From 13417cf9c6eec555b51da49742e47939d2f5715b Mon Sep 17 00:00:00 2001
From: James Moger <james.moger@gitblit.com>
Date: Fri, 19 Oct 2012 22:47:33 -0400
Subject: [PATCH] Exclude submodules from zip downloads (issue 151)

---
 src/com/gitblit/utils/JGitUtils.java | 1447 +++++++++++++++++++++++++++++++++++++++++++++++++--------
 1 files changed, 1,227 insertions(+), 220 deletions(-)

diff --git a/src/com/gitblit/utils/JGitUtils.java b/src/com/gitblit/utils/JGitUtils.java
index 5656efb..bc44f00 100644
--- a/src/com/gitblit/utils/JGitUtils.java
+++ b/src/com/gitblit/utils/JGitUtils.java
@@ -20,22 +20,23 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
-import java.nio.charset.Charset;
+import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.regex.Pattern;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
 import org.eclipse.jgit.api.CloneCommand;
 import org.eclipse.jgit.api.FetchCommand;
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.diff.DiffEntry;
 import org.eclipse.jgit.diff.DiffEntry.ChangeType;
 import org.eclipse.jgit.diff.DiffFormatter;
@@ -44,23 +45,30 @@
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.errors.StopWalkException;
+import org.eclipse.jgit.lib.BlobBasedConfig;
+import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectInserter;
 import org.eclipse.jgit.lib.ObjectLoader;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefUpdate;
+import org.eclipse.jgit.lib.RefUpdate.Result;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryCache.FileKey;
-import org.eclipse.jgit.lib.StoredConfig;
+import org.eclipse.jgit.lib.TreeFormatter;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevSort;
 import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.revwalk.filter.CommitTimeRevFilter;
 import org.eclipse.jgit.revwalk.filter.RevFilter;
 import org.eclipse.jgit.storage.file.FileRepository;
+import org.eclipse.jgit.transport.CredentialsProvider;
 import org.eclipse.jgit.transport.FetchResult;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.treewalk.TreeWalk;
@@ -79,11 +87,48 @@
 import com.gitblit.models.PathModel;
 import com.gitblit.models.PathModel.PathChangeModel;
 import com.gitblit.models.RefModel;
+import com.gitblit.models.SubmoduleModel;
 
+/**
+ * Collection of static methods for retrieving information from a repository.
+ * 
+ * @author James Moger
+ * 
+ */
 public class JGitUtils {
 
 	static final Logger LOGGER = LoggerFactory.getLogger(JGitUtils.class);
 
+	/**
+	 * Log an error message and exception.
+	 * 
+	 * @param t
+	 * @param repository
+	 *            if repository is not null it MUST be the {0} parameter in the
+	 *            pattern.
+	 * @param pattern
+	 * @param objects
+	 */
+	private static void error(Throwable t, Repository repository, String pattern, Object... objects) {
+		List<Object> parameters = new ArrayList<Object>();
+		if (objects != null && objects.length > 0) {
+			for (Object o : objects) {
+				parameters.add(o);
+			}
+		}
+		if (repository != null) {
+			parameters.add(0, repository.getDirectory().getAbsolutePath());
+		}
+		LOGGER.error(MessageFormat.format(pattern, parameters.toArray()), t);
+	}
+
+	/**
+	 * Returns the displayable name of the person in the form "Real Name <email
+	 * address>".  If the email address is empty, just "Real Name" is returned.
+	 * 
+	 * @param person
+	 * @return "Real Name <email address>" or "Real Name"
+	 */
 	public static String getDisplayName(PersonIdent person) {
 		if (StringUtils.isEmpty(person.getEmailAddress())) {
 			return person.getName();
@@ -96,37 +141,98 @@
 		return r.toString().trim();
 	}
 
-	public static FetchResult cloneRepository(File repositoriesFolder, String name, String fromUrl)
+	/**
+	 * Encapsulates the result of cloning or pulling from a repository.
+	 */
+	public static class CloneResult {
+		public String name;
+		public FetchResult fetchResult;
+		public boolean createdRepository;
+	}
+
+	/**
+	 * Clone or Fetch a repository. If the local repository does not exist,
+	 * clone is called. If the repository does exist, fetch is called. By
+	 * default the clone/fetch retrieves the remote heads, tags, and notes.
+	 * 
+	 * @param repositoriesFolder
+	 * @param name
+	 * @param fromUrl
+	 * @return CloneResult
+	 * @throws Exception
+	 */
+	public static CloneResult cloneRepository(File repositoriesFolder, String name, String fromUrl)
 			throws Exception {
-		FetchResult result = null;
-		if (!name.toLowerCase().endsWith(Constants.DOT_GIT_EXT)) {
-			name += Constants.DOT_GIT_EXT;
+		return cloneRepository(repositoriesFolder, name, fromUrl, true, null);
+	}
+
+	/**
+	 * Clone or Fetch a repository. If the local repository does not exist,
+	 * clone is called. If the repository does exist, fetch is called. By
+	 * default the clone/fetch retrieves the remote heads, tags, and notes.
+	 * 
+	 * @param repositoriesFolder
+	 * @param name
+	 * @param fromUrl
+	 * @param bare
+	 * @param credentialsProvider
+	 * @return CloneResult
+	 * @throws Exception
+	 */
+	public static CloneResult cloneRepository(File repositoriesFolder, String name, String fromUrl,
+			boolean bare, CredentialsProvider credentialsProvider) throws Exception {
+		CloneResult result = new CloneResult();
+		if (bare) {
+			// bare repository, ensure .git suffix
+			if (!name.toLowerCase().endsWith(Constants.DOT_GIT_EXT)) {
+				name += Constants.DOT_GIT_EXT;
+			}
+		} else {
+			// normal repository, strip .git suffix
+			if (name.toLowerCase().endsWith(Constants.DOT_GIT_EXT)) {
+				name = name.substring(0, name.indexOf(Constants.DOT_GIT_EXT));
+			}
 		}
+		result.name = name;
+
 		File folder = new File(repositoriesFolder, name);
 		if (folder.exists()) {
 			File gitDir = FileKey.resolve(new File(repositoriesFolder, name), FS.DETECTED);
 			FileRepository repository = new FileRepository(gitDir);
-			result = fetchRepository(repository);
+			result.fetchResult = fetchRepository(credentialsProvider, repository);
 			repository.close();
 		} else {
 			CloneCommand clone = new CloneCommand();
-			clone.setBare(true);
+			clone.setBare(bare);
 			clone.setCloneAllBranches(true);
 			clone.setURI(fromUrl);
 			clone.setDirectory(folder);
-			clone.call();
+			if (credentialsProvider != null) {
+				clone.setCredentialsProvider(credentialsProvider);
+			}
+			Repository repository = clone.call().getRepository();
+			
 			// Now we have to fetch because CloneCommand doesn't fetch
 			// refs/notes nor does it allow manual RefSpec.
-			File gitDir = FileKey.resolve(new File(repositoriesFolder, name), FS.DETECTED);
-			FileRepository repository = new FileRepository(gitDir);
-			result = fetchRepository(repository);
+			result.createdRepository = true;
+			result.fetchResult = fetchRepository(credentialsProvider, repository);
 			repository.close();
 		}
 		return result;
 	}
 
-	public static FetchResult fetchRepository(Repository repository, RefSpec... refSpecs)
-			throws Exception {
+	/**
+	 * Fetch updates from the remote repository. If refSpecs is unspecifed,
+	 * remote heads, tags, and notes are retrieved.
+	 * 
+	 * @param credentialsProvider
+	 * @param repository
+	 * @param refSpecs
+	 * @return FetchResult
+	 * @throws Exception
+	 */
+	public static FetchResult fetchRepository(CredentialsProvider credentialsProvider,
+			Repository repository, RefSpec... refSpecs) throws Exception {
 		Git git = new Git(repository);
 		FetchCommand fetch = git.fetch();
 		List<RefSpec> specs = new ArrayList<RefSpec>();
@@ -137,153 +243,311 @@
 		} else {
 			specs.addAll(Arrays.asList(refSpecs));
 		}
+		if (credentialsProvider != null) {
+			fetch.setCredentialsProvider(credentialsProvider);
+		}
 		fetch.setRefSpecs(specs);
-		FetchResult result = fetch.call();
-		repository.close();
-		return result;
+		FetchResult fetchRes = fetch.call();
+		return fetchRes;
 	}
 
