package org.argeo.build;

import static java.lang.System.Logger.Level.DEBUG;
import static org.argeo.build.Repackage.ManifestConstants.BUNDLE_SYMBOLICNAME;
import static org.argeo.build.Repackage.ManifestConstants.BUNDLE_VERSION;
import static org.argeo.build.Repackage.ManifestConstants.EXPORT_PACKAGE;
import static org.argeo.build.Repackage.ManifestConstants.SLC_ORIGIN_M2;
import static org.argeo.build.Repackage.ManifestConstants.SLC_ORIGIN_M2_REPO;

import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.lang.System.Logger;
import java.lang.System.Logger.Level;
import java.net.MalformedURLException;
import java.net.URL;
import java.nio.file.DirectoryStream;
import java.nio.file.FileSystem;
import java.nio.file.FileSystems;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.PathMatcher;
import java.nio.file.Paths;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.StandardOpenOption;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Properties;
import java.util.TreeMap;
import java.util.jar.Attributes;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
import java.util.jar.Manifest;
import java.util.zip.Deflater;

import aQute.bnd.osgi.Analyzer;
import aQute.bnd.osgi.Jar;

/** The central class for A2 packaging. */
public class Repackage {
	private final static Logger logger = System.getLogger(Repackage.class.getName());

	/** Main entry point. */
	public static void main(String[] args) {
		if (args.length < 2) {
			System.err.println("Usage: <path to a2 output dir> <category1> <category2> ...");
			System.exit(1);
		}
		Path a2Base = Paths.get(args[0]).toAbsolutePath().normalize();
		Path descriptorsBase = Paths.get(".").toAbsolutePath().normalize();
		Repackage factory = new Repackage(a2Base, descriptorsBase, true);

		for (int i = 1; i < args.length; i++) {
			Path p = Paths.get(args[i]);
			factory.processCategory(p);
		}
	}

	private final static String COMMON_BND = "common.bnd";
	private final static String MERGE_BND = "merge.bnd";

	private Path originBase;
	private Path a2Base;
	private Path a2LibBase;
	private Path descriptorsBase;

	private Properties uris = new Properties();

	private boolean includeSources = true;

	/** key is URI prefix, value list of base URLs */
	private Map<String, List<String>> mirrors = new HashMap<String, List<String>>();

	public Repackage(Path a2Base, Path descriptorsBase, boolean includeSources) {
		Objects.requireNonNull(a2Base);
		Objects.requireNonNull(descriptorsBase);
		this.originBase = Paths.get(System.getProperty("user.home"), ".cache", "argeo/build/origin");
		// TODO define and use a build base
		this.a2Base = a2Base;
		this.a2LibBase = a2Base.resolve("lib");
		this.descriptorsBase = descriptorsBase;
		if (!Files.exists(this.descriptorsBase))
			throw new IllegalArgumentException(this.descriptorsBase + " does not exist");
		this.includeSources = includeSources;

		Path urisPath = this.descriptorsBase.resolve("uris.properties");
		if (Files.exists(urisPath)) {
			try (InputStream in = Files.newInputStream(urisPath)) {
				uris.load(in);
			} catch (IOException e) {
				throw new IllegalStateException("Cannot load " + urisPath, e);
			}
		}

		// TODO make it configurable
		List<String> eclipseMirrors = new ArrayList<>();
		eclipseMirrors.add("https://archive.eclipse.org/");
		eclipseMirrors.add("http://ftp-stud.hs-esslingen.de/Mirrors/eclipse/");
		eclipseMirrors.add("http://ftp.fau.de/eclipse/");

		mirrors.put("http://www.eclipse.org/downloads", eclipseMirrors);
	}

	/*
	 * MAVEN ORIGIN
	 */

	/** Process a whole category/group id. */
	public void processCategory(Path categoryRelativePath) {
		try {
			Path targetCategoryBase = descriptorsBase.resolve(categoryRelativePath);
			DirectoryStream<Path> bnds = Files.newDirectoryStream(targetCategoryBase,
					(p) -> p.getFileName().toString().endsWith(".bnd") && !p.getFileName().toString().equals(COMMON_BND)
							&& !p.getFileName().toString().equals(MERGE_BND));
			for (Path p : bnds) {
				processSingleM2ArtifactDistributionUnit(p);
			}

			DirectoryStream<Path> dus = Files.newDirectoryStream(targetCategoryBase, (p) -> Files.isDirectory(p));
			for (Path duDir : dus) {
				if (duDir.getFileName().toString().startsWith("eclipse-")) {
					processEclipseArchive(duDir);
				} else {
					processM2BasedDistributionUnit(duDir);
				}
			}
		} catch (IOException e) {
			throw new RuntimeException("Cannot process category " + categoryRelativePath, e);
		}
	}

	/** Process a standalone Maven artifact. */
	public void processSingleM2ArtifactDistributionUnit(Path bndFile) {
		try {
//			String category = bndFile.getParent().getFileName().toString();
			Path categoryRelativePath = descriptorsBase.relativize(bndFile.getParent());
			Path targetCategoryBase = a2Base.resolve(categoryRelativePath);

