upstream

README.md

@@ -1,8 +1,9 @@
 # Welcome to JNode!
 
-[![Build Status](https://travis-ci.org/jnode/jnode.svg?branch=master)](https://travis-ci.org/jnode/jnode)
+## Archived
+
+This project has been archived, and moved to https://github.com/Nuix/jnode-fs
 
-In this file, you find the instructions needed to setup a JNode development environment.
 
 ## Sub-Projects
 

core/src/core/org/jnode/util/LittleEndian.java

@@ -126,6 +126,23 @@ public static int getInt32(byte[] src, int offset) {
         return ((v3 << 24) | (v2 << 16) | (v1 << 8) | v0);
     }
 
+    /**
+     * Gets a 40-bit signed integer from the given byte array at the given offset.
+     *
+     * @param src
+     * @param offset
+     */
+    public static long getInt40(byte[] src, int offset) {
+        final long v0 = src[offset + 0] & 0xFF;
+        final long v1 = src[offset + 1] & 0xFF;
+        final long v2 = src[offset + 2] & 0xFF;
+        final long v3 = src[offset + 3] & 0xFF;
+        final long v4 = src[offset + 4] & 0xFF;
+        long tmp = (v4 << 32) | (v3 << 24) | (v2 << 16) | (v1 << 8) | v0;
+        tmp <<= 24; // Shift the value to the top of the 8 bytes in the long, and back to extend any -ve sign
+        return tmp >> 24;
+    }
+
     /**
      * Gets a 48-bit unsigned integer from the given byte array at the given offset.
      *

fs/src/fs/org/jnode/fs/exfat/DirectoryParser.java

@@ -51,13 +51,13 @@ public class DirectoryParser {
     private static final int FLAG_CONTIGUOUS = 3;
 
     public static DirectoryParser create(Node node) throws IOException {
-        return create(node, false);
+        return create(node, false, false);
     }
 
-    public static DirectoryParser create(Node node, boolean showDeleted) throws IOException {
+    public static DirectoryParser create(Node node, boolean showDeleted, boolean performChecks) throws IOException {
         assert (node.isDirectory()) : "not a directory"; //NOI18N
 
-        final DirectoryParser result = new DirectoryParser(node, showDeleted);
+        final DirectoryParser result = new DirectoryParser(node, showDeleted, performChecks);
         result.init();
         return result;
     }
@@ -66,13 +66,15 @@ public static DirectoryParser create(Node node, boolean showDeleted) throws IOEx
     private final ByteBuffer chunk;
     private final Node node;
     private boolean showDeleted;
+    private boolean performChecks;
     private long cluster;
     private UpcaseTable upcase;
     private int index;
 
-    private DirectoryParser(Node node, boolean showDeleted) {
+    private DirectoryParser(Node node, boolean showDeleted, boolean performChecks) {
         this.node = node;
         this.showDeleted = showDeleted;
+        this.performChecks = performChecks;
         this.sb = node.getSuperBlock();
         this.chunk = ByteBuffer.allocate(sb.getBytesPerCluster());
         this.chunk.order(ByteOrder.LITTLE_ENDIAN);
@@ -232,14 +234,10 @@ private void parseFile(Visitor v, boolean deleted) throws IOException {
         int nameLen = DeviceAccess.getUint8(chunk);
         final int nameHash = DeviceAccess.getUint16(chunk);
         skip(2); /* unknown */
-        final long realSize = DeviceAccess.getUint64(chunk);
+        final long size = DeviceAccess.getUint64(chunk);
         skip(4); /* unknown */
         final long startCluster = DeviceAccess.getUint32(chunk);
-        final long size = DeviceAccess.getUint64(chunk);
-
-        if (realSize != size) {
-            throw new IOException("real size does not equal size");
-        }
+        final long allocatedSize = DeviceAccess.getUint64(chunk);
 
         conts--;
 
