r/org.eclipse.statet.r.core/src/org/eclipse/statet/internal/r/core/pkgmanager/RPkgScanner.java - statet/org.eclipse.statet-r - Git at Google

 /*=============================================================================#
  # Copyright (c) 2012, 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.r.core.pkgmanager;

 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;

 import org.eclipse.osgi.util.NLS;

 import org.eclipse.statet.jcommons.lang.Nullable;
 import org.eclipse.statet.jcommons.status.ErrorStatus;
 import org.eclipse.statet.jcommons.status.ProgressMonitor;
 import org.eclipse.statet.jcommons.status.StatusException;

 import org.eclipse.statet.r.core.RCore;
 import org.eclipse.statet.r.core.pkgmanager.IRPkgData;
 import org.eclipse.statet.r.core.pkgmanager.IRPkgInfo;
 import org.eclipse.statet.r.core.pkgmanager.ISelectedRepos;
 import org.eclipse.statet.r.core.pkgmanager.RPkgInfo;
 import org.eclipse.statet.r.core.pkgmanager.RPkgUtils;
 import org.eclipse.statet.r.core.pkgmanager.RRepo;
 import org.eclipse.statet.rj.data.RArray;
 import org.eclipse.statet.rj.data.RCharacterStore;
 import org.eclipse.statet.rj.data.RDataUtils;
 import org.eclipse.statet.rj.data.UnexpectedRDataException;
 import org.eclipse.statet.rj.renv.core.BasicRPkg;
 import org.eclipse.statet.rj.renv.core.BasicRPkgCompilation;
 import org.eclipse.statet.rj.renv.core.REnv;
 import org.eclipse.statet.rj.renv.core.RLibLocation;
 import org.eclipse.statet.rj.renv.core.RNumVersion;
 import org.eclipse.statet.rj.renv.core.RPkg;
 import org.eclipse.statet.rj.renv.core.RPkgCompilation;
 import org.eclipse.statet.rj.renv.core.RPkgList;
 import org.eclipse.statet.rj.renv.runtime.RLibLocationInfo;
 import org.eclipse.statet.rj.renv.runtime.RuntimeRLibPaths;
 import org.eclipse.statet.rj.services.FunctionCall;
 import org.eclipse.statet.rj.services.RService;


 final class RPkgScanner {

 	private static final String AVAIL_LIST_FNAME= "rj:::renv.getAvailPkgs"; //$NON-NLS-1$
 	private static final int AVAIL_LIST_COUNT1= 9;
 	private static final int AVAIL_LIST_IDX1_NAME= 0;
 	private static final int AVAIL_LIST_IDX1_VERSION= 1;
 	private static final int AVAIL_LIST_IDX1_PRIORITY= 2;
 	private static final int AVAIL_LIST_IDX1_LICENSE= 3;
 	private static final int AVAIL_LIST_IDX1_DEPENDS= 4;
 	private static final int AVAIL_LIST_IDX1_IMPORTS= 5;
 	private static final int AVAIL_LIST_IDX1_LINKINGTO= 6;
 	private static final int AVAIL_LIST_IDX1_SUGGESTS= 7;
 	private static final int AVAIL_LIST_IDX1_ENHANCES= 8;

 	private static final String INST_LIST_FNAME= "rj:::renv.getInstPkgs"; //$NON-NLS-1$
 	private static final int INST_LIST_COUNT1= 4;
 	private static final int INST_LIST_IDX1_NAME= 0;
 	private static final int INST_LIST_IDX1_VERSION= 1;
 	private static final int INST_LIST_IDX1_TITLE= 2;
 	private static final int INST_LIST_IDX1_BUILT= 3;

 	private static final String INST_DETAIL_FNAME= "rj:::renv.getInstPkgDetail"; //$NON-NLS-1$
 	private static final int INST_DETAIL_LENGTH= 7;
 	private static final int INST_DETAIL_IDX_PRIORITY= 0;
 	private static final int INST_DETAIL_IDX_LICENSE= 1;
 	private static final int INST_DETAIL_IDX_DEPENDS= 2;
 	private static final int INST_DETAIL_IDX_IMPORTS= 3;
 	private static final int INST_DETAIL_IDX_LINKINGTO= 4;
 	private static final int INST_DETAIL_IDX_SUGGESTS= 5;
 	private static final int INST_DETAIL_IDX_ENHANCES= 6;

 	private static @Nullable String decodeDescrField(final @Nullable String s) {
 		if (s == null) {
 			return null;
 		}
 		int mode= 0; // 1= single space, 2= chars to replace
 		int idxMode= 0;
 		int idxDone= 0;
 		StringBuilder sb= null;
 		for (int idx = 0; idx < s.length(); idx++) {
 			switch (s.charAt(idx)) {
 			case 0x00: case 0x01: case 0x02: case 0x03: case 0x04: case 0x05: case 0x06: case 0x07:
 			case 0x08: case 0x09: case 0x0A: case 0x0B: case 0x0C: case 0x0D: case 0x0E: case 0x0F:
 			case 0x7F:
 				switch (mode) {
 				case 0:
 					mode= 2;
 					idxMode= idx;
 					continue;
 				case 1:
 					mode= 2;
 					continue;
 //				case 2:
 				default:
 					continue;
 				}
 			case ' ':
 				switch (mode) {
 				case 0:
 					mode= 1;
 					idxMode= idx;
 					continue;
 				case 1:
 					mode= 2;
 					continue;
 //				case 2:
 				default:
 					continue;
 				}
 			default:
 				switch (mode) {
 				case 0:
 					continue;
 				case 1:
 					mode= 0;
 					continue;
 //				case 2:
 				default:
 					if (sb == null) {
 						sb= new StringBuilder(s.length());
 					}
 					sb.append(s, idxDone, idxMode);
 					sb.append(' ');
 					idxDone= idx + 1;
 					mode= 0;
 					continue;
 				}
 			}
 		}
 		if (sb != null) {
 			sb.append(s, idxDone, (mode == 0) ? s.length() : idxMode);
 			return sb.toString();
 		}
 		else {
 			return (mode == 0) ? s : s.substring(0, idxMode);
 		}
 	}


