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'

docker-entrypoint.sh

@@ -1,47 +1,61 @@
 #!/bin/bash
+set -e
 
-# # Run freshclam to update virus definitions
-# freshclam
+echo "Starting ClamAV services..."
 
-# # Sleep for a few seconds to give ClamAV time to start
-# sleep 5
 
-# # Start the ClamAV daemon
-# /etc/init.d/clamav-daemon start
-
-# bootstrap clam av service and clam av database updater
-set -m
-
-function process_file() {
-    if [[ ! -z "$1" ]]; then
-        local SETTING_LIST=$(echo "$1" | tr ',' '\n' | grep "^[A-Za-z][A-Za-z]*=.*$")
-        local SETTING
-        
-        for SETTING in ${SETTING_LIST}; do
-            # Remove any existing copies of this setting.  We do this here so that
-            # settings with multiple values (e.g. ExtraDatabase) can still be added
-            # multiple times below
-            local KEY=${SETTING%%=*}
-            sed -i $2 -e "/^${KEY} /d"
-        done
-
-        for SETTING in ${SETTING_LIST}; do
-            # Split on first '='
-            local KEY=${SETTING%%=*}
-            local VALUE=${SETTING#*=}
-            echo "${KEY} ${VALUE}" >> "$2"
-        done
+# Try to download database if missing
+if [ ! "$(ls -A /var/lib/clamav 2>/dev/null)" ]; then
+    echo "Downloading ClamAV database (this may take a while)..."
+    
+    # Simple freshclam run without complex config
+    if sg clamav -c "freshclam --datadir=/var/lib/clamav --quiet"; then
+        echo "✓ Database downloaded successfully"
+    else
+        echo "⚠ Database download failed - creating minimal setup"
+        # Create a dummy file so clamd doesn't immediately fail
+        sg clamav -c "touch /var/lib/clamav/.dummy"
     fi
-}
+fi
 
-# process_file "${CLAMD_SETTINGS_CSV}" /etc/clamav/clamd.conf
-# process_file "${FRESHCLAM_SETTINGS_CSV}" /etc/clamav/freshclam.conf
+# Start freshclam daemon for automatic updates
+echo "Starting freshclam daemon for automatic updates..."
+sg clamav -c "freshclam -d" &
 
-# start in background
-freshclam -d &
 # /etc/init.d/clamav-freshclam start &
-clamd
+# Start clamd in background
+# Start clamd in foreground (so dumb-init can supervise it)
 # /etc/init.d/clamav-daemon start &
 
-# change back to CMD of dockerfile
-exec "$@"
+# Start clamd daemon in background using sg
+echo "Starting ClamAV daemon..."
+# sg clamav -c "clamd" &
+# Use sg to run clamd with proper group permissions
+# sg clamav -c "clamd" &
+sg clamav -c "clamd --config-file=/etc/clamav/clamd.conf" &
+
+
+# Give services time to start
+echo "Waiting for services to initialize..."
+sleep 8
+
+# simple check
+if pgrep clamd > /dev/null; then
+    echo "✓ ClamAV daemon is running"
+else
+    echo "⚠ ClamAV daemon status uncertain, but continuing..."
+fi
+
+# Check if freshclam daemon is running
+if pgrep freshclam > /dev/null; then
+    echo "✓ Freshclam daemon is running"
+else
+    echo "⚠ Freshclam daemon status uncertain, but continuing..."
+fi
+
+# # change back to CMD of dockerfile
+# exec "$@"
+
+echo "✓ ClamAV setup complete"
+echo "Starting main application..."
+exec dumb-init -- "$@"