rhelp/org.eclipse.statet.rhelp.core/src/org/eclipse/statet/internal/rhelp/core/SerUtil.java - statet/org.eclipse.statet-r - Git at Google

 /*=============================================================================#
  # Copyright (c) 2010, 2019 Stephan Wahlbrink and others.
  #
  # This program and the accompanying materials are made available under the
  # terms of the Eclipse Public License 2.0 which is available at
  # https://www.eclipse.org/legal/epl-2.0, or the Apache License, Version 2.0
  # which is available at https://www.apache.org/licenses/LICENSE-2.0.
  #
  # SPDX-License-Identifier: EPL-2.0 OR Apache-2.0
  #
  # Contributors:
  #     Stephan Wahlbrink <sw@wahlbrink.eu> - initial API and implementation
  #=============================================================================*/

 package org.eclipse.statet.internal.rhelp.core;

 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
 import java.nio.file.StandardOpenOption;
 import java.util.List;

 import org.eclipse.statet.jcommons.collections.ImCollections;
 import org.eclipse.statet.jcommons.collections.ImList;
 import org.eclipse.statet.jcommons.lang.NonNull;
 import org.eclipse.statet.jcommons.lang.NonNullByDefault;
 import org.eclipse.statet.jcommons.lang.Nullable;
 import org.eclipse.statet.jcommons.status.ErrorStatus;

 import org.eclipse.statet.rhelp.core.DocResource;
 import org.eclipse.statet.rhelp.core.REnvHelpConfiguration;
 import org.eclipse.statet.rhelp.core.RHelpCore;
 import org.eclipse.statet.rhelp.core.RHelpKeyword;
 import org.eclipse.statet.rhelp.core.RHelpKeywordGroup;
 import org.eclipse.statet.rhelp.core.RHelpPage;
 import org.eclipse.statet.rhelp.core.RPkgHelp;
 import org.eclipse.statet.rj.renv.core.BasicRLibLocation;
 import org.eclipse.statet.rj.renv.core.BasicRPkgDescription;
 import org.eclipse.statet.rj.renv.core.REnvConfiguration;
 import org.eclipse.statet.rj.renv.core.RLibLocation;
 import org.eclipse.statet.rj.renv.core.RNumVersion;
 import org.eclipse.statet.rj.renv.core.RPkgDescription;


 @NonNullByDefault
 public class SerUtil {


 	private static final int VERSION_11= 11;
 	private static final int VERSION_10= 10;
 	private static final int VERSION= VERSION_11;

 	public static final String READABLE_SERVER= "" + VERSION_11 + ',' + VERSION_10; //$NON-NLS-1$

 	private static final int COMPRESS= 1 << 4;


 	private boolean canRead(final int version, final REnvHelpConfiguration rEnvConfig) {
 		switch (version) {
 		case VERSION_11:
 			return true;
 		case VERSION_10:
 			return (rEnvConfig.getStateSharedType() == REnvConfiguration.SHARED_SERVER);
 		default:
 			return false;
 		}
 	}


 	private static final String RHELP_SER_FILE= "rhelp.ser"; //$NON-NLS-1$


 	private static class UnsupportedVersionException extends IOException {

 		private static final long serialVersionUID= 1L;

 		public UnsupportedVersionException(final int inputVersion) {
 			super("input= " + inputVersion);
 		}

 	}

 	public static interface Controller {

 		Object getFileLock();

 		boolean shouldSave();
 		void onSaved();

 	}


 	public static @Nullable Path getIndexDirectoryPath(final REnvHelpConfiguration rEnvConfig) {
 		try {
 			final Path stateDirectory= rEnvConfig.getStateSharedDirectoryPath();
 			if (stateDirectory != null) {
 				return stateDirectory.resolve("index"); //$NON-NLS-1$
 			}
 		}
 		catch (final Exception e) {}
 		return null;
 	}

 	public static Path getIndexDirectoryChecked(final REnvHelpConfiguration rEnvConfig) {
 		Exception e1= null;
 		try {
 			final Path stateDirectory= rEnvConfig.getStateSharedDirectoryPath();
 			if (stateDirectory != null) {
 				final Path indexDirectory= stateDirectory.resolve("index"); //$NON-NLS-1$
 				if (!Files.isDirectory(indexDirectory)) {
 					Files.createDirectories(indexDirectory);
 				}
 				return indexDirectory;
 			}
 		}
 		catch (final Exception e) {
 			e1= e;
 		}
 		throw new RuntimeException(
 				String.format("Index directory could not be resolved: '%1$s'.",
 						rEnvConfig.getStateSharedDirectory() ),
 				e1 );
 	}