 	private static List<RPkg> parsePkgRefs(final String s) {
 		if (s == null || s.isEmpty()) {
 			return Collections.emptyList();
 		}
 		final List<RPkg> list= new ArrayList<>(4);
 		String name= null;
 		String version= null;
 		boolean ws;
 		final StringBuilder sb= new StringBuilder();
 		ITER_S: for (int i= 0; i <= s.length();) {
 			int c= (i < s.length()) ? s.charAt(i) : -1;

 			if (c == -1 || c == ',') {
 				if (name != null) {
 					list.add(new BasicRPkg(name, RNumVersion.create(version)));
 				}
 				name= null;
 				version= null;
 				i++;
 				continue ITER_S;
 			}
 			if (Character.isLetterOrDigit(c)) {
 				if (name != null) {
 					// ?
 				}
 				name= null;
 				version= null;
 				int j= i + 1;
 				while (true) {
 					c= (j < s.length()) ? s.charAt(j) : -1;
 					if (c < 0 || Character.isWhitespace(c) || c == '(' || c == ',') {
 						name= s.substring(i, j).intern();
 						i= j;
 						continue ITER_S;
 					}
 					j++;
 				}
 			}
 			if (c == '(') {
 				if (name == null || version != null) {
 					// ?
 					name= null;
 					version= null;
 				}
 				sb.setLength(0);
 				ws= false;
 				int j= ++i;
 				while (true) {
 					c= (j < s.length()) ? s.charAt(j) : -1;
 					if (c < 0 || c == ')') {
 						version= sb.toString();
 						i= j + 1;
 						continue ITER_S;
 					}
 					if (Character.isWhitespace(c)) {
 						ws= true;
 					}
 					else {
 						if (ws) {
 							sb.append(' ');
 							ws= false;
 						}
 						sb.append((char) c);
 					}
 					j++;
 				}
 			}

 			i++;
 			continue ITER_S;
 		}
 		return list;
 	}


 	private final BasicRPkgCompilation<IRPkgData> expectedPkgs= new BasicRPkgCompilation<IRPkgData>(4) {
 		@Override
 		protected RPkgList<IRPkgData> newPkgList() {
 			return new RPkgListImpl<>(4);
 		}
 	};


 	public RPkgScanner() {
 	}


 	void addExpectedPkg(final RLibLocation location, final IRPkgData pkg) {
 		final String path= location.getDirectory();
 		final RPkgListImpl<IRPkgData> list= (RPkgListImpl<IRPkgData>) this.expectedPkgs.getOrAdd(path);
 		list.set(pkg);
 	}

 	private void clearExpected() {
 		final List<RPkgList<IRPkgData>> all= this.expectedPkgs.getAll();
 		for (final RPkgList<IRPkgData> list : all) {
 			((RPkgListImpl<IRPkgData>) list).clear();
 		}
 	}


 	RPkgCompilation<IRPkgData> loadAvailable(final REnv rEnv, final ISelectedRepos repoSettings,
 			final RService r, final ProgressMonitor m) throws StatusException {
 		m.beginSubTask("Loading available R packages...");
 		try {
 			final RCharacterStore repos= RDataUtils.checkRCharVector(r.evalData(
 					"options('repos')[[1L]]", m)).getData(); //$NON-NLS-1$
 			final int l= RDataUtils.checkIntLength(repos);

 			final BasicRPkgCompilation<IRPkgData> newAvailable= new BasicRPkgCompilation<>(l);
 			for (int idxRepos= 0; idxRepos < l; idxRepos++) {
 				final String repoURL= repos.getChar(idxRepos);
 				if (repoURL == null || repoURL.isEmpty()) {
 					continue;
 				}
 				final RRepo repo= Util.getRepoByURL(repoSettings.getRepos(), repoURL);
 				m.beginSubTask(NLS.bind("Loading available R packages from {0}...", repoURL));

 				RArray<RCharacterStore> data;
 				{	final FunctionCall call= r.createFunctionCall(AVAIL_LIST_FNAME);
 					call.addChar("repo", repoURL); //$NON-NLS-1$
 					if (repo.getPkgType() != null) {
 						final String key= RPkgUtils.getPkgTypeInstallKey(r.getPlatform(), repo.getPkgType());
 						if (key == null) {
 							continue;
 						}
 					}
 					data= RDataUtils.checkRCharArray(call.evalData(m), 2);
 					RDataUtils.checkColumnCountEqual(data, AVAIL_LIST_COUNT1);
 				}

 				final RCharacterStore store= data.getData();
 				final int nPkgs= data.getDim().getInt(0);
 				final RPkgListImpl<IRPkgData> list= new RPkgListImpl<>(nPkgs);
 				newAvailable.add(repo.getId(), list);

 				for (int idxPkgs= 0; idxPkgs < nPkgs; idxPkgs++) {
 					String name= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_NAME));
 					final String version= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_VERSION));
 					if (name != null && !name.isEmpty() && version != null) {
 						name= name.intern();
 						final RPkgData pkg= new RPkgData(name, RNumVersion.create(version), repo.getId());

