Fix handling of symlinked projects

- HistoryGuru etc. will operate correctly and no
  longer throw exceptions.
- index.jsp will show symlinked projects.
- Fix macOS regression in Oracle PR #1846.

Author: idodeclare

src/org/opensolaris/opengrok/configuration/RuntimeEnvironment.java

@@ -100,6 +100,7 @@
 import static java.nio.file.StandardWatchEventKinds.ENTRY_DELETE;
 import static java.nio.file.StandardWatchEventKinds.ENTRY_MODIFY;
 import static org.opensolaris.opengrok.configuration.Configuration.makeXMLStringAsConfiguration;
+import org.opensolaris.opengrok.util.PathUtils;
 
 /**
  * The RuntimeEnvironment class is used as a placeholder for the current
@@ -135,7 +136,7 @@ public final class RuntimeEnvironment {
 
     private Statistics statistics = new Statistics();
 
-    private static IndexTimestamp indexTime = new IndexTimestamp();
+    private static final IndexTimestamp indexTime = new IndexTimestamp();
 
     /**
      * Instance of authorization framework.
@@ -390,24 +391,24 @@ public String getPathRelativeToSourceRoot(File file) throws IOException {
      * @return Path relative to source root
      */
     public String getPathRelativeToSourceRoot(File file, int stripCount) throws IOException {
-        String canonicalPath = file.getCanonicalPath();
         String sourceRoot = getSourceRootPath();
-        
-        if(sourceRoot == null){
+        if (sourceRoot == null) {
             throw new FileNotFoundException("Source Root Not Found");
         }
-        
-        if (canonicalPath.startsWith(sourceRoot)) {
-            return canonicalPath.substring(sourceRoot.length() + stripCount);
-        }
-        for (String allowedSymlink : getAllowedSymlinks()) {
-            String allowedTarget = new File(allowedSymlink).getCanonicalPath();
-            if (canonicalPath.startsWith(allowedTarget)) {
-                return canonicalPath.substring(allowedTarget.length()
-                        + stripCount);
-            }
+
+        String maybeRelPath = PathUtils.getRelativeToCanonical(file.getPath(),
+            sourceRoot, getAllowedSymlinks());
+        File maybeRelFile = new File(maybeRelPath);
+        if (!maybeRelFile.isAbsolute()) {
+            // N.b. OpenGrok has a weird convention that
+            // source-root "relative" paths must start with a '/' as they are
+            // elsewhere directly appended to env.getSourceRootPath() and also
+            // stored as such.
+            maybeRelPath = File.separator + maybeRelPath;
+            return maybeRelPath.substring(stripCount);
         }
-        throw new FileNotFoundException("Failed to resolve [" + canonicalPath
+
+        throw new FileNotFoundException("Failed to resolve [" + file.getPath()
                 + "] relative to source root [" + sourceRoot + "]");
     }
 
@@ -1717,7 +1718,7 @@ public void applyConfig(Message m, boolean reindex) {
         try {
             config = makeXMLStringAsConfiguration(m.getText());
         } catch (IOException ex) {
-            LOGGER.log(Level.WARNING, "Configuration decoding failed" + ex);
+            LOGGER.log(Level.WARNING, "Configuration decoding failed", ex);
             return;
         }
 

src/org/opensolaris/opengrok/history/BazaarRepository.java

@@ -19,6 +19,7 @@
 
 /*
  * Copyright (c) 2008, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 package org.opensolaris.opengrok.history;
 
@@ -80,11 +81,7 @@ public BazaarRepository() {
      */
     Executor getHistoryLogExecutor(final File file, final String sinceRevision)
             throws IOException {
-        String abs = file.getCanonicalPath();
-        String filename = "";
-        if (abs.length() > getDirectoryName().length()) {
-            filename = abs.substring(getDirectoryName().length() + 1);
-        }
+        String filename = getRepoRelativePath(file);
 
         List<String> cmd = new ArrayList<String>();
         ensureCommand(CMD_PROPERTY_KEY, CMD_FALLBACK);

src/org/opensolaris/opengrok/history/CVSRepository.java

@@ -19,6 +19,7 @@
 
 /*
  * Copyright (c) 2008, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 package org.opensolaris.opengrok.history;
 