 	public static Path getBasicDataFilePath(final Path indexDirectory) {
 		return indexDirectory.resolve(RHELP_SER_FILE);
 	}

 	public static @Nullable Path getBasicDataFilePath(final REnvHelpConfiguration rEnvConfig) {
 		final Path directory= getIndexDirectoryPath(rEnvConfig);
 		if (directory != null) {
 			return getBasicDataFilePath(directory);
 		}
 		return null;
 	}


 	public SerUtil() {
 	}

 	public boolean save(final REnvHelpConfiguration rEnvConfig, final REnvHelpImpl help,
 			final Controller controller) {
 		try {
 			final Path directory= getIndexDirectoryChecked(rEnvConfig);
 			final Path newFile= directory.resolve(RHELP_SER_FILE + ".new"); //$NON-NLS-1$
 			Files.deleteIfExists(newFile);

 			try (final FIO fio= FIO.get(new BufferedOutputStream(
 					Files.newOutputStream(newFile, StandardOpenOption.CREATE_NEW) ))) {
 				save(help, fio, COMPRESS);
 				fio.flush();
 			}

 			synchronized (controller.getFileLock()) {
 				if (!controller.shouldSave()) {
 					return false;
 				}
 				final Path serFile= directory.resolve(RHELP_SER_FILE);
 				Files.move(newFile, serFile, StandardCopyOption.REPLACE_EXISTING);
 				controller.onSaved();
 				return true;
 			}
 		}
 		catch (final Exception e) {
 			RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
 					String.format("An error occurred when saving R help data for '%1$s'.",
 							rEnvConfig.getName() ),
 					e ));
 			return false;
 		}
 	}

 	public boolean save(final REnvHelpConfiguration rEnvConfig, final InputStream in,
 			final Controller controller) {
 		try {
 			final Path directory= getIndexDirectoryChecked(rEnvConfig);
 			final Path newFile= directory.resolve(RHELP_SER_FILE + ".new"); //$NON-NLS-1$
 			Files.deleteIfExists(newFile);

 			try (final OutputStream out= new BufferedOutputStream(
 					Files.newOutputStream(newFile, StandardOpenOption.CREATE_NEW) )) {
 				FIO.copy(in, out);
 			}

 			synchronized (controller.getFileLock()) {
 				if (!controller.shouldSave()) {
 					return false;
 				}
 				final Path serFile= directory.resolve(RHELP_SER_FILE);
 				Files.move(newFile, serFile, StandardCopyOption.REPLACE_EXISTING);
 				controller.onSaved();
 				return true;
 			}
 		}
 		catch (final Exception e) {
 			RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
 					String.format("An error occurred when saving R help data for '%1$s'.",
 							rEnvConfig.getName() ),
 					e ));
 			return false;
 		}
 	}

 	public long getStamp(final REnvHelpConfiguration rEnvConfig) {
 		try {
 			final Path serFile= getBasicDataFilePath(rEnvConfig);
 			if (!Files.isRegularFile(serFile)) {
 				return REnvHelpImpl.NOT_AVAILABLE_STAMP;
 			}

 			try (final FIO fio= FIO.get(new BufferedInputStream(
 					Files.newInputStream(serFile), 64 ))) {
 				final int version= fio.readInt();
 				if (version != VERSION && !canRead(version, rEnvConfig)) {
 					return REnvHelpImpl.NOT_AVAILABLE_STAMP;
 				}
 				return fio.readLong();
 			}
 		}
 		catch (final Throwable e) {
 			if (e instanceof Error && !(e instanceof UnsupportedVersionException)) {
 				throw (Error) e;
 			}
 			RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
 					String.format("An error occurred when loading R help data for '%1$s'.",
 							rEnvConfig.getName() ),
 					e ));
 			return REnvHelpImpl.NOT_AVAILABLE_STAMP;
 		}
 	}

 	public @Nullable REnvHelpImpl load(final REnvHelpConfiguration rEnvConfig) {
 		try {
 			final Path serFile= getBasicDataFilePath(rEnvConfig);
 			if (!Files.isRegularFile(serFile)) {
 				return null;
 			}

 			try (final FIO fio= FIO.get(new BufferedInputStream(
 					Files.newInputStream(serFile) ))) {
 				return load(rEnvConfig, fio);
 			}
 		}
 		catch (final Throwable e) {
 			if (e instanceof Error) {
 				throw (Error) e;
 			}
 			RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
 					String.format("An error occurred when loading R help data for '%1$s'.",
 							rEnvConfig.getName() ),
 					e ));
 			return null;
 		}
 	}

 	public void save(final REnvHelpImpl help, final FIO fio, final int flags)
 			throws IOException {
 		fio.writeInt(VERSION);
 		fio.writeLong(help.getStamp());

 		fio.writeInt(flags);
 		if ((flags & COMPRESS) != 0) {
 			fio.enableCompression();
 		}

 		fio.writeString(help.getDocDir());
 		{	final ImList<DocResource> resources= help.getManuals();
 			final int count= resources.size();
 			fio.writeInt(count);
 			for (int i= 0; i < count; i++) {
 				saveDocResource(resources.get(i), fio);
 			}
 		}
 		{	final ImList<DocResource> resources= help.getMiscResources();
 			final int count= resources.size();
 			fio.writeInt(count);
 			for (int i= 0; i < count; i++) {
 				saveDocResource(resources.get(i), fio);
 			}
 		}

