net.imagej.maven.AbstractCopyJarsMojo Maven / Gradle / Ivy

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A plugin helping with installing ImageJ 1.x plugins and dependencies. In ImageJ 1.x, .jar files containing an underscore are automatically scanned for classes whose names contain underscores. Every such class is considered to be a plugin. That is not true, however, for jai_codec.jar's classes. Therefore, Fiji introduced the split between plugins/ and jars/, where third-party libraries are expected to live in jars/. ImageJ2 uses the same structure since it is backwards compatible.
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package net.imagej.maven;

/*
 * #%L
 * ImageJ software for multidimensional image processing and analysis.
 * %%
 * Copyright (C) 2012 - 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.
 * %%
 * 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%
 */

import java.io.File;
import java.io.FilenameFilter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.jar.JarEntry;
import java.util.jar.JarFile;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.maven.artifact.Artifact;
import org.apache.maven.artifact.repository.ArtifactRepository;
import org.apache.maven.artifact.resolver.ArtifactNotFoundException;
import org.apache.maven.artifact.resolver.ArtifactResolutionException;
import org.apache.maven.artifact.resolver.ArtifactResolver;
import org.apache.maven.execution.MavenSession;
import org.apache.maven.model.Dependency;
import org.apache.maven.plugin.AbstractMojo;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.project.MavenProject;
import org.codehaus.plexus.interpolation.EnvarBasedValueSource;
import org.codehaus.plexus.interpolation.ObjectBasedValueSource;
import org.codehaus.plexus.interpolation.PrefixAwareRecursionInterceptor;
import org.codehaus.plexus.interpolation.PrefixedValueSourceWrapper;
import org.codehaus.plexus.interpolation.PropertiesBasedValueSource;
import org.codehaus.plexus.interpolation.RecursionInterceptor;
import org.codehaus.plexus.interpolation.RegexBasedInterpolator;
import org.codehaus.plexus.util.FileUtils;

/**
 * Base class for mojos to copy .jar artifacts and their dependencies into an
 * ImageJ.app/ directory structure.
 * 
 * @author Johannes Schindelin
 */
public abstract class AbstractCopyJarsMojo extends AbstractMojo {

	protected boolean hasIJ1Dependency(final MavenProject project) {
		@SuppressWarnings("unchecked")
		final List dependencies = project.getDependencies();
		for (final Dependency dependency : dependencies) {
			final String artifactId = dependency.getArtifactId();
			if ("ij".equals(artifactId) || "imagej".equals(artifactId)) return true;
		}
		return false;
	}

	protected String interpolate(final String original,
		final MavenProject project, final MavenSession session)
		throws MojoExecutionException
	{
		if (original == null || original.indexOf("${") < 0) return original;
		try {
			RegexBasedInterpolator interpolator = new RegexBasedInterpolator();

			interpolator.addValueSource(new EnvarBasedValueSource());
			interpolator.addValueSource(new PropertiesBasedValueSource(System
				.getProperties()));

			List synonymPrefixes = new ArrayList();
			synonymPrefixes.add("project.");
			synonymPrefixes.add("pom.");

			if (project != null) {
				PrefixedValueSourceWrapper modelWrapper =
					new PrefixedValueSourceWrapper(new ObjectBasedValueSource(project
						.getModel()), synonymPrefixes, true);
				interpolator.addValueSource(modelWrapper);

				PrefixedValueSourceWrapper pomPropertyWrapper =
					new PrefixedValueSourceWrapper(new PropertiesBasedValueSource(project
						.getModel().getProperties()), synonymPrefixes, true);
				interpolator.addValueSource(pomPropertyWrapper);
			}

			if (session != null) {
				interpolator.addValueSource(new PropertiesBasedValueSource(session
					.getExecutionProperties()));
			}

