allow @files and externalModules dirs to persist on mounted storage

Dockerfile

@@ -188,7 +188,6 @@ RUN [ -n "${DEBUG}" ] && set -x; \
     mkdir -pv \
         "${LABKEY_FILES_ROOT}/@files" \
         "config" \
-        "externalModules" \
         "logs" \
         "startup" \
         "${TOMCAT_BASE_DIR}" \
@@ -259,8 +258,6 @@ HEALTHCHECK \
             "https://localhost:${LABKEY_PORT}${HEALTHCHECK_ENDPOINT}" \
             || exit 1
 
-VOLUME "${LABKEY_FILES_ROOT}/@files"
-VOLUME "${LABKEY_HOME}/externalModules"
 VOLUME "${LABKEY_HOME}/logs"
 
 EXPOSE ${LABKEY_PORT}

application.properties

@@ -90,6 +90,8 @@ context.resources.jdbc.labkeyDataSource.maxWaitMillis=${POSTGRES_MAX_WAIT_MILLIS
 context.resources.jdbc.labkeyDataSource.accessToUnderlyingConnectionAllowed=${POSTGRES_ACCESS_UNDERLYING_CONNECTIONS}
 context.resources.jdbc.labkeyDataSource.validationQuery=${POSTGRES_VALIDATION_QUERY}
 
+context.externalModules=${LABKEY_EXTERNAL_MODULES}
+
 # send access logs to file:
 # server.tomcat.accesslog.directory=/tmp
 # server.tomcat.accesslog.enabled=true

docker-compose.yml

@@ -18,7 +18,6 @@ services:
     volumes:
       - ./mounts/files:/labkey/files
       # - files:/labkey/files
-      - ./mounts/modules:/labkey/externalModules
       - ./mounts/logs:/labkey/logs
     environment:
       # - DEBUG=1
@@ -132,7 +131,6 @@ services:
     volumes:
       - ./mounts/files:/labkey/files
       # - files:/labkey/files
-      - ./mounts/modules:/labkey/externalModules
       - ./mounts/logs:/labkey/logs
     environment:
       # - DEBUG=1
@@ -244,7 +242,6 @@ services:
     volumes:
       - ./mounts/files:/labkey/files
       # - files:/labkey/files
-      - ./mounts/modules:/labkey/externalModules
       - ./mounts/logs:/labkey/logs
     environment:
       # - DEBUG=1
@@ -357,7 +354,6 @@ services:
     volumes:
       - ./mounts/files:/labkey/files
       # - files:/labkey/files
-      - ./mounts/modules:/labkey/externalModules
       - ./mounts/logs:/labkey/logs
     environment:
       # - DEBUG=1
@@ -427,6 +423,8 @@ services:
       - DD_COLLECT_APM=${DD_COLLECT_APM-false}
       - SLEEP=${SLEEP:-0}
       - PURGE_HEAP_AND_ERROR_LOGS_OLDER_THAN_DAYS=${PURGE_HEAP_AND_ERROR_LOGS_OLDER_THAN_DAYS:-90}
+      - PURGE_MTNC_LOGS_OLDER_THAN_DAYS=${PURGE_MTNC_LOGS_OLDER_THAN_DAYS:-90}
+      - LABKEY_EXTERNAL_MODULES=${LABKEY_EXTERNAL_MODULES:-/labkey/files/externalModules}
 
   pg-lims_starter:
     image: postgres:15

entrypoint.sh

@@ -25,8 +25,12 @@ JSON_OUTPUT="${JSON_OUTPUT:-false}"
 DD_COLLECT_APM="${DD_COLLECT_APM:-false}"
 JAVA_RMI_SERVER_HOSTNAME="${JAVA_RMI_SERVER_HOSTNAME:-}"
 
-# set age past which old heap and error log directories are removed
+# set age past which old heap and error log directories and system maintenance files are removed
 PURGE_HEAP_AND_ERROR_LOGS_OLDER_THAN_DAYS="${PURGE_HEAP_AND_ERROR_LOGS_OLDER_THAN_DAYS:-90}"
+PURGE_MTNC_LOGS_OLDER_THAN_DAYS="${PURGE_MTNC_LOGS_OLDER_THAN_DAYS:-90}"
+
+# set path to external modules)
+LABKEY_EXTERNAL_MODULES="${LABKEY_EXTERNAL_MODULES:-/labkey/files/externalModules}"
 
 SLEEP="${SLEEP:=0}"
 
