From 8d7d4a05bce1d09e9f207d9d472c57b400777b0b Mon Sep 17 00:00:00 2001
From: Tony <tony@saagie.com>
Date: Thu, 27 Jul 2023 14:25:26 +0200
Subject: [PATCH] Add Rstudio 4.3

---
 .../app/rstudio/rstudio-4.2/context.yaml      |   2 +-
 .../app/rstudio/rstudio-4.3/Dockerfile        |  25 ++++
 .../app/rstudio/rstudio-4.3/build.gradle.kts  |  31 +++++
 .../app/rstudio/rstudio-4.3/context.yaml      |  12 ++
 .../app/rstudio/rstudio-4.3/dockerInfo.yaml   |   2 +
 .../app/rstudio/rstudio-4.3/image_test.yaml   |  96 +++++++++++++++
 .../rstudio-4.3/resources/entrypoint.sh       |  21 ++++
 .../rstudio-4.3/resources/init_rstudio.sh     |  98 +++++++++++++++
 .../rstudio/rstudio-4.3/resources/server.conf |  24 ++++
 .../rstudio/rstudio-4.3/resources/userconf    | 114 ++++++++++++++++++
 10 files changed, 424 insertions(+), 1 deletion(-)
 create mode 100644 technologies/app/rstudio/rstudio-4.3/Dockerfile
 create mode 100644 technologies/app/rstudio/rstudio-4.3/build.gradle.kts
 create mode 100644 technologies/app/rstudio/rstudio-4.3/context.yaml
 create mode 100644 technologies/app/rstudio/rstudio-4.3/dockerInfo.yaml
 create mode 100644 technologies/app/rstudio/rstudio-4.3/image_test.yaml
 create mode 100755 technologies/app/rstudio/rstudio-4.3/resources/entrypoint.sh
 create mode 100644 technologies/app/rstudio/rstudio-4.3/resources/init_rstudio.sh
 create mode 100644 technologies/app/rstudio/rstudio-4.3/resources/server.conf
 create mode 100644 technologies/app/rstudio/rstudio-4.3/resources/userconf

diff --git a/technologies/app/rstudio/rstudio-4.2/context.yaml b/technologies/app/rstudio/rstudio-4.2/context.yaml
index 8659d678c..3d26b2793 100644
--- a/technologies/app/rstudio/rstudio-4.2/context.yaml
+++ b/technologies/app/rstudio/rstudio-4.2/context.yaml
@@ -3,7 +3,7 @@ label: "4.2"
 releaseNotes: First version of RStudio 4.2 into Saagie.
 available: true
 trustLevel: stable
-recommended: true
+recommended: false
 ports:
   - port: 80
     name: Rstudio
diff --git a/technologies/app/rstudio/rstudio-4.3/Dockerfile b/technologies/app/rstudio/rstudio-4.3/Dockerfile
new file mode 100644
index 000000000..1eaec4d9f
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/Dockerfile
@@ -0,0 +1,25 @@
+ARG base_img
+
+FROM ${base_img} AS BASE_IMG
+
+# Nginx isntall and remove default conf
+RUN apt-get update -qq && apt-get install -yqq --no-install-recommends nginx \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/ \
+    && rm /etc/nginx/sites-enabled/default
+COPY resources/server.conf /etc/nginx/sites-enabled/rstudio.conf
+COPY resources/userconf /etc/cont-init.d/userconf
+COPY resources/init_rstudio.sh /init_rstudio.sh
+
+# Be sure rstudio user has full access to his home directory
+RUN mkdir -p /home/rstudio && \
+    chown -R rstudio:rstudio /home/rstudio && \
+    chmod -R 755 /home/rstudio && \
+    chmod 500 /init_rstudio.sh
+
+EXPOSE 80
+
+COPY resources/entrypoint.sh /entrypoint.sh
+ENTRYPOINT ["/entrypoint.sh"]
+
+CMD ["/bin/sh", "-c", "/init_rstudio.sh"]
diff --git a/technologies/app/rstudio/rstudio-4.3/build.gradle.kts b/technologies/app/rstudio/rstudio-4.3/build.gradle.kts
new file mode 100644
index 000000000..036a6e380
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/build.gradle.kts
