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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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/*
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 * 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.
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 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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package org.scijava.script;

import java.io.File;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.scijava.AbstractContextual;
import org.scijava.MenuEntry;
import org.scijava.MenuPath;
import org.scijava.log.LogService;
import org.scijava.plugin.Parameter;

/**
 * Discovers scripts.
 * 
 * To accomplish this, we crawl the directories specified by
 * {@link ScriptService#getScriptDirectories()}. By default, those directories
 * include the {@code scripts} and {@code plugins/Scripts} folders off the
 * SciJava application's base directory.
 * 
 * 
 * @author Johannes Schindelin
 * @author Curtis Rueden
 */
public class ScriptFinder extends AbstractContextual {

	private static final String SCRIPT_ICON = "/icons/script_code.png";

	private final ScriptService scriptService;

	@Parameter
	private LogService log;

	public ScriptFinder(final ScriptService scriptService) {
		this.scriptService = scriptService;
		setContext(scriptService.getContext());
	}

	// -- ScriptFinder methods --

	/**
	 * Discovers the scripts.
	 * 
	 * @param scripts The collection to which the discovered scripts are added.
	 */
	public void findScripts(final List scripts) {
		final List directories = scriptService.getScriptDirectories();

		int scriptCount = 0;

		final HashSet scriptFiles = new HashSet();
		for (final File directory : directories) {
			if (!directory.exists()) {
				log.debug("Ignoring non-existent scripts directory: " +
					directory.getAbsolutePath());
				continue;
			}
			final MenuPath prefix = scriptService.getMenuPrefix(directory);
			final MenuPath menuPath = prefix == null ? new MenuPath() : prefix;
			scriptCount +=
				discoverScripts(scripts, scriptFiles, directory, menuPath);
		}

		log.debug("Found " + scriptCount + " scripts");
	}

	// -- Helper methods --

	/**
	 * Looks through a directory, discovering and adding scripts.
	 * 
	 * @param scripts The collection to which the discovered scripts are added.
	 * @param directory The directory in which to look for scripts recursively.
	 * @param menuPath The menu path, which must not be {@code null}.
	 */
	private int discoverScripts(final List scripts,
		final Set scriptFiles, final File directory, final MenuPath menuPath)
	{
		final File[] fileList = directory.listFiles();
		if (fileList == null) return 0; // directory does not exist
		Arrays.sort(fileList);

		int scriptCount = 0;
		final boolean isTopLevel = menuPath.size() == 0;

		for (final File file : fileList) {
			if (scriptFiles.contains(file)) continue; // script already added

			final String name = file.getName().replace('_', ' ');
			if (file.isDirectory()) {
				// recurse into subdirectory
				discoverScripts(scripts, scriptFiles, file, subMenuPath(menuPath, name));
			}
			else if (isTopLevel) {
				// ignore scripts in toplevel script directories
				continue;
			}
			else if (scriptService.canHandleFile(file)) {
				// found a script!
				final int dot = name.lastIndexOf('.');
				final String noExt = dot <= 0 ? name : name.substring(0, dot);
				scripts.add(createEntry(file, subMenuPath(menuPath, noExt)));
				scriptFiles.add(file);
				scriptCount++;
			}
		}

		return scriptCount;
	}

	private MenuPath
		subMenuPath(final MenuPath menuPath, final String subMenuName)
	{
		final MenuPath result = new MenuPath(menuPath);
		result.add(new MenuEntry(subMenuName));
		return result;
	}

	private ScriptInfo
		createEntry(final File scriptFile, final MenuPath menuPath)
	{
		final ScriptInfo info = new ScriptInfo(getContext(), scriptFile);
		info.setMenuPath(menuPath);

		// flag script with special icon
		menuPath.getLeaf().setIconPath(SCRIPT_ICON);

		return info;
	}

}