Propagate IOException where possible when getting refs.

Currently, Repository.getAllRefs() and Repository.getTags() silently
ignores an IOException and instead returns an empty map. Repository
is a public API and as such cannot be changed until the next major
revision change. Where possible, update the internal jgit APIs to
use the RefDatabase directly, since it propagates the error.

Change-Id: I4e4537d8bd0fa772f388262684c5c4ca1929dc4c

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/InfoRefsServlet.java

@@ -44,6 +44,7 @@
 package org.eclipse.jgit.http.server;
 
 import static org.eclipse.jgit.http.server.ServletUtils.getRepository;
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
 
 import java.io.IOException;
 import java.io.OutputStreamWriter;
@@ -91,7 +92,7 @@ protected void end() {
 		adv.init(db);
 		adv.setDerefTags(true);
 
-		Map<String, Ref> refs = db.getAllRefs();
+		Map<String, Ref> refs = db.getRefDatabase().getRefs(ALL);
 		refs.remove(Constants.HEAD);
 		adv.send(refs);
 		out.close();

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Branch.java

@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.pgm;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
@@ -175,7 +177,7 @@ protected void run() throws Exception {
 	}
 
 	private void list() throws Exception {
-		Map<String, Ref> refs = db.getAllRefs();
+		Map<String, Ref> refs = db.getRefDatabase().getRefs(ALL);
 		Ref head = refs.get(Constants.HEAD);
 		// This can happen if HEAD is stillborn
 		if (head != null) {

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevParse.java

@@ -44,6 +44,8 @@
 
 package org.eclipse.jgit.pgm;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
@@ -64,7 +66,7 @@ class RevParse extends TextBuiltin {
 	@Override
 	protected void run() throws Exception {
 		if (all) {
-			Map<String, Ref> allRefs = db.getAllRefs();
+			Map<String, Ref> allRefs = db.getRefDatabase().getRefs(ALL);
 			for (final Ref r : allRefs.values())
 				outw.println(r.getObjectId().name());
 		} else {

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/RevWalkTextBuiltin.java

@@ -47,6 +47,7 @@
 import java.util.ArrayList;
 import java.util.EnumSet;
 import java.util.List;
+import java.util.Map;
 
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
@@ -55,6 +56,7 @@
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.pgm.opt.PathTreeFilterHandler;
 import org.eclipse.jgit.revwalk.FollowFilter;
@@ -164,8 +166,10 @@ protected void run() throws Exception {
 		else if (revLimiter.size() > 1)
 			walk.setRevFilter(AndRevFilter.create(revLimiter));
 
-		if (all)
+		if (all) {
-			for (Ref a : db.getAllRefs().values()) {
+			Map<String, Ref> refs =
+				db.getRefDatabase().getRefs(RefDatabase.ALL);
+			for (Ref a : refs.values()) {
 				ObjectId oid = a.getPeeledObjectId();
 				if (oid == null)
 					oid = a.getObjectId();
@@ -175,6 +179,7 @@ else if (revLimiter.size() > 1)
 					// Ignore all refs which are not commits
 				}
 			}
+		}
 
 		if (commits.isEmpty()) {
 			final ObjectId head = db.resolve(Constants.HEAD);

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/ShowRef.java

@@ -45,6 +45,8 @@
 
 package org.eclipse.jgit.pgm;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.IOException;
 import java.util.Map;
 import java.util.SortedMap;
@@ -65,8 +67,8 @@ protected void run() throws Exception {
 		}
 	}
 
-	private Iterable<Ref> getSortedRefs() {
+	private Iterable<Ref> getSortedRefs() throws Exception {
-		Map<String, Ref> all = db.getAllRefs();
+		Map<String, Ref> all = db.getRefDatabase().getRefs(ALL);
 		if (all instanceof RefMap
 				|| (all instanceof SortedMap && ((SortedMap) all).comparator() == null))
 			return all.values();

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java

@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.pgm.debug;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -114,7 +116,7 @@ class RebuildCommitGraph extends TextBuiltin {
 
