feat: Enhance ClamAV Docker entrypoint and configuration

- Updated docker-entrypoint.sh to improve ClamAV service initialization and logging.
- Added checks for ClamAV and freshclam daemon status.
- Optimized freshclam configuration for container usage, including logging to stdout and setting database directory.
- Introduced caching mechanism for enabled file extensions in vinejs_provider.ts to reduce database queries.
- Implemented a new command to list datasets needing DataCite DOI updates, with options for verbose output, count only, and IDs only.
- Updated package dependencies to include p-limit and pino-pretty.
- finalized ace command 'detect:missing-cross-references'

Dockerfile

@@ -1,55 +1,61 @@
 ################## First Stage - Creating base #########################
 
 # Created a variable to hold our node base image
-ARG NODE_IMAGE=node:22-bookworm-slim
+ARG NODE_IMAGE=node:22-trixie-slim
 
 FROM $NODE_IMAGE AS base
+
 # Install dumb-init and ClamAV, and perform ClamAV database update
-RUN apt update \
-    && apt-get install -y dumb-init clamav clamav-daemon nano \ 
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    dumb-init \
+    clamav \
+    clamav-daemon \
+    ca-certificates \   
     && rm -rf /var/lib/apt/lists/* \
     # Creating folders and changing ownerships
-    && mkdir -p /home/node/app && chown node:node /home/node/app \
+    && mkdir -p /home/node/app \
     &&  mkdir -p /var/lib/clamav \
     && mkdir /usr/local/share/clamav \
-    && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav \
-    # permissions
     && mkdir /var/run/clamav \
-    && chown node:clamav /var/run/clamav \
-    && chmod 750 /var/run/clamav
-# -----------------------------------------------
-# --- ClamAV & FeshClam -------------------------
-# -----------------------------------------------
-# RUN \
-#   chmod 644 /etc/clamav/freshclam.conf && \
-#   freshclam && \
-#   mkdir /var/run/clamav && \
-  # chown -R clamav:root /var/run/clamav
+    && mkdir -p /var/log/clamav \
+    && mkdir -p /tmp/clamav-logs \
+   
+    # Set ownership and permissions
+    && chown node:node /home/node/app \
+    # && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav \
+    && chown -R clamav:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav /var/log/clamav \
+    && chmod 755 /tmp/clamav-logs \
+    && chmod 750 /var/run/clamav \
+    && chmod 755 /var/lib/clamav \
+    && chmod 755 /var/log/clamav \
+     # Add node user to clamav group and allow sudo for clamav commands
+    && usermod -a -G clamav node \
+    && chmod g+w /var/run/clamav /var/lib/clamav /var/log/clamav /tmp/clamav-logs
 
-# # initial update of av databases
-# RUN freshclam
 
-# Configure Clam AV...
-COPY --chown=node:clamav ./*.conf /etc/clamav/
+# Configure ClamAV - copy config files before switching user
+# COPY --chown=node:clamav ./*.conf /etc/clamav/
+COPY --chown=clamav:clamav ./*.conf /etc/clamav/
+
+# Copy entrypoint script
+COPY --chown=node:node docker-entrypoint.sh /home/node/app/docker-entrypoint.sh
+RUN chmod +x /home/node/app/docker-entrypoint.sh
+
+ENV TZ="Europe/Vienna"
 
-# # permissions
-# RUN mkdir /var/run/clamav && \
-#     chown node:clamav /var/run/clamav && \
-#     chmod 750 /var/run/clamav
 # Setting the working directory
 WORKDIR /home/node/app
 # Changing the current active user to "node"
+
+# Download initial ClamAV database as root before switching users
+USER root
+RUN freshclam --quiet || echo "Initial database download failed - will retry at runtime"
+
 USER node
 
-# initial update of av databases
-RUN freshclam
-
-# VOLUME /var/lib/clamav
-COPY --chown=node:clamav docker-entrypoint.sh /home/node/app/docker-entrypoint.sh
-RUN chmod +x /home/node/app/docker-entrypoint.sh
-ENV TZ="Europe/Vienna"
-
-
+# Initial update of AV databases (moved after USER directive)
+# RUN freshclam || true
 
 
 ################## Second Stage - Installing dependencies ##########
@@ -70,14 +76,13 @@ ENV NODE_ENV=production
 # We run "node ace build" to build the app (dist folder) for production
 RUN node ace build --ignore-ts-errors
 # RUN node ace build --production
-# RUN node ace build --ignore-ts-errors
 
 
 ################## Final Stage - Production #########################
 # In this final stage, we will start running the application
 FROM base AS production
 # Here, we include all the required environment variables
-# ENV NODE_ENV=production
+ENV NODE_ENV=production
 # ENV PORT=$PORT
 # ENV HOST=0.0.0.0
 
@@ -91,4 +96,4 @@ COPY --chown=node:node --from=build /home/node/app/build .
 EXPOSE 3333
 ENTRYPOINT ["/home/node/app/docker-entrypoint.sh"]
 # Run the command to start the server using "dumb-init"
-CMD [ "dumb-init", "node", "bin/server.js" ]
+CMD [ "node", "bin/server.js" ]