Add a managment tool for Coffee file system images.

tools/coffee-manager/LICENSE

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+Copyright (c) 2009, Swedish Institute of Computer Science
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+3. Neither the name of the Institute nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.

tools/coffee-manager/MANIFEST.MF

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+Manifest-Version: 1.0
+Main-Class: se.sics.coffee.CoffeeManager

tools/coffee-manager/README.TXT

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+se.sics.coffee is a library for the Coffee File System. It is able to 
+generate file system images and to extract information from existing 
+images.
+
+Building:
+
+./build.sh
+
+Usage:
+
+java -jar coffee.jar [-i|e <Coffee file> <file>] [-r <Coffee file>]
+                     [-l|s] <file system image>
+
+Options:
+
+-i   Inserts a new file into the file system.
+-e   Extracts a file from the file system and saves it locally.
+-r   Removes a file from the file system.
+-l   Lists all files.
+-s   Prints file system statistics.
+
+Author:
+
+Nicols Tsiftes <nvt@sics.se>

tools/coffee-manager/build.sh

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+#!/bin/sh
+(cd se/sics/coffee && javac *.java) && jar cvfm coffee.jar MANIFEST.MF se/

tools/coffee-manager/se/sics/coffee/CoffeeConfiguration.java

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+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * This file is part of the Contiki operating system.
+ *
+ * $Id: CoffeeConfiguration.java,v 1.1 2009/08/04 10:36:53 nvt-se Exp $
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package se.sics.coffee;
+
+import java.io.*;
+import java.util.Properties;
+
+public class CoffeeConfiguration {
+	public static final int FD_SET_SIZE = 256;
+	public static final int MAX_OPEN_FILES = 256;
+	public static final int LOG_TABLE_LIMIT = 256;
+	public static final int DIR_CACHE_ENTRIES = 256;
+	public static final int NAME_LENGTH = 16;
+	public static int fsSize, sectorSize, pageSize;
+	public static int startOffset, pageTypeSize;
+	public static int defaultFileSize, defaultLogSize;
+	public static int pagesPerSector;
+	public static boolean useMicroLogs;
+
+	public CoffeeConfiguration(String filename)
+			throws CoffeeException, IOException {
+		String[] validParameters = {"use_micro_logs", "fs_size", 
+					    "page_size", "sector_size", 
+					    "start_offset", "default_file_size",
+					    "default_log_size", "page_type_size"};
+		String property;
+		Properties prop = new Properties();
+		FileInputStream fstream =
+			new FileInputStream(filename);
+
+		prop.load(fstream);
+		for(int i = 0; i < validParameters.length; i++) {
+			if(prop.getProperty(validParameters[i]) == null) {
+				throw new CoffeeException("missing the parameter \"" + validParameters[i] + "\" in the configuration file " + filename);
+			}
+		}
+
+		useMicroLogs = new Boolean(prop.getProperty("use_micro_logs")).booleanValue();
+		fsSize = new Integer(prop.getProperty("fs_size")).intValue();
+		sectorSize = new Integer(prop.getProperty("sector_size")).intValue();
+		pageSize = new Integer(prop.getProperty("page_size")).intValue();
+		defaultFileSize = new Integer(prop.getProperty("default_file_size")).intValue();
+		defaultLogSize = new Integer(prop.getProperty("default_log_size")).intValue();
+		startOffset = new Integer(prop.getProperty("start_offset")).intValue();
+		pageTypeSize = new Integer(prop.getProperty("page_type_size")).intValue();
+
+		pagesPerSector = sectorSize / pageSize;
+	}
+}