@@ -147,9 +151,6 @@ main() {
     awsclibin/aws s3 cp $LABKEY_OPTIONAL_APP_PROPERTIES_S3_URI config/
   fi
 
-  echo "sleeping for $SLEEP seconds..."
-  sleep $SLEEP
-
   # echo "deleting awscli and unsetting AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, & AWS_SESSION_TOKEN, if set..."
   # rm -rf awsclibin aws-cli
   unset AWS_ACCESS_KEY_ID AWS_SECRET_ACCESS_KEY AWS_SESSION_TOKEN
@@ -258,20 +259,30 @@ main() {
         -Djava.rmi.server.hostname=${JAVA_RMI_SERVER_HOSTNAME}" 
   fi
 
-  echo "Purging secrets and other bits from environment variables..."
-  unset POSTGRES_USER POSTGRES_PASSWORD POSTGRES_HOST POSTGRES_PORT POSTGRES_DB POSTGRES_PARAMETERS
-  unset SMTP_HOST SMTP_USER SMTP_PORT SMTP_PASSWORD SMTP_AUTH SMTP_FROM SMTP_STARTTLS
-  unset LABKEY_CREATE_INITIAL_USER LABKEY_CREATE_INITIAL_USER_APIKEY LABKEY_INITIAL_USER_APIKEY LABKEY_INITIAL_USER_EMAIL LABKEY_INITIAL_USER_GROUP LABKEY_INITIAL_USER_ROLE
-  unset LABKEY_EK SLEEP CONTAINER_PRIVATE_IP
-
   echo "Creating new heap/error log directory..."
   HEAP_AND_ERROR_PATH="$LABKEY_HOME/files/heap_dumps_and_errors_$(date +%Y%m%d_%H%M%S)"
   mkdir -pv $HEAP_AND_ERROR_PATH
 
+  echo "Creating externalModules directory if it does not already exist..."
+  mkdir -pv $LABKEY_EXTERNAL_MODULES
+
   # purge old heap/error directories
   echo "Purging heap/error log directories older than $PURGE_HEAP_AND_ERROR_LOGS_OLDER_THAN_DAYS days..."
   find "$LABKEY_HOME/files/" -mindepth 1 -maxdepth 1 -type d -ctime +${PURGE_HEAP_AND_ERROR_LOGS_OLDER_THAN_DAYS} -name "heap*" | xargs rm -rf 
 
+  # purge old system maintenance files
+  echo "Purging system maintenance files older than $PURGE_MTNC_LOGS_OLDER_THAN_DAYS days..."
+  find "$LABKEY_HOME/files/@files" -mindepth 1 -maxdepth 1 -type d -ctime +${PURGE_MTNC_LOGS_OLDER_THAN_DAYS} -name "system_maintenance*" | xargs rm -rf 
+
+  echo "sleeping for $SLEEP seconds..."
+  sleep $SLEEP
+
+  echo "Purging secrets and other bits from environment variables..."
+  unset POSTGRES_USER POSTGRES_PASSWORD POSTGRES_HOST POSTGRES_PORT POSTGRES_DB POSTGRES_PARAMETERS
+  unset SMTP_HOST SMTP_USER SMTP_PORT SMTP_PASSWORD SMTP_AUTH SMTP_FROM SMTP_STARTTLS
+  unset LABKEY_CREATE_INITIAL_USER LABKEY_CREATE_INITIAL_USER_APIKEY LABKEY_INITIAL_USER_APIKEY LABKEY_INITIAL_USER_EMAIL LABKEY_INITIAL_USER_GROUP LABKEY_INITIAL_USER_ROLE
+  unset LABKEY_EK SLEEP CONTAINER_PRIVATE_IP
+
   # shellcheck disable=SC2086
   exec java \
     \
@@ -290,7 +301,6 @@ main() {
     \
     -Dlabkey.home="$LABKEY_HOME" \
     -Dlabkey.log.home="${LABKEY_HOME}/logs" \
-    -Dlabkey.externalModulesDir="${LABKEY_HOME}/externalModules" \
     \
     -Djava.library.path=/usr/lib:/usr/lib/x86_64-linux-gnu \
     \

quickstart_envs.sh

@@ -3,7 +3,7 @@
 # example minimal set of environment variables to get started - see readme for additional envs you may wish to set
 
 # embedded tomcat LabKey .jar version to build container with
-export LABKEY_VERSION="25.7"
+export LABKEY_VERSION="25.8"
 
 # minimal SMTP settings
 export SMTP_HOST="localhost"