 		{	final List<RHelpKeywordGroup> keywordGroups= help.getKeywords();
 			final int count= keywordGroups.size();
 			fio.writeInt(count);
 			for (int i= 0; i < keywordGroups.size(); i++) {
 				saveKeywordGroup(keywordGroups.get(i), fio);
 			}
 		}
 		{	final List<RPkgHelp> packages= help.getPkgs();
 			final int count= packages.size();
 			fio.writeInt(count);
 			for (int i= 0; i < packages.size(); i++) {
 				savePackage(packages.get(i), fio);
 			}
 		}
 	}

 	public REnvHelpImpl load(final REnvHelpConfiguration rEnvConfig, final FIO fio)
 			throws IOException {
 		final int version= fio.readInt();
 		if (version != VERSION && !canRead(version, rEnvConfig)) {
 			throw new UnsupportedVersionException(version);
 		}

 		final long stamp= fio.readLong();

 		final int flags= fio.readInt();
 		if ((flags & COMPRESS) != 0) {
 			fio.enableCompression();
 		}

 		final String docDir= fio.readString();
 		final ImList<DocResource> manuals;
 		{	final int count= fio.readInt();
 			final DocResource[] array= new org.eclipse.statet.rhelp.core.DocResource[count];
 			for (int i= 0; i < count; i++) {
 				array[i]= readDocResource(fio);
 			}
 			manuals= ImCollections.newList(array);
 		}
 		final ImList<DocResource> miscRes;
 		{	final int count= fio.readInt();
 			final DocResource[] array= new @NonNull DocResource[count];
 			for (int i= 0; i < count; i++) {
 				array[i]= readDocResource(fio);
 			}
 			miscRes= ImCollections.newList(array);
 		}

 		final ImList<RHelpKeywordGroup> keywordGroups;
 		{	final int count= fio.readInt();
 			final RHelpKeywordGroup[] array= new @NonNull RHelpKeywordGroup[count];
 			for (int i= 0; i < count; i++) {
 				array[i]= loadKeywordGroup(fio);
 			}
 			keywordGroups= ImCollections.newList(array);
 		}

 		final ImList<RPkgHelp> pkgHelps;
 		{	final int count= fio.readInt();
 			final RPkgHelp[] array= new @NonNull RPkgHelp[count];
 			for (int i= 0; i < count; i++) {
 				array[i]= loadPackage(rEnvConfig, fio);
 			}
 			pkgHelps= ImCollections.newList(array);
 		}

 		return new REnvHelpImpl(rEnvConfig.getREnv(), stamp,
 				docDir, manuals, miscRes,
 				keywordGroups, pkgHelps );
 	}


 	private void saveDocResource(final DocResource res,
 			final FIO fio) throws IOException {
 		fio.writeString(res.getTitle());
 		fio.writeString(res.getPath());
 		fio.writeString(res.getPdfPath());
 	}

 	private DocResource readDocResource(final FIO fio) throws IOException {
 		return new DocResource(
 				fio.readNonNullString(),
 				fio.readNonNullString(),
 				fio.readString() );
 	}


 	private void saveKeywordGroup(final RHelpKeywordGroup group,
 			final FIO fio) throws IOException {
 		fio.writeString(group.getLabel());
 		fio.writeString(group.getDescription());
 		final List<RHelpKeyword> keywords= group.getNestedKeywords();
 		final int count= keywords.size();
 		fio.writeInt(count);
 		for (int i= 0; i < count; i++) {
 			saveKeyword(keywords.get(i), fio);
 		}
 	}

 	private RHelpKeywordGroup loadKeywordGroup(final FIO fio) throws IOException {
 		final String label= fio.readString();
 		final String description= fio.readString();
 		final int count= fio.readInt();
 		final RHelpKeyword[] keywords= new @NonNull RHelpKeyword[count];
 		for (int i= 0; i < count; i++) {
 			keywords[i]= loadKeyword(fio);
 		}
 		return new RHelpKeywordGroupImpl(label, description, ImCollections.newList(keywords));
 	}