tools/coffee-manager/se/sics/coffee/CoffeeFS.java

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+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * This file is part of the Contiki operating system.
+ *
+ * $Id: CoffeeFS.java,v 1.1 2009/08/04 10:36:53 nvt-se Exp $
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package se.sics.coffee;
+
+import java.io.*;
+import java.util.Map;
+import java.util.TreeMap;
+
+class CoffeeException extends RuntimeException {
+	public CoffeeException(String message) {
+		super("Coffee error: " + message);
+	}
+}
+
+class CoffeeFileException extends RuntimeException {
+	public CoffeeFileException(String message) {
+		super("Coffee file error: " + message);
+	}
+}
+
+public class CoffeeFS {
+	private CoffeeImage image;
+	private CoffeeConfiguration conf;
+	private int currentPage;
+	private Map<String, CoffeeFile> files;
+	private static final int INVALID_PAGE = -1;
+
+	public CoffeeFS(CoffeeImage image) throws IOException {
+		this.image = image;
+		conf = image.getConfiguration();
+		currentPage = 0;
+		files = new TreeMap<String, CoffeeFile>();
+
+		while(currentPage < (conf.fsSize / conf.pageSize)) {
+			CoffeeHeader header = readHeader(currentPage);
+			if(header.isActive()) {
+				CoffeeFile file = new CoffeeFile(this, header);
+				files.put(file.getName(), file);
+			}
+			currentPage = nextFile(header, currentPage);
+		}
+	}
+
+	private int pageCount(long size) {
+		int headerSize = conf.NAME_LENGTH + conf.pageTypeSize * 2 + 6;
+		return (int)(size + headerSize + conf.pageSize - 1) / conf.pageSize;
+	}
+
+	private int findFreeExtent(int pages) throws IOException {
+		CoffeeHeader header;
+		int currentPage = 0;
+		int start = INVALID_PAGE;
+
+		while(currentPage < (conf.fsSize / conf.pageSize)) {
+			header = readHeader(currentPage);
+			if(header.isFree()) {
+				if(start == INVALID_PAGE) {
+					start = currentPage;
+				}
+				currentPage = nextFile(header, currentPage);
+				if(start + pages <= currentPage) {
+					return start;
+				}
+			} else {
+				start = INVALID_PAGE;
+				currentPage = nextFile(header, currentPage);
+			}
+		}
+		return INVALID_PAGE;
+	}
+
+	public CoffeeImage getImage() {
+		return image;
+	}
+
+	public CoffeeConfiguration getConfiguration() {
+		return conf;
+	}
+
+	private CoffeeHeader readHeader(int page) throws IOException {
+		byte[] bytes = new byte[conf.NAME_LENGTH + conf.pageTypeSize * 2 + 6];
+		int index = 0;
+
+		image.read(bytes, bytes.length, page * conf.pageSize);
+		CoffeeHeader header = new CoffeeHeader(this, page, bytes);
+
+		return header;
+	}
+
+	private void writeHeader(CoffeeHeader header) throws IOException {
+		byte[] bytes = header.toRawHeader();
+
+		image.write(bytes, bytes.length, header.getPage() * conf.pageSize);
+	}
+
+	private int nextFile(CoffeeHeader header, int page) {
+		if(header.isFree()) {
+			return page + conf.pagesPerSector & ~(conf.pagesPerSector - 1);
+		} else if(header.isIsolated()) {
+			return page + 1;
+		}
+
+		return page + header.maxPages;
+	}
+
+	public final Map<String, CoffeeFile> getFiles() {
+		return files;
+	}
+
+	public CoffeeFile insertFile(String filename) throws IOException {
+		CoffeeFile coffeeFile;
+		try {
+			File file = new File(filename);
+			FileInputStream input = new FileInputStream(file);
+System.out.println("file length: " + file.length() + ", page count: " + pageCount(file.length()));
+			int allocatePages = pageCount(file.length());
+			int start = findFreeExtent(allocatePages);
+			if(start == INVALID_PAGE) {
+				return null;
+			}
+			CoffeeHeader header = new CoffeeHeader(this, start);
+			header.setName(filename);
+			header.setReservedSize(allocatePages);
+			header.allocate();
+			coffeeFile = new CoffeeFile(this, header);
+			writeHeader(header);
+			coffeeFile.insertContents(input);
+			input.close();
+			return coffeeFile;
+		} catch (FileNotFoundException e) {
+		}
+		return null;
+	}
+
+	public void removeFile(String filename)
+			throws CoffeeFileException, IOException {
+		CoffeeFile file = files.get(filename);
+		if(file == null) {
+			throw new CoffeeFileException("Coffee: attempt to remove inexistent file");
+		}
+
+		file.remove();
+		writeHeader(file.getHeader());
+		files.remove(file.getName());
+	}
+
+	public boolean extractFile(String inputFile, String outputFile) throws IOException {
+		CoffeeFile file = files.get(inputFile);
+
+		if(file == null) {
+			return false;
+		}
+
+		file.saveContents(outputFile);
+		return true;
+	}
+}