@@ -276,19 +274,19 @@ private void parseFile(Visitor v, boolean deleted) throws IOException {
             }
         }
 
-        if (!deleted && referenceChecksum != actualChecksum) {
+        if (performChecks && !deleted && referenceChecksum != actualChecksum) {
             throw new IOException("checksum mismatch");
         }
 
         final String name = nameBuilder.toString();
 
-        if ((this.upcase != null) && (hashName(name) != nameHash)) {
+        if (performChecks && (this.upcase != null) && (hashName(name) != nameHash)) {
             throw new IOException("name hash mismatch ("
                 + Integer.toHexString(hashName(name)) +
                 " != " + Integer.toHexString(nameHash) + ")");
         }
 
-        v.foundNode(Node.create(sb, startCluster, attrib, name, (flag == FLAG_CONTIGUOUS), realSize, times, deleted),
+        v.foundNode(Node.create(sb, startCluster, attrib, name, (flag == FLAG_CONTIGUOUS), size, allocatedSize, times, deleted),
             index);
     }
 

fs/src/fs/org/jnode/fs/exfat/Node.java

@@ -21,6 +21,7 @@
 package org.jnode.fs.exfat;
 
 import java.io.IOException;
+import org.apache.log4j.Logger;
 
 /**
  * @author Matthias Treydte <waldheinz at gmail.com>
@@ -47,16 +48,21 @@ public static Node createRoot(ExFatSuperBlock sb)
 
     public static Node create(
         ExFatSuperBlock sb, long startCluster, int flags,
-        String name, boolean isContiguous, long size, EntryTimes times, boolean deleted) {
+        String name, boolean isContiguous, long size, long allocatedSize, EntryTimes times, boolean deleted) {
 
         final Node result = new Node(sb, startCluster, times);
 
         result.name = name;
         result.isContiguous = isContiguous;
         result.size = size;
+        result.allocatedSize = allocatedSize;
         result.flags = flags;
         result.deleted = deleted;
 
+        if (allocatedSize < size) {
+            Logger.getLogger(Node.class).warn("Allocated size less than file size: " + result);
+        }
+
         return result;
     }
 
@@ -69,7 +75,17 @@ public static Node create(
     private long clusterCount;
     private int flags;
     private String name;
+
+    /**
+     * The size of the file in bytes.
+     */
     private long size;
+
+    /**
+     * The size allocated for the file in bytes. This may be larger than {@code size} if the OS has reserved some space
+     * for the file to grow into.
+     */
+    private long allocatedSize;
     private boolean deleted;
 
     private Node(ExFatSuperBlock sb, long startCluster, EntryTimes times) {
@@ -125,6 +141,10 @@ public long getSize() {
         return size;
     }
 
+    public long getAllocatedSize() {
+        return allocatedSize;
+    }
+
     public boolean isDeleted() {
         return deleted;
     }
@@ -170,6 +190,10 @@ public String toString() {
         result.append(this.name);
         result.append(", contiguous=");
         result.append(this.isContiguous);
+        result.append(", size=");
+        result.append(size);
+        result.append(", allocated-size=");
+        result.append(allocatedSize);
         result.append("]");
 
         return result.toString();

fs/src/fs/org/jnode/fs/exfat/NodeDirectory.java

@@ -43,10 +43,10 @@ public class NodeDirectory extends AbstractFSObject implements FSDirectory, FSDi
     public NodeDirectory(ExFatFileSystem fs, NodeEntry nodeEntry)
         throws IOException {
 
-        this(fs, nodeEntry, false);
+        this(fs, nodeEntry, false, false);
     }
 
-    public NodeDirectory(ExFatFileSystem fs, NodeEntry nodeEntry, boolean showDeleted)
+    public NodeDirectory(ExFatFileSystem fs, NodeEntry nodeEntry, boolean showDeleted, boolean performChecks)
         throws IOException {
 
         super(fs);
@@ -57,7 +57,7 @@ public NodeDirectory(ExFatFileSystem fs, NodeEntry nodeEntry, boolean showDelete
         this.idToNode = new LinkedHashMap<String, NodeEntry>();
 