 						pkg.setLicense(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_LICENSE)));

 						pkg.setDepends(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_DEPENDS))));
 						pkg.setImports(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_IMPORTS))));
 						pkg.setLinkingTo(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_LINKINGTO))));
 						pkg.setSuggests(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_SUGGESTS))));
 						pkg.setEnhances(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_ENHANCES))));

 						pkg.setPriority(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_PRIORITY)));

 						list.add(pkg);
 					}
 				}
 			}

 			return newAvailable;
 		}
 		catch (final UnexpectedRDataException | StatusException e) {
 			throw new StatusException(new ErrorStatus(RCore.BUNDLE_ID,
 					"An error occurred when loading list of available R packages.",
 					e ));
 		}
 	}

 	RPkgCompilation<IRPkgInfo> loadInstalled(final RuntimeRLibPaths rLibPaths, final boolean[] update,
 			final Change event,
 			final RService r, final ProgressMonitor m) throws StatusException {
 		m.beginSubTask("Updating installed R packages...");
 		try {
 			final BasicRPkgCompilation<IRPkgInfo> newInstalled= new BasicRPkgCompilation<>(
 					rLibPaths.getRLibLocations().size() );
 			final RPkgCompilation<IRPkgInfo> prevInstalled= (RPkgCompilation<IRPkgInfo>)
 					((event.oldPkgs != null) ? event.oldPkgs.getInstalled() : null);
 			final RPkgChangeSet changeSet= new RPkgChangeSet();
 			event.installedPkgs= changeSet;
 			for (final RLibLocation libLocation : rLibPaths.getRLibLocations()) {
 				final RLibLocationInfo locationInfo= rLibPaths.getInfo(libLocation);
 				if (locationInfo == null || locationInfo.getLibPathsIndex() < 0) {
 					continue;
 				}
 				if (newInstalled.getBySource(libLocation.getDirectory()) != null) {
 					continue;
 				}
 				if (update == null || update[locationInfo.getLibPathsIndex()] || prevInstalled == null) {
 					final RArray<RCharacterStore> data;
 					{	final FunctionCall call= r.createFunctionCall(INST_LIST_FNAME);
 						call.addChar("lib", locationInfo.getDirectoryRPath()); //$NON-NLS-1$
 						data= RDataUtils.checkRCharArray(call.evalData(m), 2);
 						RDataUtils.checkColumnCountEqual(data, INST_LIST_COUNT1);
 					}
 					final RCharacterStore store= data.getData();
 					final int nPkgs= data.getDim().getInt(0);

 					final RPkgList<IRPkgInfo> oldList= (prevInstalled != null) ?
 							prevInstalled.getBySource(libLocation.getDirectory()) : null;
 					final RPkgListImpl<IRPkgInfo> newList= new RPkgListImpl<>(nPkgs);
 					final RPkgList<IRPkgData> expectedList= this.expectedPkgs.getBySource(libLocation.getDirectory());
 					for (int idxPkg= 0; idxPkg < nPkgs; idxPkg++) {
 						String name= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_NAME));
 						final String version= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_VERSION));
 						if (name != null && !name.isEmpty() && version != null && !version.isEmpty()) {
 							name= name.intern();
 							String built= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_BUILT));
 							if (built == null) {
 								built= ""; //$NON-NLS-1$
 							}
 							final IRPkgInfo oldPkg= (oldList != null) ? oldList.get(name) : null;
 							final IRPkgInfo newPkg;
 							final boolean changed= (oldPkg == null
 									|| !oldPkg.getVersion().toString().equals(version)
 									|| !oldPkg.getBuilt().equals(built) );

 							if (!changed) {
 								newPkg= oldPkg;
 							}
 							else {
 								final IRPkgData expectedData =
 										(expectedList != null) ? expectedList.get(name) : null;
 								newPkg= new RPkgInfo(name, RNumVersion.create(version), built,
 										decodeDescrField(
 												store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_TITLE)) ),
 										libLocation,
 										0,
 										event.stamp,
 										(expectedData != null) ? expectedData.getRepoId() : null );

 								changeSet.names.add(name);
 								if (oldPkg == null) {
 									changeSet.added.add(newPkg);
 								}
 								else {
 									changeSet.changed.add(oldPkg);
 								}
 							}

 							newList.add(newPkg);
 						}
 					}
 					if (oldList != null) {
 						int i= 0, j= 0;
 						final int in= oldList.size(), jn= newList.size();
 						while (i < in) {
 							final IRPkgInfo oldPkg= oldList.get(i++);
 							final String name= oldPkg.getName();
 							if (j < jn) {
 								if (newList.get(j).getName() == name) {
 									j++;
 									continue;
 								}
 								final int idx= newList.indexOf(name, j + 1);
 								if (idx >= 0) {
 									j= idx + 1;
 									continue;
 								}
 							}
 							changeSet.names.add(name);
 							changeSet.deleted.add(oldPkg);
 						}
 					}

 					newInstalled.add(libLocation.getDirectory(), newList);
 				}
 				else {
 					final RPkgList<IRPkgInfo> prevList= prevInstalled.getBySource(libLocation.getDirectory());
 					if (prevList != null) {
 						newInstalled.add(libLocation.getDirectory(), prevList);
 					}
 					else {
 						// error/warning?
 					}
 				}
 			}

 			clearExpected();