tools/coffee-manager/se/sics/coffee/CoffeeFile.java

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+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * This file is part of the Contiki operating system.
+ *
+ * $Id: CoffeeFile.java,v 1.1 2009/08/04 10:36:53 nvt-se Exp $
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package se.sics.coffee;
+
+import java.io.*;
+
+public class CoffeeFile {
+	private CoffeeFS coffeeFS;
+	private CoffeeHeader header;
+	private String name;
+	private int length;
+	private int startPage;
+	private int reservedSize;
+	private CoffeeFile logFile;
+	private boolean knownLength;
+
+	public CoffeeFile(CoffeeFS coffeeFS, CoffeeHeader header) {
+		this.coffeeFS = coffeeFS;
+		this.header = header;
+		name = header.name;
+		startPage = header.getPage();
+		reservedSize = header.maxPages * coffeeFS.getConfiguration().pageSize;
+	}
+
+	private int calculateLength() throws IOException {
+		byte[] bytes = new byte[1];
+		int i;
+
+		for(i = reservedSize; i >= header.rawLength(); i--) {
+			coffeeFS.getImage().read(bytes, 1, header.getPage() * coffeeFS.getConfiguration().pageSize + i);
+			if(bytes[0] != 0) {
+				return i - header.rawLength() + 1;
+			}
+		}
+		return 0;
+	}
+
+	public void insertContents(FileInputStream input) throws IOException {
+		byte[] bytes = new byte[1];
+		int ch;
+		int startOffset = header.getPage() *
+				  coffeeFS.getConfiguration().pageSize +
+				  header.rawLength();
+
+		length = 0;
+		knownLength = true;
+
+		while((ch = input.read()) != -1) {
+			bytes[0] = (byte) ch;
+
+			coffeeFS.getImage().write(bytes, 1,
+				startOffset + length);
+			length++;
+		}
+System.out.println("inserted bytes: " + length);
+	}
+
+	public void saveContents(String filename) throws IOException {
+		byte[] bytes = new byte[1];
+		int startOffset = header.getPage() *
+				  coffeeFS.getConfiguration().pageSize +
+				  header.rawLength();
+		int i;
+
+		FileOutputStream fOut = new FileOutputStream(filename);
+		for(i = 0; i < getLength(); i++) {
+			coffeeFS.getImage().read(bytes, 1, startOffset + i);
+			fOut.write(bytes);
+		}
+
+		fOut.close();
+	}
+
+	public void remove() {
+		header.makeObsolete();
+	}
+
+	public CoffeeHeader getHeader() {
+		return header;
+	}
+
+	public int getLength() throws IOException {
+		if(!knownLength) {
+			length = calculateLength();
+			knownLength = true;
+		}
+		return length;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public int getReservedSize() {
+		return reservedSize;
+	}
+}

