GP-4341 Force retained checkout if file is in-use during checkin or add-to-version-control. Deprecated upgrade concept during checkin. Revised manner in which file open for update is updated following a version control operation (perform DBHandle update).

Ghidra/Framework/DB/src/main/java/db/DBHandle.java

@@ -18,7 +18,6 @@ package db;
 import java.io.File;
 import java.io.IOException;
 import java.util.Hashtable;
-import java.util.Iterator;
 
 import db.buffers.*;
 import db.util.ErrorHandler;
@@ -439,8 +438,7 @@ public class DBHandle {
 	 * @throws IllegalStateException if transaction is already active or this {@link DBHandle} has 
 	 * already been closed.
 	 */
-	public Transaction openTransaction(ErrorHandler errorHandler)
-			throws IllegalStateException {
+	public Transaction openTransaction(ErrorHandler errorHandler) throws IllegalStateException {
 		return new Transaction() {
 
 			long txId = startTransaction();
@@ -542,6 +540,33 @@ public class DBHandle {
 		return (bufferMgr != null && !bufferMgr.atCheckpoint());
 	}
 
+	/**
+	 * Set the DB source buffer file with a newer local buffer file version.
+	 * Intended for use following a merge or commit operation only where a local checkout has been
+	 * retained.
+	 * @param versionedSourceBufferFile updated local DB source buffer file opened for versioning 
+	 * update (NOTE: file itself is read-only).  File must be an instance of 
+	 * {@link LocalManagedBufferFile}.
+	 * @throws IOException if an IO error occurs
+	 */
+	public void setDBVersionedSourceFile(BufferFile versionedSourceBufferFile) throws IOException {
+		if (!(versionedSourceBufferFile instanceof LocalManagedBufferFile bf) ||
+			!versionedSourceBufferFile.isReadOnly()) {
+			throw new IllegalArgumentException(
+				"Requires local versioned buffer file opened for versioning update");
+		}
+		synchronized (this) {
+			if (isTransactionActive()) {
+				throw new IOException("transaction is active");
+			}
+			bufferMgr.clearRecoveryFiles();
+			bufferMgr.setDBVersionedSourceFile(bf);
+			++checkpointNum;
+			reloadTables();
+		}
+		notifyDbRestored();
+	}
+
 	/**
 	 * Terminate current transaction.  If commit is false a rollback may occur followed by
 	 * {@link DBListener#dbRestored(DBHandle)} notification to listeners.  This method is very 
@@ -1022,10 +1047,9 @@ public class DBHandle {
 	public Table[] getTables() {
 		Table[] t = new Table[tables.size()];
 
-		Iterator<Table> it = tables.values().iterator();
 		int i = 0;
-		while (it.hasNext()) {
-			t[i++] = it.next();
+		for (Table element : tables.values()) {
+			t[i++] = element;
 		}
 		return t;
 	}
@@ -1050,8 +1074,7 @@ public class DBHandle {
 	 * @return new table instance
 	 * @throws IOException if IO error occurs during table creation
 	 */
-	public Table createTable(String name, Schema schema, int[] indexedColumns)
-			throws IOException {
+	public Table createTable(String name, Schema schema, int[] indexedColumns) throws IOException {
 		Table table;
 		synchronized (this) {
 			if (tables.containsKey(name)) {

Ghidra/Framework/DB/src/main/java/db/buffers/BufferMgr.java

@@ -223,6 +223,22 @@ public class BufferMgr {
 			approxCacheSize < MINIMUM_CACHE_SIZE ? MINIMUM_CACHE_SIZE : approxCacheSize;
 		maxCacheSize = (int) (approxCacheSize / bufferSize);
 
+		// Setup baseline - checkpoint 0
+		startCheckpoint();
+		baselineCheckpointHead = currentCheckpointHead;
+		currentCheckpointHead = null;
+
+		initializeCache();
+
+		addInstance(this);
+	}
+
+	private void initializeCache() throws IOException {
+
+		if (cacheFile != null) {
+			cacheFile.delete();
+		}
+
 		// Setup memory cache list
 		cacheHead = new BufferNode(HEAD, -1);
 		cacheTail = new BufferNode(TAIL, -1);
@@ -234,11 +250,6 @@ public class BufferMgr {
 
 		cacheIndexProvider = new IndexProvider();
 