			Properties fileProps = new Properties();
			try (InputStream in = Files.newInputStream(bndFile)) {
				fileProps.load(in);
			}
			String repoStr = fileProps.containsKey(SLC_ORIGIN_M2_REPO.toString())
					? fileProps.getProperty(SLC_ORIGIN_M2_REPO.toString())
					: null;

			if (!fileProps.containsKey(BUNDLE_SYMBOLICNAME.toString())) {
				// use file name as symbolic name
				String symbolicName = bndFile.getFileName().toString();
				symbolicName = symbolicName.substring(0, symbolicName.length() - ".bnd".length());
				fileProps.put(BUNDLE_SYMBOLICNAME.toString(), symbolicName);
			}

			String m2Coordinates = fileProps.getProperty(SLC_ORIGIN_M2.toString());
			if (m2Coordinates == null)
				throw new IllegalArgumentException("No M2 coordinates available for " + bndFile);
			M2Artifact artifact = new M2Artifact(m2Coordinates);
			URL url = M2ConventionsUtils.mavenRepoUrl(repoStr, artifact);
			Path downloaded = download(url, originBase, artifact);

			Path targetBundleDir = processBndJar(downloaded, targetCategoryBase, fileProps, artifact);

			downloadAndProcessM2Sources(repoStr, artifact, targetBundleDir);

			createJar(targetBundleDir);
		} catch (Exception e) {
			throw new RuntimeException("Cannot process " + bndFile, e);
		}
	}

	/** Process multiple Maven artifacts. */
	public void processM2BasedDistributionUnit(Path duDir) {
		try {
			// String category = duDir.getParent().getFileName().toString();
			Path categoryRelativePath = descriptorsBase.relativize(duDir.getParent());
			Path targetCategoryBase = a2Base.resolve(categoryRelativePath);

			// merge
			Path mergeBnd = duDir.resolve(MERGE_BND);
			if (Files.exists(mergeBnd)) {
				mergeM2Artifacts(mergeBnd);
//				return;
			}

			Path commonBnd = duDir.resolve(COMMON_BND);
			if (!Files.exists(commonBnd)) {
				return;
			}
			Properties commonProps = new Properties();
			try (InputStream in = Files.newInputStream(commonBnd)) {
				commonProps.load(in);
			}

			String m2Version = commonProps.getProperty(SLC_ORIGIN_M2.toString());
			if (m2Version == null) {
				logger.log(Level.WARNING, "Ignoring " + duDir + " as it is not an M2-based distribution unit");
				return;// ignore, this is probably an Eclipse archive
			}
			if (!m2Version.startsWith(":")) {
				throw new IllegalStateException("Only the M2 version can be specified: " + m2Version);
			}
			m2Version = m2Version.substring(1);

			DirectoryStream<Path> ds = Files.newDirectoryStream(duDir,
					(p) -> p.getFileName().toString().endsWith(".bnd") && !p.getFileName().toString().equals(COMMON_BND)
							&& !p.getFileName().toString().equals(MERGE_BND));
			for (Path p : ds) {
				Properties fileProps = new Properties();
				try (InputStream in = Files.newInputStream(p)) {
					fileProps.load(in);
				}
				String m2Coordinates = fileProps.getProperty(SLC_ORIGIN_M2.toString());
				M2Artifact artifact = new M2Artifact(m2Coordinates);

				artifact.setVersion(m2Version);

				// prepare manifest entries
				Properties mergeProps = new Properties();
				mergeProps.putAll(commonProps);

				fileEntries: for (Object key : fileProps.keySet()) {
					if (ManifestConstants.SLC_ORIGIN_M2.toString().equals(key))
						continue fileEntries;
					String value = fileProps.getProperty(key.toString());
					Object previousValue = mergeProps.put(key.toString(), value);
					if (previousValue != null) {
						logger.log(Level.WARNING,
								commonBnd + ": " + key + " was " + previousValue + ", overridden with " + value);
					}
				}
				mergeProps.put(ManifestConstants.SLC_ORIGIN_M2.toString(), artifact.toM2Coordinates());
				if (!mergeProps.containsKey(BUNDLE_SYMBOLICNAME.toString())) {
					// use file name as symbolic name
					String symbolicName = p.getFileName().toString();
					symbolicName = symbolicName.substring(0, symbolicName.length() - ".bnd".length());
					mergeProps.put(BUNDLE_SYMBOLICNAME.toString(), symbolicName);
				}

				String repoStr = mergeProps.containsKey(SLC_ORIGIN_M2_REPO.toString())
						? mergeProps.getProperty(SLC_ORIGIN_M2_REPO.toString())
						: null;

				// download
				URL url = M2ConventionsUtils.mavenRepoUrl(repoStr, artifact);
				Path downloaded = download(url, originBase, artifact);

				Path targetBundleDir = processBndJar(downloaded, targetCategoryBase, mergeProps, artifact);
//				logger.log(Level.DEBUG, () -> "Processed " + downloaded);

				// sources
				downloadAndProcessM2Sources(repoStr, artifact, targetBundleDir);

				createJar(targetBundleDir);
			}
		} catch (IOException e) {
			throw new RuntimeException("Cannot process " + duDir, e);
		}

	}

	/** Merge multiple Maven artifacts. */
	protected void mergeM2Artifacts(Path mergeBnd) throws IOException {
		Path duDir = mergeBnd.getParent();
		String category = duDir.getParent().getFileName().toString();
		Path targetCategoryBase = a2Base.resolve(category);

		Properties mergeProps = new Properties();
		try (InputStream in = Files.newInputStream(mergeBnd)) {
			mergeProps.load(in);
		}

