06-fuse-logback.xml

@@ -0,0 +1,24 @@
+<?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>

06_workspace_mount.sh

@@ -0,0 +1,43 @@
+#!/usr/bin/with-contenv bash
+
+echo "Manage the user's workspace"
+workspace_dir='/workspace'
+workspace_logdir='/var/log/workspace-lib'
+workspace_libdir='/opt/workspace-lib'
+workspace_fuse_jar="$workspace_libdir/fuse-workspace.jar"
+
+_decode_base64_url() {
+  local len=$((${#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 ${2:-2}) | jq .; }
+
+
+[[ ! -d "$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} $workspace_logdir
+
+_retval=
+/bin/rm /home/${USER}/workspace
+_retval=$?
+if [ $_retval -ne 0 ]; then
+    echo "The user has a directory named 'workspace' inside their home directory"
+    echo "Not starting the workspace mount"
+    exit
+else
+    ln -s /home/${USER}/workspace $workspace_dir
+fi
+
+echo "Mount the workspace"
+su - "$USER" -c "/usr/bin/java  -cp .:${workspace_dir}:${workspace_logdir}/ -Dlogback.configurationFile=${workspace_logdir}/logback.xml -jar $workspace_fuse_jar $SHINYPROXY_OIDC_ACCESS_TOKEN $workspace_dir" >/dev/null 2>&1 &
+
+exit ?$

Dockerfile

@@ -12,12 +12,10 @@ ENV DEFAULT_USER=rstudio
 ENV PANDOC_VERSION=default
 ENV PATH=/usr/lib/rstudio-server/bin:$PATH
 
-
 RUN /rocker_scripts/install_rstudio.sh
 RUN /rocker_scripts/install_pandoc.sh
 
-# Add the mountpoint for the workspace
+RUN apt-get update && apt-get install -y fuse zip jq
-RUN mkdir /workspace
 
 # 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
@@ -32,6 +30,13 @@ ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path
 #ADD 04_copy_env.sh /etc/cont-init.d/04_copy_env
 ADD 05_setup_rsession_parameters.sh /etc/cont-init.d/05_setup_rsession_parameters
 
+# Prepare the workspace environment
+RUN mkdir -p /opt/workspace-lib
+RUN mkdir /var/log/workspace-lib
+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 /workspace-lib/fuse-workspace.jar
+ADD 06_workspace_mount.sh /etc/cont-init.d/06_workspace_mount
+ADD 06-fuse-logback.xml /workspace-lib/logback.xml
+
 EXPOSE 8787
 
 CMD ["/init"]