+	/**
+	 * Creates a bare repository.
+	 * 
+	 * @param repositoriesFolder
+	 * @param name
+	 * @return Repository
+	 */
 	public static Repository createRepository(File repositoriesFolder, String name) {
-		Git git = Git.init().setDirectory(new File(repositoriesFolder, name)).setBare(true).call();
-		return git.getRepository();
+		try {
+			Git git = Git.init().setDirectory(new File(repositoriesFolder, name)).setBare(true).call();
+			return git.getRepository();
+		} catch (GitAPIException e) {
+			throw new RuntimeException(e);
+		}
 	}
 
-	public static List<String> getRepositoryList(File repositoriesFolder, boolean exportAll,
-			boolean searchSubfolders) {
+	/**
+	 * Returns a list of repository names in the specified folder.
+	 * 
+	 * @param repositoriesFolder
+	 * @param onlyBare
+	 *            if true, only bare repositories repositories are listed. If
+	 *            false all repositories are included.
+	 * @param searchSubfolders
+	 *            recurse into subfolders to find grouped repositories
+	 * @param depth
+	 *            optional recursion depth, -1 = infinite recursion
+	 * @param exclusions
+	 *            list of regex exclusions for matching to folder names
+	 * @return list of repository names
+	 */
+	public static List<String> getRepositoryList(File repositoriesFolder, boolean onlyBare,
+			boolean searchSubfolders, int depth, List<String> exclusions) {
 		List<String> list = new ArrayList<String>();
 		if (repositoriesFolder == null || !repositoriesFolder.exists()) {
 			return list;
 		}
+		List<Pattern> patterns = new ArrayList<Pattern>();
+		if (!ArrayUtils.isEmpty(exclusions)) {
+			for (String regex : exclusions) {
+				patterns.add(Pattern.compile(regex));
+			}
+		}
 		list.addAll(getRepositoryList(repositoriesFolder.getAbsolutePath(), repositoriesFolder,
-				exportAll, searchSubfolders));
-		Collections.sort(list);
+				onlyBare, searchSubfolders, depth, patterns));
+		StringUtils.sortRepositorynames(list);
 		return list;
 	}
 
+	/**
+	 * Recursive function to find git repositories.
+	 * 
+	 * @param basePath
+	 *            basePath is stripped from the repository name as repositories
+	 *            are relative to this path
+	 * @param searchFolder
+	 * @param onlyBare
+	 *            if true only bare repositories will be listed. if false all
+	 *            repositories are included.
+	 * @param searchSubfolders
+	 *            recurse into subfolders to find grouped repositories
+	 * @param depth
+	 *            recursion depth, -1 = infinite recursion
+	 * @param patterns
+	 *            list of regex patterns for matching to folder names
+	 * @return
+	 */
 	private static List<String> getRepositoryList(String basePath, File searchFolder,
-			boolean exportAll, boolean searchSubfolders) {
+			boolean onlyBare, boolean searchSubfolders, int depth, List<Pattern> patterns) {
+		File baseFile = new File(basePath);
 		List<String> list = new ArrayList<String>();
+		if (depth == 0) {
+			return list;
+		}
+		
+		int nextDepth = (depth == -1) ? -1 : depth - 1;
 		for (File file : searchFolder.listFiles()) {
 			if (file.isDirectory()) {
+				boolean exclude = false;
+				for (Pattern pattern : patterns) {
+					String path = FileUtils.getRelativePath(baseFile, file).replace('\\',  '/');
+					if (pattern.matcher(path).matches()) {
+						LOGGER.debug(MessageFormat.format("excluding {0} because of rule {1}", path, pattern.pattern()));
+						exclude = true;
+						break;
+					}
+				}
+				if (exclude) {
+					// skip to next file
+					continue;
+				}
+
 				File gitDir = FileKey.resolve(new File(searchFolder, file.getName()), FS.DETECTED);
 				if (gitDir != null) {
-					boolean exportRepository = exportAll
-							|| new File(gitDir, "git-daemon-export-ok").exists();
-
-					if (!exportRepository) {
+					if (onlyBare && gitDir.getName().equals(".git")) {
 						continue;
 					}
-					// determine repository name relative to base path
-					String repository = StringUtils.getRelativePath(basePath,
-							file.getAbsolutePath());
-					list.add(repository);
-				} else if (searchSubfolders) {
+					if (gitDir.equals(file) || gitDir.getParentFile().equals(file)) {
+						// determine repository name relative to base path
+						String repository = FileUtils.getRelativePath(baseFile, file);
+						list.add(repository);
+					} else if (searchSubfolders && file.canRead()) {
+						// look for repositories in subfolders
+						list.addAll(getRepositoryList(basePath, file, onlyBare, searchSubfolders,
+								nextDepth, patterns));
+					}
+				} else if (searchSubfolders && file.canRead()) {
 					// look for repositories in subfolders
-					list.addAll(getRepositoryList(basePath, file, exportAll, searchSubfolders));
+					list.addAll(getRepositoryList(basePath, file, onlyBare, searchSubfolders,
+							nextDepth, patterns));
 				}
 			}
 		}
 		return list;
 	}
 
-	public static RevCommit getFirstCommit(Repository r, String branch) {
-		if (!hasCommits(r)) {
+	/**
+	 * Returns the first commit on a branch. If the repository does not exist or
+	 * is empty, null is returned.
+	 * 
+	 * @param repository
+	 * @param branch
+	 *            if unspecified, HEAD is assumed.
+	 * @return RevCommit
+	 */
+	public static RevCommit getFirstCommit(Repository repository, String branch) {
+		if (!hasCommits(repository)) {
 			return null;
-		}
-		if (StringUtils.isEmpty(branch)) {
-			branch = Constants.HEAD;
 		}
 		RevCommit commit = null;
 		try {
-			RevWalk walk = new RevWalk(r);
+			// resolve branch
+			ObjectId branchObject;
+			if (StringUtils.isEmpty(branch)) {
+				branchObject = getDefaultBranch(repository);
+			} else {
+				branchObject = repository.resolve(branch);
+			}
+
+			RevWalk walk = new RevWalk(repository);
 			walk.sort(RevSort.REVERSE);
-			RevCommit head = walk.parseCommit(r.resolve(branch));
+			RevCommit head = walk.parseCommit(branchObject);
 			walk.markStart(head);
 			commit = walk.next();
 			walk.dispose();
 		} catch (Throwable t) {
-			LOGGER.error("Failed to determine first commit", t);
+			error(t, repository, "{0} failed to determine first commit");
 		}
 		return commit;
 	}
 
-	public static Date getFirstChange(Repository r, String branch) {
-		RevCommit commit = getFirstCommit(r, branch);
+	/**
+	 * Returns the date of the first commit on a branch. If the repository does
+	 * not exist, Date(0) is returned. If the repository does exist bit is
+	 * empty, the last modified date of the repository folder is returned.
+	 * 
+	 * @param repository
+	 * @param branch
+	 *            if unspecified, HEAD is assumed.
+	 * @return Date of the first commit on a branch
+	 */
+	public static Date getFirstChange(Repository repository, String branch) {
+		RevCommit commit = getFirstCommit(repository, branch);
 		if (commit == null) {
-			if (r == null || !r.getDirectory().exists()) {
+			if (repository == null || !repository.getDirectory().exists()) {
 				return new Date(0);
 			}
 			// fresh repository
-			return new Date(r.getDirectory().lastModified());
+			return new Date(repository.getDirectory().lastModified());
 		}
 		return getCommitDate(commit);
 	}
 
-	public static boolean hasCommits(Repository r) {
-		if (r != null && r.getDirectory().exists()) {
-			return new File(r.getDirectory(), Constants.R_HEADS).list().length > 0;
+	/**
+	 * Determine if a repository has any commits. This is determined by checking
+	 * the for loose and packed objects.
+	 * 
+	 * @param repository
+	 * @return true if the repository has commits
+	 */
+	public static boolean hasCommits(Repository repository) {
+		if (repository != null && repository.getDirectory().exists()) {
+			return (new File(repository.getDirectory(), "objects").list().length > 2)
+					|| (new File(repository.getDirectory(), "objects/pack").list().length > 0);
 		}
 		return false;
 	}
 