 	private void saveKeyword(final RHelpKeyword keyword, final FIO fio)
 			throws IOException {
 		fio.writeString(keyword.getKeyword());
 		fio.writeString(keyword.getDescription());
 		final List<RHelpKeyword> nestedKeywords= keyword.getNestedKeywords();
 		final int count= nestedKeywords.size();
 		fio.writeInt(count);
 		for (int i= 0; i < nestedKeywords.size(); i++) {
 			saveKeyword(nestedKeywords.get(i), fio);
 		}
 	}

 	private RHelpKeyword loadKeyword(final FIO fio)
 			throws IOException {
 		final String keyword= fio.readString();
 		final String description= fio.readString();
 		final int n= fio.readInt();
 		final RHelpKeyword[] nestedKeywords= new @NonNull RHelpKeyword[n];
 		for (int i= 0; i < n; i++) {
 			nestedKeywords[i]= loadKeyword(fio);
 		}
 		return new RHelpKeywordImpl(keyword, description, ImCollections.newList(nestedKeywords));
 	}

 	private void savePackage(final RPkgHelp pkgHelp, final FIO fio)
 			throws IOException {
 		savePkgDescription(pkgHelp.getPkgDescription(), fio);

 		final List<RHelpPage> pages= pkgHelp.getPages();
 		final int nPages= pages.size();
 		fio.writeInt(nPages);
 		for (int i= 0; i < nPages; i++) {
 			savePage(pages.get(i), fio);
 		}
 	}

 	private RPkgHelp loadPackage(final REnvHelpConfiguration rEnvConfig, final FIO fio)
 			throws IOException {
 		final RPkgDescription pkgDescription= loadPkgDescription(rEnvConfig, fio);

 		final int nPages= fio.readInt();
 		final RHelpPage[] pages= new @NonNull RHelpPage[nPages];
 		final RPkgHelpImpl pkg= new RPkgHelpImpl(pkgDescription, rEnvConfig.getREnv());
 		for (int i= 0; i < nPages; i++) {
 			pages[i]= loadPage(pkg, fio);
 		}
 		pkg.setPages(ImCollections.newList(pages));
 		return pkg;
 	}

 	private void savePkgDescription(final RPkgDescription pkgDescription,
 			final FIO fio) throws IOException {
 		fio.writeString(pkgDescription.getName());
 		fio.writeString(pkgDescription.getVersion().toString());
 		fio.writeString(pkgDescription.getTitle());
 		fio.writeString(pkgDescription.getDescription());
 		fio.writeString(pkgDescription.getAuthor());
 		fio.writeString(pkgDescription.getMaintainer());
 		fio.writeString(pkgDescription.getUrl());
 		fio.writeString(pkgDescription.getBuilt());
 		fio.writeString(pkgDescription.getLibLocation().getDirectory());
 	}

 	private RPkgDescription loadPkgDescription(final REnvHelpConfiguration rEnvConfig,
 			final FIO fio) throws IOException {
 		final String name= fio.readNonNullString().intern();
 		final String version= fio.readNonNullString();
 		final String title= fio.readNonNullString();
 		final String description= fio.readNonNullString();
 		final String author= fio.readString();
 		final String maintainer= fio.readString();
 		final String url= fio.readString();
 		final String built= fio.readNonNullString();
 		final RLibLocation libLocation= getLibLocationSafe(rEnvConfig, fio.readNonNullString());

 		return new BasicRPkgDescription(name, RNumVersion.create(version),
 				title, description,
 				author, maintainer,
 				url,
 				built, libLocation);
 	}

 	private RLibLocation getLibLocationSafe(final REnvHelpConfiguration rEnvConfig, final String directory) {
 		RLibLocation libLocation= rEnvConfig.getRLibLocationByDirectory(directory);
 		if (libLocation == null) {
 			libLocation= new BasicRLibLocation(RLibLocation.MISSING, directory, null);
 		}
 		return libLocation;
 	}

 	private void savePage(final RHelpPage page, final FIO fio)
 			throws IOException {
 		fio.writeString(page.getName());
 		{	final ImList<String> topics= page.getTopics();
 			final int nTopics= topics.size();
 			fio.writeInt(nTopics);
 			for (int i= 0; i < nTopics; i++) {
 				final String topic= topics.get(i);
 				fio.writeString((topic == page.getName()) ? null : topic);
 			}
 		}
 		fio.writeString(page.getTitle());
 	}

 	private RHelpPage loadPage(final RPkgHelp pkg, final FIO fio)
 			throws IOException {
 		final String name= fio.readNonNullString().intern();
 		final ImList<String> topics;
 		{	final int nTopics= fio.readInt();
 			final String[] array= new @NonNull String[nTopics];
 			for (int i= 0; i < array.length; i++) {
 				final String topic= fio.readString();
 				array[i]= (topic == null) ? name : topic.intern();
 			}
 			topics= ImCollections.newList(array);
 		}
 		final String title= fio.readNonNullString();
 		return new RHelpPageImpl(pkg, name, topics, title);
 	}

