science.image.source="https://code-repo.d4science.org/gCubeSystem/rstudio-d4science" \
+      org.d4science.image.vendor="D4Science <https://www.d4science.org>" \
+      org.d4science.image.authors="Andrea Dell'Amico <andrea.dellamico@isti.cnr.it>
+
+COPY rsession.conf /etc/rstudio/rsession.conf
+RUN chmod 0644 /etc/rstudio/rsession.conf
+RUN curl -o "${R_HOME}/etc/Rprofile.site" "https://code-repo.d4science.org/gCubeSystem/rstudio-rprofile/raw/branch/master/jupyter-Rprofile.site"
+
diff --git a/Jenkinsfile b/Jenkinsfile
new file mode 100644
index 0000000..d4900c3
--- /dev/null
+++ b/Jenkinsfile
@@ -0,0 +1,66 @@
+// REMEMBER TO FILL THE environment section with your values.
+// the following filed should be filled: imagename, git_url
+// REMEMBER to put your Dockerfile in the root folder of your project
+// The related jenkinsjob template is here: 
+
+
+pipeline {
+  agent {
+      label 'docker'
+  }
+  environment {
+    imagename = "d4science/r-studio-test"
+    registryCredential = 'e348bfab-5580-4db6-b0e0-d854966bde08'
+    dockerImage = ''
+    git_url='https://code-repo.d4science.org/gCubeSystem/r-studio-test.git'
+  }
+  stages {
+    stage('Cloning Git') {
+      steps {
+        git([url: git_url, branch: 'master', credentialsId: '88b54962-1c0e-49cb-8155-22276860f346'])
+
+      }
+    }
+    stage('Building image') {
+      steps{
+        script {
+          dockerImage = docker.build imagename
+        }
+      }
+    }
+    stage('Deploy Image') {
+      steps{
+        script {
+          docker.withRegistry( '', registryCredential ) {
+            dockerImage.push("$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}"
+        }
+    }
+}
diff --git a/README.md b/README.md
index dd856b6..61c752b 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,6 @@
 # rstudio-d4science
 
-Rstudio docker images. Used through JupyterHub in the D4Science VREs.
\ No newline at end of file
+Rstudio image that builds from "r-full"
+
+One branch for each corresponding *major.minor* `R` version and for each
+customization on top of the R version.
diff --git a/fix-permissions b/fix-permissions
new file mode 100644
index 0000000..08436da
--- /dev/null
+++ b/fix-permissions
@@ -0,0 +1,36 @@
+#!/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
diff --git a/rsession.conf b/rsession.conf
new file mode 100644
index 0000000..b3b8532
--- /dev/null
+++ b/rsession.conf
@@ -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=0
+allow-terminal-websockets=0
+limit-cpu-time-minutes=0
+limit-file-upload-size-mb=0
+limit-xfs-disk-quota=no