-	public static Date getLastChange(Repository r) {
-		if (!hasCommits(r)) {
+	/**
+	 * Returns the date of the most recent commit on a branch. If the repository
+	 * does not exist Date(0) is returned. If it does exist but is empty, the
+	 * last modified date of the repository folder is returned.
+	 * 
+	 * @param repository
+	 * @return
+	 */
+	public static Date getLastChange(Repository repository) {
+		if (!hasCommits(repository)) {
 			// null repository
-			if (r == null) {
+			if (repository == null) {
 				return new Date(0);
 			}
 			// fresh repository
-			return new Date(r.getDirectory().lastModified());
+			return new Date(repository.getDirectory().lastModified());
 		}
-		RevCommit commit = getCommit(r, Constants.HEAD);
-		return getCommitDate(commit);
+
+		List<RefModel> branchModels = getLocalBranches(repository, true, -1);
+		if (branchModels.size() > 0) {
+			// find most recent branch update
+			Date lastChange = new Date(0);
+			for (RefModel branchModel : branchModels) {
+				if (branchModel.getDate().after(lastChange)) {
+					lastChange = branchModel.getDate();
+				}
+			}
+			return lastChange;
+		}
+		
+		// default to the repository folder modification date
+		return new Date(repository.getDirectory().lastModified());
 	}
 
+	/**
+	 * Retrieves a Java Date from a Git commit.
+	 * 
+	 * @param commit
+	 * @return date of the commit or Date(0) if the commit is null
+	 */
 	public static Date getCommitDate(RevCommit commit) {
+		if (commit == null) {
+			return new Date(0);
+		}
 		return new Date(commit.getCommitTime() * 1000L);
 	}
 
-	public static RevCommit getCommit(Repository r, String objectId) {
-		if (!hasCommits(r)) {
+	/**
+	 * Retrieves a Java Date from a Git commit.
+	 * 
+	 * @param commit
+	 * @return date of the commit or Date(0) if the commit is null
+	 */
+	public static Date getAuthorDate(RevCommit commit) {
+		if (commit == null) {
+			return new Date(0);
+		}
+		return commit.getAuthorIdent().getWhen();
+	}
+
+	/**
+	 * Returns the specified commit from the repository. If the repository does
+	 * not exist or is empty, null is returned.
+	 * 
+	 * @param repository
+	 * @param objectId
+	 *            if unspecified, HEAD is assumed.
+	 * @return RevCommit
+	 */
+	public static RevCommit getCommit(Repository repository, String objectId) {
+		if (!hasCommits(repository)) {
 			return null;
 		}
 		RevCommit commit = null;
 		try {
+			// resolve object id
+			ObjectId branchObject;
 			if (StringUtils.isEmpty(objectId)) {
-				objectId = Constants.HEAD;
+				branchObject = getDefaultBranch(repository);
+			} else {
+				branchObject = repository.resolve(objectId);
 			}
-			ObjectId object = r.resolve(objectId);
-			RevWalk walk = new RevWalk(r);
-			RevCommit rev = walk.parseCommit(object);
+			RevWalk walk = new RevWalk(repository);
+			RevCommit rev = walk.parseCommit(branchObject);
 			commit = rev;
 			walk.dispose();
 		} catch (Throwable t) {
-			LOGGER.error("Failed to get commit " + objectId, t);
+			error(t, repository, "{0} failed to get commit {1}", objectId);
 		}
 		return commit;
 	}
 
-	public static Map<ObjectId, List<RefModel>> getAllRefs(Repository r) {
-		List<RefModel> list = getRefs(r, org.eclipse.jgit.lib.RefDatabase.ALL, true, -1);
-		Map<ObjectId, List<RefModel>> refs = new HashMap<ObjectId, List<RefModel>>();
-		for (RefModel ref : list) {
-			ObjectId objectid = ref.getReferencedObjectId();
-			if (!refs.containsKey(objectid)) {
-				refs.put(objectid, new ArrayList<RefModel>());
-			}
-			refs.get(objectid).add(ref);
-		}
-		return refs;
-	}
-
-	public static byte[] getByteContent(Repository r, RevTree tree, final String path) {
-		RevWalk rw = new RevWalk(r);
-		TreeWalk tw = new TreeWalk(r);
+	/**
+	 * Retrieves the raw byte content of a file in the specified tree.
+	 * 
+	 * @param repository
+	 * @param tree
+	 *            if null, the RevTree from HEAD is assumed.
+	 * @param path
+	 * @return content as a byte []
+	 */
+	public static byte[] getByteContent(Repository repository, RevTree tree, final String path) {
+		RevWalk rw = new RevWalk(repository);
+		TreeWalk tw = new TreeWalk(repository);
 		tw.setFilter(PathFilterGroup.createFromStrings(Collections.singleton(path)));
 		byte[] content = null;
 		try {
 			if (tree == null) {
-				ObjectId object = r.resolve(Constants.HEAD);
+				ObjectId object = getDefaultBranch(repository);
 				RevCommit commit = rw.parseCommit(object);
 				tree = commit.getTree();
 			}
@@ -295,21 +559,23 @@
 				}
 				ObjectId entid = tw.getObjectId(0);
 				FileMode entmode = tw.getFileMode(0);
-				RevObject ro = rw.lookupAny(entid, entmode.getObjectType());
-				rw.parseBody(ro);
-				ByteArrayOutputStream os = new ByteArrayOutputStream();
-				ObjectLoader ldr = r.open(ro.getId(), Constants.OBJ_BLOB);
-				byte[] tmp = new byte[4096];
-				InputStream in = ldr.openStream();
-				int n;
-				while ((n = in.read(tmp)) > 0) {
-					os.write(tmp, 0, n);
+				if (entmode != FileMode.GITLINK) {
+					RevObject ro = rw.lookupAny(entid, entmode.getObjectType());
+					rw.parseBody(ro);
+					ByteArrayOutputStream os = new ByteArrayOutputStream();
+					ObjectLoader ldr = repository.open(ro.getId(), Constants.OBJ_BLOB);
+					byte[] tmp = new byte[4096];
+					InputStream in = ldr.openStream();
+					int n;
+					while ((n = in.read(tmp)) > 0) {
+						os.write(tmp, 0, n);
+					}
+					in.close();
+					content = os.toByteArray();
 				}
-				in.close();
-				content = os.toByteArray();
 			}
 		} catch (Throwable t) {
-			LOGGER.error("Can't find " + path + " in tree " + tree.name(), t);
+			error(t, repository, "{0} can't find {1} in tree {2}", path, tree.name());
 		} finally {
 			rw.dispose();
 			tw.release();
@@ -317,22 +583,39 @@
 		return content;
 	}
 
-	public static String getStringContent(Repository r, RevTree tree, String blobPath) {
-		byte[] content = getByteContent(r, tree, blobPath);
+	/**
+	 * Returns the UTF-8 string content of a file in the specified tree.
+	 * 
+	 * @param repository
+	 * @param tree
+	 *            if null, the RevTree from HEAD is assumed.
+	 * @param blobPath
+	 * @param charsets optional
+	 * @return UTF-8 string content
+	 */
+	public static String getStringContent(Repository repository, RevTree tree, String blobPath, String... charsets) {
+		byte[] content = getByteContent(repository, tree, blobPath);
 		if (content == null) {
 			return null;
 		}
-		return new String(content, Charset.forName(Constants.CHARACTER_ENCODING));
+		return StringUtils.decodeString(content, charsets);
 	}
 
-	public static byte[] getByteContent(Repository r, String objectId) {
-		RevWalk rw = new RevWalk(r);
+	/**
+	 * Gets the raw byte content of the specified blob object.
+	 * 
+	 * @param repository
+	 * @param objectId
+	 * @return byte [] blob content
+	 */
+	public static byte[] getByteContent(Repository repository, String objectId) {
+		RevWalk rw = new RevWalk(repository);
 		byte[] content = null;
 		try {
 			RevBlob blob = rw.lookupBlob(ObjectId.fromString(objectId));
 			rw.parseBody(blob);
 			ByteArrayOutputStream os = new ByteArrayOutputStream();
-			ObjectLoader ldr = r.open(blob.getId(), Constants.OBJ_BLOB);
+			ObjectLoader ldr = repository.open(blob.getId(), Constants.OBJ_BLOB);
 			byte[] tmp = new byte[4096];
 			InputStream in = ldr.openStream();
 			int n;
@@ -342,34 +625,55 @@
 			in.close();
 			content = os.toByteArray();
 		} catch (Throwable t) {
-			LOGGER.error("Can't find blob " + objectId, t);
+			error(t, repository, "{0} can't find blob {1}", objectId);
 		} finally {
 			rw.dispose();
 		}
 		return content;
 	}
 