 			return newInstalled;
 		}
 		catch (final UnexpectedRDataException | StatusException e) {
 			throw new StatusException(new ErrorStatus(RCore.BUNDLE_ID,
 					"An error occurred when loading list of installed R packages.",
 					e ));
 		}
 	}

 	void updateInstFull(final RuntimeRLibPaths rLibPaths, final boolean[] update,
 			final FullRPkgSet newPkgs, final Change event,
 			final RService r, final ProgressMonitor m) throws StatusException {
 		m.beginSubTask("Updating installed R packages...");
 		try {
 			final FullRPkgSet oldFullPkgs= (event.oldPkgs instanceof FullRPkgSet) ?
 					(FullRPkgSet) event.oldPkgs : null;
 			final RPkgChangeSet changeSet= new RPkgChangeSet();
 			event.installedPkgs= changeSet;
 			for (final RLibLocation location : rLibPaths.getRLibLocations()) {
 				final RLibLocationInfo locationInfo= rLibPaths.getInfo(location);
 				if (locationInfo == null || locationInfo.getLibPathsIndex() < 0) {
 					continue;
 				}
 				if (update == null || update[locationInfo.getLibPathsIndex()] || oldFullPkgs == null) {
 					final RArray<RCharacterStore> data;
 					{	final FunctionCall call= r.createFunctionCall(INST_LIST_FNAME);
 						call.addChar("lib", locationInfo.getDirectoryRPath()); //$NON-NLS-1$
 						data= RDataUtils.checkRCharArray(call.evalData(m), 2);
 						RDataUtils.checkColumnCountEqual(data, INST_LIST_COUNT1);
 					}
 					final RCharacterStore store= data.getData();
 					final int nPkgs= data.getDim().getInt(0);

 					final RPkgList<? extends IRPkgInfo> oldList= (event.oldPkgs != null) ?
 							event.oldPkgs.getInstalled().getBySource(location.getDirectory()) : null;
 					final RPkgListImpl<RPkgInfoAndData> newList= new RPkgListImpl<>(nPkgs);
 					final RPkgList<IRPkgData> expectedList= this.expectedPkgs.getBySource(location.getDirectory());
 					for (int idxPkg= 0; idxPkg < nPkgs; idxPkg++) {
 						String name= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_NAME));
 						final String version= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_VERSION));
 						if (name != null && !name.isEmpty() && version != null && !version.isEmpty()) {
 							name= name.intern();
 							String built= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_BUILT));
 							if (built == null) {
 								built= ""; //$NON-NLS-1$
 							}
 							final IRPkgInfo oldPkg= (oldList != null) ? oldList.get(name) : null;
 							final RPkgInfoAndData newPkg;
 							final boolean changed= (oldPkg == null
 									|| !oldPkg.getVersion().toString().equals(version)
 									|| !oldPkg.getBuilt().equals(built) );

 							if (!changed && (oldPkg instanceof RPkgInfoAndData)) {
 								newPkg= (RPkgInfoAndData) oldPkg;
 							}
 							else {
 								final IRPkgData expectedData= (changed && expectedList != null) ?
 										expectedList.get(name) : null;
 								newPkg= new RPkgInfoAndData(name,
 										(!changed) ? oldPkg.getVersion() : RNumVersion.create(version),
 										built,
 										decodeDescrField(
 												store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_TITLE)) ),
 										location,
 										(!changed) ? oldPkg.getFlags() : 0,
 										(!changed) ? oldPkg.getInstallStamp() : event.stamp,
 										(!changed) ? oldPkg.getRepoId() : ((expectedData != null) ? expectedData.getRepoId() : null) );

 								RCharacterStore detail;
 								{	final FunctionCall call= r.createFunctionCall(INST_DETAIL_FNAME);
 									call.addChar("lib", locationInfo.getDirectoryRPath()); //$NON-NLS-1$
 									call.addChar("name", name); //$NON-NLS-1$
 									detail= RDataUtils.checkRCharVector(call.evalData(m)).getData();
 									RDataUtils.checkLengthEqual(detail, INST_DETAIL_LENGTH);
 								}

 								newPkg.setPriority(detail.getChar(INST_DETAIL_IDX_PRIORITY));
 								newPkg.setLicense(detail.getChar(INST_DETAIL_IDX_LICENSE));

 								newPkg.setDepends(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_DEPENDS)));
 								newPkg.setImports(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_IMPORTS)));
 								newPkg.setLinkingTo(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_LINKINGTO)));
 								newPkg.setSuggests(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_SUGGESTS)));
 								newPkg.setEnhances(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_ENHANCES)));

 								if (changed) {
 									changeSet.names.add(name);
 									if (oldPkg == null) {
 										changeSet.added.add(newPkg);
 									}
 									else {
 										changeSet.changed.add(oldPkg);
 									}
 								}
 							}

 							newList.add(newPkg);
 						}
 					}
 					if (oldList != null) {
 						int i= 0, j= 0;
 						final int in= oldList.size(), jn= newList.size();
 						while (i < in) {
 							final IRPkgInfo oldPkg= oldList.get(i++);
 							final String name= oldPkg.getName();
 							if (j < jn) {
 								if (newList.get(j).getName() == name) {
 									j++;
 									continue;
 								}
 								final int idx= newList.indexOf(name, j + 1);
 								if (idx >= 0) {
 									j= idx + 1;
 									continue;
 								}
 							}
 							changeSet.names.add(name);
 							changeSet.deleted.add(oldPkg);
 						}
 					}

 					newPkgs.getInstalled().add(location.getDirectory(), newList);
 				}
 				else {
 					newPkgs.getInstalled().add(location.getDirectory(),
 							oldFullPkgs.getInstalled().getBySource(location.getDirectory()) );
 				}
 			}
 			return;
 		}
 		catch (final UnexpectedRDataException | StatusException e) {
 			throw new StatusException(new ErrorStatus(RCore.BUNDLE_ID,
 					"An error occurred when loading list of installed R packages.",
 					e ));
 		}
 	}