@@ -96,8 +97,8 @@ public boolean isWorking() {
     }
 
     @Override
-    public void setDirectoryName(String directoryName) {
-        super.setDirectoryName(directoryName);
+    public void setDirectoryName(File directory) {
+        super.setDirectoryName(directory);
 
         if (isWorking()) {
             File rootFile = new File(getDirectoryName() + File.separatorChar
@@ -195,11 +196,7 @@ String determineBranch() throws IOException {
      * @return An Executor ready to be started
      */
     Executor getHistoryLogExecutor(final File file) throws IOException {
-        String abs = file.getCanonicalPath();
-        String filename = "";
-        if (abs.length() > getDirectoryName().length()) {
-            filename = abs.substring(getDirectoryName().length() + 1);
-        }
+        String filename = getRepoRelativePath(file);
 
         List<String> cmd = new ArrayList<>();
         ensureCommand(CMD_PROPERTY_KEY, CMD_FALLBACK);

src/org/opensolaris/opengrok/history/ClearCaseRepository.java

@@ -19,6 +19,7 @@
 
 /*
  * Copyright (c) 2008, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 package org.opensolaris.opengrok.history;
 
@@ -93,11 +94,7 @@ public void setVerbose(boolean verbose) {
      * @return An Executor ready to be started
      */
     Executor getHistoryLogExecutor(final File file) throws IOException {
-        String abs = file.getCanonicalPath();
-        String filename = "";
-        if (abs.length() > getDirectoryName().length()) {
-            filename = abs.substring(getDirectoryName().length() + 1);
-        }
+        String filename = getRepoRelativePath(file);
 
         List<String> cmd = new ArrayList<>();
         ensureCommand(CMD_PROPERTY_KEY, CMD_FALLBACK);

src/org/opensolaris/opengrok/history/GitRepository.java

@@ -17,8 +17,9 @@
  * CDDL HEADER END
  */
 
- /*
+/*
  * Copyright (c) 2008, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 package org.opensolaris.opengrok.history;
 
@@ -31,7 +32,6 @@
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.text.ParseException;
-import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.LinkedList;
@@ -116,11 +116,7 @@ public GitRepository() {
     Executor getHistoryLogExecutor(final File file, String sinceRevision)
             throws IOException {
 
-        String abs = file.getCanonicalPath();
-        String filename = "";
-        if (abs.length() > getDirectoryName().length()) {
-            filename = abs.substring(getDirectoryName().length() + 1);
-        }
+        String filename = getRepoRelativePath(file);
 
         List<String> cmd = new ArrayList<>();
         ensureCommand(CMD_PROPERTY_KEY, CMD_FALLBACK);

src/org/opensolaris/opengrok/history/HistoryGuru.java

@@ -19,6 +19,7 @@
 
 /*
  * Copyright (c) 2005, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 package org.opensolaris.opengrok.history;
 
@@ -27,6 +28,7 @@
 import java.io.InputStream;
 import java.lang.reflect.InvocationTargetException;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -39,7 +41,6 @@
 import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
-import java.util.concurrent.Semaphore;
 import java.util.concurrent.ThreadFactory;
 import java.util.concurrent.TimeUnit;
 import java.util.logging.Level;
@@ -49,6 +50,7 @@
 import org.opensolaris.opengrok.configuration.RuntimeEnvironment;
 import org.opensolaris.opengrok.index.IgnoredNames;
 import org.opensolaris.opengrok.logger.LoggerFactory;
+import org.opensolaris.opengrok.util.PathUtils;
 import org.opensolaris.opengrok.util.Statistics;
 
 /**
@@ -76,6 +78,12 @@ public final class HistoryGuru {
      */
     private Map<String, Repository> repositories = new ConcurrentHashMap<>();
 
+    /**
+     * set of repository roots (using ConcurrentHashMap but a throwaway value)
+     * with parent of {@code DirectoryName} as key
+     */
+    private Map<String, String> repositoryRoots = new ConcurrentHashMap<>();
+
     private final int scanningDepth;
 
     /**
@@ -415,7 +423,11 @@ private Collection<RepositoryInfo> addRepositories(File[] files,
                     }
 
                     repoList.add(new RepositoryInfo(repository));
-                    repositories.put(repository.getDirectoryName(), repository);
+                    String repoDirectoryName = repository.getDirectoryName();
+                    File repoDirectoryFile = new File(repoDirectoryName);
+                    String repoDirParent = repoDirectoryFile.getParent();
+                    repositoryRoots.put(repoDirParent, "");
+                    repositories.put(repoDirectoryName, repository);
 