			RecursionInterceptor recursionInterceptor =
				new PrefixAwareRecursionInterceptor(synonymPrefixes, true);
			return interpolator.interpolate(original, recursionInterceptor);
		}
		catch (Exception e) {
			throw new MojoExecutionException("Could not interpolate '" + original +
				"'", e);
		}
	}

	protected void installArtifact(final Artifact artifact,
		final File imagejDirectory, final boolean force,
		final boolean deleteOtherVersions, final ArtifactResolver resolver,
		List remoteRepositories,
		ArtifactRepository localRepository) throws ArtifactResolutionException,
		ArtifactNotFoundException, IOException
	{
		resolver.resolve(artifact, remoteRepositories, localRepository);

		if (!"jar".equals(artifact.getType())) return;

		final File source = artifact.getFile();
		final File targetDirectory;

		if (isIJ1Plugin(source)) {
			targetDirectory = new File(imagejDirectory, "plugins");
		}
		else if ("ome".equals(artifact.getGroupId()) ||
			("loci".equals(artifact.getGroupId()) && (source.getName().startsWith(
				"scifio-4.4.") || source.getName().startsWith("jai_imageio-4.4."))))
		{
			targetDirectory = new File(imagejDirectory, "jars/bio-formats");
		}
		else {
			targetDirectory = new File(imagejDirectory, "jars");
		}
		final String fileName =
			"Fiji_Updater".equals(artifact.getArtifactId()) ? artifact
				.getArtifactId() +
				".jar" : source.getName();
		final File target = new File(targetDirectory, fileName);

		if (!force && target.exists() &&
			target.lastModified() > source.lastModified())
		{
			getLog().info("Dependency " + fileName + " is already there; skipping");
		}
		else {
			getLog().info("Copying " + fileName + " to " + targetDirectory);
			FileUtils.copyFile(source, target);
		}

		final Collection otherVersions = getEncroachingVersions(target);
		if (otherVersions != null && !otherVersions.isEmpty()) {
			for (final File file : otherVersions) {
				if (!deleteOtherVersions) {
					getLog().warn(
						"Possibly incompatible version exists: " + file.getName());
				}
				else if (file.delete()) {
					getLog().info("Deleted overridden " + file.getName());
				}
				else {
					getLog().warn("Could not delete overridden " + file.getName());
				}
			}
		}

	}

	private static boolean isIJ1Plugin(final File file) {
		final String name = file.getName();
		if (name.indexOf('_') < 0 || !file.exists()) return false;
		if (file.isDirectory()) return new File(file,
			"src/main/resources/plugins.config").exists();
		if (name.endsWith(".jar")) try {
			final JarFile jar = new JarFile(file);
			for (JarEntry entry : Collections.list(jar.entries()))
				if (entry.getName().equals("plugins.config")) {
					jar.close();
					return true;
				}
			jar.close();
		}
		catch (Throwable t) {
			// obviously not a plugin...
		}
		return false;
	}

	private final static Pattern versionPattern = Pattern.compile("(.+?)"
		+ "(-\\d+(\\.\\d+|\\d{7})+[a-z]?\\d?(-[A-Za-z0-9.]+?|\\.GA)*?)?"
		+ "((-(swing|swt|sources|javadoc|native|linux-x86|linux-x86_64|macosx-x86_64|windows-x86|windows-x86_64|android-arm|android-x86))?(\\.jar(-[a-z]*)?))");
	private final static int PREFIX_INDEX = 1;
	private final static int SUFFIX_INDEX = 5;

	private static Collection getEncroachingVersions(final File file) {
		// TODO reuse FileUtils.stripFilenameVersion logic
		final Matcher matcher = versionPattern.matcher(file.getName());
		if (!matcher.matches()) return null;

		final String prefix = matcher.group(PREFIX_INDEX);
		final String suffix = matcher.group(SUFFIX_INDEX);
		final File parent = file.getParentFile();
		final File directory =
			parent != null ? parent : file.getAbsoluteFile().getParentFile();
		if (directory == null) return null;
		final File[] candidates = directory.listFiles(new FilenameFilter() {

			public boolean accept(File dir, String name) {
				if (!name.startsWith(prefix)) return false;
				final Matcher matcher = versionPattern.matcher(name);
				return matcher.matches() &&
					prefix.equals(matcher.group(PREFIX_INDEX)) &&
					suffix.equals(matcher.group(SUFFIX_INDEX));
			}
		});
		if (candidates == null || candidates.length == (file.exists() ? 1 : 0)) return null;

		final Collection result = new ArrayList();
		for (final File candidate : candidates) {
			if (!candidate.equals(file)) result.add(candidate);
		}
		return result;
	}
}