r_connector: add script and cron job that unmount stale sessions.

smartgears/r_connector/defaults/main.yml

@@ -10,6 +10,7 @@ r_connector_usershome: /home/
 r_connector_userconfig: userconfig.csv
 r_connector_adduserscript: /usr/local/bin/rusersadd
 r_connector_workspace_unmount: /usr/local/bin/rconnector_unmount
+r_connector_check_stale_sessions: /usr/local/bin/rconnector_check_stale_sessions
 r_connector_workspace_mountpoint: workspace
 r_connector_sleep_after_mount: 5
 r_connector_rstudio_cookie_key: /var/lib/rstudio-server/secure-cookie-key
@@ -42,3 +43,6 @@ fuse_integration_name: sh-fuse-integration
 fuse_integration_group_id: org.gcube.data-access
 fuse_integration_version: latest
 fuse_integration_classifier: 'jar-with-dependencies'
+r_connector_fuse_packages: 
+  - fuse
+  - libfuse2

smartgears/r_connector/tasks/main.yml

@@ -69,29 +69,29 @@
       become_user: root
       template: src=rconnector_unmount dest={{ r_connector_workspace_unmount }} owner=root group=root mode=0555
 
+    - name: Install the script that checks for stale workspace mounts
+      become_user: root
+      template: src=rconnector_check_stale_sessions dest={{ r_connector_check_stale_sessions }} owner=root group=root mode=0555
+
+    - name: Install the cron job that regulary wipes out the stale workspace mounts
+      become: root
+      cron: name="Unmount the stale workspace sessions" special_time=hourly job="{{ r_connector_check_stale_sessions }} >/dev/null 2>&1"
+
     - name: Crete the directory that will host the RConfiguration stuff
       become_user: root
       file: dest={{ r_connector_rprofile_base_dir }} owner={{ d4science_user }} group={{ d4science_user }} state=directory
 
     - name: Download the fuse jar-with-dependencies
       become_user: root
-      get_url:
-        url: '{{ fuse_integration_jar_url }}'
-        dest: /usr/local/lib/{{ fuse_integration_file }}
-        force: yes
-        mode: 0555
-   
-    - name: Download the fuse jar-with-dependencies
-      maven_artifact: artifact_id={{ fuse_integration_name }} version={{ fuse_integration_version | default(omit) }} group_id={{ fuse_integration_group_id }} extension={{ fuse_integration_extension | default('jar') }} repository_url={{ smartgears_global_base_url }} classifier={{ fuse_integration_classifier }} dest=/usr/local/lib/{{ fuse_integration_file } 
-
-#      shell: cd /usr/local/lib/ ; wget http://maven.research-infrastructures.eu/nexus/content/repositories/gcube-snapshots/org/gcube/data-access/sh-fuse-integration/1.0.0-SNAPSHOT/sh-fuse-integration-1.0.0-20190312.161452-1-jar-with-dependencies.jar
-#      args:
-#        creates: /usr/local/lib/sh-fuse-integration-jar-with-dependencies.jar
-
+      maven_artifact: artifact_id={{ fuse_integration_name }} version={{ fuse_integration_version }} group_id={{ fuse_integration_group_id }} extension={{ fuse_integration_extension }} repository_url={{ smartgears_global_base_url }} classifier={{ fuse_integration_classifier }} dest=/usr/local/lib/{{ fuse_integration_file }}
 
     - name: Get the svn repository that provides the .Rprofile
       subversion: repo={{ r_connector_rprofile_svn_url }} dest={{ r_connector_rprofile_path }}
 
+    - name: Install /etc/R/Rprofile.site as a symlink to the svn repository
+      become_user: root
+      file: src={{ r_connector_rprofile_path }}/.Rprofile dest=/etc/R/Rprofile.site state=link force=yes
+
     - name: Install the cron job that regulary updates the Rprofile
       cron: name="Update the RStudioConfiguration repo" special_time=daily job="cd {{ r_connector_rprofile_path }} ; svn update >/dev/null 2>&1"
 
@@ -102,15 +102,15 @@
 
 - block:
 # Additional fuse packages 
-    - name: Install the libfuse package 
-      apt: pkg=libfuse2 state=present update_cache=yes cache_valid_time=3600
+    - name: Install the fuse required packages
+      apt: pkg={{ r_connector_fuse_packages }} state=present update_cache=yes cache_valid_time=3600
 
-    - name: Install the fuse package
-      apt: pkg=fuse state=present update_cache=yes cache_valid_time=3600
+  when: r_connector_install
+  tags: [ 'smartgears', 'r_connector', 'tomcat' ]
 