		// Version
		String m2Version = mergeProps.getProperty(SLC_ORIGIN_M2.toString());
		if (m2Version == null) {
			logger.log(Level.WARNING, "Ignoring " + duDir + " as it is not an M2-based distribution unit");
			return;// ignore, this is probably an Eclipse archive
		}
		if (!m2Version.startsWith(":")) {
			throw new IllegalStateException("Only the M2 version can be specified: " + m2Version);
		}
		m2Version = m2Version.substring(1);
		mergeProps.put(ManifestConstants.BUNDLE_VERSION.toString(), m2Version);

		String artifactsStr = mergeProps.getProperty(ManifestConstants.SLC_ORIGIN_M2_MERGE.toString());
		String repoStr = mergeProps.containsKey(SLC_ORIGIN_M2_REPO.toString())
				? mergeProps.getProperty(SLC_ORIGIN_M2_REPO.toString())
				: null;

		String bundleSymbolicName = mergeProps.getProperty(ManifestConstants.BUNDLE_SYMBOLICNAME.toString());
		if (bundleSymbolicName == null)
			throw new IllegalArgumentException("Bundle-SymbolicName must be set in " + mergeBnd);
		CategoryNameVersion nameVersion = new M2Artifact(category + ":" + bundleSymbolicName + ":" + m2Version);
		Path targetBundleDir = targetCategoryBase.resolve(bundleSymbolicName + "." + nameVersion.getBranch());

		String[] artifacts = artifactsStr.split(",");
		artifacts: for (String str : artifacts) {
			String m2Coordinates = str.trim();
			if ("".equals(m2Coordinates))
				continue artifacts;
			M2Artifact artifact = new M2Artifact(m2Coordinates.trim());
			if (artifact.getVersion() == null)
				artifact.setVersion(m2Version);
			URL url = M2ConventionsUtils.mavenRepoUrl(repoStr, artifact);
			Path downloaded = download(url, originBase, artifact);
			JarEntry entry;
			try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(downloaded), false)) {
				entries: while ((entry = jarIn.getNextJarEntry()) != null) {
					if (entry.isDirectory())
						continue entries;
					else if (entry.getName().endsWith(".RSA") || entry.getName().endsWith(".SF"))
						continue entries;
					else if (entry.getName().startsWith("META-INF/versions/"))
						continue entries;
					else if (entry.getName().startsWith("META-INF/maven/"))
						continue entries;
					else if (entry.getName().equals("module-info.class"))
						continue entries;
					else if (entry.getName().equals("META-INF/NOTICE"))
						continue entries;
					else if (entry.getName().equals("META-INF/NOTICE.txt"))
						continue entries;
					else if (entry.getName().equals("META-INF/LICENSE"))
						continue entries;
					else if (entry.getName().equals("META-INF/LICENSE.md"))
						continue entries;
					else if (entry.getName().equals("META-INF/LICENSE-notice.md"))
						continue entries;
					else if (entry.getName().equals("META-INF/DEPENDENCIES"))
						continue entries;
					if (entry.getName().startsWith(".cache/")) // Apache SSHD
						continue entries;
					Path target = targetBundleDir.resolve(entry.getName());
					Files.createDirectories(target.getParent());
					if (!Files.exists(target)) {
						Files.copy(jarIn, target);
					} else {
						if (entry.getName().startsWith("META-INF/services/")) {
							try (OutputStream out = Files.newOutputStream(target, StandardOpenOption.APPEND)) {
								out.write("\n".getBytes());
								jarIn.transferTo(out);
								if (logger.isLoggable(DEBUG))
									logger.log(DEBUG, artifact.getArtifactId() + " - Appended " + entry.getName());
							}
						} else if (entry.getName().startsWith("org/apache/batik/")) {
							logger.log(Level.WARNING, "Skip " + entry.getName());
							continue entries;
						} else {
							throw new IllegalStateException("File " + target + " from " + artifact + " already exists");
						}
					}
					logger.log(Level.TRACE, () -> "Copied " + target);
				}

			}
			downloadAndProcessM2Sources(repoStr, artifact, targetBundleDir);
		}

		// additional service files
		Path servicesDir = duDir.resolve("services");
		if (Files.exists(servicesDir)) {
			for (Path p : Files.newDirectoryStream(servicesDir)) {
				Path target = targetBundleDir.resolve("META-INF/services/").resolve(p.getFileName());
				try (InputStream in = Files.newInputStream(p);
						OutputStream out = Files.newOutputStream(target, StandardOpenOption.APPEND);) {
					out.write("\n".getBytes());
					in.transferTo(out);
					if (logger.isLoggable(DEBUG))
						logger.log(DEBUG, "Appended " + p);
				}
			}
		}

		Map<String, String> entries = new TreeMap<>();
		try (Analyzer bndAnalyzer = new Analyzer()) {
			bndAnalyzer.setProperties(mergeProps);
			Jar jar = new Jar(targetBundleDir.toFile());
			bndAnalyzer.setJar(jar);
			Manifest manifest = bndAnalyzer.calcManifest();

			keys: for (Object key : manifest.getMainAttributes().keySet()) {
				Object value = manifest.getMainAttributes().get(key);

				switch (key.toString()) {
				case "Tool":
				case "Bnd-LastModified":
				case "Created-By":
					continue keys;
				}
				if ("Require-Capability".equals(key.toString())
						&& value.toString().equals("osgi.ee;filter:=\"(&(osgi.ee=JavaSE)(version=1.1))\""))
					continue keys;// hack for very old classes
				entries.put(key.toString(), value.toString());
				// logger.log(DEBUG, () -> key + "=" + value);