@@ -0,0 +1,31 @@
+/*
+ * SPDX-License-Identifier: Apache-2.0
+ *
+ * Copyright 2019-2021.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import com.bmuschko.gradle.docker.DockerRemoteApiPlugin
+import com.saagie.technologies.SaagieTechnologiesGradlePlugin
+
+
+apply<DockerRemoteApiPlugin>()
+apply<SaagieTechnologiesGradlePlugin>()
+
+
+tasks.withType(com.bmuschko.gradle.docker.tasks.image.DockerBuildImage::class) {
+     this.buildArgs.put(
+        "base_img",
+        "saagie/r-image:4.3-1.163.0_sdktechno-238"
+    )
+}
diff --git a/technologies/app/rstudio/rstudio-4.3/context.yaml b/technologies/app/rstudio/rstudio-4.3/context.yaml
new file mode 100644
index 000000000..9c4d38d5b
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/context.yaml
@@ -0,0 +1,12 @@
+id: rstudio-4.3
+label: "4.3"
+releaseNotes: First version of RStudio 4.3 into Saagie.
+available: true
+trustLevel: stable
+recommended: true
+ports:
+  - port: 80
+    name: Rstudio
+    rewriteUrl: false
+    basePath: SAAGIE_BASE_PATH
+volumes: ["/home"]
diff --git a/technologies/app/rstudio/rstudio-4.3/dockerInfo.yaml b/technologies/app/rstudio/rstudio-4.3/dockerInfo.yaml
new file mode 100644
index 000000000..2f44f12f5
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/dockerInfo.yaml
@@ -0,0 +1,2 @@
+image: saagie/rstudio
+baseTag: 4.3
diff --git a/technologies/app/rstudio/rstudio-4.3/image_test.yaml b/technologies/app/rstudio/rstudio-4.3/image_test.yaml
new file mode 100644
index 000000000..b20d3a15c
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/image_test.yaml
@@ -0,0 +1,96 @@
+schemaVersion: "2.0.0"
+
+metadataTest:
+  env:
+    - key: LANG
+      value: en_US.UTF-8
+    - key: JAVA_HOME
+      value: /usr/lib/jvm/java-11-openjdk-amd64
+    - key: HADOOP_HOME
+      value: /hadoop/hadoop-2.7.0
+    - key: HIVE_HOME
+      value: /apache-hive-1.2.2-bin
+
+fileExistenceTests:
+  - name: "entrypoint"
+    path: "/entrypoint.sh"
+    shouldExist: true
+    permissions: "-rwxr-xr-x"
+  - name: "init_rstudio"
+    path: "/init_rstudio.sh"
+    shouldExist: true
+    permissions: "-r-x------"
+  - name: "rstudio_home"
+    path: "/home/rstudio"
+    shouldExist: true
+    permissions: "drwxr-xr-x"
+    uid: 1000
+    gid: 1000
+  - name: No default nginx conf
+    path: /etc/nginx/sites-enabled/default
+    shouldExist: false
+  - name: rstudio nginx conf
+    path: "/etc/nginx/sites-enabled/rstudio.conf"
+    shouldExist: true
+    permissions: "-rw-r--r--"
+  - name: Impala ODBC dependecy
+    path: "/opt/cloudera/impalaodbc/Setup/odbcinst.ini"
+    shouldExist: true
+
+fileContentTests:
+  - name: "OBBC Impala content"
+    path: "/opt/cloudera/impalaodbc/Setup/odbcinst.ini"
+    expectedContents:
+      [
+        "Cloudera ODBC Driver for Impala 32-bit=Installed",
+        "Cloudera ODBC Driver for Impala 64-bit=Installed",
+        "Driver=/opt/cloudera/impalaodbc/lib/32/libclouderaimpalaodbc32.so",
+        "Driver=/opt/cloudera/impalaodbc/lib/64/libclouderaimpalaodbc64.so"
+      ]
+  - name: "RStudio conf"
+    path: "/etc/nginx/sites-enabled/rstudio.conf"
+    expectedContents:
+      [
+        "listen 80 default_server;",
+        "listen \\[::\\]:80 default_server",
