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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.
/*
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* SciJava Common shared library for SciJava software.
* %%
* Copyright (C) 2009 - 2015 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.
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* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
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* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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package org.scijava.module;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
import org.scijava.MenuPath;
import org.scijava.Priority;
import org.scijava.convert.ConvertService;
import org.scijava.event.EventService;
import org.scijava.input.Accelerator;
import org.scijava.log.LogService;
import org.scijava.module.event.ModulesAddedEvent;
import org.scijava.module.event.ModulesRemovedEvent;
import org.scijava.module.process.ModulePostprocessor;
import org.scijava.module.process.ModulePreprocessor;
import org.scijava.module.process.PostprocessorPlugin;
import org.scijava.module.process.PreprocessorPlugin;
import org.scijava.object.ObjectService;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.plugin.PluginService;
import org.scijava.prefs.PrefService;
import org.scijava.service.AbstractService;
import org.scijava.service.Service;
import org.scijava.thread.ThreadService;
import org.scijava.util.ClassUtils;
/**
* Default service for keeping track of and executing available modules.
*
* @author Curtis Rueden
* @see Module
* @see ModuleInfo
*/
@Plugin(type = Service.class)
public class DefaultModuleService extends AbstractService implements
ModuleService
{
@Parameter
private LogService log;
@Parameter
private EventService eventService;
@Parameter
private PluginService pluginService;
@Parameter
private ObjectService objectService;
@Parameter
private ThreadService threadService;
@Parameter
private PrefService prefService;
@Parameter
private ConvertService convertService;
/** Index of registered modules. */
private ModuleIndex moduleIndex;
// -- ModuleService methods --
@Override
public ModuleIndex getIndex() {
return moduleIndex;
}
@Override
public void addModule(final ModuleInfo module) {
if (moduleIndex.add(module)) {
eventService.publish(new ModulesAddedEvent(module));
}
}
@Override
public void removeModule(final ModuleInfo module) {
if (moduleIndex.remove(module)) {
eventService.publish(new ModulesRemovedEvent(module));
}
}
@Override
public void addModules(final Collection modules) {
if (moduleIndex.addAll(modules)) {
eventService.publish(new ModulesAddedEvent(modules));
}
}
@Override
public void removeModules(final Collection modules) {
if (moduleIndex.removeAll(modules)) {
eventService.publish(new ModulesRemovedEvent(modules));
}
}
@Override
public List getModules() {
return moduleIndex.getAll();
}
@Override
public ModuleInfo getModuleForAccelerator(final Accelerator acc) {
for (final ModuleInfo info : getModules()) {
final MenuPath menuPath = info.getMenuPath();
if (menuPath == null || menuPath.isEmpty()) continue;
if (acc.equals(menuPath.getLeaf().getAccelerator())) return info;
}
return null;
}
@Override
public Module createModule(final ModuleInfo info) {
final Module existing = getRegisteredModuleInstance(info);
if (existing != null) return existing;
try {
final Module module = info.createModule();
getContext().inject(module);
Priority.inject(module, info.getPriority());
return module;
}
catch (final ModuleException exc) {
log.error("Cannot create module: " + info.getDelegateClassName(), exc);
}
return null;
}
@Override
public Future run(final ModuleInfo info, final boolean process,
final Object... inputs)
{
return run(info, pre(process), post(process), inputs);
}
@Override
public Future run(final ModuleInfo info, final boolean process,
final Map inputMap)
{
return run(info, pre(process), post(process), inputMap);
}
@Override
public Future run(final ModuleInfo info,
final List pre,
final List post, final Object... inputs)
{
return run(info, pre, post, createMap(inputs));
}
@Override
public Future run(final ModuleInfo info,
final List pre,
final List post,
final Map inputMap)
{
final Module module = createModule(info);
if (module == null) return null;
return run(module, pre, post, inputMap);
}
@Override
public Future run(final M module,
final boolean process, final Object... inputs)
{
return run(module, pre(process), post(process), inputs);
}
@Override
public Future run(final M module,
final boolean process, final Map inputMap)
{
return run(module, pre(process), post(process), inputMap);
}
@Override
public Future run(final M module,
final List pre,
final List post, final Object... inputs)
{
return run(module, pre, post, createMap(inputs));
}
@Override
public Future run(final M module,
final List pre,
final List post,
final Map inputMap)
{
assignInputs(module, inputMap);
final ModuleRunner runner =
new ModuleRunner(getContext(), module, pre, post);
@SuppressWarnings("unchecked")
final Callable callable = (Callable) runner;
final Future future = threadService.run(callable);
return future;
}
@Override
public M waitFor(final Future future) {
try {
return future.get();
}
catch (final InterruptedException e) {
log.error("Module execution interrupted", e);
}
catch (final ExecutionException e) {
log.error("Error during module execution", e);
}
return null;
}
@Override
public ModuleItem getSingleInput(final Module module,
final Class type)
{
return getSingleItem(module, type, module.getInfo().inputs());
}
@Override
public ModuleItem getSingleOutput(final Module module,
final Class type)
{
return getSingleItem(module, type, module.getInfo().outputs());
}
@Override
public void save(final ModuleItem item, final T value) {
if (!item.isPersisted()) return;
