Update catalogue MD5 for PFNs with blank / null checksums

src/main/java/alien/api/catalogue/UpdateGUIDMD5.java

+package alien.api.catalogue;
+
+import alien.api.Request;
+import alien.catalogue.GUIDUtils;
+import alien.user.AliEnPrincipal;
+import java.util.Arrays;
+import java.util.List;
+import java.util.UUID;
+
+public class UpdateGUIDMD5 extends Request {
+	private UUID uuid;
+	private String md5;
+	private boolean updateSuccessful;
+
+	public UpdateGUIDMD5(final AliEnPrincipal user, final UUID uuid, String md5) {
+		setRequestUser(user);
+		this.uuid = uuid;
+		this.md5 = md5;
+	}
+
+	@Override
+	public List<String> getArguments() {
+		return Arrays.asList(uuid.toString(), md5);
+	}
+
+	@Override
+	public void run() {
+		this.updateSuccessful = GUIDUtils.updateMd5(uuid, md5);
+	}
+
+	public boolean isUpdateSuccessful() {
+		return updateSuccessful;
+	}
+}

src/main/java/alien/catalogue/GUIDUtils.java

 package alien.catalogue;
 
+import alien.api.Dispatcher;
+import alien.api.ServerException;
+import alien.api.catalogue.UpdateGUIDMD5;
+import alien.catalogue.access.AccessType;
+import alien.catalogue.access.AuthorizationFactory;
+import alien.config.ConfigUtils;
+import alien.io.IOUtils;
+import alien.io.protocols.TempFileManager;
+import alien.monitoring.Monitor;
+import alien.monitoring.MonitorFactory;
+import alien.user.AliEnPrincipal;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
@@ -19,16 +30,8 @@ import java.util.UUID;
 import java.util.concurrent.TimeUnit;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-
-import alien.catalogue.access.AccessType;
-import alien.catalogue.access.AuthorizationFactory;
-import alien.config.ConfigUtils;
-import alien.io.IOUtils;
-import alien.io.protocols.TempFileManager;
-import alien.monitoring.Monitor;
-import alien.monitoring.MonitorFactory;
-import alien.user.AliEnPrincipal;
 import lazyj.DBFunctions;
+import lazyj.Format;
 import lia.util.process.ExternalProcesses;
 
 /**
@@ -706,6 +709,62 @@ public final class GUIDUtils {
 		return true;
 	}
 
+	/**
+	 * @param guid
+	 * @param md5
+	 * @return <code>true</code> if the MD5 was already set or if it could be now set, <code>false</code> if there was any error setting it
+	 */
+	public static boolean updateMd5(UUID guid, String md5) {
+
+		if (guid == null || md5 == null)
+			return false;
+
+		if (!ConfigUtils.isCentralService())
+			try {
+				final UpdateGUIDMD5 request = new UpdateGUIDMD5(null, guid, md5);
+				return Dispatcher.execute(request).isUpdateSuccessful();
+			}
+			catch (@SuppressWarnings("unused") final ServerException se) {
+				return false;
+			}
+
+		final int host = getGUIDHost(guid);
+
+		if (host < 0)
+			return false;
+
+		final Host h = CatalogueUtils.getHost(host);
+
+		if (h == null)
+			return false;
+
+		try (DBFunctions db = h.getDB()) {
+			if (db == null)
+				return false;
+
+			final int tableName = GUIDUtils.getTableNameForGUID(guid);
+
+			if (tableName < 0)
+				return false;
+
+			if (!db.query("UPDATE G" + tableName + "L SET md5='" + Format.escSQL(md5) + "' WHERE guid=string2binary('" + Format.escSQL(guid.toString()) + "') AND (md5 is null OR length(md5) = 0)"))
+				return false;
+
+			if (db.getUpdateCount() == 0)
+				return false;
+
+			List<LFN> lfns = LFNUtils.getLFNsFromUUIDs(Set.of(guid));
+
+			for(LFN lfn : lfns) {
+				String guidMD5 = GUIDUtils.getGUID(lfn).getMD5();
+				if (guidMD5 != null && guidMD5.length() > 0)
+					GUIDUtils.checkMD5(lfn);
+			}
+		}
+
+		return true;
+	}
+
 	/**
 	 * @param pfn
 	 * @return the GUID, or <code>null</code> if it cannot be located

src/main/java/utils/crawler/SEFileCrawler.java

@@ -11,7 +11,18 @@ import static utils.crawler.CrawlingStatusCode.E_PFN_XRDSTAT_FAILED;
 import static utils.crawler.CrawlingStatusCode.E_UNEXPECTED_ERROR;
 import static utils.crawler.CrawlingStatusCode.S_FILE_CHECKSUM_MATCH;
 import static utils.crawler.CrawlingStatusCode.S_FILE_CHECKSUM_MISMATCH;
-
+import alien.catalogue.GUID;
+import alien.catalogue.PFN;
+import alien.config.ConfigUtils;
+import alien.io.IOUtils;
+import alien.io.protocols.Factory;
+import alien.io.protocols.SourceException;
+import alien.io.protocols.SourceExceptionCode;
+import alien.io.protocols.Xrootd;
+import alien.se.SE;
+import alien.se.SEUtils;
+import alien.shell.commands.JAliEnCOMMander;
+import alien.user.JAKeyStore;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -24,22 +35,8 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
-
-import alien.catalogue.GUID;
-import alien.catalogue.PFN;
-import alien.config.ConfigUtils;
-import alien.io.IOUtils;
-import alien.io.protocols.Factory;
-import alien.io.protocols.SourceException;
-import alien.io.protocols.SourceExceptionCode;
-import alien.io.protocols.Xrootd;
-import alien.se.SE;
-import alien.se.SEUtils;
-import alien.shell.commands.JAliEnCOMMander;
-import alien.user.JAKeyStore;
 import utils.StatusType;
 
 /**
@@ -431,10 +428,14 @@ public class SEFileCrawler {
 
 					if (Long.valueOf(0).equals(catalogueFileSize))
 						status = new CrawlingStatus(E_FILE_EMPTY, "Catalogue file size is 0");
-					else if (catalogueMD5 == null)
+					else if (catalogueMD5 == null) {
+//						GUIDUtils.updateMd5(guid.guid, observedMD5);
 						status = new CrawlingStatus(E_CATALOGUE_MD5_IS_NULL, "Catalogue MD5 is null");
-					else if (catalogueMD5.isBlank())
+					}
+					else if (catalogueMD5.isBlank()) {
+//						GUIDUtils.updateMd5(guid.guid, observedMD5);
 						status = new CrawlingStatus(E_CATALOGUE_MD5_IS_BLANK, "Catalogue MD5 is blank");
+					}
 					else if (!catalogueMD5.equalsIgnoreCase(observedMD5))
 						status = new CrawlingStatus(S_FILE_CHECKSUM_MISMATCH, "Recomputed checksum does not match catalogue checksum");
 					else