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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 - 2016 Board of Regents of the University of
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
* Institute of Molecular Cell Biology and Genetics.
* %%
* 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
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*/
package org.scijava.annotations;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PrintStream;
import java.lang.annotation.Annotation;
import java.lang.reflect.Array;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TreeMap;
import java.util.concurrent.ConcurrentSkipListMap;
import javax.lang.model.element.AnnotationValue;
/**
* Writes annotations as JSON-formatted files.
*
* The file names are the names of the annotations, and the serialized data
* describe the class which was annotated together with the specific annotation
* fields.
*
*
* @author Johannes Schindelin
*/
public abstract class AbstractIndexWriter {
private final Map> map =
new ConcurrentSkipListMap<>();
protected synchronized boolean foundAnnotations() {
return !map.isEmpty();
}
protected synchronized void add(final Map annotationValues,
final String annotationName, final String className)
{
Map list = map.get(annotationName);
if (list == null) {
list = new LinkedHashMap<>();
map.put(annotationName, list);
}
final Map o = new TreeMap<>();
o.put("class", className);
o.put("values", annotationValues);
list.put(className, o);
}
public interface StreamFactory {
InputStream openInput(String annotationName) throws IOException;
OutputStream openOutput(String annotationName) throws IOException;
boolean isClassObsolete(String className);
}
protected synchronized void write(final StreamFactory factory)
throws IOException
{
for (Entry> entry : map.entrySet()) {
final String annotationName = entry.getKey();
merge(annotationName, factory);
final PrintStream out =
new PrintStream(factory.openOutput(annotationName));
for (Object o : entry.getValue().values()) {
writeObject(out, adapt(o));
}
out.close();
}
map.clear();
}
/**
* Merges an existing annotation index into the currently-generated one.
*
* This method is used to read previously-indexed annotations and reconcile
* them with the newly-generated ones just.
*
*
* @param annotationName the name of the annotation for which the index
* contains the annotated classes
* @param factory the factory to generate input and output streams given an
* annotation name
* @throws IOException
*/
protected synchronized void merge(final String annotationName,
final StreamFactory factory) throws IOException
{
final InputStream in = factory.openInput(annotationName);
if (in == null) {
return;
}
Map m = map.get(annotationName);
if (m == null) {
m = new LinkedHashMap<>();
map.put(annotationName, m);
}
/*
* To determine whether the index needs to be written out,
* we need to keep track of changed entries.
*/
int changedCount = m.size();
boolean hasObsoletes = false;
final IndexReader reader =
new IndexReader(in, annotationName + " from " + in);
try {
for (;;) {
@SuppressWarnings("unchecked")
final Map entry = (Map) reader.next();
if (entry == null) {
break;
}
final String className = (String) entry.get("class");
if (factory.isClassObsolete(className)) {
hasObsoletes = true;
}
else if (m.containsKey(className)) {
if (!hasObsoletes && entry.equals(m.get(className))) {
changedCount--;
}
}
else {
m.put(className, entry);
}
}
}
finally {
reader.close();
}
// if this annotation index is unchanged, no need to write it out again
if (changedCount == 0 && !hasObsoletes) {
map.remove(annotationName);
}
}
protected Object adapt(final Object o) {
if (o instanceof Annotation) {
return adapt((Annotation) o);
}
else if (o instanceof AnnotationValue) {
return adapt(((AnnotationValue) o).getValue());
}
else if (o instanceof Enum) {
return adapt((Enum) o);
}
return o;
}
protected Map adapt(A annotation) {
Map result = new TreeMap<>();
for (Method method : annotation.annotationType().getMethods())
try {
if (method.getDeclaringClass() == annotation.annotationType()) {
result.put(method.getName(), adapt(method.invoke(annotation)));
}
}
catch (IllegalArgumentException e) {
e.printStackTrace();
}
catch (IllegalAccessException e) {
e.printStackTrace();
}
catch (InvocationTargetException e) {
e.printStackTrace();
}
return result;
}
private static Map adapt(Enum e) {
Map result = new TreeMap<>();
result.put("enum", e.getClass().getName());
result.put("value", e.name());
return result;
}
private void writeObject(final PrintStream out, final Object o)
throws IOException
{
if (o == null) {
out.print("null");
}
else if (o instanceof Boolean) {
out.print((Boolean) o ? "true" : "false");
}
else if (o instanceof Byte) {
out.print((byte) (Byte) o);
}
else if (o instanceof Short) {
out.print((short) (Short) o);
}
else if (o instanceof Integer) {
out.print((int) (Integer) o);
}
else if (o instanceof Long) {
out.print((long) (Long) o);
}
else if (o instanceof Float) {
out.print((float) (Float) o);
}
else if (o instanceof Double) {
out.print((double) (Double) o);
}
else if (o instanceof Character) {
writeString(out, "" + o);
}
else if (o instanceof String) {
writeString(out, (String) o);
}
else if (o instanceof Class) {
writeString(out, ((Class) o).getName());
}
else if (o instanceof List) {
writeArray(out, (List) o);
}
else if (o.getClass().isArray()) {
writeArray(out, o);
}
else if (o instanceof Map) {
writeMap(out, (Map) o);
}
else {
throw new IOException("Cannot handle object of type " + o.getClass());
}
}
protected void writeMap(final PrintStream out, final Object... pairs)
throws IOException
{
if ((pairs.length % 2) != 0) {
throw new IOException("Key without value!");
}
out.write('{');
for (int i = 0; i < pairs.length; i += 2) {
if (i > 0) {
out.write(',');
}
writeString(out, (String) pairs[i]);
out.write(':');
writeObject(out, pairs[i + 1]);
}
out.write('}');
}
private void writeMap(final PrintStream out, final Map m)
throws IOException
{
out.write('{');
boolean first = true;
for (Map.Entry entry : m.entrySet()) {
if (first) {
first = false;
}
else {
out.write(',');
}
writeString(out, entry.getKey().toString());
out.write(':');
writeObject(out, entry.getValue());
}
out.write('}');
}
private void writeArray(final PrintStream out, final List list)
throws IOException
{
out.write('[');
boolean first = true;
for (Object o : list) {
if (first) {
first = false;
}
else {
out.write(',');
}
o = adapt(o);
writeObject(out, o);
}
out.write(']');
}
private void writeArray(final PrintStream out, final Object o)
throws IOException
{
out.write('[');
int length = Array.getLength(o);
for (int i = 0; i < length; i++) {
if (i > 0) {
out.write(',');
}
writeObject(out, adapt(Array.get(o, i)));
}
out.write(']');
}
private void writeString(final PrintStream out, final String string) {
out.write('"');
for (char c : string.toCharArray()) {
if (c == '"' || c == '\\') {
out.write('\\');
out.write(c);
}
else if (c >= ' ' && c <= 0x7f) {
out.write(c);
}
else {
String hex = Integer.toHexString(c);
out.print("\\u");
if (hex.length() < 4) {
out.print("0000".substring(hex.length()));
}
out.print(hex);
}
}
out.write('"');
}
}