 	@Override
 	protected void run() throws Exception {
-		if (!really && !db.getAllRefs().isEmpty()) {
+		if (!really && !db.getRefDatabase().getRefs(ALL).isEmpty()) {
 			System.err.println(
 				MessageFormat.format(CLIText.get().fatalThisProgramWillDestroyTheRepository
 					, db.getDirectory().getAbsolutePath(), REALLY));
@@ -241,7 +243,8 @@ private void detachHead() throws IOException {
 
 	private void deleteAllRefs() throws Exception {
 		final RevWalk rw = new RevWalk(db);
-		for (final Ref r : db.getAllRefs().values()) {
+		Map<String, Ref> refs = db.getRefDatabase().getRefs(ALL);
+		for (final Ref r : refs.values()) {
 			if (Constants.HEAD.equals(r.getName()))
 				continue;
 			final RefUpdate u = db.updateRef(r.getName());

org.eclipse.jgit/src/org/eclipse/jgit/api/DescribeCommand.java

@@ -152,7 +152,8 @@ public String call() throws GitAPIException {
 				throw new IllegalArgumentException(JGitText.get().targetIsNotSet);
 
 			Map<ObjectId, Ref> tags = new HashMap<ObjectId, Ref>();
-			for (Ref r : repo.getTags().values()) {
+
+			for (Ref r : repo.getRefDatabase().getRefs(R_TAGS).values()) {
 				ObjectId key = repo.peel(r).getPeeledObjectId();
 				if (key == null)
 					key = r.getObjectId();

org.eclipse.jgit/src/org/eclipse/jgit/api/LogCommand.java

@@ -42,10 +42,13 @@
  */
 package org.eclipse.jgit.api;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.IOException;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
@@ -252,7 +255,8 @@ public LogCommand addRange(AnyObjectId since, AnyObjectId until)
 	 *             the references could not be accessed
 	 */
 	public LogCommand all() throws IOException {
-		for (Ref ref : getRepository().getAllRefs().values()) {
+		Map<String, Ref> refs = getRepository().getRefDatabase().getRefs(ALL);
+		for (Ref ref : refs.values()) {
 			if(!ref.isPeeled())
 				ref = getRepository().peel(ref);
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java

@@ -48,6 +48,7 @@
 import static org.eclipse.jgit.internal.storage.pack.PackExt.BITMAP_INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.PACK;
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -194,7 +195,7 @@ public boolean pack(ProgressMonitor pm) throws IOException {
 			refdb.clearCache();
 			objdb.clearCache();
 
-			refsBefore = repo.getAllRefs();
+			refsBefore = refdb.getRefs(ALL);
 			packsBefore = packsToRebuild();
 			if (packsBefore.isEmpty())
 				return true;

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java

@@ -46,6 +46,8 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.File;
 import java.io.IOException;
 import java.text.MessageFormat;
@@ -382,7 +384,7 @@ public void openPack(final File pack) throws IOException {
 
 	@Override
 	public void scanForRepoChanges() throws IOException {
-		getAllRefs(); // This will look for changes to refs
+		getRefDatabase().getRefs(ALL); // This will look for changes to refs
 		detectIndexChanges();
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java

@@ -45,6 +45,7 @@
 
 import static org.eclipse.jgit.internal.storage.pack.PackExt.BITMAP_INDEX;
 import static org.eclipse.jgit.internal.storage.pack.PackExt.INDEX;
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -457,7 +458,7 @@ private static boolean equals(Ref r1, Ref r2) {
 	 * @throws IOException
 	 */
 	public void packRefs() throws IOException {
-		Collection<Ref> refs = repo.getAllRefs().values();
+		Collection<Ref> refs = repo.getRefDatabase().getRefs(ALL).values();
 		List<String> refsToBePacked = new ArrayList<String>(refs.size());
 		pm.beginTask(JGitText.get().packRefs, refs.size());
 		try {
@@ -574,7 +575,7 @@ private Set<ObjectId> listRefLogObjects(Ref ref, long minTime) throws IOExceptio
 	 * @throws IOException
 	 */
 	private Map<String, Ref> getAllRefs() throws IOException {
-		Map<String, Ref> ret = repo.getAllRefs();
+		Map<String, Ref> ret = repo.getRefDatabase().getRefs(ALL);
 		for (Ref ref : repo.getRefDatabase().getAdditionalRefs())
 			ret.put(ref.getName(), ref);
 		return ret;

org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java

@@ -45,6 +45,8 @@
 
 package org.eclipse.jgit.transport;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -52,6 +54,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
+import java.util.Map;
 import java.util.Set;
 