-	public static String getStringContent(Repository r, String objectId) {
-		byte[] content = getByteContent(r, objectId);
+	/**
+	 * Gets the UTF-8 string content of the blob specified by objectId.
+	 * 
+	 * @param repository
+	 * @param objectId
+	 * @param charsets optional
+	 * @return UTF-8 string content
+	 */
+	public static String getStringContent(Repository repository, String objectId, String... charsets) {
+		byte[] content = getByteContent(repository, objectId);
 		if (content == null) {
 			return null;
 		}
-		return new String(content, Charset.forName(Constants.CHARACTER_ENCODING));
+		return StringUtils.decodeString(content, charsets);
 	}
 
-	public static List<PathModel> getFilesInPath(Repository r, String basePath, RevCommit commit) {
+	/**
+	 * Returns the list of files in the specified folder at the specified
+	 * commit. If the repository does not exist or is empty, an empty list is
+	 * returned.
+	 * 
+	 * @param repository
+	 * @param path
+	 *            if unspecified, root folder is assumed.
+	 * @param commit
+	 *            if null, HEAD is assumed.
+	 * @return list of files in specified path
+	 */
+	public static List<PathModel> getFilesInPath(Repository repository, String path,
+			RevCommit commit) {
 		List<PathModel> list = new ArrayList<PathModel>();
-		if (!hasCommits(r)) {
+		if (!hasCommits(repository)) {
 			return list;
 		}
 		if (commit == null) {
-			commit = getCommit(r, Constants.HEAD);
+			commit = getCommit(repository, null);
 		}
-		final TreeWalk tw = new TreeWalk(r);
+		final TreeWalk tw = new TreeWalk(repository);
 		try {
 			tw.addTree(commit.getTree());
-			if (!StringUtils.isEmpty(basePath)) {
-				PathFilter f = PathFilter.create(basePath);
+			if (!StringUtils.isEmpty(path)) {
+				PathFilter f = PathFilter.create(path);
 				tw.setFilter(f);
 				tw.setRecursive(false);
 				boolean foundFolder = false;
@@ -377,12 +681,12 @@
 					if (!foundFolder && tw.isSubtree()) {
 						tw.enterSubtree();
 					}
-					if (tw.getPathString().equals(basePath)) {
+					if (tw.getPathString().equals(path)) {
 						foundFolder = true;
 						continue;
 					}
 					if (foundFolder) {
-						list.add(getPathModel(tw, basePath, commit));
+						list.add(getPathModel(tw, path, commit));
 					}
 				}
 			} else {
@@ -392,7 +696,7 @@
 				}
 			}
 		} catch (IOException e) {
-			LOGGER.error("Failed to get files for commit " + commit.getName(), e);
+			error(e, repository, "{0} failed to get files for commit {1}", commit.getName());
 		} finally {
 			tw.release();
 		}
@@ -400,60 +704,109 @@
 		return list;
 	}
 
-	public static List<PathChangeModel> getFilesInCommit(Repository r, RevCommit commit) {
+	/**
+	 * Returns the list of files changed in a specified commit. If the
+	 * repository does not exist or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param commit
+	 *            if null, HEAD is assumed.
+	 * @return list of files changed in a commit
+	 */
+	public static List<PathChangeModel> getFilesInCommit(Repository repository, RevCommit commit) {
 		List<PathChangeModel> list = new ArrayList<PathChangeModel>();
-		RevWalk rw = new RevWalk(r);		
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		RevWalk rw = new RevWalk(repository);
 		try {
 			if (commit == null) {
-				ObjectId object = r.resolve(Constants.HEAD);
+				ObjectId object = getDefaultBranch(repository);
 				commit = rw.parseCommit(object);
-			}			
+			}
 
 			if (commit.getParentCount() == 0) {
-				TreeWalk tw = new TreeWalk(r);
+				TreeWalk tw = new TreeWalk(repository);
 				tw.reset();
 				tw.setRecursive(true);
 				tw.addTree(commit.getTree());
 				while (tw.next()) {
 					list.add(new PathChangeModel(tw.getPathString(), tw.getPathString(), 0, tw
-							.getRawMode(0), commit.getId().getName(), ChangeType.ADD));
+							.getRawMode(0), tw.getObjectId(0).getName(), commit.getId().getName(),
+							ChangeType.ADD));
 				}
 				tw.release();
 			} else {
 				RevCommit parent = rw.parseCommit(commit.getParent(0).getId());
 				DiffFormatter df = new DiffFormatter(DisabledOutputStream.INSTANCE);
-				df.setRepository(r);
+				df.setRepository(repository);
 				df.setDiffComparator(RawTextComparator.DEFAULT);
 				df.setDetectRenames(true);
 				List<DiffEntry> diffs = df.scan(parent.getTree(), commit.getTree());
 				for (DiffEntry diff : diffs) {
+					String objectId = null;
+					if (FileMode.GITLINK.equals(diff.getNewMode())) {
+						objectId = diff.getNewId().name();
+					}
+
 					if (diff.getChangeType().equals(ChangeType.DELETE)) {
 						list.add(new PathChangeModel(diff.getOldPath(), diff.getOldPath(), 0, diff
-								.getNewMode().getBits(), commit.getId().getName(), diff
+								.getNewMode().getBits(), objectId, commit.getId().getName(), diff
+								.getChangeType()));
+					} else if (diff.getChangeType().equals(ChangeType.RENAME)) {
+						list.add(new PathChangeModel(diff.getOldPath(), diff.getNewPath(), 0, diff
+								.getNewMode().getBits(), objectId, commit.getId().getName(), diff
 								.getChangeType()));
 					} else {
 						list.add(new PathChangeModel(diff.getNewPath(), diff.getNewPath(), 0, diff
-								.getNewMode().getBits(), commit.getId().getName(), diff
+								.getNewMode().getBits(), objectId, commit.getId().getName(), diff
 								.getChangeType()));
 					}
 				}
 			}
 		} catch (Throwable t) {
-			LOGGER.error("failed to determine files in commit!", t);
+			error(t, repository, "{0} failed to determine files in commit!");
 		} finally {
-			rw.dispose();			
+			rw.dispose();
 		}
 		return list;
 	}
 
-	public static List<PathModel> getDocuments(Repository r, List<String> extensions) {
+	/**
+	 * Returns the list of files in the repository on the default branch that
+	 * match one of the specified extensions. This is a CASE-SENSITIVE search.
+	 * If the repository does not exist or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param extensions
+	 * @return list of files in repository with a matching extension
+	 */
+	public static List<PathModel> getDocuments(Repository repository, List<String> extensions) {
+		return getDocuments(repository, extensions, null);
+	}
+
+	/**
+	 * Returns the list of files in the repository in the specified commit that
+	 * match one of the specified extensions. This is a CASE-SENSITIVE search.
+	 * If the repository does not exist or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param extensions
+	 * @param objectId
+	 * @return list of files in repository with a matching extension
+	 */
+	public static List<PathModel> getDocuments(Repository repository, List<String> extensions,
+			String objectId) {
 		List<PathModel> list = new ArrayList<PathModel>();
-		RevCommit commit = getCommit(r, Constants.HEAD);
-		final TreeWalk tw = new TreeWalk(r);
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		RevCommit commit = getCommit(repository, objectId);
+		final TreeWalk tw = new TreeWalk(repository);
 		try {
 			tw.addTree(commit.getTree());
 			if (extensions != null && extensions.size() > 0) {
-				Collection<TreeFilter> suffixFilters = new ArrayList<TreeFilter>();
+				List<TreeFilter> suffixFilters = new ArrayList<TreeFilter>();
 				for (String extension : extensions) {
 					if (extension.charAt(0) == '.') {
 						suffixFilters.add(PathSuffixFilter.create("\\" + extension));
@@ -462,7 +815,12 @@
 						suffixFilters.add(PathSuffixFilter.create("\\." + extension));
 					}
 				}
-				TreeFilter filter = OrTreeFilter.create(suffixFilters);
+				TreeFilter filter;
+				if (suffixFilters.size() == 1) {
+					filter = suffixFilters.get(0);
+				} else {
+					filter = OrTreeFilter.create(suffixFilters);
+				}
 				tw.setFilter(filter);
 				tw.setRecursive(true);
 			}
@@ -470,7 +828,7 @@
 				list.add(getPathModel(tw, null, commit));
 			}
 		} catch (IOException e) {
-			LOGGER.error("Failed to get documents for commit " + commit.getName(), e);
+			error(e, repository, "{0} failed to get documents for commit {1}", commit.getName());
 		} finally {
 			tw.release();
 		}
@@ -478,6 +836,14 @@
 		return list;
 	}
 