 }
	/*=============================================================================#
	# Copyright (c) 2012, 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.r.core.pkgmanager;

	import java.util.ArrayList;
	import java.util.Collections;
	import java.util.List;

	import org.eclipse.osgi.util.NLS;

	import org.eclipse.statet.jcommons.lang.Nullable;
	import org.eclipse.statet.jcommons.status.ErrorStatus;
	import org.eclipse.statet.jcommons.status.ProgressMonitor;
	import org.eclipse.statet.jcommons.status.StatusException;

	import org.eclipse.statet.r.core.RCore;
	import org.eclipse.statet.r.core.pkgmanager.IRPkgData;
	import org.eclipse.statet.r.core.pkgmanager.IRPkgInfo;
	import org.eclipse.statet.r.core.pkgmanager.ISelectedRepos;
	import org.eclipse.statet.r.core.pkgmanager.RPkgInfo;
	import org.eclipse.statet.r.core.pkgmanager.RPkgUtils;
	import org.eclipse.statet.r.core.pkgmanager.RRepo;
	import org.eclipse.statet.rj.data.RArray;
	import org.eclipse.statet.rj.data.RCharacterStore;
	import org.eclipse.statet.rj.data.RDataUtils;
	import org.eclipse.statet.rj.data.UnexpectedRDataException;
	import org.eclipse.statet.rj.renv.core.BasicRPkg;
	import org.eclipse.statet.rj.renv.core.BasicRPkgCompilation;
	import org.eclipse.statet.rj.renv.core.REnv;
	import org.eclipse.statet.rj.renv.core.RLibLocation;
	import org.eclipse.statet.rj.renv.core.RNumVersion;
	import org.eclipse.statet.rj.renv.core.RPkg;
	import org.eclipse.statet.rj.renv.core.RPkgCompilation;
	import org.eclipse.statet.rj.renv.core.RPkgList;
	import org.eclipse.statet.rj.renv.runtime.RLibLocationInfo;
	import org.eclipse.statet.rj.renv.runtime.RuntimeRLibPaths;
	import org.eclipse.statet.rj.services.FunctionCall;
	import org.eclipse.statet.rj.services.RService;


	final class RPkgScanner {

	private static final String AVAIL_LIST_FNAME= "rj:::renv.getAvailPkgs"; //$NON-NLS-1$
	private static final int AVAIL_LIST_COUNT1= 9;
	private static final int AVAIL_LIST_IDX1_NAME= 0;
	private static final int AVAIL_LIST_IDX1_VERSION= 1;
	private static final int AVAIL_LIST_IDX1_PRIORITY= 2;
	private static final int AVAIL_LIST_IDX1_LICENSE= 3;
	private static final int AVAIL_LIST_IDX1_DEPENDS= 4;
	private static final int AVAIL_LIST_IDX1_IMPORTS= 5;
	private static final int AVAIL_LIST_IDX1_LINKINGTO= 6;
	private static final int AVAIL_LIST_IDX1_SUGGESTS= 7;
	private static final int AVAIL_LIST_IDX1_ENHANCES= 8;

	private static final String INST_LIST_FNAME= "rj:::renv.getInstPkgs"; //$NON-NLS-1$
	private static final int INST_LIST_COUNT1= 4;
	private static final int INST_LIST_IDX1_NAME= 0;
	private static final int INST_LIST_IDX1_VERSION= 1;
	private static final int INST_LIST_IDX1_TITLE= 2;
	private static final int INST_LIST_IDX1_BUILT= 3;

	private static final String INST_DETAIL_FNAME= "rj:::renv.getInstPkgDetail"; //$NON-NLS-1$
	private static final int INST_DETAIL_LENGTH= 7;
	private static final int INST_DETAIL_IDX_PRIORITY= 0;
	private static final int INST_DETAIL_IDX_LICENSE= 1;
	private static final int INST_DETAIL_IDX_DEPENDS= 2;
	private static final int INST_DETAIL_IDX_IMPORTS= 3;
	private static final int INST_DETAIL_IDX_LINKINGTO= 4;
	private static final int INST_DETAIL_IDX_SUGGESTS= 5;
	private static final int INST_DETAIL_IDX_ENHANCES= 6;

	private static @Nullable String decodeDescrField(final @Nullable String s) {
	if (s == null) {
	return null;
	}
	int mode= 0; // 1= single space, 2= chars to replace
	int idxMode= 0;
	int idxDone= 0;
	StringBuilder sb= null;
	for (int idx = 0; idx < s.length(); idx++) {
	switch (s.charAt(idx)) {
	case 0x00: case 0x01: case 0x02: case 0x03: case 0x04: case 0x05: case 0x06: case 0x07:
	case 0x08: case 0x09: case 0x0A: case 0x0B: case 0x0C: case 0x0D: case 0x0E: case 0x0F:
	case 0x7F:
	switch (mode) {
	case 0:
	mode= 2;
	idxMode= idx;
	continue;
	case 1:
	mode= 2;
	continue;
	// case 2:
	default:
	continue;
	}
	case ' ':
	switch (mode) {
	case 0:
	mode= 1;
	idxMode= idx;
	continue;
	case 1:
	mode= 2;
	continue;
	// case 2:
	default:
	continue;
	}
	default:
	switch (mode) {
	case 0:
	continue;
	case 1:
	mode= 0;
	continue;
	// case 2:
	default:
	if (sb == null) {
	sb= new StringBuilder(s.length());
	}
	sb.append(s, idxDone, idxMode);
	sb.append(' ');
	idxDone= idx + 1;
	mode= 0;
	continue;
	}
	}
	}
	if (sb != null) {
	sb.append(s, idxDone, (mode == 0) ? s.length() : idxMode);
	return sb.toString();
	}
	else {
	return (mode == 0) ? s : s.substring(0, idxMode);
	}
	}