 }
	/*=============================================================================#
	# Copyright (c) 2010, 2019 Stephan Wahlbrink and others.
	#
	# This program and the accompanying materials are made available under the
	# terms of the Eclipse Public License 2.0 which is available at
	# https://www.eclipse.org/legal/epl-2.0, or the Apache License, Version 2.0
	# which is available at https://www.apache.org/licenses/LICENSE-2.0.
	#
	# SPDX-License-Identifier: EPL-2.0 OR Apache-2.0
	#
	# Contributors:
	# Stephan Wahlbrink <sw@wahlbrink.eu> - initial API and implementation
	#=============================================================================*/

	package org.eclipse.statet.internal.rhelp.core;

	import java.io.BufferedInputStream;
	import java.io.BufferedOutputStream;
	import java.io.IOException;
	import java.io.InputStream;
	import java.io.OutputStream;
	import java.nio.file.Files;
	import java.nio.file.Path;
	import java.nio.file.StandardCopyOption;
	import java.nio.file.StandardOpenOption;
	import java.util.List;

	import org.eclipse.statet.jcommons.collections.ImCollections;
	import org.eclipse.statet.jcommons.collections.ImList;
	import org.eclipse.statet.jcommons.lang.NonNull;
	import org.eclipse.statet.jcommons.lang.NonNullByDefault;
	import org.eclipse.statet.jcommons.lang.Nullable;
	import org.eclipse.statet.jcommons.status.ErrorStatus;

	import org.eclipse.statet.rhelp.core.DocResource;
	import org.eclipse.statet.rhelp.core.REnvHelpConfiguration;
	import org.eclipse.statet.rhelp.core.RHelpCore;
	import org.eclipse.statet.rhelp.core.RHelpKeyword;
	import org.eclipse.statet.rhelp.core.RHelpKeywordGroup;
	import org.eclipse.statet.rhelp.core.RHelpPage;
	import org.eclipse.statet.rhelp.core.RPkgHelp;
	import org.eclipse.statet.rj.renv.core.BasicRLibLocation;
	import org.eclipse.statet.rj.renv.core.BasicRPkgDescription;
	import org.eclipse.statet.rj.renv.core.REnvConfiguration;
	import org.eclipse.statet.rj.renv.core.RLibLocation;
	import org.eclipse.statet.rj.renv.core.RNumVersion;
	import org.eclipse.statet.rj.renv.core.RPkgDescription;


	@NonNullByDefault
	public class SerUtil {


	private static final int VERSION_11= 11;
	private static final int VERSION_10= 10;
	private static final int VERSION= VERSION_11;

	public static final String READABLE_SERVER= "" + VERSION_11 + ',' + VERSION_10; //$NON-NLS-1$

	private static final int COMPRESS= 1 << 4;


	private boolean canRead(final int version, final REnvHelpConfiguration rEnvConfig) {
	switch (version) {
	case VERSION_11:
	return true;
	case VERSION_10:
	return (rEnvConfig.getStateSharedType() == REnvConfiguration.SHARED_SERVER);
	default:
	return false;
	}
	}


	private static final String RHELP_SER_FILE= "rhelp.ser"; //$NON-NLS-1$


	private static class UnsupportedVersionException extends IOException {

	private static final long serialVersionUID= 1L;

	public UnsupportedVersionException(final int inputVersion) {
	super("input= " + inputVersion);
	}

	}

	public static interface Controller {

	Object getFileLock();

	boolean shouldSave();
	void onSaved();

	}


	public static @Nullable Path getIndexDirectoryPath(final REnvHelpConfiguration rEnvConfig) {
	try {
	final Path stateDirectory= rEnvConfig.getStateSharedDirectoryPath();
	if (stateDirectory != null) {
	return stateDirectory.resolve("index"); //$NON-NLS-1$
	}
	}
	catch (final Exception e) {}
	return null;
	}

	public static Path getIndexDirectoryChecked(final REnvHelpConfiguration rEnvConfig) {
	Exception e1= null;
	try {
	final Path stateDirectory= rEnvConfig.getStateSharedDirectoryPath();
	if (stateDirectory != null) {
	final Path indexDirectory= stateDirectory.resolve("index"); //$NON-NLS-1$
	if (!Files.isDirectory(indexDirectory)) {
	Files.createDirectories(indexDirectory);
	}
	return indexDirectory;
	}
	}
	catch (final Exception e) {
	e1= e;
	}
	throw new RuntimeException(
	String.format("Index directory could not be resolved: '%1$s'.",
	rEnvConfig.getStateSharedDirectory() ),
	e1 );
	}