         DirectoryParser.
-            create(nodeEntry.getNode(), showDeleted).
+            create(nodeEntry.getNode(), showDeleted, performChecks).
             setUpcase(this.upcase).
             parse(new VisitorImpl());
 
@@ -145,7 +145,7 @@ public void foundBitmap(
         @Override
         public void foundUpcaseTable(DirectoryParser parser, long checksum,
                                      long startCluster, long size) {
-            
+
             /* ignore */
         }
 

fs/src/fs/org/jnode/fs/exfat/NodeFile.java

@@ -39,6 +39,10 @@ public NodeFile(ExFatFileSystem fs, Node node) {
         this.node = node;
     }
 
+    public Node getNode() {
+        return node;
+    }
+
     @Override
     public long getLength() {
         return this.node.getSize();

fs/src/fs/org/jnode/fs/ext2/Ext2DirectoryRecord.java

@@ -59,8 +59,8 @@ public Ext2DirectoryRecord(Ext2FileSystem fs, byte[] data, int offset, int fileO
         synchronized (data) {
             byte[] newData = new byte[Math.max(8, getRecLen())];
             int copySize = getRecLen();
-            if (copySize + offset > data.length) {
-                copySize = Math.max(0, copySize - offset);
+            if (offset + copySize > data.length) {
+                copySize = data.length - offset;
             }
             System.arraycopy(data, offset, newData, 0, copySize);
             this.data = newData;

fs/src/fs/org/jnode/fs/ext2/INode.java

@@ -166,7 +166,7 @@ public Ext2FileSystem getExt2FileSystem() {
      * @return the extra size.
      */
     public int getExtraISize() {
-        if (getExt2FileSystem().hasROFeature(Ext2Constants.EXT4_FEATURE_RO_COMPAT_EXTRA_ISIZE)) {
+        if (getExt2FileSystem().hasROFeature(Ext2Constants.EXT4_FEATURE_RO_COMPAT_EXTRA_ISIZE) && data.length > 0x82) {
             return LittleEndian.getInt16(data, 0x80);
         }
 

fs/src/fs/org/jnode/fs/hfsplus/HfsPlusDirectory.java

@@ -218,7 +218,7 @@ private FSEntryTable readEntries() throws IOException {
         List<FSEntry> pathList = new LinkedList<FSEntry>();
         HfsPlusFileSystem fs = getFileSystem();
         if (fs.getVolumeHeader().getFolderCount() > 0) {
-            LeafRecord[] records;
+            List<LeafRecord> records;
 
             if ((folder.getFlags() & CatalogFile.FLAGS_HARDLINK_CHAIN) != 0) {
                 records = fs.getCatalog().getRecords(getHardLinkFolder().getFolderId());

fs/src/fs/org/jnode/fs/hfsplus/HfsPlusFileSystemType.java

@@ -32,18 +32,17 @@
 public class HfsPlusFileSystemType implements BlockDeviceFileSystemType<HfsPlusFileSystem> {
     public static final Class<HfsPlusFileSystemType> ID = HfsPlusFileSystemType.class;
 
-    public final HfsPlusFileSystem create(final Device device, final boolean readOnly) throws FileSystemException {
+    public HfsPlusFileSystem create(final Device device, final boolean readOnly) throws FileSystemException {
         HfsPlusFileSystem fs = new HfsPlusFileSystem(device, readOnly, this);
         fs.read();
         return fs;
     }
 
-    public final String getName() {
+    public String getName() {
         return "HFS+";
     }
 