	private static List<RPkg> parsePkgRefs(final String s) {
	if (s == null \|\| s.isEmpty()) {
	return Collections.emptyList();
	}
	final List<RPkg> list= new ArrayList<>(4);
	String name= null;
	String version= null;
	boolean ws;
	final StringBuilder sb= new StringBuilder();
	ITER_S: for (int i= 0; i <= s.length();) {
	int c= (i < s.length()) ? s.charAt(i) : -1;

	if (c == -1 \|\| c == ',') {
	if (name != null) {
	list.add(new BasicRPkg(name, RNumVersion.create(version)));
	}
	name= null;
	version= null;
	i++;
	continue ITER_S;
	}
	if (Character.isLetterOrDigit(c)) {
	if (name != null) {
	// ?
	}
	name= null;
	version= null;
	int j= i + 1;
	while (true) {
	c= (j < s.length()) ? s.charAt(j) : -1;
	if (c < 0 \|\| Character.isWhitespace(c) \|\| c == '(' \|\| c == ',') {
	name= s.substring(i, j).intern();
	i= j;
	continue ITER_S;
	}
	j++;
	}
	}
	if (c == '(') {
	if (name == null \|\| version != null) {
	// ?
	name= null;
	version= null;
	}
	sb.setLength(0);
	ws= false;
	int j= ++i;
	while (true) {
	c= (j < s.length()) ? s.charAt(j) : -1;
	if (c < 0 \|\| c == ')') {
	version= sb.toString();
	i= j + 1;
	continue ITER_S;
	}
	if (Character.isWhitespace(c)) {
	ws= true;
	}
	else {
	if (ws) {
	sb.append(' ');
	ws= false;
	}
	sb.append((char) c);
	}
	j++;
	}
	}

	i++;
	continue ITER_S;
	}
	return list;
	}


	private final BasicRPkgCompilation<IRPkgData> expectedPkgs= new BasicRPkgCompilation<IRPkgData>(4) {
	@Override
	protected RPkgList<IRPkgData> newPkgList() {
	return new RPkgListImpl<>(4);
	}
	};


	public RPkgScanner() {
	}


	void addExpectedPkg(final RLibLocation location, final IRPkgData pkg) {
	final String path= location.getDirectory();
	final RPkgListImpl<IRPkgData> list= (RPkgListImpl<IRPkgData>) this.expectedPkgs.getOrAdd(path);
	list.set(pkg);
	}

	private void clearExpected() {
	final List<RPkgList<IRPkgData>> all= this.expectedPkgs.getAll();
	for (final RPkgList<IRPkgData> list : all) {
	((RPkgListImpl<IRPkgData>) list).clear();
	}
	}


	RPkgCompilation<IRPkgData> loadAvailable(final REnv rEnv, final ISelectedRepos repoSettings,
	final RService r, final ProgressMonitor m) throws StatusException {
	m.beginSubTask("Loading available R packages...");
	try {
	final RCharacterStore repos= RDataUtils.checkRCharVector(r.evalData(
	"options('repos')[[1L]]", m)).getData(); //$NON-NLS-1$
	final int l= RDataUtils.checkIntLength(repos);

	final BasicRPkgCompilation<IRPkgData> newAvailable= new BasicRPkgCompilation<>(l);
	for (int idxRepos= 0; idxRepos < l; idxRepos++) {
	final String repoURL= repos.getChar(idxRepos);
	if (repoURL == null \|\| repoURL.isEmpty()) {
	continue;
	}
	final RRepo repo= Util.getRepoByURL(repoSettings.getRepos(), repoURL);
	m.beginSubTask(NLS.bind("Loading available R packages from {0}...", repoURL));

	RArray<RCharacterStore> data;
	{ final FunctionCall call= r.createFunctionCall(AVAIL_LIST_FNAME);
	call.addChar("repo", repoURL); //$NON-NLS-1$
	if (repo.getPkgType() != null) {
	final String key= RPkgUtils.getPkgTypeInstallKey(r.getPlatform(), repo.getPkgType());
	if (key == null) {
	continue;
	}
	}
	data= RDataUtils.checkRCharArray(call.evalData(m), 2);
	RDataUtils.checkColumnCountEqual(data, AVAIL_LIST_COUNT1);
	}

	final RCharacterStore store= data.getData();
	final int nPkgs= data.getDim().getInt(0);
	final RPkgListImpl<IRPkgData> list= new RPkgListImpl<>(nPkgs);
	newAvailable.add(repo.getId(), list);

	for (int idxPkgs= 0; idxPkgs < nPkgs; idxPkgs++) {
	String name= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_NAME));
	final String version= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_VERSION));
	if (name != null && !name.isEmpty() && version != null) {
	name= name.intern();
	final RPkgData pkg= new RPkgData(name, RNumVersion.create(version), repo.getId());

	pkg.setLicense(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_LICENSE)));

	pkg.setDepends(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_DEPENDS))));
	pkg.setImports(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_IMPORTS))));
	pkg.setLinkingTo(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_LINKINGTO))));
	pkg.setSuggests(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_SUGGESTS))));
	pkg.setEnhances(RPkgScanner.parsePkgRefs(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_ENHANCES))));

	pkg.setPriority(store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkgs, AVAIL_LIST_IDX1_PRIORITY)));

	list.add(pkg);
	}
	}
	}

	return newAvailable;
	}
	catch (final UnexpectedRDataException \| StatusException e) {
	throw new StatusException(new ErrorStatus(RCore.BUNDLE_ID,
	"An error occurred when loading list of available R packages.",
	e ));
	}
	}

