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org.scijava.annotations.legacy.LegacyReader Maven / Gradle / Ivy
/*
* #%L
* SciJava Common shared library for SciJava software.
* %%
* Copyright (C) 2009 - 2017 Board of Regents of the University of
* Wisconsin-Madison, Broad Institute of MIT and Harvard, Max Planck
* Institute of Molecular Cell Biology and Genetics, University of
* Konstanz, and KNIME GmbH.
* %%
* 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.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS 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 COPYRIGHT HOLDERS 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.
* #L%
*/
package org.scijava.annotations.legacy;
import java.io.BufferedInputStream;
import java.io.EOFException;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
/**
* Reads legacy annotation indexes.
*
* For backwards-compatibility with SezPoz, this reader falls back to a custom
* deserializer designed to gracefully handle serialized classes even when the
* current class path library is incompatible with the one used to serialize the
* data.
*
*
* @author Johannes Schindelin
*/
public class LegacyReader {
private final static short STREAM_MAGIC = (short) 0xaced;
private final static short STREAM_VERSION = 5;
private final static byte TC_NULL = (byte) 0x70;
private final static byte TC_REFERENCE = (byte) 0x71;
private final static byte TC_CLASSDESC = (byte) 0x72;
private final static byte TC_OBJECT = (byte) 0x73;
private final static byte TC_STRING = (byte) 0x74;
private final static byte TC_BLOCKDATA = (byte) 0x77;
private final static byte TC_ENDBLOCKDATA = (byte) 0x78;
private final static byte SC_WRITE_METHOD = 0x01; // if SC_SERIALIZABLE
private final static byte SC_SERIALIZABLE = 0x02;
private final static int HANDLE_OFFSET = 0x7e0000;
private final InputStream in;
private final List references;
public LegacyReader(final InputStream in) throws IOException {
this.in = new BufferedInputStream(in);
short signature = (short) read16();
if (signature != STREAM_MAGIC) {
throw new IOException("Unrecognized signature: 0x" +
Integer.toHexString(signature));
}
int version = read16();
if (version != STREAM_VERSION) {
throw new IOException("Unsupported version: " + version);
}
references = new ArrayList<>();
}
public void close() throws IOException {
in.close();
}
public Object readObject() throws IOException {
int c = read8();
if (c == TC_NULL) {
return null;
}
if (c == TC_STRING) {
int length = read16();
byte[] bytes = new byte[length];
readFully(bytes);
String s = new String(bytes, "UTF-8");
references.add(s);
return s;
}
if (c == TC_REFERENCE) {
int handle = read32() - HANDLE_OFFSET;
return references.get(handle);
}
if (c != TC_OBJECT) {
throw new IOException("Unexpected token: 0x" + Integer.toHexString(c));
}
return readClassDesc().readWithoutClassDesc();
}
private ClassDesc readClassDesc() throws IOException {
int c = read8();
if (c == TC_REFERENCE) {
int handle = read32() - HANDLE_OFFSET;
return (ClassDesc) references.get(handle);
}
else if (c == TC_CLASSDESC) {
return newClassDesc();
}
else {
throw new UnsupportedOperationException("Unexpected token: 0x" +
Integer.toHexString(c));
}
}
private void expectToken(int token) throws IOException {
int c = read8();
if (c != token) {
throw new UnsupportedOperationException("Unexpected token: 0x" +
Integer.toHexString(c));
}
}
private int read8() throws IOException {
return in.read() & 0xff;
}
private int read16() throws IOException {
return (read8() << 8) | read8();
}
private int read32() throws IOException {
return (read16() << 16) | read16();
}
private long read64() throws IOException {
return ((read32() & 0xffffffffl) << 32) | read32();
}
private String readString() throws IOException {
int length = read16();
byte[] array = new byte[length];
readFully(array);
return new String(array);
}
private void readFully(byte[] b) throws IOException {
readFully(b, 0, b.length);
}