			}
		} catch (Exception e) {
			throw new RuntimeException("Cannot process " + mergeBnd, e);
		}

		Manifest manifest = new Manifest();
		Path manifestPath = targetBundleDir.resolve("META-INF/MANIFEST.MF");
		Files.createDirectories(manifestPath.getParent());
		for (String key : entries.keySet()) {
			String value = entries.get(key);
			manifest.getMainAttributes().putValue(key, value);
		}

		try (OutputStream out = Files.newOutputStream(manifestPath)) {
			manifest.write(out);
		}
		createJar(targetBundleDir);
	}

	/** Generate MANIFEST using BND. */
	protected Path processBndJar(Path downloaded, Path targetCategoryBase, Properties fileProps, M2Artifact artifact) {

		try {
			Map<String, String> additionalEntries = new TreeMap<>();
			boolean doNotModify = Boolean.parseBoolean(fileProps
					.getOrDefault(ManifestConstants.SLC_ORIGIN_MANIFEST_NOT_MODIFIED.toString(), "false").toString());

			// we always force the symbolic name

			if (doNotModify) {
				fileEntries: for (Object key : fileProps.keySet()) {
					if (ManifestConstants.SLC_ORIGIN_M2.toString().equals(key))
						continue fileEntries;
					String value = fileProps.getProperty(key.toString());
					additionalEntries.put(key.toString(), value);
				}
			} else {
				if (artifact != null) {
					if (!fileProps.containsKey(BUNDLE_SYMBOLICNAME.toString())) {
						fileProps.put(BUNDLE_SYMBOLICNAME.toString(), artifact.getName());
					}
					if (!fileProps.containsKey(BUNDLE_VERSION.toString())) {
						fileProps.put(BUNDLE_VERSION.toString(), artifact.getVersion());
					}
				}

				if (!fileProps.containsKey(EXPORT_PACKAGE.toString())) {
					fileProps.put(EXPORT_PACKAGE.toString(),
							"*;version=\"" + fileProps.getProperty(BUNDLE_VERSION.toString()) + "\"");
				}

				try (Analyzer bndAnalyzer = new Analyzer()) {
					bndAnalyzer.setProperties(fileProps);
					Jar jar = new Jar(downloaded.toFile());
					bndAnalyzer.setJar(jar);
					Manifest manifest = bndAnalyzer.calcManifest();

					keys: for (Object key : manifest.getMainAttributes().keySet()) {
						Object value = manifest.getMainAttributes().get(key);

						switch (key.toString()) {
						case "Tool":
						case "Bnd-LastModified":
						case "Created-By":
							continue keys;
						}
						if ("Require-Capability".equals(key.toString())
								&& value.toString().equals("osgi.ee;filter:=\"(&(osgi.ee=JavaSE)(version=1.1))\""))
							continue keys;// hack for very old classes
						additionalEntries.put(key.toString(), value.toString());
						// logger.log(DEBUG, () -> key + "=" + value);

					}
				}
			}
			Path targetBundleDir = processBundleJar(downloaded, targetCategoryBase, additionalEntries);
			logger.log(Level.DEBUG, () -> "Processed " + downloaded);
			return targetBundleDir;
		} catch (Exception e) {
			throw new RuntimeException("Cannot BND process " + downloaded, e);
		}

	}

	/** Download and integrates sources for a single Maven artifact. */
	protected void downloadAndProcessM2Sources(String repoStr, M2Artifact artifact, Path targetBundleDir)
			throws IOException {
		if (!includeSources)
			return;
		M2Artifact sourcesArtifact = new M2Artifact(artifact.toM2Coordinates(), "sources");
		URL sourcesUrl = M2ConventionsUtils.mavenRepoUrl(repoStr, sourcesArtifact);
		Path sourcesDownloaded = download(sourcesUrl, originBase, artifact, true);
		processM2SourceJar(sourcesDownloaded, targetBundleDir);
		logger.log(Level.TRACE, () -> "Processed source " + sourcesDownloaded);

	}

	/** Integrate sources from a downloaded jar file. */
	protected void processM2SourceJar(Path file, Path targetBundleDir) throws IOException {
		try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(file), false)) {
			Path targetSourceDir = targetBundleDir.resolve("OSGI-OPT/src");

			// TODO make it less dangerous?
			if (Files.exists(targetSourceDir)) {
//				deleteDirectory(targetSourceDir);
			} else {
				Files.createDirectories(targetSourceDir);
			}

			// copy entries
			JarEntry entry;
			entries: while ((entry = jarIn.getNextJarEntry()) != null) {
				if (entry.isDirectory())
					continue entries;
				if (entry.getName().startsWith("META-INF"))// skip META-INF entries
					continue entries;
				if (entry.getName().startsWith("module-info.java"))// skip META-INF entries
					continue entries;
				if (entry.getName().startsWith("/")) // absolute paths
					continue entries;
				Path target = targetSourceDir.resolve(entry.getName());
				Files.createDirectories(target.getParent());
				if (!Files.exists(target)) {
					Files.copy(jarIn, target);
					logger.log(Level.TRACE, () -> "Copied source " + target);
				} else {
					logger.log(Level.WARNING, () -> target + " already exists, skipping...");
				}
			}
		}