                     // @TODO: Search only for one type of repository - the one found here
                     if (recursiveSearch && repository.supportsSubRepositories()) {
@@ -829,12 +841,27 @@ public void ensureHistoryCacheExists(File file) throws HistoryException {
 
     protected Repository getRepository(File path) {
         File file = path;
+        Set<String> rootKeys = repositoryRoots.keySet();
 
         while (file != null) {
-            Repository r = repositories.get(file.getAbsolutePath());
-            if (r != null) {
-                return r;
+            String nextPath = file.getPath();
+            for (String rootKey : rootKeys) {
+                String rel;
+                try {
+                    rel = PathUtils.getRelativeToCanonical(nextPath, rootKey);
+                } catch (IOException e) {
+                    LOGGER.log(Level.WARNING,
+                        "Failed to get relative to canonical for " + nextPath,
+                        e);
+                    return null;
+                }
+                String inRootPath = Paths.get(rootKey, rel).toString();
+                Repository r = repositories.get(inRootPath);
+                if (r != null) {
+                    return r;
+                }
             }
+
             file = file.getParentFile();
         }
 

src/org/opensolaris/opengrok/history/MercurialRepository.java

@@ -19,6 +19,7 @@
 
 /*
  * Copyright (c) 2006, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 package org.opensolaris.opengrok.history;
 
@@ -152,14 +153,9 @@ String determineBranch() throws IOException {
      */
     Executor getHistoryLogExecutor(File file, String sinceRevision)
             throws HistoryException, IOException {
-        String abs = file.getCanonicalPath();
-        String filename = "";
+        String filename = getRepoRelativePath(file);
         RuntimeEnvironment env = RuntimeEnvironment.getInstance();
 
-        if (abs.length() > getDirectoryName().length()) {
-            filename = abs.substring(getDirectoryName().length() + 1);
-        }
-
         List<String> cmd = new ArrayList<>();
         ensureCommand(CMD_PROPERTY_KEY, CMD_FALLBACK);
         cmd.add(RepoCommand);

src/org/opensolaris/opengrok/history/MonotoneRepository.java

@@ -19,6 +19,7 @@
 
 /*
  * Copyright (c) 2009, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 package org.opensolaris.opengrok.history;
 
@@ -124,11 +125,7 @@ public InputStream getHistoryGet(String parent, String basename, String rev) {
      */
     Executor getHistoryLogExecutor(File file, String sinceRevision)
             throws IOException {
-        String abs = file.getCanonicalPath();
-        String filename = "";
-        if (abs.length() > getDirectoryName().length()) {
-            filename = abs.substring(getDirectoryName().length() + 1);
-        }
+        String filename = getRepoRelativePath(file);
 
         List<String> cmd = new ArrayList<>();
         ensureCommand(CMD_PROPERTY_KEY, CMD_FALLBACK);

src/org/opensolaris/opengrok/history/RazorRepository.java

@@ -19,6 +19,7 @@
 
 /*
  * Copyright (c) 2008, 2017, Oracle and/or its affiliates. All rights reserved.
+ * Portions Copyright (c) 2017, Chris Fraire <[email protected]>.
  */
 /* Portions Copyright 2008 Peter Bray */
 package org.opensolaris.opengrok.history;
@@ -157,13 +158,12 @@ public RazorRepository() {
     }
 
     @Override
-    public void setDirectoryName(String directoryName) {
-        super.setDirectoryName(directoryName);
-        File opengrokBaseDirectory = new File(directoryName);
+    public void setDirectoryName(File directory) {
+        super.setDirectoryName(directory);
         opengrokSourceRootDirectoryPath
-                = opengrokBaseDirectory.getParentFile().getAbsolutePath();
+                = directory.getParentFile().getAbsolutePath();
         razorGroupBaseDirectoryPath
-                = new File(directoryName, RAZOR_DIR).getAbsolutePath();
+                = new File(directory, RAZOR_DIR).getAbsolutePath();
     }
 
     public String getOpengrokSourceRootDirectoryPath() {

src/org/opensolaris/opengrok/history/Repository.java

@@ -526,4 +526,25 @@ protected String ensureCommand(String propertyKey, String fallbackCommand) {
         }
         return RepoCommand;
     }
+
+    protected String getRepoRelativePath(final File file)
+            throws IOException {
+
+        String filename = file.getPath();
+        String repoDirName = getDirectoryName();
+
+        String abs = file.getCanonicalPath();
+        if (abs.startsWith(repoDirName)) {
+            if (abs.length() > repoDirName.length()) {
+                filename = abs.substring(repoDirName.length() + 1);
+            }
+        } else {
+            abs = file.getAbsolutePath();
+            if (abs.startsWith(repoDirName) && abs.length() >
+                repoDirName.length()) {
+                filename = abs.substring(repoDirName.length() + 1);
+            }
+        }
+        return filename;
+    }
 }