final String sValue = value == null ? "" : value.toString();
// do not persist if object cannot be converted back from a string
if (!convertService.supports(sValue, item.getType())) return;
final String persistKey = item.getPersistKey();
if (persistKey == null || persistKey.isEmpty()) {
final Class prefClass = delegateClass(item);
final String prefKey = item.getName();
prefService.put(prefClass, prefKey, sValue);
}
else prefService.put(persistKey, sValue);
}
@Override
public T load(final ModuleItem item) {
// if there is nothing to load from persistence return nothing
if (!item.isPersisted()) return null;
final String sValue;
final String persistKey = item.getPersistKey();
if (persistKey == null || persistKey.isEmpty()) {
final Class prefClass = delegateClass(item);
final String prefKey = item.getName();
sValue = prefService.get(prefClass, prefKey);
}
else sValue = prefService.get(persistKey);
// if persisted value has never been set before return null
if (sValue == null) return null;
return convertService.convert(sValue, item.getType());
}
@Override
public T getDefaultValue(final ModuleItem item) {
final T defaultValue = item.getDefaultValue();
if (defaultValue != null) return defaultValue;
final T min = item.getMinimumValue();
if (min != null) return min;
final T softMin = item.getSoftMinimum();
if (softMin != null) return softMin;
final T max = item.getMaximumValue();
if (max != null) return max;
final T softMax = item.getSoftMaximum();
if (softMax != null) return softMax;
if (Number.class.isAssignableFrom(item.getType())) {
final T zero = convertService.convert("0", item.getType());
if (zero != null) return zero;
}
// no known default value
return null;
}
// -- Service methods --
@Override
public void initialize() {
moduleIndex = new ModuleIndex();
}
// -- Helper methods --
/** Creates the preprocessor chain. */
private List pre(final boolean process) {
if (!process) return null;
return pluginService.createInstancesOfType(PreprocessorPlugin.class);
}
/** Creates the postprocessor chain. */
private List post(final boolean process) {
if (!process) return null;
return pluginService.createInstancesOfType(PostprocessorPlugin.class);
}
/**
* Checks the {@link ObjectService} for a single registered {@link Module}
* instance of the given {@link ModuleInfo}. In this way, if you want to
* repeatedly reuse the same module instance instead of creating a new one
* with each execution, you can register it with the {@link ObjectService} and
* it will be automatically returned by the {@link #createModule(ModuleInfo)}
* method (and hence automatically used whenever a {@link #run} method with
* {@link ModuleInfo} argument is called).
*/
private Module getRegisteredModuleInstance(final ModuleInfo info) {
final Class type = ClassUtils.loadClass(info.getDelegateClassName());
if (type == null || !Module.class.isAssignableFrom(type)) return null;
// the module metadata's delegate class extends Module, so there is hope
@SuppressWarnings("unchecked")
final Class moduleType = (Class) type;
// ask the object service for an instance of the delegate type
final List objects = objectService.getObjects(moduleType);
if (objects == null || objects.isEmpty()) {
// the object service has no such instances
return null;
}
if (objects.size() > 1) {
// there are multiple instances; it's not clear which one to use
log.warn("Ignoring multiple candidate module instances for class: " +
type.getName());
return null;
}
// found exactly one instance; return it!
return objects.get(0);
}
/** Converts the given list of name/value pairs into an input map. */
private Map createMap(final Object[] values) {
if (values == null || values.length == 0) return null;
final HashMap inputMap = new HashMap();
if (values.length % 2 != 0) {
log.error("Ignoring extraneous argument: " + values[values.length - 1]);
}
// loop over list of key/value pairs
final int numPairs = values.length / 2;
for (int i = 0; i < numPairs; i++) {
final Object key = values[2 * i];
final Object value = values[2 * i + 1];
if (!(key instanceof String)) {
log.error("Invalid input name: " + key);
continue;
}
final String name = (String) key;
inputMap.put(name, value);
}
return inputMap;
}
/** Sets the given module's input values to those in the given map. */
private void assignInputs(final Module module,
final Map inputMap)
{
if (inputMap == null) return; // no inputs to assign
for (final String name : inputMap.keySet()) {
final ModuleItem input = module.getInfo().getInput(name);
final Object value = inputMap.get(name);
final Object converted;
if (input == null) {
// inputs whose name starts with a dot are implicitly known by convention
if (!name.startsWith(".")) {
log.warn("Unmatched input: " + name);
}
converted = value;
}
else {
final Class type = input.getType();
converted = convertService.convert(value, type);
if (value != null && converted == null) {
log.error("For input " + name + ": incompatible object " +
value.getClass().getName() + " for type " + type.getName());
continue;
}
}
module.setInput(name, converted);
module.setResolved(name, true);
}
}
private ModuleItem getSingleItem(final Module module,
final Class type, final Iterable> items)
{
ModuleItem result = null;
for (final ModuleItem item : items) {
final String name = item.getName();
final boolean resolved = module.isResolved(name);
if (resolved) continue; // skip resolved inputs
if (!item.isAutoFill()) continue; // skip unfillable inputs
if (!type.isAssignableFrom(item.getType())) continue;
if (result != null) return null; // multiple matching items
@SuppressWarnings("unchecked")
final ModuleItem typedItem = (ModuleItem) item;
result = typedItem;
}
return result;
}
private Class delegateClass(final ModuleItem item) {
try {
return item.getInfo().loadDelegateClass();
}
catch (final ClassNotFoundException exc) {
throw new IllegalStateException(exc);
}
}
}