	}

	/** Download a Maven artifact. */
	protected Path download(URL url, Path dir, M2Artifact artifact) throws IOException {
		return download(url, dir, artifact, false);
	}

	/** Download a Maven artifact. */
	protected Path download(URL url, Path dir, M2Artifact artifact, boolean sources) throws IOException {
		return download(url, dir, artifact.getGroupId() + '/' + artifact.getArtifactId() + "-" + artifact.getVersion()
				+ (sources ? "-sources" : "") + ".jar");
	}

	/*
	 * ECLIPSE ORIGIN
	 */

	/** Process an archive in Eclipse format. */
	public void processEclipseArchive(Path duDir) {
		try {
			Path categoryRelativePath = descriptorsBase.relativize(duDir.getParent());
			// String category = categoryRelativePath.getFileName().toString();
			Path targetCategoryBase = a2Base.resolve(categoryRelativePath);
			Files.createDirectories(targetCategoryBase);
			// first delete all directories from previous builds
			for (Path dir : Files.newDirectoryStream(targetCategoryBase, (p) -> Files.isDirectory(p))) {
				deleteDirectory(dir);
			}

			Files.createDirectories(originBase);

			Path commonBnd = duDir.resolve(COMMON_BND);
			Properties commonProps = new Properties();
			try (InputStream in = Files.newInputStream(commonBnd)) {
				commonProps.load(in);
			}
			String url = commonProps.getProperty(ManifestConstants.SLC_ORIGIN_URI.toString());
			if (url == null) {
				url = uris.getProperty(duDir.getFileName().toString());
				if (url == null)
					throw new IllegalStateException("No url available for " + duDir);
				commonProps.put(ManifestConstants.SLC_ORIGIN_URI.toString(), url);
			}
			Path downloaded = tryDownload(url, originBase);

			FileSystem zipFs = FileSystems.newFileSystem(downloaded, (ClassLoader) null);

			// filters
			List<PathMatcher> includeMatchers = new ArrayList<>();
			Properties includes = new Properties();
			try (InputStream in = Files.newInputStream(duDir.resolve("includes.properties"))) {
				includes.load(in);
			}
			for (Object pattern : includes.keySet()) {
				PathMatcher pathMatcher = zipFs.getPathMatcher("glob:/" + pattern);
				includeMatchers.add(pathMatcher);
			}

			List<PathMatcher> excludeMatchers = new ArrayList<>();
			Path excludeFile = duDir.resolve("excludes.properties");
			if (Files.exists(excludeFile)) {
				Properties excludes = new Properties();
				try (InputStream in = Files.newInputStream(excludeFile)) {
					excludes.load(in);
				}
				for (Object pattern : excludes.keySet()) {
					PathMatcher pathMatcher = zipFs.getPathMatcher("glob:/" + pattern);
					excludeMatchers.add(pathMatcher);
				}
			}

			Files.walkFileTree(zipFs.getRootDirectories().iterator().next(), new SimpleFileVisitor<Path>() {

				@Override
				public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
					includeMatchers: for (PathMatcher includeMatcher : includeMatchers) {
						if (includeMatcher.matches(file)) {
							for (PathMatcher excludeMatcher : excludeMatchers) {
								if (excludeMatcher.matches(file)) {
									logger.log(Level.WARNING, "Skipping excluded " + file);
									return FileVisitResult.CONTINUE;
								}
							}
							if (includeSources && file.getFileName().toString().contains(".source_")) {
								processEclipseSourceJar(file, targetCategoryBase);
								logger.log(Level.DEBUG, () -> "Processed source " + file);

							} else {
								Map<String, String> map = new HashMap<>();
								for (Object key : commonProps.keySet())
									map.put(key.toString(), commonProps.getProperty(key.toString()));
								processBundleJar(file, targetCategoryBase, map);
								logger.log(Level.DEBUG, () -> "Processed " + file);
							}
							break includeMatchers;
						}
					}
					return FileVisitResult.CONTINUE;
				}
			});

			DirectoryStream<Path> dirs = Files.newDirectoryStream(targetCategoryBase,
					(p) -> Files.isDirectory(p) && p.getFileName().toString().indexOf('.') >= 0);
			for (Path dir : dirs) {
				createJar(dir);
			}
		} catch (IOException e) {
			throw new RuntimeException("Cannot process " + duDir, e);
		}

	}

	/** Process sources in Eclipse format. */
	protected void processEclipseSourceJar(Path file, Path targetBase) throws IOException {
		try {
			Path targetBundleDir;
			try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(file), false)) {
				Manifest manifest = jarIn.getManifest();

				String[] relatedBundle = manifest.getMainAttributes().getValue("Eclipse-SourceBundle").split(";");
				String version = relatedBundle[1].substring("version=\"".length());
				version = version.substring(0, version.length() - 1);
				NameVersion nameVersion = new NameVersion(relatedBundle[0], version);
				targetBundleDir = targetBase.resolve(nameVersion.getName() + "." + nameVersion.getBranch());

				Path targetSourceDir = targetBundleDir.resolve("OSGI-OPT/src");

				// TODO make it less dangerous?
				if (Files.exists(targetSourceDir)) {
//				deleteDirectory(targetSourceDir);
				} else {
					Files.createDirectories(targetSourceDir);
				}