+	/**
+	 * Returns a path model of the current file in the treewalk.
+	 * 
+	 * @param tw
+	 * @param basePath
+	 * @param commit
+	 * @return a path model of the current file in the treewalk
+	 */
 	private static PathModel getPathModel(TreeWalk tw, String basePath, RevCommit commit) {
 		String name;
 		long size = 0;
@@ -486,17 +852,24 @@
 		} else {
 			name = tw.getPathString().substring(basePath.length() + 1);
 		}
+		ObjectId objectId = tw.getObjectId(0);
 		try {
-			if (!tw.isSubtree()) {
-				size = tw.getObjectReader().getObjectSize(tw.getObjectId(0), Constants.OBJ_BLOB);
+			if (!tw.isSubtree() && (tw.getFileMode(0) != FileMode.GITLINK)) {
+				size = tw.getObjectReader().getObjectSize(objectId, Constants.OBJ_BLOB);
 			}
 		} catch (Throwable t) {
-			LOGGER.error("Failed to retrieve blob size", t);
+			error(t, null, "failed to retrieve blob size for " + tw.getPathString());
 		}
 		return new PathModel(name, tw.getPathString(), size, tw.getFileMode(0).getBits(),
-				commit.getName());
+				objectId.getName(), commit.getName());
 	}
 
+	/**
+	 * Returns a permissions representation of the mode bits.
+	 * 
+	 * @param mode
+	 * @return string representation of the mode bits
+	 */
 	public static String getPermissionsFromMode(int mode) {
 		if (FileMode.TREE.equals(mode)) {
 			return "drwxr-xr-x";
@@ -505,37 +878,123 @@
 		} else if (FileMode.EXECUTABLE_FILE.equals(mode)) {
 			return "-rwxr-xr-x";
 		} else if (FileMode.SYMLINK.equals(mode)) {
-			// FIXME symlink permissions
 			return "symlink";
 		} else if (FileMode.GITLINK.equals(mode)) {
-			// FIXME gitlink permissions
-			return "gitlink";
+			return "submodule";
 		}
-		// FIXME missing permissions
 		return "missing";
 	}
 
-	public static List<RevCommit> getRevLog(Repository r, int maxCount) {
-		return getRevLog(r, Constants.HEAD, 0, maxCount);
-	}
-
-	public static List<RevCommit> getRevLog(Repository r, String objectId, int offset, int maxCount) {
-		return getRevLog(r, objectId, null, offset, maxCount);
-	}
-
-	public static List<RevCommit> getRevLog(Repository r, String objectId, String path, int offset,
-			int maxCount) {
+	/**
+	 * Returns a list of commits since the minimum date starting from the
+	 * specified object id.
+	 * 
+	 * @param repository
+	 * @param objectId
+	 *            if unspecified, HEAD is assumed.
+	 * @param minimumDate
+	 * @return list of commits
+	 */
+	public static List<RevCommit> getRevLog(Repository repository, String objectId, Date minimumDate) {
 		List<RevCommit> list = new ArrayList<RevCommit>();
-		if (!hasCommits(r)) {
+		if (!hasCommits(repository)) {
 			return list;
 		}
 		try {
+			// resolve branch
+			ObjectId branchObject;
 			if (StringUtils.isEmpty(objectId)) {
-				objectId = Constants.HEAD;
+				branchObject = getDefaultBranch(repository);
+			} else {
+				branchObject = repository.resolve(objectId);
 			}
-			RevWalk rw = new RevWalk(r);
-			ObjectId object = r.resolve(objectId);
-			rw.markStart(rw.parseCommit(object));
+
+			RevWalk rw = new RevWalk(repository);
+			rw.markStart(rw.parseCommit(branchObject));
+			rw.setRevFilter(CommitTimeRevFilter.after(minimumDate));
+			Iterable<RevCommit> revlog = rw;
+			for (RevCommit rev : revlog) {
+				list.add(rev);
+			}
+			rw.dispose();
+		} catch (Throwable t) {
+			error(t, repository, "{0} failed to get {1} revlog for minimum date {2}", objectId,
+					minimumDate);
+		}
+		return list;
+	}
+
+	/**
+	 * Returns a list of commits starting from HEAD and working backwards.
+	 * 
+	 * @param repository
+	 * @param maxCount
+	 *            if < 0, all commits for the repository are returned.
+	 * @return list of commits
+	 */
+	public static List<RevCommit> getRevLog(Repository repository, int maxCount) {
+		return getRevLog(repository, null, 0, maxCount);
+	}
+
+	/**
+	 * Returns a list of commits starting from the specified objectId using an
+	 * offset and maxCount for paging. This is similar to LIMIT n OFFSET p in
+	 * SQL. If the repository does not exist or is empty, an empty list is
+	 * returned.
+	 * 
+	 * @param repository
+	 * @param objectId
+	 *            if unspecified, HEAD is assumed.
+	 * @param offset
+	 * @param maxCount
+	 *            if < 0, all commits are returned.
+	 * @return a paged list of commits
+	 */
+	public static List<RevCommit> getRevLog(Repository repository, String objectId, int offset,
+			int maxCount) {
+		return getRevLog(repository, objectId, null, offset, maxCount);
+	}
+
+	/**
+	 * Returns a list of commits for the repository or a path within the
+	 * repository. Caller may specify ending revision with objectId. Caller may
+	 * specify offset and maxCount to achieve pagination of results. If the
+	 * repository does not exist or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param objectId
+	 *            if unspecified, HEAD is assumed.
+	 * @param path
+	 *            if unspecified, commits for repository are returned. If
+	 *            specified, commits for the path are returned.
+	 * @param offset
+	 * @param maxCount
+	 *            if < 0, all commits are returned.
+	 * @return a paged list of commits
+	 */
+	public static List<RevCommit> getRevLog(Repository repository, String objectId, String path,
+			int offset, int maxCount) {
+		List<RevCommit> list = new ArrayList<RevCommit>();
+		if (maxCount == 0) {
+			return list;
+		}
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		try {
+			// resolve branch
+			ObjectId branchObject;
+			if (StringUtils.isEmpty(objectId)) {
+				branchObject = getDefaultBranch(repository);
+			} else {
+				branchObject = repository.resolve(objectId);
+			}
+			if (branchObject == null) {
+				return list;
+			}
+
+			RevWalk rw = new RevWalk(repository);
+			rw.markStart(rw.parseCommit(branchObject));
 			if (!StringUtils.isEmpty(path)) {
 				TreeFilter filter = AndTreeFilter.create(
 						PathFilterGroup.createFromStrings(Collections.singleton(path)),
@@ -564,45 +1023,98 @@
 			}
 			rw.dispose();
 		} catch (Throwable t) {
-			LOGGER.error("Failed to get revlog", t);
+			error(t, repository, "{0} failed to get {1} revlog for path {2}", objectId, path);
 		}
 		return list;
 	}
 