 import org.eclipse.jgit.errors.PackProtocolException;
@@ -400,7 +403,8 @@ private int maxTimeWanted(final Collection<Ref> wants) {
 
 	private void markReachable(final Set<ObjectId> have, final int maxTime)
 			throws IOException {
-		for (final Ref r : local.getAllRefs().values()) {
+		Map<String, Ref> refs = local.getRefDatabase().getRefs(ALL);
+		for (final Ref r : refs.values()) {
 			ObjectId id = r.getPeeledObjectId();
 			if (id == null)
 				id = r.getObjectId();

org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleFetchConnection.java

@@ -47,6 +47,8 @@
 
 package org.eclipse.jgit.transport;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -242,7 +244,13 @@ private void verifyPrerequisites() throws TransportException {
 				throw new MissingBundlePrerequisiteException(transport.uri,
 						missing);
 
-			for (final Ref r : transport.local.getAllRefs().values()) {
+			Map<String, Ref> localRefs;
+			try {
+				localRefs = transport.local.getRefDatabase().getRefs(ALL);
+			} catch (IOException e) {
+				throw new TransportException(transport.uri, e.getMessage(), e);
+			}
+			for (final Ref r : localRefs.values()) {
 				try {
 					rw.markStart(rw.parseCommit(r.getObjectId()));
 				} catch (IOException readError) {

org.eclipse.jgit/src/org/eclipse/jgit/transport/Transport.java

@@ -46,6 +46,8 @@
 
 package org.eclipse.jgit.transport;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStream;
@@ -644,8 +646,9 @@ public static Collection<RemoteRefUpdate> findRemoteRefUpdatesFor(
 	}
 
 	private static Collection<RefSpec> expandPushWildcardsFor(
-			final Repository db, final Collection<RefSpec> specs) {
+			final Repository db, final Collection<RefSpec> specs)
-		final Map<String, Ref> localRefs = db.getAllRefs();
+			throws IOException {
+		final Map<String, Ref> localRefs = db.getRefDatabase().getRefs(ALL);
 		final Collection<RefSpec> procRefs = new HashSet<RefSpec>();
 
 		for (final RefSpec spec : specs) {

org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java

@@ -43,6 +43,8 @@
 
 package org.eclipse.jgit.transport;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.EOFException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -1129,7 +1131,7 @@ public void checkWants(UploadPack up, List<ObjectId> wants)
 				new ReachableCommitTipRequestValidator().checkWants(up, wants);
 			else if (!wants.isEmpty()) {
 				Set<ObjectId> refIds =
-					refIdSet(up.getRepository().getAllRefs().values());
+					refIdSet(up.getRepository().getRefDatabase().getRefs(ALL).values());
 				for (ObjectId obj : wants) {
 					if (!refIds.contains(obj))
 						throw new PackProtocolException(MessageFormat.format(
@@ -1149,7 +1151,7 @@ public static final class ReachableCommitTipRequestValidator
 		public void checkWants(UploadPack up, List<ObjectId> wants)
 				throws PackProtocolException, IOException {
 			checkNotAdvertisedWants(up.getRevWalk(), wants,
-					refIdSet(up.getRepository().getAllRefs().values()));
+					refIdSet(up.getRepository().getRefDatabase().getRefs(ALL).values()));
 		}
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java

@@ -44,6 +44,8 @@
 
 package org.eclipse.jgit.transport;
 
+import static org.eclipse.jgit.lib.RefDatabase.ALL;
+
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -56,6 +58,7 @@
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import org.eclipse.jgit.errors.CompoundException;
@@ -668,7 +671,13 @@ private Collection<WalkRemoteObjectDatabase> expandOneAlternate(
 	}
 
 	private void markLocalRefsComplete(final Set<ObjectId> have) throws TransportException {
-		for (final Ref r : local.getAllRefs().values()) {
+		Map<String, Ref> refs;
+		try {
+			refs = local.getRefDatabase().getRefs(ALL);
+		} catch (IOException e) {
+			throw new TransportException(e.getMessage(), e);
+		}
+		for (final Ref r : refs.values()) {
 			try {
 				markLocalObjComplete(revWalk.parseAny(r.getObjectId()));
 			} catch (IOException readError) {