				// copy entries
				JarEntry entry;
				entries: while ((entry = jarIn.getNextJarEntry()) != null) {
					if (entry.isDirectory())
						continue entries;
					if (entry.getName().startsWith("META-INF"))// skip META-INF entries
						continue entries;
					Path target = targetSourceDir.resolve(entry.getName());
					Files.createDirectories(target.getParent());
					Files.copy(jarIn, target);
					logger.log(Level.TRACE, () -> "Copied source " + target);
				}

				// copy MANIFEST
			}
		} catch (IOException e) {
			throw new IllegalStateException("Cannot process " + file, e);
		}

	}

	/*
	 * COMMON PROCESSING
	 */
	/** Normalise a bundle. */
	protected Path processBundleJar(Path file, Path targetBase, Map<String, String> entries) throws IOException {
		NameVersion nameVersion;
		Path targetBundleDir;
		try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(file), false)) {
			Manifest sourceManifest = jarIn.getManifest();
			Manifest manifest = sourceManifest != null ? new Manifest(sourceManifest) : new Manifest();

			// remove problematic entries in MANIFEST
			manifest.getEntries().clear();

			String ourSymbolicName = entries.get(BUNDLE_SYMBOLICNAME.toString());
			String ourVersion = entries.get(BUNDLE_VERSION.toString());

			if (ourSymbolicName != null && ourVersion != null) {
				nameVersion = new NameVersion(ourSymbolicName, ourVersion);
			} else {
				nameVersion = nameVersionFromManifest(manifest);
				if (ourVersion != null && !nameVersion.getVersion().equals(ourVersion)) {
					logger.log(Level.WARNING,
							"Original version is " + nameVersion.getVersion() + " while new version is " + ourVersion);
					entries.put(BUNDLE_VERSION.toString(), ourVersion);
				}
				if (ourSymbolicName != null) {
					// we always force our symbolic name
					nameVersion.setName(ourSymbolicName);
				}
			}
			targetBundleDir = targetBase.resolve(nameVersion.getName() + "." + nameVersion.getBranch());

			// force Java 9 module name
			entries.put(ManifestConstants.AUTOMATIC_MODULE_NAME.toString(), nameVersion.getName());

			boolean isNative = false;
			String os = null;
			String arch = null;
			if (targetBundleDir.startsWith(a2LibBase)) {
				isNative = true;
				Path libRelativePath = a2LibBase.relativize(targetBundleDir);
				os = libRelativePath.getName(0).toString();
				arch = libRelativePath.getName(1).toString();
			}

			// copy entries
			JarEntry entry;
			entries: while ((entry = jarIn.getNextJarEntry()) != null) {
				if (entry.isDirectory())
					continue entries;
				if (entry.getName().endsWith(".RSA") || entry.getName().endsWith(".SF"))
					continue entries;
				if (entry.getName().endsWith("module-info.class")) // skip Java 9 module info
					continue entries;
				if (entry.getName().startsWith("META-INF/versions/")) // skip multi-version
					continue entries;
				// skip file system providers as they cause issues with native image
				if (entry.getName().startsWith("META-INF/services/java.nio.file.spi.FileSystemProvider"))
					continue entries;
				if (entry.getName().startsWith("OSGI-OPT/src/")) // skip embedded sources
					continue entries;
				Path target = targetBundleDir.resolve(entry.getName());
				Files.createDirectories(target.getParent());
				Files.copy(jarIn, target);

				// native libraries
				if (isNative && (entry.getName().endsWith(".so") || entry.getName().endsWith(".dll")
						|| entry.getName().endsWith(".jnilib"))) {
					Path categoryDir = targetBundleDir.getParent();
//					String[] segments = categoryDir.getFileName().toString().split("\\.");
//					String arch = segments[segments.length - 1];
//					String os = segments[segments.length - 2];
					boolean copyDll = false;
					Path targetDll = categoryDir.resolve(targetBundleDir.relativize(target));
					if (nameVersion.getName().equals("com.sun.jna")) {
						if (arch.equals("x86_64"))
							arch = "x86-64";
						if (os.equals("macosx"))
							os = "darwin";
						if (target.getParent().getFileName().toString().equals(os + "-" + arch)) {
							copyDll = true;
						}
						targetDll = categoryDir.resolve(target.getFileName());
					} else {
						copyDll = true;
					}
					if (copyDll) {
						Files.createDirectories(targetDll.getParent());
						if (Files.exists(targetDll))
							Files.delete(targetDll);
						Files.copy(target, targetDll);
					}
					Files.delete(target);
				}
				logger.log(Level.TRACE, () -> "Copied " + target);
			}

			// copy MANIFEST
			Path manifestPath = targetBundleDir.resolve("META-INF/MANIFEST.MF");
			Files.createDirectories(manifestPath.getParent());
			for (String key : entries.keySet()) {
				String value = entries.get(key);
				Object previousValue = manifest.getMainAttributes().putValue(key, value);
				if (previousValue != null && !previousValue.equals(value)) {
					if (ManifestConstants.IMPORT_PACKAGE.toString().equals(key)
							|| ManifestConstants.EXPORT_PACKAGE.toString().equals(key))
						logger.log(Level.TRACE, file.getFileName() + ": " + key + " was modified");
					else
						logger.log(Level.WARNING, file.getFileName() + ": " + key + " was " + previousValue
								+ ", overridden with " + value);
				}