-	public static enum SearchType {
-		AUTHOR, COMMITTER, COMMIT;
-
-		public static SearchType forName(String name) {
-			for (SearchType type : values()) {
-				if (type.name().equalsIgnoreCase(name)) {
-					return type;
-				}
-			}
-			return COMMIT;
-		}
-
-		@Override
-		public String toString() {
-			return name().toLowerCase();
-		}
-	}
-
-	public static List<RevCommit> searchRevlogs(Repository r, String objectId, String value,
-			final SearchType type, int offset, int maxCount) {
-		final String lcValue = value.toLowerCase();
+	/**
+	 * Returns a list of commits for the repository within the range specified
+	 * by startRangeId and endRangeId. If the repository does not exist or is
+	 * empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param startRangeId
+	 *            the first commit (not included in results)
+	 * @param endRangeId
+	 *            the end commit (included in results)
+	 * @return a list of commits
+	 */
+	public static List<RevCommit> getRevLog(Repository repository, String startRangeId,
+			String endRangeId) {
 		List<RevCommit> list = new ArrayList<RevCommit>();
-		if (!hasCommits(r)) {
+		if (!hasCommits(repository)) {
 			return list;
 		}
 		try {
-			if (StringUtils.isEmpty(objectId)) {
-				objectId = Constants.HEAD;
+			ObjectId endRange = repository.resolve(endRangeId);
+			ObjectId startRange = repository.resolve(startRangeId);
+
+			RevWalk rw = new RevWalk(repository);
+			rw.markStart(rw.parseCommit(endRange));
+			if (startRange.equals(ObjectId.zeroId())) {
+				// maybe this is a tag or an orphan branch
+				list.add(rw.parseCommit(endRange));
+				rw.dispose();
+				return list;
+			} else {
+				rw.markUninteresting(rw.parseCommit(startRange));
 			}
-			RevWalk rw = new RevWalk(r);
+
+			Iterable<RevCommit> revlog = rw;
+			for (RevCommit rev : revlog) {
+				list.add(rev);
+			}
+			rw.dispose();
+		} catch (Throwable t) {
+			error(t, repository, "{0} failed to get revlog for {1}..{2}", startRangeId, endRangeId);
+		}
+		return list;
+	}
+
+	/**
+	 * Search the commit history for a case-insensitive match to the value.
+	 * Search results require a specified SearchType of AUTHOR, COMMITTER, or
+	 * COMMIT. Results may be paginated using offset and maxCount. If the
+	 * repository does not exist or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param objectId
+	 *            if unspecified, HEAD is assumed.
+	 * @param value
+	 * @param type
+	 *            AUTHOR, COMMITTER, COMMIT
+	 * @param offset
+	 * @param maxCount
+	 *            if < 0, all matches are returned
+	 * @return matching list of commits
+	 */
+	public static List<RevCommit> searchRevlogs(Repository repository, String objectId,
+			String value, final com.gitblit.Constants.SearchType type, int offset, int maxCount) {
+		final String lcValue = value.toLowerCase();
+		List<RevCommit> list = new ArrayList<RevCommit>();
+		if (maxCount == 0) {
+			return list;
+		}
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		try {
+			// resolve branch
+			ObjectId branchObject;
+			if (StringUtils.isEmpty(objectId)) {
+				branchObject = getDefaultBranch(repository);
+			} else {
+				branchObject = repository.resolve(objectId);
+			}
+
+			RevWalk rw = new RevWalk(repository);
 			rw.setRevFilter(new RevFilter() {
 
 				@Override
 				public RevFilter clone() {
+					// FindBugs complains about this method name.
+					// This is part of JGit design and unrelated to Cloneable.
 					return this;
 				}
 
@@ -630,8 +1142,7 @@
 				}
 
 			});
-			ObjectId object = r.resolve(objectId);
-			rw.markStart(rw.parseCommit(object));
+			rw.markStart(rw.parseCommit(branchObject));
 			Iterable<RevCommit> revlog = rw;
 			if (offset > 0) {
 				int count = 0;
@@ -654,32 +1165,328 @@
 			}
 			rw.dispose();
 		} catch (Throwable t) {
-			LOGGER.error("Failed to search revlogs", t);
+			error(t, repository, "{0} failed to {1} search revlogs for {2}", type.name(), value);
 		}
 		return list;
 	}
 
-	public static List<RefModel> getTags(Repository r, boolean fullName, int maxCount) {
-		return getRefs(r, Constants.R_TAGS, fullName, maxCount);
+	/**
+	 * Returns the default branch to use for a repository. Normally returns
+	 * whatever branch HEAD points to, but if HEAD points to nothing it returns
+	 * the most recently updated branch.
+	 * 
+	 * @param repository
+	 * @return the objectid of a branch
+	 * @throws Exception
+	 */
+	public static ObjectId getDefaultBranch(Repository repository) throws Exception {
+		ObjectId object = repository.resolve(Constants.HEAD);
+		if (object == null) {
+			// no HEAD
+			// perhaps non-standard repository, try local branches
+			List<RefModel> branchModels = getLocalBranches(repository, true, -1);
+			if (branchModels.size() > 0) {
+				// use most recently updated branch
+				RefModel branch = null;
+				Date lastDate = new Date(0);
+				for (RefModel branchModel : branchModels) {
+					if (branchModel.getDate().after(lastDate)) {
+						branch = branchModel;
+						lastDate = branch.getDate();
+					}
+				}
+				object = branch.getReferencedObjectId();
+			}
+		}
+		return object;
 	}
 