 - block:
     - name: Reconfigure the Java environment for R
-      shell: export JAVA_HOME={{ jdk_java_home }} ; export J2SDKDIR={{ jdk_java_home ; export J2REDIR={{ jdk_java_home }}/jre ; R CMD javareconf
+      shell: export JAVA_HOME={{ jdk_java_home }} ; export J2SDKDIR={{ jdk_java_home }} ; export J2REDIR={{ jdk_java_home }}/jre ; R CMD javareconf
       when: jdk_java_home is defined
 
   become: True

smartgears/r_connector/templates/rconnector_check_stale_sessions

@@ -0,0 +1,49 @@
+#!/bin/bash
+DEBUG=1
+if [ $DEBUG -eq 0 ] ; then
+    set -x
+    exec 2>/var/tmp/rconnector_check_stale_sessions.log
+fi
+# We use logger to log directly to syslog
+LOG_PREFIX="r-connector check_stale_sessions:"
+
+UNMOUNT_SCRIPT="{{ r_connector_workspace_unmount }}"
+RSTUDIO_BIN="/usr/sbin/rstudio-server"
+ACTIVE_MOUNTS=
+ACTIVE_MOUNTS_F=$( mktemp /tmp/active_mounts.XXXXX )
+ACTIVE_SESSIONS_LIST=
+ACTIVE_SESSIONS_LIST_F=$( mktemp /tmp/active_sessions.XXXXX )
+STALE_SESSIONS_LIST=
+
+list_mounts() {
+        ACTIVE_MOUNTS=$( /bin/ps auwwx | grep -i java | grep "fuse-integration" | grep sudo | grep -v grep | awk '{print $13}' | sort > "$ACTIVE_MOUNTS_F" )
+        if [ $DEBUG -eq 0 ] ; then
+                for m in $ACTIVE_MOUNTS ; do
+                        logger "$LOG_PREFIX Active session: $m"
+                done
+        fi
+}
+check_running_sessions() {
+        ACTIVE_SESSIONS_LIST=$( $RSTUDIO_BIN active-sessions | grep rsession | grep -v grep | awk '{print $5 }' | sort > "$ACTIVE_SESSIONS_LIST_F" )
+        if [ $DEBUG -eq 0 ] ; then
+                for ses in $ACTIVE_SESSIONS_LIST ; do
+                        logger "$LOG_PREFIX Active mount: $ses"
+                done
+        fi
+}
+
+umount_stale_sessions() {
+        STALE_SESSIONS_LIST=$( /usr/bin/comm -23 "$ACTIVE_MOUNTS_F" "$ACTIVE_SESSIONS_LIST_F" )
+        for stale_s in $STALE_SESSIONS_LIST ; do
+                if [ $DEBUG -eq 0 ] ; then
+                        logger "$LOG_PREFIX Stale session: $stale_s"
+                fi
+                $UNMOUNT_SCRIPT "$stale_s"
+        done
+}
+
+list_mounts
+check_running_sessions
+umount_stale_sessions
+rm -f "$ACTIVE_MOUNTS_F" "$ACTIVE_SESSIONS_LIST_F"
+exit 0

smartgears/r_connector/templates/rusersadd.j2

@@ -30,13 +30,13 @@ WORKSPACE_MOUNT_DIR="$HDIR/{{ r_connector_workspace_mountpoint }}"
 
 workspace_mount () {
     if [ $REMOTE_WORKSPACE_MOUNT -eq 0 ] ; then
-        {{ r_connector_workspace_unmount }} "$USER"
+        "{{ r_connector_workspace_unmount }}" "$USER"
         logger "$LOG_PREFIX: Trying to mount the remote workspace"
         [ $DEBUG -eq 0 ] && logger "$LOG_PREFIX: Mount command is sudo -u $USER /usr/bin/java -jar $FUSE_INTEGRATION_JAR $GCUBE_TOKEN $GCUBE_SCOPES $WORKSPACE_MOUNT_DIR"
         sudo /bin/mkdir -p "$WORKSPACE_MOUNT_DIR"
         sudo /bin/chown "${USER}" "$WORKSPACE_MOUNT_DIR"
         sudo -u "$USER" /usr/bin/java -jar $FUSE_INTEGRATION_JAR $GCUBE_TOKEN $GCUBE_SCOPES $WORKSPACE_MOUNT_DIR > "/var/tmp/workspace_${USER}.log" 2>&1 &
-        sleep $SLEEP_AFTER_MOUNT
+        sleep "$SLEEP_AFTER_MOUNT"
     fi
 }