A few queries that could be easily converted to prepared statements

src/main/java/alien/catalogue/CatalogueUtils.java

@@ -116,7 +116,7 @@ public final class CatalogueUtils {
 	 */
 	public static final long CACHE_TIMEOUT = 1000 * 60 * 5;
 
-	private static final void updateGuidIndexCache() {
+	private static void updateGuidIndexCache() {
 		guidIndexReadLock.lock();
 
 		try {
@@ -465,9 +465,9 @@ public final class CatalogueUtils {
 					do {
 						read = 0;
 
-						final String q = "select guid,size from G" + idx.tableName + "L LIMIT " + LIMIT + " OFFSET " + offset + ";";
+						final String q = "select guid,size from G" + idx.tableName + "L LIMIT ? OFFSET ?;";
 
-						while (!gdb.query(q))
+						while (!gdb.query(q, false, Long.valueOf(LIMIT), Long.valueOf(offset)))
 							System.err.println("Retrying query " + q);
 
 						while (gdb.moveNext()) {

src/main/java/alien/catalogue/GUID.java

@@ -270,8 +270,8 @@ public class GUID implements Comparable<GUID>, CatalogEntity {
 			}
 
 			// only the SE list can change, and the size for a collection, and md5 when it was missing
-			if (!db.query("UPDATE G" + tableName + "L SET seStringlist=" + setToString(seStringList) + ", size=" + size + ", md5='" + Format.escSQL(md5) + "', owner='" + Format.escSQL(owner)
-					+ "', gowner='" + Format.escSQL(gowner) + "',perm='" + Format.escSQL(perm) + "' WHERE guidId=" + guidId))
+			if (!db.query("UPDATE G" + tableName + "L SET seStringlist=?, size=?, md5=?, owner=?, gowner=?,perm=? WHERE guidId=?", false, setToString(seStringList),
+					Long.valueOf(size), md5, owner, gowner, perm, Integer.valueOf(guidId)))
 				// wrong table name or what?
 				return false;
 
@@ -537,21 +537,12 @@ public class GUID implements Comparable<GUID>, CatalogEntity {
 
 			guidIDs.drainTo(toExecute);
 
-			final StringBuilder sb = new StringBuilder(guidIDs.size() * 10);
-
-			for (final Integer id : toExecute) {
-				if (sb.length() > 0)
-					sb.append(",");
-
-				sb.append(id.toString());
-			}
-
 			if (monitor != null)
 				monitor.incrementCounter("GUID_flush");
 
-			if (sb.length() > 0)
+			if (toExecute.size() > 0)
 				try (DBFunctions db = host.getDB()) {
-					db.query("DELETE FROM G" + tableName + "L" + tableSuffix + " WHERE guidId IN (" + sb.toString() + ")");
+					db.query("DELETE FROM G" + tableName + "L" + tableSuffix + " WHERE guidId IN (" + Format.toCommaList(toExecute) + ")");
 				}
 
 			return true;
@@ -787,7 +778,7 @@ public class GUID implements Comparable<GUID>, CatalogEntity {
 
 					final SE se = SEUtils.getSE(pfn.seNumber);
 
-					if (se != null && !(se.getName().equalsIgnoreCase("no_se"))) {
+					if (se != null && !("no_se".equalsIgnoreCase(se.getName()))) {
 						final GUID g = pfn.getGuid();
 
 						if (g != null && g.guid != null) {
@@ -874,7 +865,7 @@ public class GUID implements Comparable<GUID>, CatalogEntity {
 	/**
 	 * This method is _not_ authoritative, if you want to do the actual lookup to see which LFNs point to this GUID then use {@link LFNUtils#getLFN(GUID)}.
 	 * Should only be called when the previous code has filled the cache with known LFN objects.
-	 * 
+	 *
 	 * @return the <b>cached</b> LFNs associated to this GUID, from either the internal cache or the G*L_REF tables.
 	 */
 	public Set<LFN> getLFNs() {
@@ -1020,7 +1011,7 @@ public class GUID implements Comparable<GUID>, CatalogEntity {
 
 	/**
 	 * Change the access permissions on this LFN
-	 * 
+	 *
 	 * @param newPermissions
 	 * @return the previous permissions, if anything changed and the change was successfully propagated to the database, or <code>null</code> if nothing was touched
 	 */
@@ -1065,7 +1056,7 @@ public class GUID implements Comparable<GUID>, CatalogEntity {
 
 	/**
 	 * Get the two digit hash (first level of folders in a storage)
-	 * 
+	 *
 	 * @param guid
 	 * @return chash
 	 */
@@ -1152,7 +1143,7 @@ public class GUID implements Comparable<GUID>, CatalogEntity {
 
 	/**
 	 * Get the replica from a particular SE
-	 * 
+	 *
 	 * @param seNumber
 	 * @return the PFN to the replica on this storage element, if it exists
 	 */

src/main/java/alien/io/TransferUtils.java

@@ -133,7 +133,7 @@ public final class TransferUtils {
 			final String orderClause = (orderAsc ? " ORDER BY transferId ASC" : " ORDER BY transferId DESC");
 			final String limitClause = (count != null ? " LIMIT " + count.toString() : "");
 