+        "location SAAGIE_BASE_PATH {",
+        "proxy_pass http:\\/\\/localhost:8787;",
+      ]
+
+commandTests:
+  - name: "Workdir"
+    command: "pwd"
+    expectedOutput: ["/"]
+  - name: "R version"
+    command: "R"
+    args: ["--version"]
+    expectedOutput: ['R version 4.3.*']
+  - name: "java version"
+    command: "java"
+    args: ["-version"]
+    expectedError: ['openjdk version "11.*']
+  - name: "java installation"
+    command: "which"
+    args: ["java"]
+    expectedOutput: ["/usr/lib/jvm/java-11-openjdk-amd64/bin/java"]
+  - name: "Hadoop installation"
+    command: "which"
+    args: ["hadoop"]
+    expectedOutput: ["/hadoop/hadoop-2.7.0/bin/hadoop"]
+  - name: "Beeline installation"
+    command: "which"
+    args: ["beeline"]
+    expectedOutput: ["/apache-hive-1.2.2-bin/bin/beeline"]
+  - name: check All libs
+    command: "bash"
+    args: [
+      "-c",
+      "
+        Rscript -e 'library(tidyverse)' &&
+        Rscript -e 'library(aws.s3)' &&
+        Rscript -e 'library(arrow)' &&
+        Rscript -e 'library(openxlsx)' &&
+        Rscript -e 'library(data.table)' &&
+        Rscript -e 'library(odbc)';",
+    ]
+    exitCode: 0
diff --git a/technologies/app/rstudio/rstudio-4.3/resources/entrypoint.sh b/technologies/app/rstudio/rstudio-4.3/resources/entrypoint.sh
new file mode 100755
index 000000000..2ff277711
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/resources/entrypoint.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+if [[ -z ${RSTUDIO_ADMIN_PASSWORD} || -z ${RSTUDIO_PASSWORD} ]]; then
+  echo "ERROR : Missing environment variables. In order to work, this app needs the following environment variables set : "
+  echo "RSTUDIO_ADMIN_PASSWORD : Password for the user admin, with root permissions"
+  echo "RSTUDIO_PASSWORD : Password for the user rstudio"
+  exit 1
+fi
+
+R_HOME=$(Rscript -e 'Sys.getenv("R_HOME")' | sed -rn 's/^\[[[:digit:]]+\] "(.*)"/\1/p')
+
+# Change default CRAN to ENV VAR if present
+if [[ -z "${R_CUSTOM_CRAN}" ]]; then
+    echo "No custom CRAN defined, using default, you can configure one using R_CUSTOM_CRAN env var"
+else
+    echo "Custom CRAN used: ${R_CUSTOM_CRAN}"
+    sed -ri "s#(CRAN = ')[^']*#\1${R_CUSTOM_CRAN}#g" "${R_HOME}/etc/Rprofile.site"
+fi
+
+sed -i 's:SAAGIE_BASE_PATH:'"$SAAGIE_BASE_PATH"':g' /etc/nginx/sites-enabled/rstudio.conf
+nginx && /init_rstudio.sh
\ No newline at end of file
diff --git a/technologies/app/rstudio/rstudio-4.3/resources/init_rstudio.sh b/technologies/app/rstudio/rstudio-4.3/resources/init_rstudio.sh
new file mode 100644
index 000000000..766929532
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/resources/init_rstudio.sh
@@ -0,0 +1,98 @@
+#!/bin/bash
+
+# Grab runtime parameters
+TEMP=`getopt -o p: --long port: -- "$@"`
+eval set -- "$TEMP"
+
+while true ; do
+  case "$1" in
+    -p|--port)
+      case "$2" in
+        "") shift 2 ;;
+        *) RSTUDIO_PORT=$2 ; shift 2 ;;
+      esac ;;
+    --) shift ; break ;;
+    *) echo "Internal error!" ; exit 1 ;;
+  esac
+done
+
+# check if rstudio needs to be run on a custom port
+if [ -z $RSTUDIO_PORT ];
+then
+  echo "INFO: no port given. RStudio will run on default port (8787)."