	RPkgCompilation<IRPkgInfo> loadInstalled(final RuntimeRLibPaths rLibPaths, final boolean[] update,
	final Change event,
	final RService r, final ProgressMonitor m) throws StatusException {
	m.beginSubTask("Updating installed R packages...");
	try {
	final BasicRPkgCompilation<IRPkgInfo> newInstalled= new BasicRPkgCompilation<>(
	rLibPaths.getRLibLocations().size() );
	final RPkgCompilation<IRPkgInfo> prevInstalled= (RPkgCompilation<IRPkgInfo>)
	((event.oldPkgs != null) ? event.oldPkgs.getInstalled() : null);
	final RPkgChangeSet changeSet= new RPkgChangeSet();
	event.installedPkgs= changeSet;
	for (final RLibLocation libLocation : rLibPaths.getRLibLocations()) {
	final RLibLocationInfo locationInfo= rLibPaths.getInfo(libLocation);
	if (locationInfo == null \|\| locationInfo.getLibPathsIndex() < 0) {
	continue;
	}
	if (newInstalled.getBySource(libLocation.getDirectory()) != null) {
	continue;
	}
	if (update == null \|\| update[locationInfo.getLibPathsIndex()] \|\| prevInstalled == null) {
	final RArray<RCharacterStore> data;
	{ final FunctionCall call= r.createFunctionCall(INST_LIST_FNAME);
	call.addChar("lib", locationInfo.getDirectoryRPath()); //$NON-NLS-1$
	data= RDataUtils.checkRCharArray(call.evalData(m), 2);
	RDataUtils.checkColumnCountEqual(data, INST_LIST_COUNT1);
	}
	final RCharacterStore store= data.getData();
	final int nPkgs= data.getDim().getInt(0);

	final RPkgList<IRPkgInfo> oldList= (prevInstalled != null) ?
	prevInstalled.getBySource(libLocation.getDirectory()) : null;
	final RPkgListImpl<IRPkgInfo> newList= new RPkgListImpl<>(nPkgs);
	final RPkgList<IRPkgData> expectedList= this.expectedPkgs.getBySource(libLocation.getDirectory());
	for (int idxPkg= 0; idxPkg < nPkgs; idxPkg++) {
	String name= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_NAME));
	final String version= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_VERSION));
	if (name != null && !name.isEmpty() && version != null && !version.isEmpty()) {
	name= name.intern();
	String built= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_BUILT));
	if (built == null) {
	built= ""; //$NON-NLS-1$
	}
	final IRPkgInfo oldPkg= (oldList != null) ? oldList.get(name) : null;
	final IRPkgInfo newPkg;
	final boolean changed= (oldPkg == null
	\|\| !oldPkg.getVersion().toString().equals(version)
	\|\| !oldPkg.getBuilt().equals(built) );

	if (!changed) {
	newPkg= oldPkg;
	}
	else {
	final IRPkgData expectedData =
	(expectedList != null) ? expectedList.get(name) : null;
	newPkg= new RPkgInfo(name, RNumVersion.create(version), built,
	decodeDescrField(
	store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_TITLE)) ),
	libLocation,
	0,
	event.stamp,
	(expectedData != null) ? expectedData.getRepoId() : null );

	changeSet.names.add(name);
	if (oldPkg == null) {
	changeSet.added.add(newPkg);
	}
	else {
	changeSet.changed.add(oldPkg);
	}
	}

	newList.add(newPkg);
	}
	}
	if (oldList != null) {
	int i= 0, j= 0;
	final int in= oldList.size(), jn= newList.size();
	while (i < in) {
	final IRPkgInfo oldPkg= oldList.get(i++);
	final String name= oldPkg.getName();
	if (j < jn) {
	if (newList.get(j).getName() == name) {
	j++;
	continue;
	}
	final int idx= newList.indexOf(name, j + 1);
	if (idx >= 0) {
	j= idx + 1;
	continue;
	}
	}
	changeSet.names.add(name);
	changeSet.deleted.add(oldPkg);
	}
	}

	newInstalled.add(libLocation.getDirectory(), newList);
	}
	else {
	final RPkgList<IRPkgInfo> prevList= prevInstalled.getBySource(libLocation.getDirectory());
	if (prevList != null) {
	newInstalled.add(libLocation.getDirectory(), prevList);
	}
	else {
	// error/warning?
	}
	}
	}

	clearExpected();

	return newInstalled;
	}
	catch (final UnexpectedRDataException \| StatusException e) {
	throw new StatusException(new ErrorStatus(RCore.BUNDLE_ID,
	"An error occurred when loading list of installed R packages.",
	e ));
	}
	}