private void readFully(byte[] b, int offset, int length) throws IOException {
while (length > 0) {
int count = in.read(b, offset, length);
if (count < 0) {
throw new EOFException("Reached EOF " + length + " bytes too early");
}
offset += count;
length -= count;
}
}
private ClassDesc newClassDesc() throws IOException {
String className = readString();
long serialVersionUID = read64();
String rawName = "L" + className.replace('.', '/') + ";";
ClassDesc result = classDescs.get(rawName);
if (result == null) {
throw new IOException("Could not find class for " + className +
", serial " + serialVersionUID);
}
references.add(result);
int flags = read8();
if ((flags & ~(SC_SERIALIZABLE | SC_WRITE_METHOD)) != 0) {
throw new UnsupportedOperationException("Cannot handle flags: 0x" +
Integer.toHexString(flags));
}
int fieldCount = read16();
if (fieldCount != result.fields.size()) {
throw new IOException("Incompatible field count: " + fieldCount + " vs " +
result.fields.size());
}
result.order = new String[fieldCount];
for (int i = 0; i < fieldCount; i++) {
int typeChar = read8();
String fieldName = readString();
if (!result.fields.containsKey(fieldName)) {
throw new IOException("Unexpected field " + fieldName);
}
result.order[i] = fieldName;
String type = "" + (char) typeChar;
if (typeChar == '[' || typeChar == 'L') {
type = (String) readObject();
}
if (!type.equals(result.fields.get(fieldName).className)) {
throw new IOException(fieldName + " has type " + type +
" instead of expected " + result.fields.get(fieldName).className);
}
}
expectToken(TC_ENDBLOCKDATA);
int c = read8();
@SuppressWarnings("unused")
Object superClassDesc = null;
if (c == TC_CLASSDESC) {
superClassDesc = newClassDesc();
}
else if (c == TC_REFERENCE) {
int handle = read32() - HANDLE_OFFSET;
superClassDesc = references.get(handle);
}
else if (c != TC_NULL) {
throw new UnsupportedOperationException("Unexpected token: 0x" +
Integer.toHexString(c));
}
return result;
}
private abstract class ClassDesc {
protected String[] order;
protected final String className;
protected Map fields;
protected ClassDesc(final String className) {
this.className = className;
classDescs.put(className, this);
}
protected abstract Object read() throws IOException;
protected Object readWithoutClassDesc() throws IOException {
return read();
}
}
private class NonPrimitiveClassDesc extends ClassDesc {
protected NonPrimitiveClassDesc(final String className,
final Object... fields)
{
super(className);
if ((fields.length % 2) != 0) {
throw new RuntimeException("That's odd: " + fields.length);
}
this.fields = new LinkedHashMap<>();
for (int i = 0; i < fields.length; i += 2) {
String name = (String) fields[i];
ClassDesc classDesc;
if (fields[i + 1] instanceof ClassDesc) {
classDesc = (ClassDesc) fields[i + 1];
}
else if (fields[i + 1] instanceof String) {
classDesc = classDescs.get(fields[i + 1]);
if (classDesc == null) {
throw new RuntimeException("Could not find class desc for " +
fields[i + 1]);
}
}
else {
throw new RuntimeException("Invalid class desc: " + fields[i + 1]);
}
this.fields.put(name, classDesc);
}
}
@Override
protected Object read() throws IOException {
int c = read8();
if (c == TC_NULL) {
return null;
}
else if (c != TC_OBJECT) {
throw new IOException("Unexpected token: " + Integer.toHexString(c));
}
final ClassDesc classDesc = readClassDesc();
if (classDesc != this) {
throw new IOException("ClassDesc mismatch: " + className +
" was expected, but got " + classDesc.className);
}
return readWithoutClassDesc();
}
@Override
protected final Object readWithoutClassDesc() throws IOException {
final Map map = new LinkedHashMap<>();
int index = references.size();
references.add(map);
for (final String fieldName : order) {
final ClassDesc classDesc = fields.get(fieldName);
map.put(fieldName, classDesc.read());
}
Object o = readExtra(map);
if (o != map) {
references.set(index, o);
}
return o;
}
/**
* @throws IOException If something goes wrong reading the map.