+  export PORT0=8787
+  export RSTUDIO_PORT=8787
+else
+  # If not already set, set a fake PORT0 variable (used in spark-env.sh)
+  if [ -z $PORT0 ]
+  then
+    export PORT0=$(( $RSTUDIO_PORT+1 ))
+    echo "WARNING: no PORT0 environment variable provided. $PORT0 will be used..."
+  fi
+  echo "www-port=$RSTUDIO_PORT" >> /etc/rstudio/rserver.conf
+fi
+
+echo "Running RStudio on port $RSTUDIO_PORT"
+
+/init &
+
+# wait a bit for initialization to end before modifying the users...
+sleep 5
+
+echo "Init users"
+
+# We need to make rstudio user the owner of his own home directory as it will be owned by root if we mount a docker volume to /home (weird but true...)
+mkdir -p /home/rstudio
+chown -R rstudio:rstudio /home/rstudio
+chmod -R 755 /home/rstudio
+
+# create an admin user who will be able to create new users directly from RStudio IDE
+useradd admin --home /home/admin --create-home -p $(openssl passwd -1 ${RSTUDIO_ADMIN_PASSWORD}) --groups sudo,shadow,rstudio,staff
+
+# Add backupusers script for admin user
+mkdir -p /home/admin
+echo "sudo tar cf /home/admin/users_backup.tar /etc/passwd /etc/shadow 2> /dev/null" > /home/admin/backupusers
+chown admin:admin /home/admin/backupusers
+chmod 700 /home/admin/backupusers
+
+# then restore previous users if necessary
+if [ -e /home/admin/users_backup.tar ]
+then
+    echo "Restoring users..."
+    rm -rf /tmp/userrestore
+    mkdir -p /tmp/userrestore
+
+    tar xf /home/admin/users_backup.tar -C /tmp/userrestore --strip-components=1
+
+    cat /tmp/userrestore/shadow | while read LINE
+    do
+      # echo $LINE
+
+      USER=$(echo $LINE | awk -F':' '{print $1}')
+      ENCRYPTED_PASSWD=$(echo $LINE | awk -F':' '{print $2}')
+
+      if ! grep -q "^$USER:" /etc/passwd
+      then
+        echo "- restoring $USER"
+        HOME_DIR=$(grep "^$USER:" /tmp/userrestore/passwd | awk -F':' '{print $6}')
+        echo "   home dir: $HOME_DIR"
+        useradd $USER --home $HOME_DIR --create-home -p $ENCRYPTED_PASSWD
+        chown -R $USER:$USER $HOME_DIR
+      fi
+
+    done
+fi
+
+# propagate environment variables to every user
+R_HOME=$(Rscript -e 'Sys.getenv("R_HOME")' | sed -rn 's/^\[[[:digit:]]+\] "(.*)"/\1/p')
+
+env | while read VAR
+do
+  if ! grep -q "$VAR" /ROOT_ENV_VAR && ! echo "$VAR" | grep -q "RSTUDIO_ADMIN_PASSWORD"
+  then
+    echo $VAR >> $R_HOME/etc/Renviron.site
+  fi
+done
+
+# keep the container running...