-	public static List<RefModel> getLocalBranches(Repository r, boolean fullName, int maxCount) {
-		return getRefs(r, Constants.R_HEADS, fullName, maxCount);
-	}
-
-	public static List<RefModel> getRemoteBranches(Repository r, boolean fullName, int maxCount) {
-		return getRefs(r, Constants.R_REMOTES, fullName, maxCount);
-	}
-
-	public static List<RefModel> getNotesRefs(Repository r, boolean fullName, int maxCount) {
-		return getRefs(r, Constants.R_NOTES, fullName, maxCount);
-	}
-
-	private static List<RefModel> getRefs(Repository r, String refs, boolean fullName, int maxCount) {
-		List<RefModel> list = new ArrayList<RefModel>();
+	/**
+	 * Returns the target of the symbolic HEAD reference for a repository.
+	 * Normally returns a branch reference name, but when HEAD is detached,
+	 * the commit is matched against the known tags. The most recent matching
+	 * tag ref name will be returned if it references the HEAD commit. If
+	 * no match is found, the SHA1 is returned.
+	 *
+	 * @param repository
+	 * @return the ref name or the SHA1 for a detached HEAD
+	 */
+	public static String getHEADRef(Repository repository) {
+		String target = null;
 		try {
-			Map<String, Ref> map = r.getRefDatabase().getRefs(refs);
-			RevWalk rw = new RevWalk(r);
+			target = repository.getFullBranch();
+			if (!target.startsWith(Constants.R_HEADS)) {
+				// refers to an actual commit, probably a tag
+				// find latest tag that matches the commit, if any
+				List<RefModel> tagModels = getTags(repository, true, -1);
+				if (tagModels.size() > 0) {
+					RefModel tag = null;
+					Date lastDate = new Date(0);
+					for (RefModel tagModel : tagModels) {
+						if (tagModel.getReferencedObjectId().getName().equals(target) &&
+								tagModel.getDate().after(lastDate)) {
+							tag = tagModel;
+							lastDate = tag.getDate();
+						}
+					}
+					target = tag.getName();
+				}
+			}
+		} catch (Throwable t) {
+			error(t, repository, "{0} failed to get symbolic HEAD target");
+		}
+		return target;
+	}
+	
+	/**
+	 * Sets the symbolic ref HEAD to the specified target ref. The
+	 * HEAD will be detached if the target ref is not a branch.
+	 *
+	 * @param repository
+	 * @param targetRef
+	 * @return true if successful
+	 */
+	public static boolean setHEADtoRef(Repository repository, String targetRef) {
+		try {
+			 // detach HEAD if target ref is not a branch
+			boolean detach = !targetRef.startsWith(Constants.R_HEADS);
+			RefUpdate.Result result;
+			RefUpdate head = repository.updateRef(Constants.HEAD, detach);
+			if (detach) { // Tag
+				RevCommit commit = getCommit(repository, targetRef);
+				head.setNewObjectId(commit.getId());
+				result = head.forceUpdate();
+			} else {
+				result = head.link(targetRef);
+			}
+			switch (result) {
+			case NEW:
+			case FORCED:
+			case NO_CHANGE:
+			case FAST_FORWARD:
+				return true;				
+			default:
+				LOGGER.error(MessageFormat.format("{0} HEAD update to {1} returned result {2}",
+						repository.getDirectory().getAbsolutePath(), targetRef, result));
+			}
+		} catch (Throwable t) {
+			error(t, repository, "{0} failed to set HEAD to {1}", targetRef);
+		}
+		return false;
+	}
+	
+	/**
+	 * Sets the local branch ref to point to the specified commit id.
+	 *
+	 * @param repository
+	 * @param branch
+	 * @param commitId
+	 * @return true if successful
+	 */
+	public static boolean setBranchRef(Repository repository, String branch, String commitId) {
+		String branchName = branch;
+		if (!branchName.startsWith(Constants.R_HEADS)) {
+			branchName = Constants.R_HEADS + branch;
+		}
+
+		try {
+			RefUpdate refUpdate = repository.updateRef(branchName, false);
+			refUpdate.setNewObjectId(ObjectId.fromString(commitId));
+			RefUpdate.Result result = refUpdate.forceUpdate();
+
+			switch (result) {
+			case NEW:
+			case FORCED:
+			case NO_CHANGE:
+			case FAST_FORWARD:
+				return true;				
+			default:
+				LOGGER.error(MessageFormat.format("{0} {1} update to {2} returned result {3}",
+						repository.getDirectory().getAbsolutePath(), branchName, commitId, result));
+			}
+		} catch (Throwable t) {
+			error(t, repository, "{0} failed to set {1} to {2}", branchName, commitId);
+		}
+		return false;
+	}
+	
+	/**
+	 * Deletes the specified branch ref.
+	 *  
+	 * @param repository
+	 * @param branch
+	 * @return true if successful
+	 */
+	public static boolean deleteBranchRef(Repository repository, String branch) {
+		String branchName = branch;
+		if (!branchName.startsWith(Constants.R_HEADS)) {
+			branchName = Constants.R_HEADS + branch;
+		}
+
+		try {
+			RefUpdate refUpdate = repository.updateRef(branchName, false);
+			refUpdate.setForceUpdate(true);
+			RefUpdate.Result result = refUpdate.delete();
+			switch (result) {
+			case NEW:
+			case FORCED:
+			case NO_CHANGE:
+			case FAST_FORWARD:
+				return true;				
+			default:
+				LOGGER.error(MessageFormat.format("{0} failed to delete to {1} returned result {2}",
+						repository.getDirectory().getAbsolutePath(), branchName, result));
+			}
+		} catch (Throwable t) {
+			error(t, repository, "{0} failed to delete {1}", branchName);
+		}
+		return false;
+	}
+	
+	/**
+	 * Get the full branch and tag ref names for any potential HEAD targets.
+	 *
+	 * @param repository
+	 * @return a list of ref names
+	 */
+	public static List<String> getAvailableHeadTargets(Repository repository) {
+		List<String> targets = new ArrayList<String>();
+		for (RefModel branchModel : JGitUtils.getLocalBranches(repository, true, -1)) {
+			targets.add(branchModel.getName());
+		}
+
+		for (RefModel tagModel : JGitUtils.getTags(repository, true, -1)) {
+			targets.add(tagModel.getName());
+		}
+		return targets;
+	}
+
+	/**
+	 * Returns all refs grouped by their associated object id.
+	 * 
+	 * @param repository
+	 * @return all refs grouped by their referenced object id
+	 */
+	public static Map<ObjectId, List<RefModel>> getAllRefs(Repository repository) {
+		return getAllRefs(repository, true);
+	}
+	
+	/**
+	 * Returns all refs grouped by their associated object id.
+	 * 
+	 * @param repository
+	 * @param includeRemoteRefs
+	 * @return all refs grouped by their referenced object id
+	 */
+	public static Map<ObjectId, List<RefModel>> getAllRefs(Repository repository, boolean includeRemoteRefs) {
+		List<RefModel> list = getRefs(repository, org.eclipse.jgit.lib.RefDatabase.ALL, true, -1);
+		Map<ObjectId, List<RefModel>> refs = new HashMap<ObjectId, List<RefModel>>();
+		for (RefModel ref : list) {
+			if (!includeRemoteRefs && ref.getName().startsWith(Constants.R_REMOTES)) {
+				continue;
+			}
+			ObjectId objectid = ref.getReferencedObjectId();
+			if (!refs.containsKey(objectid)) {
+				refs.put(objectid, new ArrayList<RefModel>());
+			}
+			refs.get(objectid).add(ref);
+		}
+		return refs;
+	}
+
+	/**
+	 * Returns the list of tags in the repository. If repository does not exist
+	 * or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param fullName
+	 *            if true, /refs/tags/yadayadayada is returned. If false,
+	 *            yadayadayada is returned.
+	 * @param maxCount
+	 *            if < 0, all tags are returned
+	 * @return list of tags
+	 */
+	public static List<RefModel> getTags(Repository repository, boolean fullName, int maxCount) {
+		return getRefs(repository, Constants.R_TAGS, fullName, maxCount);
+	}
+
+	/**
+	 * Returns the list of local branches in the repository. If repository does
+	 * not exist or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param fullName
+	 *            if true, /refs/heads/yadayadayada is returned. If false,
+	 *            yadayadayada is returned.
+	 * @param maxCount
+	 *            if < 0, all local branches are returned
+	 * @return list of local branches
+	 */
+	public static List<RefModel> getLocalBranches(Repository repository, boolean fullName,
+			int maxCount) {
+		return getRefs(repository, Constants.R_HEADS, fullName, maxCount);
+	}
+
+	/**
+	 * Returns the list of remote branches in the repository. If repository does
+	 * not exist or is empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param fullName
+	 *            if true, /refs/remotes/yadayadayada is returned. If false,
+	 *            yadayadayada is returned.
+	 * @param maxCount
+	 *            if < 0, all remote branches are returned
+	 * @return list of remote branches
+	 */
+	public static List<RefModel> getRemoteBranches(Repository repository, boolean fullName,
+			int maxCount) {
+		return getRefs(repository, Constants.R_REMOTES, fullName, maxCount);
+	}
+
+	/**
+	 * Returns the list of note branches. If repository does not exist or is
+	 * empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param fullName
+	 *            if true, /refs/notes/yadayadayada is returned. If false,
+	 *            yadayadayada is returned.
+	 * @param maxCount
+	 *            if < 0, all note branches are returned
+	 * @return list of note branches
+	 */
+	public static List<RefModel> getNoteBranches(Repository repository, boolean fullName,
+			int maxCount) {
+		return getRefs(repository, Constants.R_NOTES, fullName, maxCount);
+	}
+
+	/**
+	 * Returns a list of references in the repository matching "refs". If the
+	 * repository is null or empty, an empty list is returned.
+	 * 
+	 * @param repository
+	 * @param refs
+	 *            if unspecified, all refs are returned
+	 * @param fullName
+	 *            if true, /refs/something/yadayadayada is returned. If false,
+	 *            yadayadayada is returned.
+	 * @param maxCount
+	 *            if < 0, all references are returned
+	 * @return list of references
+	 */
+	private static List<RefModel> getRefs(Repository repository, String refs, boolean fullName,
+			int maxCount) {
+		List<RefModel> list = new ArrayList<RefModel>();
+		if (maxCount == 0) {
+			return list;
+		}
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		try {
+			Map<String, Ref> map = repository.getRefDatabase().getRefs(refs);
+			RevWalk rw = new RevWalk(repository);
 			for (Entry<String, Ref> entry : map.entrySet()) {
 				Ref ref = entry.getValue();
 				RevObject object = rw.parseAny(ref.getObjectId());
@@ -696,20 +1503,145 @@
 				list = new ArrayList<RefModel>(list.subList(0, maxCount));
 			}
 		} catch (IOException e) {
-			LOGGER.error("Failed to retrieve " + refs, e);
+			error(e, repository, "{0} failed to retrieve {1}", refs);
 		}
 		return list;
 	}
 