				// hack to remove unresolvable
				if (key.equals("Provide-Capability") || key.equals("Require-Capability"))
					if (nameVersion.getName().equals("osgi.core") || nameVersion.getName().equals("osgi.cmpn")) {
						manifest.getMainAttributes().remove(key);
					}
			}
			try (OutputStream out = Files.newOutputStream(manifestPath)) {
				manifest.write(out);
			}
		}
		return targetBundleDir;
	}

	/*
	 * UTILITIES
	 */

	/** Recursively deletes a directory. */
	private static void deleteDirectory(Path path) throws IOException {
		if (!Files.exists(path))
			return;
		Files.walkFileTree(path, new SimpleFileVisitor<Path>() {
			@Override
			public FileVisitResult postVisitDirectory(Path directory, IOException e) throws IOException {
				if (e != null)
					throw e;
				Files.delete(directory);
				return FileVisitResult.CONTINUE;
			}

			@Override
			public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
				Files.delete(file);
				return FileVisitResult.CONTINUE;
			}
		});
	}

	/** Extract name/version from a MANIFEST. */
	protected NameVersion nameVersionFromManifest(Manifest manifest) {
		Attributes attrs = manifest.getMainAttributes();
		// symbolic name
		String symbolicName = attrs.getValue(ManifestConstants.BUNDLE_SYMBOLICNAME.toString());
		if (symbolicName == null)
			return null;
		// make sure there is no directive
		symbolicName = symbolicName.split(";")[0];

		String version = attrs.getValue(ManifestConstants.BUNDLE_VERSION.toString());
		return new NameVersion(symbolicName, version);
	}

	/** Try to download from an URI. */
	protected Path tryDownload(String uri, Path dir) throws IOException {
		// find mirror
		List<String> urlBases = null;
		String uriPrefix = null;
		uriPrefixes: for (String uriPref : mirrors.keySet()) {
			if (uri.startsWith(uriPref)) {
				if (mirrors.get(uriPref).size() > 0) {
					urlBases = mirrors.get(uriPref);
					uriPrefix = uriPref;
					break uriPrefixes;
				}
			}
		}
		if (urlBases == null)
			try {
				return download(new URL(uri), dir);
			} catch (FileNotFoundException e) {
				throw new FileNotFoundException("Cannot find " + uri);
			}

		// try to download
		for (String urlBase : urlBases) {
			String relativePath = uri.substring(uriPrefix.length());
			URL url = new URL(urlBase + relativePath);
			try {
				return download(url, dir);
			} catch (FileNotFoundException e) {
				logger.log(Level.WARNING, "Cannot download " + url + ", trying another mirror");
			}
		}
		throw new FileNotFoundException("Cannot find " + uri);
	}

	/** Effectively download. */
	protected Path download(URL url, Path dir) throws IOException {
		return download(url, dir, (String) null);
	}

	/** Effectively download. */
	protected Path download(URL url, Path dir, String name) throws IOException {

		Path dest;
		if (name == null) {
			name = url.getPath().substring(url.getPath().lastIndexOf('/') + 1);
		}

		dest = dir.resolve(name);
		if (Files.exists(dest)) {
			logger.log(Level.TRACE, () -> "File " + dest + " already exists for " + url + ", not downloading again");
			return dest;
		} else {
			Files.createDirectories(dest.getParent());
		}

		try (InputStream in = url.openStream()) {
			Files.copy(in, dest);
			logger.log(Level.DEBUG, () -> "Downloaded " + dest + " from " + url);
		}
		return dest;
	}

	/** Create a JAR file from a directory. */
	protected Path createJar(Path bundleDir) throws IOException {
		// Create the jar
		Path jarPath = bundleDir.getParent().resolve(bundleDir.getFileName() + ".jar");
		Path manifestPath = bundleDir.resolve("META-INF/MANIFEST.MF");
		Manifest manifest;
		try (InputStream in = Files.newInputStream(manifestPath)) {
			manifest = new Manifest(in);
		}
		try (JarOutputStream jarOut = new JarOutputStream(Files.newOutputStream(jarPath), manifest)) {
			jarOut.setLevel(Deflater.DEFAULT_COMPRESSION);
			Files.walkFileTree(bundleDir, new SimpleFileVisitor<Path>() {

				@Override
				public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
					if (file.getFileName().toString().equals("MANIFEST.MF"))
						return super.visitFile(file, attrs);
					JarEntry entry = new JarEntry(bundleDir.relativize(file).toString());
					jarOut.putNextEntry(entry);
					Files.copy(file, jarOut);
					return super.visitFile(file, attrs);
				}

			});
		}
		deleteDirectory(bundleDir);
		return jarPath;
	}

	enum ManifestConstants {
		// OSGi
		BUNDLE_SYMBOLICNAME("Bundle-SymbolicName"), //
		BUNDLE_VERSION("Bundle-Version"), //
		BUNDLE_LICENSE("Bundle-License"), //
		EXPORT_PACKAGE("Export-Package"), //
		IMPORT_PACKAGE("Import-Package"), //
		// JAVA
		AUTOMATIC_MODULE_NAME("Automatic-Module-Name"), //
		// SLC
		SLC_CATEGORY("SLC-Category"), //
		SLC_ORIGIN_M2("SLC-Origin-M2"), //
		SLC_ORIGIN_M2_MERGE("SLC-Origin-M2-Merge"), //
		SLC_ORIGIN_M2_REPO("SLC-Origin-M2-Repo"), //
		SLC_ORIGIN_MANIFEST_NOT_MODIFIED("SLC-Origin-ManifestNotModified"), //
		SLC_ORIGIN_URI("SLC-Origin-URI"),//
		;

		final String value;

		private ManifestConstants(String value) {
			this.value = value;
		}

		@Override
		public String toString() {
			return value;
		}

	}

}

/** Simple representation of an M2 artifact. */
class M2Artifact extends CategoryNameVersion {
	private String classifier;