-    public final boolean supports(final PartitionTableEntry pte, final byte[] firstSector,
-                                  final FSBlockDeviceAPI devApi) {
+    public boolean supports(final PartitionTableEntry pte, final byte[] firstSector, final FSBlockDeviceAPI devApi) {
         /*
          * if (pte != null) { if (pte instanceof IBMPartitionTableEntry) { if (((IBMPartitionTableEntry)
          * pte).getSystemIndicator() != IBMPartitionTypes.PARTTYPE_LINUXNATIVE) { return false; } } }
@@ -62,5 +61,4 @@ public final boolean supports(final PartitionTableEntry pte, final byte[] firstS
         return (magicNumber == SuperBlock.HFSPLUS_SUPER_MAGIC && version == 4)
             || (magicNumber == SuperBlock.HFSX_SUPER_MAGIC && version == 5);
     }
-
 }

fs/src/fs/org/jnode/fs/hfsplus/HfsPlusForkData.java

@@ -59,7 +59,7 @@ public class HfsPlusForkData {
     /**
      * Overflow extents.
      */
-    private ExtentDescriptor[] overflowExtents;
+    private List<ExtentDescriptor> overflowExtents;
 
     /**
      * The catalog node ID that owns this fork.
@@ -178,7 +178,7 @@ public Collection<ExtentDescriptor> getAllExtents(HfsPlusFileSystem fileSystem)
 
         // Add the overflow extents if the exist
         if (overflowExtents != null) {
-            Collections.addAll(allExtents, overflowExtents);
+            allExtents.addAll(overflowExtents);
         }
 
         return allExtents;

fs/src/fs/org/jnode/fs/hfsplus/HfsUnicodeString.java

@@ -22,7 +22,7 @@
 
 import org.jnode.util.BigEndian;
 
-public class HfsUnicodeString {
+public class HfsUnicodeString implements Comparable<HfsUnicodeString> {
     /**
      * Length of string in characters.
      */
@@ -55,7 +55,7 @@ public HfsUnicodeString(final byte[] src, final int offset) {
      */
     public HfsUnicodeString(String string) {
         this.string = string;
-        this.length = string.length();
+        this.length = string == null ? 0 : string.length();
     }
 
     public final int getLength() {
@@ -83,4 +83,32 @@ public final byte[] getBytes() {
     public String toString() {
         return string;
     }
+
+    @Override
+    public int hashCode() {
+        return string == null ? 0 : string.hashCode();
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+        if (!(obj instanceof HfsUnicodeString)) {
+            return false;
+        }
+
+        HfsUnicodeString other = (HfsUnicodeString) obj;
+        return compareTo(other) == 0;
+    }
+
+    @Override
+    public int compareTo(HfsUnicodeString other) {
+        if (string == null && other.string == null) {
+            return 0;
+        } else if (string == null) {
+            return -1;
+        } else if (other.string == null) {
+            return 1;
+        }
+
+        return string.compareTo(other.string);
+    }
 }

fs/src/fs/org/jnode/fs/hfsplus/attributes/AttributeKey.java

@@ -81,8 +81,7 @@ public int compareTo(Key key) {
                 // Note: this is unlikely to be correct. See TN1150 section "Unicode Subtleties" for details
                 // For reading in data is should be safe since the B-Tree will be pre-sorted, but for adding new entries
                 // it will cause the order to be wrong.
-                result = this.getAttributeName().getUnicodeString()
-                    .compareTo(otherKey.getAttributeName().getUnicodeString());
+                result = this.getAttributeName().compareTo(otherKey.getAttributeName());
             }
         }
         return result;
@@ -103,7 +102,8 @@ public boolean equals(Object obj) {
 
         return
             fileId.getId() == otherKey.fileId.getId() &&
-            attributeName.getUnicodeString().equals(otherKey.getAttributeName().getUnicodeString());
+                (attributeName.getUnicodeString() == null || otherKey.getAttributeName().getUnicodeString() == null ||
+                    attributeName.getUnicodeString().equals(otherKey.getAttributeName().getUnicodeString()));
     }
 
     @Override