-			String query = "SELECT * FROM TRANSFERS_DIRECT WHERE " + "(? IS NULL OR user=?) AND (? IS NULL OR destination=?)" + " AND (? IS NULL OR status=?)";
+			String query = "SELECT * FROM TRANSFERS_DIRECT WHERE (? IS NULL OR user=?) AND (? IS NULL OR destination=?) AND (? IS NULL OR status=?)";
 			// db.query("SELECT * FROM TRANSFERS_DIRECT ORDER BY transferId", false);
 			query += orderClause + limitClause;
 			db.query(query, false, user, user, targetSE, targetSE, status, status);
@@ -601,7 +601,7 @@ public final class TransferUtils {
 	 * @param exitCode
 	 * @param failureReason
 	 */
-	static final void logAttempt(final Protocol p, final PFN source, final PFN target, final int exitCode, final String failureReason) {
+	static void logAttempt(final Protocol p, final PFN source, final PFN target, final int exitCode, final String failureReason) {
 		try (DBFunctions db = getDB()) {
 			if (db != null)
 				if (ConfigUtils.getConfig().getb("alien.io.TransferUtils.logReason", false))

src/main/java/alien/quotas/FileQuota.java

 package alien.quotas;
 
 import java.io.Serializable;
-import java.util.Arrays;
-import java.util.List;
+import java.util.Set;
 
 import lazyj.DBFunctions;
 import lazyj.Format;
@@ -19,7 +18,7 @@ public final class FileQuota implements Serializable, Comparable<FileQuota> {
 	 */
 
 	/**
-	 * 
+	 *
 	 */
 	private static final long serialVersionUID = 7587668615003121402L;
 
@@ -61,7 +60,7 @@ public final class FileQuota implements Serializable, Comparable<FileQuota> {
 	/**
 	 * Fields allowed to modify via fquota set command
 	 */
-	private final static List<String> allowed_to_update = Arrays.asList("maxNbFiles", "maxTotalSize");
+	private final static Set<String> allowed_to_update = Set.of("maxNbFiles", "maxTotalSize");
 
 	/**
 	 * @param db

src/main/java/alien/quotas/Quota.java

@@ -4,8 +4,7 @@
 package alien.quotas;
 
 import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
+import java.util.Set;
 import java.util.logging.Logger;
 
 import alien.config.ConfigUtils;
@@ -111,7 +110,7 @@ public class Quota implements Serializable, Comparable<Quota> {
 	/**
 	 * Fields allowed to modify via jquota set command
 	 */
-	private final static ArrayList<String> allowed_to_update = new ArrayList<>(Arrays.asList("maxUnfinishedJobs", "maxTotalCpuCost", "maxTotalRunningTime"));
+	private final static Set<String> allowed_to_update = Set.of("maxUnfinishedJobs", "maxTotalCpuCost", "maxTotalRunningTime");
 
 	/**
 	 * @param db

src/main/java/alien/quotas/QuotaUtilities.java

@@ -178,13 +178,13 @@ public final class QuotaUtilities {
 	public static boolean saveJobQuota(final String username, final String fld, final String val) {
 		if (!Quota.canUpdateField(fld))
 			return false;
+
 		try (DBFunctions db = ConfigUtils.getDB("processes")) {
-			final String query = "UPDATE PRIORITY p LEFT JOIN QUEUE_USER qu " + "ON qu.user='" + Format.escSQL(username) + "' SET p." + Format.escSQL(fld) + "=" + Format.escSQL(val)
-					+ " WHERE qu.userid=p.userid";
+			final String query = "UPDATE PRIORITY p LEFT JOIN QUEUE_USER qu ON qu.user=? SET p." + Format.escSQL(fld) + "=? WHERE qu.userid=p.userid";
 
 			db.setQueryTimeout(120);
 
-			if (db.query(query)) {
+			if (db.query(query, false, username, val)) {
 				jobQuotasLastUpdated = 0;
 				updateJobQuotasCache();
 			}
@@ -226,11 +226,11 @@ public final class QuotaUtilities {
 			return false;
 
 		try (DBFunctions db = ConfigUtils.getDB("alice_users")) {
-			final String query = "UPDATE FQUOTAS SET " + Format.escSQL(fld) + "='" + Format.escSQL(val) + "'" + " WHERE user='" + Format.escSQL(username) + "'";
+			final String query = "UPDATE FQUOTAS SET " + Format.escSQL(fld) + "=? WHERE user=?";
 
 			db.setQueryTimeout(120);
 
-			if (db.query(query)) {
+			if (db.query(query, false, val, username)) {
 				fileQuotasLastUpdated = 0;
 				updateFileQuotasCache();
 			}
@@ -246,7 +246,7 @@ public final class QuotaUtilities {
 	 *
 	 * @return file quota for all accounts, sorted by username
 	 */
-	public static final List<Quota> getJobQuotas() {
+	public static List<Quota> getJobQuotas() {
 		updateJobQuotasCache();
 
 		if (jobQuotas == null)
@@ -264,7 +264,7 @@ public final class QuotaUtilities {
 	 *
 	 * @return file quota for all accounts, sorted by username
 	 */
-	public static final List<FileQuota> getFileQuotas() {
+	public static List<FileQuota> getFileQuotas() {
 		updateFileQuotasCache();
 
 		if (fileQuotas == null)
@@ -279,13 +279,13 @@ public final class QuotaUtilities {
 
