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org.scijava.annotations.legacy.LegacyReader Maven / Gradle / Ivy
SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by downstream projects in the SciJava ecosystem, such as ImageJ and SCIFIO.
/*
* #%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");
}
};
}
}
