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'

commands/update_datacite.ts

@@ -122,58 +122,53 @@ export default class UpdateDatacite extends BaseCommand {
 
     private async shouldUpdateDataset(dataset: Dataset): Promise<boolean> {
         try {
-            // Check if dataset has a DOI identifier (HasOne relationship)
             let doiIdentifier = dataset.identifier;
 
             if (!doiIdentifier) {
-                // Try to load the relationship if not already loaded
                 await dataset.load('identifier');
                 doiIdentifier = dataset.identifier;
             }
 
             if (!doiIdentifier || doiIdentifier.type !== 'doi') {
-                logger.warn(`Dataset ${dataset.publish_id}: No DOI identifier found`);
                 return false;
             }
 
-            // Validate dataset modification date
             const datasetModified = dataset.server_date_modified;
             const now = DateTime.now();
 
             if (!datasetModified) {
-                logger.error(`Dataset ${dataset.publish_id}: server_date_modified is null or undefined`);
-                return true; // Update anyway if modification date is missing
+                return true; // Update if modification date is missing
             }
 
             if (datasetModified > now) {
-                logger.error(
-                    `Dataset ${dataset.publish_id}: server_date_modified (${datasetModified.toISO()}) is in the future! ` +
-                        `Current time: ${now.toISO()}. This indicates a data integrity issue. Skipping update.`,
-                );
-                return false; // Do not update when modification date is invalid
+                return false; // Skip invalid future dates
             }
 
-            // Get DOI information from DataCite using DoiClient
+            // Check DataCite DOI modification date
             const doiClient = new DoiClient();
             const doiLastModified = await doiClient.getDoiLastModified(doiIdentifier.value);
 
             if (!doiLastModified) {
-                logger.warn(`Dataset ${dataset.publish_id}: Could not retrieve DOI modification date from DataCite`);
-                return true; // Update anyway if we can't get DOI info
+                return false; // not Update if we can't get DOI info
             }
 
-            // Compare dataset modification date with DOI modification date
             const doiModified = DateTime.fromJSDate(doiLastModified);
+            if (datasetModified > doiModified) {
+                // if dataset was modified after DOI creation 
+                // Calculate the difference in seconds
+                const diffInSeconds = Math.abs(datasetModified.diff(doiModified, 'seconds').seconds);
 
-            logger.debug(
-                `Dataset ${dataset.publish_id}: Dataset modified: ${datasetModified.toISO()}, DOI modified: ${doiModified.toISO()}`,
-            );
+                // Define tolerance threshold (60 seconds = 1 minute)
+                const toleranceSeconds = 60;
 
-            // Update if dataset was modified after the DOI record
-            return datasetModified > doiModified;
+                // Only update if the difference is greater than the tolerance
+                // This prevents unnecessary updates for minor timestamp differences
+                return diffInSeconds > toleranceSeconds;
+            } else {
+                return false; // No update needed
+            }
         } catch (error) {
-            logger.warn(`Error checking update status for dataset ${dataset.publish_id}: ${error.message}`);
-            return true; // Update anyway if we can't determine status
+            return false; // not update if we can't determine status or other error
         }
     }