	M2Artifact(String m2coordinates) {
		this(m2coordinates, null);
	}

	M2Artifact(String m2coordinates, String classifier) {
		String[] parts = m2coordinates.split(":");
		setCategory(parts[0]);
		setName(parts[1]);
		if (parts.length > 2) {
			setVersion(parts[2]);
		}
		this.classifier = classifier;
	}

	String getGroupId() {
		return super.getCategory();
	}

	String getArtifactId() {
		return super.getName();
	}

	String toM2Coordinates() {
		return getCategory() + ":" + getName() + (getVersion() != null ? ":" + getVersion() : "");
	}

	String getClassifier() {
		return classifier != null ? classifier : "";
	}

	String getExtension() {
		return "jar";
	}
}

/** Utilities around Maven (conventions based). */
class M2ConventionsUtils {
	final static String MAVEN_CENTRAL_BASE_URL = "https://repo1.maven.org/maven2/";

	/** The file name of this artifact when stored */
	static String artifactFileName(M2Artifact artifact) {
		return artifact.getArtifactId() + '-' + artifact.getVersion()
				+ (artifact.getClassifier().equals("") ? "" : '-' + artifact.getClassifier()) + '.'
				+ artifact.getExtension();
	}

	/** Absolute path to the file */
	static String artifactPath(String artifactBasePath, M2Artifact artifact) {
		return artifactParentPath(artifactBasePath, artifact) + '/' + artifactFileName(artifact);
	}

	/** Absolute path to the file */
	static String artifactUrl(String repoUrl, M2Artifact artifact) {
		if (repoUrl.endsWith("/"))
			return repoUrl + artifactPath("/", artifact).substring(1);
		else
			return repoUrl + artifactPath("/", artifact);
	}

	/** Absolute path to the file */
	static URL mavenRepoUrl(String repoBase, M2Artifact artifact) {
		String url = artifactUrl(repoBase == null ? MAVEN_CENTRAL_BASE_URL : repoBase, artifact);
		try {
			return new URL(url);
		} catch (MalformedURLException e) {
			// it should not happen
			throw new IllegalStateException(e);
		}
	}

	/** Absolute path to the directories where the files will be stored */
	static String artifactParentPath(String artifactBasePath, M2Artifact artifact) {
		return artifactBasePath + (artifactBasePath.endsWith("/") ? "" : "/") + artifactParentPath(artifact);
	}

	/** Relative path to the directories where the files will be stored */
	static String artifactParentPath(M2Artifact artifact) {
		return artifact.getGroupId().replace('.', '/') + '/' + artifact.getArtifactId() + '/' + artifact.getVersion();
	}

	/** Singleton */
	private M2ConventionsUtils() {
	}
}

class CategoryNameVersion extends NameVersion {
	private String category;

	CategoryNameVersion() {
	}

	CategoryNameVersion(String category, String name, String version) {
		super(name, version);
		this.category = category;
	}

	CategoryNameVersion(String category, NameVersion nameVersion) {
		super(nameVersion);
		this.category = category;
	}

	String getCategory() {
		return category;
	}

	void setCategory(String category) {
		this.category = category;
	}

	@Override
	public String toString() {
		return category + ":" + super.toString();
	}

}

class NameVersion implements Comparable<NameVersion> {
	private String name;
	private String version;

	NameVersion() {
	}

	/** Interprets string in OSGi-like format my.module.name;version=0.0.0 */
	NameVersion(String nameVersion) {
		int index = nameVersion.indexOf(";version=");
		if (index < 0) {
			setName(nameVersion);
			setVersion(null);
		} else {
			setName(nameVersion.substring(0, index));
			setVersion(nameVersion.substring(index + ";version=".length()));
		}
	}

	NameVersion(String name, String version) {
		this.name = name;
		this.version = version;
	}

	NameVersion(NameVersion nameVersion) {
		this.name = nameVersion.getName();
		this.version = nameVersion.getVersion();
	}

	String getName() {
		return name;
	}

	void setName(String name) {
		this.name = name;
	}

	String getVersion() {
		return version;
	}

	void setVersion(String version) {
		this.version = version;
	}

	String getBranch() {
		String[] parts = getVersion().split("\\.");
		if (parts.length < 2)
			throw new IllegalStateException("Version " + getVersion() + " cannot be interpreted as branch.");
		return parts[0] + "." + parts[1];
	}

	@Override
	public boolean equals(Object obj) {
		if (obj instanceof NameVersion) {
			NameVersion nameVersion = (NameVersion) obj;
			return name.equals(nameVersion.getName()) && version.equals(nameVersion.getVersion());
		} else
			return false;
	}

	@Override
	public int hashCode() {
		return name.hashCode();
	}

	@Override
	public String toString() {
		return name + ":" + version;
	}

	public int compareTo(NameVersion o) {
		if (o.getName().equals(name))
			return version.compareTo(o.getVersion());
		else
			return name.compareTo(o.getName());
	}
}