tools/coffee-manager/se/sics/coffee/CoffeeHeader.java

@@ -0,0 +1,259 @@
+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * This file is part of the Contiki operating system.
+ *
+ * $Id: CoffeeHeader.java,v 1.1 2009/08/04 10:36:53 nvt-se Exp $
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package se.sics.coffee;
+
+class CoffeeHeader {
+	private CoffeeFS coffeeFS;
+	private CoffeeConfiguration conf;
+	private int page;
+
+	private static final int HDR_FLAG_VALID		= 0x1;
+	private static final int HDR_FLAG_ALLOCATED	= 0x2;
+	private static final int HDR_FLAG_OBSOLETE	= 0x4;
+	private static final int HDR_FLAG_MODIFIED	= 0x8;
+	private static final int HDR_FLAG_LOG		= 0x10;
+	private static final int HDR_FLAG_ISOLATED	= 0x20;
+
+	int logPage;
+	int logRecords;
+	int logRecordSize;
+	int maxPages;
+	String name;
+
+	private boolean valid;
+	private boolean allocated;
+	private boolean obsolete;
+	private boolean modified;
+	private boolean log;
+	private boolean isolated;
+
+	public CoffeeHeader(CoffeeFS coffeeFS, int page) {
+		this.coffeeFS = coffeeFS;
+		this.page = page;
+		conf = coffeeFS.getConfiguration();
+	}
+
+	public CoffeeHeader(CoffeeFS coffeeFS, int page, byte[] bytes) {
+		this.coffeeFS = coffeeFS;
+		this.page = page;
+
+		processRawHeader(bytes);
+	}
+
+	private void processRawHeader(byte[] bytes) {
+		int index = 0;
+
+		logPage = getPageValue(bytes, 0);
+		index += conf.pageTypeSize;
+
+		logRecords = bytes[index] + (bytes[index + 1] << 8);
+		index += 2;
+
+		logRecordSize = bytes[index] + (bytes[index + 1] << 8);
+		index += 2;
+
+		maxPages = getPageValue(bytes, index);
+		index += conf.pageTypeSize;
+
+		index++; // Skip deprecated EOF hint field.
+
+		processFlags((int)bytes[index]);
+		index++;
+
+		name = new String(bytes).substring(index,
+				index + conf.NAME_LENGTH);
+		int nullCharOffset = name.indexOf(0);
+		if(nullCharOffset >= 0) {
+			name = name.substring(0, nullCharOffset);
+		}
+	}
+
+	private byte composeFlags() {
+		byte flags = 0;
+
+		if(valid) {
+			flags |= HDR_FLAG_VALID;
+		}
+		if(allocated) {
+			flags |= HDR_FLAG_ALLOCATED;
+		}
+		if(obsolete) {
+			flags |= HDR_FLAG_OBSOLETE;
+		}
+		if(modified) {
+			flags |= HDR_FLAG_MODIFIED;
+		}
+		if(log) {
+			flags |= HDR_FLAG_LOG;
+		}
+
+		if(isolated) {
+			flags |= HDR_FLAG_ISOLATED;
+		}
+
+		return flags;
+	}
+
+	private void processFlags(int flags) {
+		if((flags & HDR_FLAG_VALID) != 0) {
+			valid = true;
+		}
+		if((flags & HDR_FLAG_ALLOCATED) != 0) {
+			allocated = true;
+		}
+		if((flags & HDR_FLAG_OBSOLETE) != 0) {
+			obsolete = true;
+		}
+		if((flags & HDR_FLAG_MODIFIED) != 0) {
+			modified = true;
+		}
+		if((flags & HDR_FLAG_LOG) != 0) {
+			log = true;
+		}
+		if((flags & HDR_FLAG_ISOLATED) != 0) {
+			isolated = true;
+		}
+	}
+
+	private byte[] setPageValue(int page) {
+		byte[] bytes = new byte[conf.pageTypeSize];
+
+		for(int i = conf.pageTypeSize - 1; i >= 0; i--) {
+			bytes[i] = (byte) (page >> (8 * i));
+		}
+		return bytes;
+	}
+
+	private int getPageValue(byte[] bytes, int offset) {
+		int page = 0;
+
+		for(int i = 0; i < conf.pageTypeSize; i++) {
+			page |= bytes[offset + i] << (8 * i);
+		}
+		return page;
+	}
+
+	public byte[] toRawHeader() {
+		byte[] bytes = new byte[2 * conf.pageTypeSize + 
+					conf.NAME_LENGTH + 6];
+		int index = 0;
+
+		System.arraycopy(setPageValue(logPage), 0, bytes, 0, 
+			conf.pageTypeSize);
+		index += conf.pageTypeSize;
+
+		bytes[index++] = (byte) (logRecords >> 8);
+		bytes[index++] = (byte) logRecords;
+
+		bytes[index++] = (byte) (logRecordSize >> 8);
+		bytes[index++] = (byte) logRecordSize;
+
+		System.arraycopy(setPageValue(maxPages), 0, bytes, index,
+			conf.pageTypeSize);
+		index += conf.pageTypeSize;
+
+		bytes[index++] = 0; // Deprecated EOF hint field.
+		bytes[index++] = composeFlags();
+
+		byte[] nameBytes = name.getBytes();
+		int copyLength = nameBytes.length > conf.NAME_LENGTH ?
+					conf.NAME_LENGTH : nameBytes.length;
+		System.arraycopy(nameBytes, 0, bytes, index, copyLength);
+
+		return bytes;
+	}
+
+	public int rawLength() {
+		return 2 * conf.pageTypeSize + conf.NAME_LENGTH + 6;
+	}
+
+	public int getPage() {
+		return page;
+	}
+
+	public boolean isValid() {
+		return valid;
+	}
+
+	public boolean isAllocated() {
+		return allocated;
+	}
+
+	public boolean isObsolete() {
+		return obsolete;
+	}
+
+	public boolean isModified() {
+		return modified;
+	}
+
+	public boolean isIsolated() {
+		return isolated;
+	}
+
+	public boolean isLog() {
+		return log;
+	}
+
+	public boolean isFree() {
+		return !isAllocated();
+	}
+
+	public boolean isActive() {
+		return isAllocated() && !isObsolete() && !isIsolated();
+	}
+
+	public void allocate() {
+		allocated = true;
+	}
+
+	public void makeObsolete() {
+		obsolete = true;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public void setReservedSize(int pages) {
+		maxPages = pages;
+	}
+
+	public int getReservedSize() {
+		return maxPages;
+	}
+}