*/
protected Object readExtra(Map o) throws IOException {
return o;
}
}
private class BoxedPrimitiveClassDesc extends NonPrimitiveClassDesc {
private final Class clazz;
public BoxedPrimitiveClassDesc(final Class clazz, final String simpleName)
{
super(toSimpleName(clazz), "value", simpleName);
this.clazz =
clazz == Double.class || clazz == Float.class ? Double.class
: clazz == Boolean.class ? Boolean.class : Long.class;
}
@Override
public Object readExtra(final Map map) throws IOException {
return clazz.cast(map.get("value"));
}
}
private class InterfaceClassDesc extends NonPrimitiveClassDesc {
protected InterfaceClassDesc(final Class clazz) {
super(toSimpleName(clazz));
}
@Override
public Object read() throws IOException {
return readObject();
}
}
public static String toSimpleName(Class clazz) {
return "L" + clazz.getName().replace('.', '/') + ";";
}
private final Map classDescs =
new HashMap<>();
{
new ClassDesc("B") {
@Override
public Object read() throws IOException {
return (long) (byte) read8();
}
};
new ClassDesc("C") {
@Override
public Object read() throws IOException {
return "" + (char) read16();
}
};
new ClassDesc("D") {
@Override
public Object read() throws IOException {
return Double.longBitsToDouble(read64());
}
};
new ClassDesc("F") {
@Override
public Object read() throws IOException {
return (double) Float.intBitsToFloat(read32());
}
};
new ClassDesc("I") {
@Override
public Object read() throws IOException {
return (long) read32();
}
};
new ClassDesc("J") {
@Override
public Object read() throws IOException {
return read64();
}
};
new ClassDesc("S") {
@Override
public Object read() throws IOException {
return (long) (short) read16();
}
};
new ClassDesc("Z") {
@Override
public Object read() throws IOException {
return read8() != 0;
}
};
new ClassDesc("Ljava/lang/String;") {
@Override
public Object read() throws IOException {
return readObject();
}
};
new BoxedPrimitiveClassDesc(Boolean.class, "Z");
new BoxedPrimitiveClassDesc(Byte.class, "B");
new BoxedPrimitiveClassDesc(Short.class, "S");
new BoxedPrimitiveClassDesc(Integer.class, "I");
new BoxedPrimitiveClassDesc(Long.class, "J");
new BoxedPrimitiveClassDesc(Float.class, "F");
new BoxedPrimitiveClassDesc(Double.class, "D");
new InterfaceClassDesc(Number.class);
new InterfaceClassDesc(Comparator.class);
new NonPrimitiveClassDesc(toSimpleName(Character.class), "value", "C") {
@Override
public Object readExtra(final Map map) {
return map.get("value");
}
};
new NonPrimitiveClassDesc(toSimpleName(TreeMap.class), "comparator",
"Ljava/util/Comparator;")
{
// implements serialVersionUID = 919286545866124006L
@Override
public Map readExtra(final Map map)
throws IOException
{
if (map.size() != 1 || !map.containsKey("comparator")) {
throw new IOException("Unexpected comparator");
}
map.clear(); // might just as well re-use it
expectToken(TC_BLOCKDATA);
expectToken(4);
int size = read32();
for (int i = 0; i < size; i++) {
final String key = (String) readObject();
final Object value = readObject();
map.put(key, value);
}
expectToken(TC_ENDBLOCKDATA);
return map;
}
};
new NonPrimitiveClassDesc(toSimpleName(ArrayList.class), "size", "I") {
// implements serialVersionUID 8683452581122892189L
@Override
public Object readExtra(final Map map) throws IOException
{
int size = (int) (long) (Long) map.get("size");
map.clear(); // might just as well re-use it
expectToken(TC_BLOCKDATA);
expectToken(4);
int capacity = read32();
final List list = new ArrayList<>(capacity);
for (int i = 0; i < size; i++) {
list.add(readObject());
}
expectToken(TC_ENDBLOCKDATA);
return list;
}
};
new NonPrimitiveClassDesc("Lnet/java/sezpoz/impl/SerAnnotatedElement;",
"isMethod", "Z", "className", "Ljava/lang/String;", "memberName",
"Ljava/lang/String;", "values", "Ljava/util/TreeMap;")
{
@Override
public Object readExtra(final Map map) throws IOException
{
map.put("class", map.get("className"));
return map;
}
};
new NonPrimitiveClassDesc("Lnet/java/sezpoz/impl/SerAnnConst;", "name",
"Ljava/lang/String;", "values", "Ljava/util/TreeMap;")
{
@Override
public Object readExtra(final Map map) throws IOException
{
return map.get("values");
}
};
new NonPrimitiveClassDesc("Lnet/java/sezpoz/impl/SerEnumConst;",
"enumName", "Ljava/lang/String;", "constName", "Ljava/lang/String;")
{
@Override
public Object readExtra(final Map map) throws IOException
{
map.put("enum", map.get("enumName"));
map.put("value", map.get("constName"));
return map;
}
};
new NonPrimitiveClassDesc("Lnet/java/sezpoz/impl/SerTypeConst;", "name",
"Ljava/lang/String;")
{
@Override
public Object readExtra(final Map map) throws IOException
{
return map.get("name");
}
};
}
}