	public static Path getBasicDataFilePath(final Path indexDirectory) {
	return indexDirectory.resolve(RHELP_SER_FILE);
	}

	public static @Nullable Path getBasicDataFilePath(final REnvHelpConfiguration rEnvConfig) {
	final Path directory= getIndexDirectoryPath(rEnvConfig);
	if (directory != null) {
	return getBasicDataFilePath(directory);
	}
	return null;
	}


	public SerUtil() {
	}

	public boolean save(final REnvHelpConfiguration rEnvConfig, final REnvHelpImpl help,
	final Controller controller) {
	try {
	final Path directory= getIndexDirectoryChecked(rEnvConfig);
	final Path newFile= directory.resolve(RHELP_SER_FILE + ".new"); //$NON-NLS-1$
	Files.deleteIfExists(newFile);

	try (final FIO fio= FIO.get(new BufferedOutputStream(
	Files.newOutputStream(newFile, StandardOpenOption.CREATE_NEW) ))) {
	save(help, fio, COMPRESS);
	fio.flush();
	}

	synchronized (controller.getFileLock()) {
	if (!controller.shouldSave()) {
	return false;
	}
	final Path serFile= directory.resolve(RHELP_SER_FILE);
	Files.move(newFile, serFile, StandardCopyOption.REPLACE_EXISTING);
	controller.onSaved();
	return true;
	}
	}
	catch (final Exception e) {
	RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
	String.format("An error occurred when saving R help data for '%1$s'.",
	rEnvConfig.getName() ),
	e ));
	return false;
	}
	}

	public boolean save(final REnvHelpConfiguration rEnvConfig, final InputStream in,
	final Controller controller) {
	try {
	final Path directory= getIndexDirectoryChecked(rEnvConfig);
	final Path newFile= directory.resolve(RHELP_SER_FILE + ".new"); //$NON-NLS-1$
	Files.deleteIfExists(newFile);

	try (final OutputStream out= new BufferedOutputStream(
	Files.newOutputStream(newFile, StandardOpenOption.CREATE_NEW) )) {
	FIO.copy(in, out);
	}

	synchronized (controller.getFileLock()) {
	if (!controller.shouldSave()) {
	return false;
	}
	final Path serFile= directory.resolve(RHELP_SER_FILE);
	Files.move(newFile, serFile, StandardCopyOption.REPLACE_EXISTING);
	controller.onSaved();
	return true;
	}
	}
	catch (final Exception e) {
	RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
	String.format("An error occurred when saving R help data for '%1$s'.",
	rEnvConfig.getName() ),
	e ));
	return false;
	}
	}

	public long getStamp(final REnvHelpConfiguration rEnvConfig) {
	try {
	final Path serFile= getBasicDataFilePath(rEnvConfig);
	if (!Files.isRegularFile(serFile)) {
	return REnvHelpImpl.NOT_AVAILABLE_STAMP;
	}

	try (final FIO fio= FIO.get(new BufferedInputStream(
	Files.newInputStream(serFile), 64 ))) {
	final int version= fio.readInt();
	if (version != VERSION && !canRead(version, rEnvConfig)) {
	return REnvHelpImpl.NOT_AVAILABLE_STAMP;
	}
	return fio.readLong();
	}
	}
	catch (final Throwable e) {
	if (e instanceof Error && !(e instanceof UnsupportedVersionException)) {
	throw (Error) e;
	}
	RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
	String.format("An error occurred when loading R help data for '%1$s'.",
	rEnvConfig.getName() ),
	e ));
	return REnvHelpImpl.NOT_AVAILABLE_STAMP;
	}
	}

	public @Nullable REnvHelpImpl load(final REnvHelpConfiguration rEnvConfig) {
	try {
	final Path serFile= getBasicDataFilePath(rEnvConfig);
	if (!Files.isRegularFile(serFile)) {
	return null;
	}

	try (final FIO fio= FIO.get(new BufferedInputStream(
	Files.newInputStream(serFile) ))) {
	return load(rEnvConfig, fio);
	}
	}
	catch (final Throwable e) {
	if (e instanceof Error) {
	throw (Error) e;
	}
	RHelpCoreInternals.log(new ErrorStatus(RHelpCore.BUNDLE_ID,
	String.format("An error occurred when loading R help data for '%1$s'.",
	rEnvConfig.getName() ),
	e ));
	return null;
	}
	}