-		// Setup baseline - checkpoint 0
-		startCheckpoint();
-		baselineCheckpointHead = currentCheckpointHead;
-		currentCheckpointHead = null;
-
 		// Copy file parameters into cache file
 		if (sourceFile != null) {
 			String[] parmNames = sourceFile.getParameterNames();
@@ -247,8 +258,6 @@ public class BufferMgr {
 			}
 		}
 
-		addInstance(this);
-
 		if (alwaysPreCache) {
 			startPreCacheIfNeeded();
 		}
@@ -417,9 +426,7 @@ public class BufferMgr {
 
 				// Dispose all buffer nodes - speeds up garbage collection
 				if (checkpointHeads != null) {
-					Iterator<BufferNode> iter = checkpointHeads.iterator();
-					while (iter.hasNext()) {
-						BufferNode node = iter.next();
+					for (BufferNode node : checkpointHeads) {
 						while (node != null) {
 							BufferNode next = node.nextInCheckpoint;
 							node.buffer = null;
@@ -435,9 +442,7 @@ public class BufferMgr {
 					checkpointHeads = null;
 				}
 				if (redoCheckpointHeads != null) {
-					Iterator<BufferNode> iter = redoCheckpointHeads.iterator();
-					while (iter.hasNext()) {
-						BufferNode node = iter.next();
+					for (BufferNode node : redoCheckpointHeads) {
 						while (node != null) {
 							BufferNode next = node.nextInCheckpoint;
 							node.buffer = null;
@@ -702,24 +707,7 @@ public class BufferMgr {
 			return; // only pre-cache remote buffer files
 		}
 		synchronized (preCacheLock) {
-			preCacheThread = new Thread(() -> {
-				try {
-					preCacheSourceFile();
-				}
-				catch (InterruptedIOException e) {
-					// ignore
-				}
-				catch (IOException e) {
-					Msg.error(BufferMgr.this, "pre-cache failure: " + e.getMessage(), e);
-				}
-				finally {
-					synchronized (preCacheLock) {
-						preCacheStatus = PreCacheStatus.STOPPED;
-						preCacheThread = null;
-						preCacheLock.notifyAll();
-					}
-				}
-			});
+			preCacheThread = new Thread(() -> preCacheSourceFile());
 			preCacheThread.setName("Pre-Cache");
 			preCacheThread.setPriority(Thread.MIN_PRIORITY);
 			preCacheThread.start();
@@ -731,23 +719,38 @@ public class BufferMgr {
 	 * Pre-cache source file into cache file.  This is intended to be run in a
 	 * dedicated thread when the source file is remote.
 	 */
-	private void preCacheSourceFile() throws IOException {
-		if (!(sourceFile instanceof BufferFileAdapter)) {
-			throw new UnsupportedOperationException("unsupported use of preCacheSourceFile");
-		}
-		Msg.trace(BufferMgr.this, "Pre-cache started...");
-		int cacheCount = 0;
-		BufferFileAdapter sourceAdapter = (BufferFileAdapter) sourceFile;
-		try (InputBlockStream inputBlockStream = sourceAdapter.getInputBlockStream()) {
-			BufferFileBlock block;
-			while (!Thread.interrupted() && (block = inputBlockStream.readBlock()) != null) {
-				DataBuffer buf = LocalBufferFile.getDataBuffer(block);
-				if (buf != null && !buf.isEmpty() && preCacheBuffer(buf)) { // skip head block and empty blocks
-					++cacheCount;
-				}
+	private void preCacheSourceFile() {
+		try {
+			if (!(sourceFile instanceof BufferFileAdapter)) {
+				throw new UnsupportedOperationException("unsupported use of preCacheSourceFile");
+			}
+			Msg.trace(BufferMgr.this, "Pre-cache started...");
+			int cacheCount = 0;
+			BufferFileAdapter sourceAdapter = (BufferFileAdapter) sourceFile;
+			try (InputBlockStream inputBlockStream = sourceAdapter.getInputBlockStream()) {
+				BufferFileBlock block;
+				while (!Thread.interrupted() && (block = inputBlockStream.readBlock()) != null) {
+					DataBuffer buf = LocalBufferFile.getDataBuffer(block);
+					if (buf != null && !buf.isEmpty() && preCacheBuffer(buf)) { // skip head block and empty blocks
+						++cacheCount;
+					}
+				}
+				Msg.trace(BufferMgr.this, "Pre-cache added " + cacheCount + " of " +
+					sourceFile.getIndexCount() + " buffers to cache");
+			}
+		}
+		catch (InterruptedIOException e) {
+			// ignore
+		}
+		catch (IOException e) {
+			Msg.error(BufferMgr.this, "pre-cache failure: " + e.getMessage(), e);
+		}
+		finally {
+			synchronized (preCacheLock) {
+				preCacheStatus = PreCacheStatus.STOPPED;
+				preCacheThread = null;
+				preCacheLock.notifyAll();
 			}
-			Msg.trace(BufferMgr.this, "Pre-cache added " + cacheCount + " of " +
-				sourceFile.getIndexCount() + " buffers to cache");
 		}
 	}
 