tools/coffee-manager/se/sics/coffee/CoffeeImage.java

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * This file is part of the Contiki operating system.
+ *
+ * $Id: CoffeeImage.java,v 1.1 2009/08/04 10:36:53 nvt-se Exp $
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package se.sics.coffee;
+
+import java.io.IOException;
+
+interface CoffeeImage {
+	CoffeeConfiguration getConfiguration();
+	void read(byte[] bytes, int size, int offset) throws IOException;
+	void write(byte[] bytes, int size, int offset) throws IOException;
+	void erase(int size, int offset) throws IOException;
+}

tools/coffee-manager/se/sics/coffee/CoffeeImageFile.java

@@ -0,0 +1,86 @@
+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * This file is part of the Contiki operating system.
+ *
+ * $Id: CoffeeImageFile.java,v 1.1 2009/08/04 10:36:53 nvt-se Exp $
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package se.sics.coffee;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.RandomAccessFile;
+
+public class CoffeeImageFile implements CoffeeImage {
+	private String filename;
+	private RandomAccessFile imageFile;
+	private CoffeeConfiguration conf;
+
+	public CoffeeImageFile(String filename, CoffeeConfiguration conf) throws IOException {
+		this.filename = filename;
+		this.conf = conf;
+		File file = new File(filename);
+		imageFile = new RandomAccessFile(file, "rw");
+		if(imageFile.length() == 0) {
+			// Allocate a full file system image.
+			imageFile.setLength(conf.fsSize);
+		}
+	}
+
+	public CoffeeConfiguration getConfiguration() {
+		return conf;
+	}
+
+	public void read(byte[] bytes, int size, int offset) throws IOException {
+		imageFile.seek(conf.startOffset + offset);
+		imageFile.read(bytes, 0, size);
+	}
+
+	public void write(byte[] bytes, int size, int offset) throws IOException {
+		imageFile.seek(conf.startOffset + offset);
+		imageFile.write(bytes, 0, size);
+	}
+
+	public void erase(int size, int offset) throws IOException {
+		byte[] bytes = new byte[256];
+		int chunkSize;
+
+		while(size > 0) {
+			chunkSize = size > bytes.length ? bytes.length : size;
+			imageFile.seek(conf.startOffset + offset);
+			imageFile.write(bytes, 0, chunkSize);
+			size -= chunkSize;
+			offset += chunkSize;
+		}
+	}
+
+}