	public void save(final REnvHelpImpl help, final FIO fio, final int flags)
	throws IOException {
	fio.writeInt(VERSION);
	fio.writeLong(help.getStamp());

	fio.writeInt(flags);
	if ((flags & COMPRESS) != 0) {
	fio.enableCompression();
	}

	fio.writeString(help.getDocDir());
	{ final ImList<DocResource> resources= help.getManuals();
	final int count= resources.size();
	fio.writeInt(count);
	for (int i= 0; i < count; i++) {
	saveDocResource(resources.get(i), fio);
	}
	}
	{ final ImList<DocResource> resources= help.getMiscResources();
	final int count= resources.size();
	fio.writeInt(count);
	for (int i= 0; i < count; i++) {
	saveDocResource(resources.get(i), fio);
	}
	}

	{ final List<RHelpKeywordGroup> keywordGroups= help.getKeywords();
	final int count= keywordGroups.size();
	fio.writeInt(count);
	for (int i= 0; i < keywordGroups.size(); i++) {
	saveKeywordGroup(keywordGroups.get(i), fio);
	}
	}
	{ final List<RPkgHelp> packages= help.getPkgs();
	final int count= packages.size();
	fio.writeInt(count);
	for (int i= 0; i < packages.size(); i++) {
	savePackage(packages.get(i), fio);
	}
	}
	}

	public REnvHelpImpl load(final REnvHelpConfiguration rEnvConfig, final FIO fio)
	throws IOException {
	final int version= fio.readInt();
	if (version != VERSION && !canRead(version, rEnvConfig)) {
	throw new UnsupportedVersionException(version);
	}

	final long stamp= fio.readLong();

	final int flags= fio.readInt();
	if ((flags & COMPRESS) != 0) {
	fio.enableCompression();
	}

	final String docDir= fio.readString();
	final ImList<DocResource> manuals;
	{ final int count= fio.readInt();
	final DocResource[] array= new org.eclipse.statet.rhelp.core.DocResource[count];
	for (int i= 0; i < count; i++) {
	array[i]= readDocResource(fio);
	}
	manuals= ImCollections.newList(array);
	}
	final ImList<DocResource> miscRes;
	{ final int count= fio.readInt();
	final DocResource[] array= new @NonNull DocResource[count];
	for (int i= 0; i < count; i++) {
	array[i]= readDocResource(fio);
	}
	miscRes= ImCollections.newList(array);
	}

	final ImList<RHelpKeywordGroup> keywordGroups;
	{ final int count= fio.readInt();
	final RHelpKeywordGroup[] array= new @NonNull RHelpKeywordGroup[count];
	for (int i= 0; i < count; i++) {
	array[i]= loadKeywordGroup(fio);
	}
	keywordGroups= ImCollections.newList(array);
	}

	final ImList<RPkgHelp> pkgHelps;
	{ final int count= fio.readInt();
	final RPkgHelp[] array= new @NonNull RPkgHelp[count];
	for (int i= 0; i < count; i++) {
	array[i]= loadPackage(rEnvConfig, fio);
	}
	pkgHelps= ImCollections.newList(array);
	}

	return new REnvHelpImpl(rEnvConfig.getREnv(), stamp,
	docDir, manuals, miscRes,
	keywordGroups, pkgHelps );
	}


	private void saveDocResource(final DocResource res,
	final FIO fio) throws IOException {
	fio.writeString(res.getTitle());
	fio.writeString(res.getPath());
	fio.writeString(res.getPdfPath());
	}

	private DocResource readDocResource(final FIO fio) throws IOException {
	return new DocResource(
	fio.readNonNullString(),
	fio.readNonNullString(),
	fio.readString() );
	}


	private void saveKeywordGroup(final RHelpKeywordGroup group,
	final FIO fio) throws IOException {
	fio.writeString(group.getLabel());
	fio.writeString(group.getDescription());
	final List<RHelpKeyword> keywords= group.getNestedKeywords();
	final int count= keywords.size();
	fio.writeInt(count);
	for (int i= 0; i < count; i++) {
	saveKeyword(keywords.get(i), fio);
	}
	}

	private RHelpKeywordGroup loadKeywordGroup(final FIO fio) throws IOException {
	final String label= fio.readString();
	final String description= fio.readString();
	final int count= fio.readInt();
	final RHelpKeyword[] keywords= new @NonNull RHelpKeyword[count];
	for (int i= 0; i < count; i++) {
	keywords[i]= loadKeyword(fio);
	}
	return new RHelpKeywordGroupImpl(label, description, ImCollections.newList(keywords));
	}