@@ -1744,6 +1747,51 @@ public class BufferMgr {
 		return false;
 	}
 
+	/**
+	 * Set the source buffer file with a newer local buffer file version.
+	 * Intended for use following a merge or commit operation only where a local checkout has been
+	 * retained.
+	 * @param versionedSourceBufferFile updated local source buffer file opened for versioning 
+	 * update (NOTE: file itself is read-only).
+	 * @throws IOException if an IO error occurs
+	 */
+	public void setDBVersionedSourceFile(LocalManagedBufferFile versionedSourceBufferFile)
+			throws IOException {
+
+		synchronized (snapshotLock) {
+			synchronized (this) {
+				if (!(sourceFile instanceof LocalManagedBufferFile)) {
+					throw new UnsupportedOperationException(getClass().getSimpleName() +
+						".setDBSourceFile not allowed: " + sourceFile.getClass());
+				}
+				if (bufferSize != sourceFile.getBufferSize()) {
+					throw new IllegalArgumentException("Buffer size mismatch");
+				}
+
+				if (corruptedState) {
+					throw new IOException("Corrupted BufferMgr state");
+				}
+
+				if (lockCount != 0) {
+					throw new IOException("Attempted checkout update while buffers are locked");
+				}
+
+				stopPreCache();
+
+				clearCheckpoints();
+
+				doSetSourceFile(versionedSourceBufferFile);
+
+				// re-initialize cached file data
+				int cnt = sourceFile.getIndexCount();
+				indexProvider = new IndexProvider(cnt, sourceFile.getFreeIndexes());
+				bufferTable = new ObjectArray(cnt + INITIAL_BUFFER_TABLE_SIZE);
+
+				initializeCache();
+			}
+		}
+	}
+
 	/**
 	 * Save the current set of buffers to a new version of the source buffer file.
 	 * If the buffer manager was not instantiated with a source file an
@@ -1825,7 +1873,7 @@ public class BufferMgr {
 					monitor.setCancelEnabled(oldCancelState & !monitor.isCancelled());
 				}
 
-				setSourceFile(outFile);
+				doSetSourceFile(outFile);
 			}
 		}
 	}
@@ -1881,7 +1929,7 @@ public class BufferMgr {
 					monitor.setCancelEnabled(true);
 				}
 				if (associateWithNewFile) {
-					setSourceFile(outFile);
+					doSetSourceFile(outFile);
 				}
 			}
 		}
@@ -1965,7 +2013,7 @@ public class BufferMgr {
 		}
 	}
 
-	private void setSourceFile(BufferFile newFile) {
+	private void doSetSourceFile(BufferFile newFile) {
 
 		// Close buffer file
 		if (sourceFile != null) {

Ghidra/Framework/DB/src/main/java/db/buffers/LocalManagedBufferFile.java

@@ -157,7 +157,6 @@ public class LocalManagedBufferFile extends LocalBufferFile implements ManagedBu
 	 * <code>preSaveThread</code> corresponds to the PreSaveTask which creates the 
 	 * preSaveFile when this buffer file is updateable.
 	 */
-	//private Thread preSaveThread;
 	private PreSaveTask preSaveTask;
 
 	/**
@@ -228,8 +227,8 @@ public class LocalManagedBufferFile extends LocalBufferFile implements ManagedBu
 		setFreeIndexes(versionFileHandler.getFreeIndexList());
 		String[] names = versionFileHandler.getOldParameterNames();
 		clearParameters();
-		for (int i = 0; i < names.length; i++) {
-			setParameter(names[i], versionFileHandler.getOldParameter(names[i]));
+		for (String name : names) {
+			setParameter(name, versionFileHandler.getOldParameter(name));
 		}
 	}