tools/coffee-manager/se/sics/coffee/CoffeeManager.java

@@ -0,0 +1,200 @@
+/*
+ * Copyright (c) 2009, Swedish Institute of Computer Science
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the distribution.
+ * 3. Neither the name of the Institute nor the names of its contributors
+ *    may be used to endorse or promote products derived from this software
+ *    without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE INSTITUTE AND CONTRIBUTORS ``AS IS'' AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED.  IN NO EVENT SHALL THE INSTITUTE OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ *
+ * This file is part of the Contiki operating system.
+ *
+ * $Id: CoffeeManager.java,v 1.1 2009/08/04 10:36:53 nvt-se Exp $
+ *
+ * @author Nicolas Tsiftes
+ *
+ */
+
+package se.sics.coffee;
+
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class CoffeeManager {
+	private static CoffeeFS coffeeFS;
+	private static final int COMMAND_NULL    = 0;
+	private static final int COMMAND_INSERT  = 1;
+	private static final int COMMAND_EXTRACT = 2;
+	private static final int COMMAND_REMOVE  = 3;
+	private static final int COMMAND_LIST    = 4;
+	private static final int COMMAND_STATS   = 5;
+
+	public static void main(String args[]) {
+		String platform = "sky";
+		String usage = "Usage: java -jar coffee.jar ";
+		int command = COMMAND_NULL;
+		String coffeeFile = "";
+		String localFile = "";
+		String fsImage = "";
+
+		usage += "[-i|e <Coffee file> <file>] ";
+		usage += "[-r <Coffee file>] ";
+		usage += "[-l|s] ";
+		usage += "<file system image>";
+
+		if(args.length < 1) {
+			System.err.println(usage);
+			System.exit(1);
+		}
+
+		if(args.length > 1) {
+			Pattern validArg = Pattern.compile("-(i|e|r|l|s)");
+			Matcher m = validArg.matcher(args[0]);
+			if(!m.matches()) {
+				System.err.println(usage);
+				System.exit(1);
+			}
+
+			if(args[0].equals("-i") || args[0].equals("-e")) {
+				if(args.length != 4) {
+					System.err.println(usage);
+					System.exit(1);
+				}
+				if(args[0].equals("-i")) {
+					command = COMMAND_INSERT;
+				} else {
+					command = COMMAND_EXTRACT;
+				}
+				coffeeFile = args[1];
+				localFile = args[2];
+				fsImage = args[3];
+			} else if (args[0].equals("-r")) {
+				if(args.length != 3) {
+					System.err.println(usage);
+					System.exit(1);
+				}
+				command = COMMAND_REMOVE;
+				coffeeFile = args[1];
+				fsImage = args[2];
+			} else {
+				if(args.length != 2) {
+					System.err.println(usage);
+					System.exit(1);
+				}
+				if(args[0].equals("-l")) {
+					command = COMMAND_LIST;
+				} else {
+					command = COMMAND_STATS;
+				}
+				fsImage = args[1];
+			}
+		}
+
+		try {
+			CoffeeConfiguration conf = new CoffeeConfiguration(platform + ".properties");
+			coffeeFS = new CoffeeFS(new CoffeeImageFile(fsImage, conf));
+			switch (command) {
+			case COMMAND_INSERT:
+				if(coffeeFS.getFiles().get(localFile) != null) {