+tail -f /dev/null
diff --git a/technologies/app/rstudio/rstudio-4.3/resources/server.conf b/technologies/app/rstudio/rstudio-4.3/resources/server.conf
new file mode 100644
index 000000000..49c2fc342
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/resources/server.conf
@@ -0,0 +1,24 @@
+map $http_connection $upgrade_requested {
+  default upgrade;
+  '' close;
+}
+server {
+  listen 80 default_server;
+  listen [::]:80 default_server;
+  server_name _;
+  
+  client_max_body_size 2G;
+
+  location SAAGIE_BASE_PATH {
+    proxy_http_version 1.1;
+    proxy_set_header Upgrade $http_upgrade;
+    proxy_set_header Connection $upgrade_requested;
+    proxy_read_timeout 20d;
+
+    rewrite ^SAAGIE_BASE_PATH/(.*)$ /$1 break;
+    rewrite ^SAAGIE_BASE_PATH$ / break;
+    proxy_pass http://localhost:8787;
+    proxy_redirect http://localhost:8787/ $scheme://$hostSAAGIE_BASE_PATH/;
+    proxy_redirect https://localhost:8787/ $scheme://$hostSAAGIE_BASE_PATH/;
+  }
+}
\ No newline at end of file
diff --git a/technologies/app/rstudio/rstudio-4.3/resources/userconf b/technologies/app/rstudio/rstudio-4.3/resources/userconf
new file mode 100644
index 000000000..cc9206275
--- /dev/null
+++ b/technologies/app/rstudio/rstudio-4.3/resources/userconf
@@ -0,0 +1,114 @@
+#!/usr/bin/with-contenv bash
+
+## Set defaults for environmental variables in case they are undefined
+USER=${USER:=rstudio}
+PASSWORD=${PASSWORD:=rstudio}
+USERID=${USERID:=1000}
+GROUPID=${GROUPID:=1000}
+ROOT=${ROOT:=FALSE}
+UMASK=${UMASK:=022}
+
+## Make sure RStudio inherits the full path
+echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron
+
+bold=$(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 [ "$RSTUDIO_ADMIN_PASSWORD" == "rstudioadmin" ]
+then
+    printf "\n\n"
+    tput bold
+    printf "\e[31mERROR\e[39m: You must set a unique ADMIN PASSWORD (not 'rstudioadmin') first! ie. define an environment variable RSTUDIO_ADMIN_PASSWORD or if manually run, run it with:\n"
+    printf "docker run -e RSTUDIO_ADMIN_PASSWORD=\e[92m<ADMIN_PASS>\e[39m -p 80:80 saagie/rstudio\n"
+    tput sgr0
+    printf "\n\n"
+    exit 1
+fi
+
+if grep --quiet "auth-none=1" /etc/rstudio/rserver.conf
+then
+	echo "Skipping authentication as requested"
+elif [ "$RSTUDIO_PASSWORD" == "rstudio" ]
+then
+    printf "\n\n"
+    tput bold
+    printf "\e[31mERROR\e[39m: You must set a unique PASSWORD (not 'rstudio') first! e.g. run with:\n"
+    printf "docker run -e RSTUDIO_PASSWORD=\e[92m<YOUR_PASS>\e[39m -p 80:80 saagie/rstudio\n"
+    tput sgr0
+    printf "\n\n"
+    exit 1
+else
+  export PASSWORD=`echo $RSTUDIO_PASSWORD`
+fi
+
+if [ "$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 user rstudio"
+    userdel rstudio
+    echo "creating new $USER with UID $USERID"
+    useradd -m $USER -u $USERID
+    mkdir /home/$USER
+    chown -R $USER /home/$USER
+    usermod -a -G staff $USER
+elif [ "$USER" != "rstudio" ]
+  then
+    ## cannot move home folder when it's a shared volume, have to copy and change permissions instead
+    cp -r /home/rstudio /home/$USER
+    ## RENAME the user
+    usermod -l $USER -d /home/$USER rstudio
+    groupmod -n $USER rstudio
+    usermod -a -G staff $USER
+    chown -R $USER:$USER /home/$USER
+    echo "USER is now $USER"
+fi
+
+if [ "$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 $GROUPID"
+fi
+
+## Add a password to user
+echo "$USER:$PASSWORD" | chpasswd
+
+# 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/$USER/.Rprofile
+fi
+
+## add these to the global environment so they are avialable to the RStudio user
+echo "HTTR_LOCALHOST=$HTTR_LOCALHOST" >> /etc/R/Renviron.site
+echo "HTTR_PORT=$HTTR_PORT" >> /etc/R/Renviron.site
\ No newline at end of file