 	/**
 	 * Check job quota authorization for a user, for n jobs
-	 * 
+	 *
 	 * @param account
 	 * @param numberOfJobsToSubmit
 	 * @return allowed or not
 	 */
-	public static final Map.Entry<Integer, String> checkJobQuota(String account, int numberOfJobsToSubmit) {
-		Quota q = getJobQuota(account);
+	public static Map.Entry<Integer, String> checkJobQuota(final String account, final int numberOfJobsToSubmit) {
+		final Quota q = getJobQuota(account);
 
 		if (q == null)
 			return new AbstractMap.SimpleEntry<>(Integer.valueOf(1), "Error: couldn't get quotas for user: " + account);

src/main/java/alien/se/SEUtils.java

@@ -1120,8 +1120,8 @@ public final class SEUtils {
 							}
 						}
 						else {
-							gdb.query("select distinct binary2string(guid),size,md5 from G" + idx.tableName + "L INNER JOIN G" + idx.tableName + "L_PFN using(guidId) where seNumber=" + se.seNumber
-									+ ";");
+							gdb.query("select distinct binary2string(guid),size,md5 from G" + idx.tableName + "L INNER JOIN G" + idx.tableName + "L_PFN using(guidId) where seNumber=?", true,
+									Integer.valueOf(se.seNumber));
 
 							while (gdb.moveNext()) {
 								final String guid = gdb.gets(1);

src/main/java/utils/FindOrphanFoldersOutput.java

@@ -20,7 +20,7 @@ public class FindOrphanFoldersOutput {
 	/**
 	 * @param args
 	 */
-	public static void main(String[] args) {
+	public static void main(final String[] args) {
 		final int nargs = args.length;
 
 		if (nargs < 1) {
@@ -29,27 +29,27 @@ public class FindOrphanFoldersOutput {
 		}
 
 		for (int i = 0; i < nargs; i++) {
-			long jobid = Long.parseLong(args[i]);
+			final long jobid = Long.parseLong(args[i]);
 			JDL jobjdl = null;
 
 			try {
 				jobjdl = new JDL(jobid);
 			}
-			catch (IOException e) {
+			catch (final IOException e) {
 				System.err.println("Can't get job JDL: " + e);
 				return;
 			}
 
-			String outputdir = jobjdl.getOutputDir();
+			final String outputdir = jobjdl.getOutputDir();
 
-			IndexTableEntry ite = CatalogueUtils.getClosestMatch(outputdir);
+			final IndexTableEntry ite = CatalogueUtils.getClosestMatch(outputdir);
 
 			if (ite == null) {
 				System.err.println("Can't find indextable for output: " + outputdir);
 				return;
 			}
 
-			String dblfn = outputdir.replaceAll(ite.lfn, "");
+			final String dblfn = outputdir.replaceAll(ite.lfn, "");
 
 			System.out.println("db pattern: " + dblfn);
 
@@ -58,11 +58,11 @@ public class FindOrphanFoldersOutput {
 
 				System.out.println("Going to select distinct dir");
 
-				if (!db.query("select distinct dir as dir from L" + ite.tableName + "L where type='d' and lfn like '" + dblfn + "/%/' order by 1 asc")) {
+				if (!db.query("select distinct dir as dir from L" + ite.tableName + "L where type='d' and lfn like ? order by 1 asc", false, dblfn + "/%/")) {
 					System.err.println("Can't get distinct dirs");
 					System.exit(-1);
 				}
-				int count = db.count();
+				final int count = db.count();
 
 				if (count <= 1) {
 					System.out.println("Only 1 dir found");
@@ -72,11 +72,11 @@ public class FindOrphanFoldersOutput {
 				System.out.println("Found several folders: " + count);
 
 				db.moveNext();
-				int mindir = db.geti("dir");
+				final int mindir = db.geti("dir");
 
 				System.out.println("select lfn from L" + ite.tableName + "L where type='d' and dir=" + mindir + " order by 1 asc");
 
-				if (!db.query("select lfn from L" + ite.tableName + "L where type='d' and dir=" + mindir + " order by 1 asc")) {
+				if (!db.query("select lfn from L" + ite.tableName + "L where type='d' and dir=? order by 1 asc", false, Integer.valueOf(mindir))) {
 					System.err.println("Can't get distinct dirs");
 					System.exit(-1);
 				}
@@ -87,7 +87,7 @@ public class FindOrphanFoldersOutput {
 						outfile.println(ite.lfn + db.gets("lfn"));
 					}
 				}
-				catch (FileNotFoundException e) {
+				catch (final FileNotFoundException e) {
 					System.err.println("Could not write to file for: " + jobid + " :" + e);
 					return;
 				}