+					System.err.println("error: file \"" + localFile + "\" already exists");
+					break;
+				}
+				if(coffeeFS.insertFile(localFile) != null) {
+					System.out.println("Inserted the local file \"" + localFile + "\" into the file system image");
+				}
+				break;
+			case COMMAND_EXTRACT:
+				if(coffeeFS.extractFile(coffeeFile, localFile) == false) {
+					System.err.println("Inexistent file: " + coffeeFile);
+					System.exit(1);
+				}
+				System.out.println("Saved the file \"" + coffeeFile + "\" from the system image into the local file \"" + localFile + "\"");
+				break;
+			case COMMAND_REMOVE:
+				coffeeFS.removeFile(coffeeFile);
+				System.out.println("Removed the file \"" + coffeeFile + "\" from the Coffee file system image");
+				break;
+			case COMMAND_LIST:
+				printFiles(coffeeFS.getFiles());
+				break;
+			case COMMAND_STATS:
+				printStatistics(coffeeFS);
+				break;
+			default:
+				System.err.println("Unknown command!");
+				System.exit(1);
+			}
+		} catch (IOException e) {
+			System.err.println(e.getMessage());
+		}
+	}
+
+	private static void printStatistics(CoffeeFS coffeeFS) {
+		int bytesWritten = 0;
+		int bytesReserved = 0;
+		int fileCount = 0;
+		CoffeeConfiguration conf = coffeeFS.getConfiguration();
+
+		try {
+			Iterator<Map.Entry<String, CoffeeFile>> iterator =
+				coffeeFS.getFiles().entrySet().iterator();
+			while (iterator.hasNext()) {
+				Map.Entry<String, CoffeeFile> pair = (Map.Entry<String, CoffeeFile>) iterator.next();
+				String key = pair.getKey();
+				CoffeeFile file = pair.getValue();
+				bytesWritten += file.getLength();
+				bytesReserved += file.getHeader().getReservedSize();
+				fileCount++;
+			}
+			bytesReserved *= conf.pageSize;
+			System.out.println("File system size: " +
+				conf.fsSize / 1024 + "kb");
+			System.out.println("Allocated files: " + fileCount);
+			System.out.println("Reserved bytes: " + bytesReserved + " (" + 
+				(100 * ((float) bytesReserved / conf.fsSize)) +
+				"%)");
+			System.out.println("Written bytes: " + bytesWritten +
+				" (" +
+				(100 * ((float) bytesWritten / conf.fsSize)) +
+				"%)");
+		} catch (IOException e) {
+			System.err.println("failed to determine the file length");
+		}
+	}
+
+	private static void printFiles(Map<String, CoffeeFile> files) {
+		try {
+			Iterator<Map.Entry<String, CoffeeFile>> iterator = files.entrySet().iterator();
+			while (iterator.hasNext()) {
+				Map.Entry<String, CoffeeFile> pair = (Map.Entry<String, CoffeeFile>) iterator.next();
+				String key = pair.getKey();
+				CoffeeFile file = pair.getValue();
+				System.out.println(file.getName() + " " + file.getLength());
+			}
+		} catch (IOException e) {
+			System.err.println("failed to determine the file length");
+		}
+	}
+}

tools/coffee-manager/sky.properties

@@ -0,0 +1,8 @@
+fs_size			983040
+sector_size		65536
+page_size		256
+start_offset		65536
+default_file_size	4096
+default_log_size	1024
+use_micro_logs		true
+page_type_size		2