	void updateInstFull(final RuntimeRLibPaths rLibPaths, final boolean[] update,
	final FullRPkgSet newPkgs, final Change event,
	final RService r, final ProgressMonitor m) throws StatusException {
	m.beginSubTask("Updating installed R packages...");
	try {
	final FullRPkgSet oldFullPkgs= (event.oldPkgs instanceof FullRPkgSet) ?
	(FullRPkgSet) event.oldPkgs : null;
	final RPkgChangeSet changeSet= new RPkgChangeSet();
	event.installedPkgs= changeSet;
	for (final RLibLocation location : rLibPaths.getRLibLocations()) {
	final RLibLocationInfo locationInfo= rLibPaths.getInfo(location);
	if (locationInfo == null \|\| locationInfo.getLibPathsIndex() < 0) {
	continue;
	}
	if (update == null \|\| update[locationInfo.getLibPathsIndex()] \|\| oldFullPkgs == null) {
	final RArray<RCharacterStore> data;
	{ final FunctionCall call= r.createFunctionCall(INST_LIST_FNAME);
	call.addChar("lib", locationInfo.getDirectoryRPath()); //$NON-NLS-1$
	data= RDataUtils.checkRCharArray(call.evalData(m), 2);
	RDataUtils.checkColumnCountEqual(data, INST_LIST_COUNT1);
	}
	final RCharacterStore store= data.getData();
	final int nPkgs= data.getDim().getInt(0);

	final RPkgList<? extends IRPkgInfo> oldList= (event.oldPkgs != null) ?
	event.oldPkgs.getInstalled().getBySource(location.getDirectory()) : null;
	final RPkgListImpl<RPkgInfoAndData> newList= new RPkgListImpl<>(nPkgs);
	final RPkgList<IRPkgData> expectedList= this.expectedPkgs.getBySource(location.getDirectory());
	for (int idxPkg= 0; idxPkg < nPkgs; idxPkg++) {
	String name= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_NAME));
	final String version= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_VERSION));
	if (name != null && !name.isEmpty() && version != null && !version.isEmpty()) {
	name= name.intern();
	String built= store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_BUILT));
	if (built == null) {
	built= ""; //$NON-NLS-1$
	}
	final IRPkgInfo oldPkg= (oldList != null) ? oldList.get(name) : null;
	final RPkgInfoAndData newPkg;
	final boolean changed= (oldPkg == null
	\|\| !oldPkg.getVersion().toString().equals(version)
	\|\| !oldPkg.getBuilt().equals(built) );

	if (!changed && (oldPkg instanceof RPkgInfoAndData)) {
	newPkg= (RPkgInfoAndData) oldPkg;
	}
	else {
	final IRPkgData expectedData= (changed && expectedList != null) ?
	expectedList.get(name) : null;
	newPkg= new RPkgInfoAndData(name,
	(!changed) ? oldPkg.getVersion() : RNumVersion.create(version),
	built,
	decodeDescrField(
	store.getChar(RDataUtils.getDataIdx(nPkgs, idxPkg, INST_LIST_IDX1_TITLE)) ),
	location,
	(!changed) ? oldPkg.getFlags() : 0,
	(!changed) ? oldPkg.getInstallStamp() : event.stamp,
	(!changed) ? oldPkg.getRepoId() : ((expectedData != null) ? expectedData.getRepoId() : null) );

	RCharacterStore detail;
	{ final FunctionCall call= r.createFunctionCall(INST_DETAIL_FNAME);
	call.addChar("lib", locationInfo.getDirectoryRPath()); //$NON-NLS-1$
	call.addChar("name", name); //$NON-NLS-1$
	detail= RDataUtils.checkRCharVector(call.evalData(m)).getData();
	RDataUtils.checkLengthEqual(detail, INST_DETAIL_LENGTH);
	}

	newPkg.setPriority(detail.getChar(INST_DETAIL_IDX_PRIORITY));
	newPkg.setLicense(detail.getChar(INST_DETAIL_IDX_LICENSE));

	newPkg.setDepends(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_DEPENDS)));
	newPkg.setImports(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_IMPORTS)));
	newPkg.setLinkingTo(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_LINKINGTO)));
	newPkg.setSuggests(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_SUGGESTS)));
	newPkg.setEnhances(RPkgScanner.parsePkgRefs(detail.getChar(INST_DETAIL_IDX_ENHANCES)));

	if (changed) {
	changeSet.names.add(name);
	if (oldPkg == null) {
	changeSet.added.add(newPkg);
	}
	else {
	changeSet.changed.add(oldPkg);
	}
	}
	}

	newList.add(newPkg);
	}
	}
	if (oldList != null) {
	int i= 0, j= 0;
	final int in= oldList.size(), jn= newList.size();
	while (i < in) {
	final IRPkgInfo oldPkg= oldList.get(i++);
	final String name= oldPkg.getName();
	if (j < jn) {
	if (newList.get(j).getName() == name) {
	j++;
	continue;
	}
	final int idx= newList.indexOf(name, j + 1);
	if (idx >= 0) {
	j= idx + 1;
	continue;
	}
	}
	changeSet.names.add(name);
	changeSet.deleted.add(oldPkg);
	}
	}

	newPkgs.getInstalled().add(location.getDirectory(), newList);
	}
	else {
	newPkgs.getInstalled().add(location.getDirectory(),
	oldFullPkgs.getInstalled().getBySource(location.getDirectory()) );
	}
	}
	return;
	}
	catch (final UnexpectedRDataException \| StatusException e) {
	throw new StatusException(new ErrorStatus(RCore.BUNDLE_ID,
	"An error occurred when loading list of installed R packages.",
	e ));
	}
	}

	}