	private void saveKeyword(final RHelpKeyword keyword, final FIO fio)
	throws IOException {
	fio.writeString(keyword.getKeyword());
	fio.writeString(keyword.getDescription());
	final List<RHelpKeyword> nestedKeywords= keyword.getNestedKeywords();
	final int count= nestedKeywords.size();
	fio.writeInt(count);
	for (int i= 0; i < nestedKeywords.size(); i++) {
	saveKeyword(nestedKeywords.get(i), fio);
	}
	}

	private RHelpKeyword loadKeyword(final FIO fio)
	throws IOException {
	final String keyword= fio.readString();
	final String description= fio.readString();
	final int n= fio.readInt();
	final RHelpKeyword[] nestedKeywords= new @NonNull RHelpKeyword[n];
	for (int i= 0; i < n; i++) {
	nestedKeywords[i]= loadKeyword(fio);
	}
	return new RHelpKeywordImpl(keyword, description, ImCollections.newList(nestedKeywords));
	}

	private void savePackage(final RPkgHelp pkgHelp, final FIO fio)
	throws IOException {
	savePkgDescription(pkgHelp.getPkgDescription(), fio);

	final List<RHelpPage> pages= pkgHelp.getPages();
	final int nPages= pages.size();
	fio.writeInt(nPages);
	for (int i= 0; i < nPages; i++) {
	savePage(pages.get(i), fio);
	}
	}

	private RPkgHelp loadPackage(final REnvHelpConfiguration rEnvConfig, final FIO fio)
	throws IOException {
	final RPkgDescription pkgDescription= loadPkgDescription(rEnvConfig, fio);

	final int nPages= fio.readInt();
	final RHelpPage[] pages= new @NonNull RHelpPage[nPages];
	final RPkgHelpImpl pkg= new RPkgHelpImpl(pkgDescription, rEnvConfig.getREnv());
	for (int i= 0; i < nPages; i++) {
	pages[i]= loadPage(pkg, fio);
	}
	pkg.setPages(ImCollections.newList(pages));
	return pkg;
	}

	private void savePkgDescription(final RPkgDescription pkgDescription,
	final FIO fio) throws IOException {
	fio.writeString(pkgDescription.getName());
	fio.writeString(pkgDescription.getVersion().toString());
	fio.writeString(pkgDescription.getTitle());
	fio.writeString(pkgDescription.getDescription());
	fio.writeString(pkgDescription.getAuthor());
	fio.writeString(pkgDescription.getMaintainer());
	fio.writeString(pkgDescription.getUrl());
	fio.writeString(pkgDescription.getBuilt());
	fio.writeString(pkgDescription.getLibLocation().getDirectory());
	}

	private RPkgDescription loadPkgDescription(final REnvHelpConfiguration rEnvConfig,
	final FIO fio) throws IOException {
	final String name= fio.readNonNullString().intern();
	final String version= fio.readNonNullString();
	final String title= fio.readNonNullString();
	final String description= fio.readNonNullString();
	final String author= fio.readString();
	final String maintainer= fio.readString();
	final String url= fio.readString();
	final String built= fio.readNonNullString();
	final RLibLocation libLocation= getLibLocationSafe(rEnvConfig, fio.readNonNullString());

	return new BasicRPkgDescription(name, RNumVersion.create(version),
	title, description,
	author, maintainer,
	url,
	built, libLocation);
	}

	private RLibLocation getLibLocationSafe(final REnvHelpConfiguration rEnvConfig, final String directory) {
	RLibLocation libLocation= rEnvConfig.getRLibLocationByDirectory(directory);
	if (libLocation == null) {
	libLocation= new BasicRLibLocation(RLibLocation.MISSING, directory, null);
	}
	return libLocation;
	}

	private void savePage(final RHelpPage page, final FIO fio)
	throws IOException {
	fio.writeString(page.getName());
	{ final ImList<String> topics= page.getTopics();
	final int nTopics= topics.size();
	fio.writeInt(nTopics);
	for (int i= 0; i < nTopics; i++) {
	final String topic= topics.get(i);
	fio.writeString((topic == page.getName()) ? null : topic);
	}
	}
	fio.writeString(page.getTitle());
	}

	private RHelpPage loadPage(final RPkgHelp pkg, final FIO fio)
	throws IOException {
	final String name= fio.readNonNullString().intern();
	final ImList<String> topics;
	{ final int nTopics= fio.readInt();
	final String[] array= new @NonNull String[nTopics];
	for (int i= 0; i < array.length; i++) {
	final String topic= fio.readString();
	array[i]= (topic == null) ? name : topic.intern();
	}
	topics= ImCollections.newList(array);
	}
	final String title= fio.readNonNullString();
	return new RHelpPageImpl(pkg, name, topics, title);
	}

	}