+	/**
+	 * Returns a RefModel for the gh-pages branch in the repository. If the
+	 * branch can not be found, null is returned.
+	 * 
+	 * @param repository
+	 * @return a refmodel for the gh-pages branch or null
+	 */
+	public static RefModel getPagesBranch(Repository repository) {
+		return getBranch(repository, "gh-pages");
+	}
+
+	/**
+	 * Returns a RefModel for a specific branch name in the repository. If the
+	 * branch can not be found, null is returned.
+	 * 
+	 * @param repository
+	 * @return a refmodel for the branch or null
+	 */
+	public static RefModel getBranch(Repository repository, String name) {
+		RefModel branch = null;
+		try {
+			// search for the branch in local heads
+			for (RefModel ref : JGitUtils.getLocalBranches(repository, false, -1)) {
+				if (ref.displayName.endsWith(name)) {
+					branch = ref;
+					break;
+				}
+			}
+
+			// search for the branch in remote heads
+			if (branch == null) {
+				for (RefModel ref : JGitUtils.getRemoteBranches(repository, false, -1)) {
+					if (ref.displayName.endsWith(name)) {
+						branch = ref;
+						break;
+					}
+				}
+			}
+		} catch (Throwable t) {
+			LOGGER.error(MessageFormat.format("Failed to find {0} branch!", name), t);
+		}
+		return branch;
+	}
+		
+	/**
+	 * Returns the list of submodules for this repository.
+	 * 
+	 * @param repository
+	 * @param commit
+	 * @return list of submodules
+	 */
+	public static List<SubmoduleModel> getSubmodules(Repository repository, String commitId) {
+		RevCommit commit = getCommit(repository, commitId);
+		return getSubmodules(repository, commit.getTree());
+	}
+	
+	/**
+	 * Returns the list of submodules for this repository.
+	 * 
+	 * @param repository
+	 * @param commit
+	 * @return list of submodules
+	 */
+	public static List<SubmoduleModel> getSubmodules(Repository repository, RevTree tree) {
+		List<SubmoduleModel> list = new ArrayList<SubmoduleModel>();
+		byte [] blob = getByteContent(repository, tree, ".gitmodules");
+		if (blob == null) {
+			return list;
+		}
+		try {
+			BlobBasedConfig config = new BlobBasedConfig(repository.getConfig(), blob);
+			for (String module : config.getSubsections("submodule")) {
+				String path = config.getString("submodule", module, "path");
+				String url = config.getString("submodule", module, "url");
+				list.add(new SubmoduleModel(module, path, url));
+			}
+		} catch (ConfigInvalidException e) {
+			LOGGER.error("Failed to load .gitmodules file for " + repository.getDirectory(), e);
+		}
+		return list;
+	}
+	
+	/**
+	 * Returns the submodule definition for the specified path at the specified
+	 * commit.  If no module is defined for the path, null is returned.
+	 * 
+	 * @param repository
+	 * @param commit
+	 * @param path
+	 * @return a submodule definition or null if there is no submodule
+	 */
+	public static SubmoduleModel getSubmoduleModel(Repository repository, String commitId, String path) {
+		for (SubmoduleModel model : getSubmodules(repository, commitId)) {
+			if (model.path.equals(path)) {
+				return model;
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Returns the list of notes entered about the commit from the refs/notes
+	 * namespace. If the repository does not exist or is empty, an empty list is
+	 * returned.
+	 * 
+	 * @param repository
+	 * @param commit
+	 * @return list of notes
+	 */
 	public static List<GitNote> getNotesOnCommit(Repository repository, RevCommit commit) {
 		List<GitNote> list = new ArrayList<GitNote>();
-		List<RefModel> notesRefs = getNotesRefs(repository, true, -1);
-		for (RefModel notesRef : notesRefs) {
+		if (!hasCommits(repository)) {
+			return list;
+		}
+		List<RefModel> noteBranches = getNoteBranches(repository, true, -1);
+		for (RefModel notesRef : noteBranches) {
 			RevTree notesTree = JGitUtils.getCommit(repository, notesRef.getName()).getTree();
+			// flat notes list
+			String notePath = commit.getName();
+			String text = getStringContent(repository, notesTree, notePath);
+			if (!StringUtils.isEmpty(text)) {
+				List<RevCommit> history = getRevLog(repository, notesRef.getName(), notePath, 0, -1);
+				RefModel noteRef = new RefModel(notesRef.displayName, null, history.get(history
+						.size() - 1));
+				GitNote gitNote = new GitNote(noteRef, text);
+				list.add(gitNote);
+				continue;
+			}
+			
+			// folder structure
 			StringBuilder sb = new StringBuilder(commit.getName());
 			sb.insert(2, '/');
-			String notePath = sb.toString();
-			String text = getStringContent(repository, notesTree, notePath);
+			notePath = sb.toString();
+			text = getStringContent(repository, notesTree, notePath);
 			if (!StringUtils.isEmpty(text)) {
 				List<RevCommit> history = getRevLog(repository, notesRef.getName(), notePath, 0, -1);
 				RefModel noteRef = new RefModel(notesRef.displayName, null, history.get(history
@@ -721,37 +1653,112 @@
 		return list;
 	}
 
-	public static StoredConfig readConfig(Repository r) {
-		StoredConfig c = r.getConfig();
-		try {
-			c.load();
-		} catch (ConfigInvalidException cex) {
-			LOGGER.error("Repository configuration is invalid!", cex);
-		} catch (IOException cex) {
-			LOGGER.error("Could not open repository configuration!", cex);
+	/**
+	 * Create an orphaned branch in a repository.
+	 * 
+	 * @param repository
+	 * @param branchName
+	 * @param author
+	 *            if unspecified, Gitblit will be the author of this new branch
+	 * @return true if successful
+	 */
+	public static boolean createOrphanBranch(Repository repository, String branchName,
+			PersonIdent author) {
+		boolean success = false;
+		String message = "Created branch " + branchName;
+		if (author == null) {
+			author = new PersonIdent("Gitblit", "gitblit@localhost");
 		}
-		return c;
+		try {
+			ObjectInserter odi = repository.newObjectInserter();
+			try {
+				// Create a blob object to insert into a tree
+				ObjectId blobId = odi.insert(Constants.OBJ_BLOB,
+						message.getBytes(Constants.CHARACTER_ENCODING));
+
+				// Create a tree object to reference from a commit
+				TreeFormatter tree = new TreeFormatter();
+				tree.append(".branch", FileMode.REGULAR_FILE, blobId);
+				ObjectId treeId = odi.insert(tree);
+
+				// Create a commit object
+				CommitBuilder commit = new CommitBuilder();
+				commit.setAuthor(author);
+				commit.setCommitter(author);
+				commit.setEncoding(Constants.CHARACTER_ENCODING);
+				commit.setMessage(message);
+				commit.setTreeId(treeId);
+
+				// Insert the commit into the repository
+				ObjectId commitId = odi.insert(commit);
+				odi.flush();
+
+				RevWalk revWalk = new RevWalk(repository);
+				try {
+					RevCommit revCommit = revWalk.parseCommit(commitId);
+					if (!branchName.startsWith("refs/")) {
+						branchName = "refs/heads/" + branchName;
+					}
+					RefUpdate ru = repository.updateRef(branchName);
+					ru.setNewObjectId(commitId);
+					ru.setRefLogMessage("commit: " + revCommit.getShortMessage(), false);
+					Result rc = ru.forceUpdate();
+					switch (rc) {
+					case NEW:
+					case FORCED:
+					case FAST_FORWARD:
+						success = true;
+						break;
+					default:
+						success = false;
+					}
+				} finally {
+					revWalk.release();
+				}
+			} finally {
+				odi.release();
+			}
+		} catch (Throwable t) {
+			error(t, repository, "Failed to create orphan branch {1} in repository {0}", branchName);
+		}
+		return success;
 	}
 
-	public static boolean zip(Repository r, String basePath, String objectId, OutputStream os)
-			throws Exception {
-		RevCommit commit = getCommit(r, objectId);
+	/**
+	 * Zips the contents of the tree at the (optionally) specified revision and
+	 * the (optionally) specified basepath to the supplied outputstream.
+	 * 
+	 * @param repository
+	 * @param basePath
+	 *            if unspecified, entire repository is assumed.
+	 * @param objectId
+	 *            if unspecified, HEAD is assumed.
+	 * @param os
+	 * @return true if repository was successfully zipped to supplied output
+	 *         stream
+	 */
+	public static boolean zip(Repository repository, String basePath, String objectId,
+			OutputStream os) {
+		RevCommit commit = getCommit(repository, objectId);
 		if (commit == null) {
 			return false;
 		}
 		boolean success = false;
-		RevWalk rw = new RevWalk(r);
-		TreeWalk tw = new TreeWalk(r);
+		RevWalk rw = new RevWalk(repository);
+		TreeWalk tw = new TreeWalk(repository);
 		try {
 			tw.addTree(commit.getTree());
 			ZipOutputStream zos = new ZipOutputStream(os);
-			zos.setComment("Generated by Git:Blit");
+			zos.setComment("Generated by Gitblit");
 			if (!StringUtils.isEmpty(basePath)) {
 				PathFilter f = PathFilter.create(basePath);
 				tw.setFilter(f);
 			}
 			tw.setRecursive(true);
 			while (tw.next()) {
+				if (tw.getFileMode(0) == FileMode.GITLINK) {
+					continue;
+				}
 				ZipEntry entry = new ZipEntry(tw.getPathString());
 				entry.setSize(tw.getObjectReader().getObjectSize(tw.getObjectId(0),
 						Constants.OBJ_BLOB));
@@ -763,7 +1770,7 @@
 				RevBlob blob = (RevBlob) rw.lookupAny(entid, entmode.getObjectType());
 				rw.parseBody(blob);
 
-				ObjectLoader ldr = r.open(blob.getId(), Constants.OBJ_BLOB);
+				ObjectLoader ldr = repository.open(blob.getId(), Constants.OBJ_BLOB);
 				byte[] tmp = new byte[4096];
 				InputStream in = ldr.openStream();
 				int n;
@@ -775,7 +1782,7 @@
 			zos.finish();
 			success = true;
 		} catch (IOException e) {
-			LOGGER.error("Failed to zip files from commit " + commit.getName(), e);
+			error(e, repository, "{0} failed to zip files from commit {1}", commit.getName());
 		} finally {
 			tw.release();
 			rw.dispose();

--
Gitblit v1.9.1