Merge branch 'stable-5.4'

* stable-5.4:
  Fix NPE in RebaseTodoFile#parseComments
  Fix NPE in ObjectIdOwnerMap#get
  Fix NPE in CommitOnlyTest#getHead
  FileUtils#lastModifiedInstant should not log error if path doesn't exist
  Cache user global and system-wide git configurations
  Avoid setup and saving FileStoreAttributes compete for ~/.gitconfig lock
  Add missing dependencies for running FS_POSIXTest in Eclipse
  Fix javadoc for SystemReader#getInstance
  Upgrade tycho-extras to 1.4.0
  Improve retry handling when saving FileStoreAttributes fails
  Ensure FSTest uses MockSystemReader
  Make supportsAtomicCreateNewFile return true as default
  Update orbit to R20190602212107-2019-06 to enable backports from master
  Handle InvalidPathException in FS_POSIX#createNewFileAtomic
  Ensure root cause of lock creation failures is logged
  Implement toString in MockSystemReader and MockConfig
  LocalDiskRefTreeDatabaseTest shall use MockSystemReader
  Ensure LocalDiskRepositoryTestCase#setup fully uses MockSystemReader
  Ensure we use MockSystemReader in tests
  Override FileBasedConfig's save method in MockConfig
  Remove FileBasedConfig.load(boolean) introduced in d45219ba
  Disable debug log for FS in org.eclipse.jgit.test
  Bazel: enable logging for tests in org.eclipse.jgit.test
  LockFile: log exception if creation of lock file failed
  Stop using deprecated Constants.CHARACTER_ENCODING

Change-Id: I709de5edb626536529a99220aae7751b127c9bff
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

11 files changed, 173 insertions, 10 deletions

diff --git a/org.eclipse.jgit.test/BUILD b/org.eclipse.jgit.test/BUILD
index fc8c53c185..f90a28030d 100644
--- a/org.eclipse.jgit.test/BUILD
+++ b/org.eclipse.jgit.test/BUILD
@@ -51,6 +51,7 @@ java_library(
     deps = [
         "//lib:jsch",
         "//lib:junit",
+        "//lib:slf4j-simple",
         "//lib:mockito",
         "//org.eclipse.jgit:jgit",
         "//org.eclipse.jgit.junit:junit",
diff --git a/org.eclipse.jgit.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
index 53b79b0cb7..e36f5e419a 100644
--- a/org.eclipse.jgit.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
@@ -10,7 +10,7 @@ Bundle-ActivationPolicy: lazy
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  com.jcraft.jsch;version="[0.1.54,0.2.0)",
- net.bytebuddy.dynamic.loading;version="[1.7.0,2.0.0)",
+ net.bytebuddy.dynamic.loading;version="[1.9.0,2.0.0)",
  org.apache.commons.compress.archivers;version="[1.15.0,2.0)",
  org.apache.commons.compress.archivers.tar;version="[1.15.0,2.0)",
  org.apache.commons.compress.archivers.zip;version="[1.15.0,2.0)",
@@ -74,10 +74,10 @@ Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  org.junit.rules;version="[4.12,5.0.0)",
  org.junit.runner;version="[4.12,5.0.0)",
  org.junit.runners;version="[4.12,5.0.0)",
- org.mockito;version="[2.13.0,3.0.0)",
- org.mockito.invocation;version="[2.13.0,3.0.0)",
- org.mockito.junit;version="[2.13.0,3.0.0)",
- org.mockito.stubbing;version="[2.13.0,3.0.0)",
+ org.mockito;version="[2.23.0,3.0.0)",
+ org.mockito.invocation;version="[2.23.0,3.0.0)",
+ org.mockito.junit;version="[2.23.0,3.0.0)",
+ org.mockito.stubbing;version="[2.23.0,3.0.0)",
  org.objenesis;version="[2.6.0,3.0.0)",
  org.slf4j;version="[1.7.0,2.0.0)",
  org.tukaani.xz;version="[1.6.0,2.0)"
diff --git a/org.eclipse.jgit.test/tst-rsrc/log4j.properties b/org.eclipse.jgit.test/tst-rsrc/log4j.properties
index ee1ac35158..856a731ab9 100644
--- a/org.eclipse.jgit.test/tst-rsrc/log4j.properties
+++ b/org.eclipse.jgit.test/tst-rsrc/log4j.properties
@@ -7,8 +7,8 @@ log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.Target=System.out
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
 log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
-#log4j.appender.fileLogger.bufferedIO = true
-#log4j.appender.fileLogger.bufferSize = 4096
+log4j.appender.fileLogger.bufferedIO = true
+log4j.appender.fileLogger.bufferSize = 4096
 
 #log4j.logger.org.eclipse.jgit.util.FS = DEBUG
 #log4j.logger.org.eclipse.jgit.internal.storage.file.FileSnapshot = DEBUG
diff --git a/org.eclipse.jgit.test/tst-rsrc/simplelogger.properties b/org.eclipse.jgit.test/tst-rsrc/simplelogger.properties
new file mode 100644
index 0000000000..011b2f8bb0
--- /dev/null
+++ b/org.eclipse.jgit.test/tst-rsrc/simplelogger.properties
@@ -0,0 +1,9 @@
+org.slf4j.simpleLogger.logFile = System.err
+org.slf4j.simpleLogger.cacheOutputStream = true
+org.slf4j.simpleLogger.defaultLogLevel = info
+org.slf4j.simpleLogger.showDateTime = true
+org.slf4j.simpleLogger.dateTimeFormat = HH:mm:ss.SSSXXX
+org.slf4j.simpleLogger.showThreadName = true
+
+#org.slf4j.simpleLogger.log.org.eclipse.jgit.util.FS = debug
+#org.slf4j.simpleLogger.log.org.eclipse.jgit.internal.storage.file.FileSnapshot = debug
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
index 74d13883e1..2270a6a8be 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CloneCommandTest.java
@@ -68,9 +68,9 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
-import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.submodule.SubmoduleStatus;
 import org.eclipse.jgit.submodule.SubmoduleStatusType;
 import org.eclipse.jgit.submodule.SubmoduleWalk;
@@ -680,8 +680,8 @@ public class CloneCommandTest extends RepositoryTestCase {
 				ConfigConstants.CONFIG_BRANCH_SECTION, "test",
 				ConfigConstants.CONFIG_KEY_REBASE, null));
 
-		FileBasedConfig userConfig = SystemReader.getInstance().openUserConfig(
-				null, git.getRepository().getFS());
+		StoredConfig userConfig = SystemReader.getInstance()
+				.getUserConfig();
 		userConfig.setString(ConfigConstants.CONFIG_BRANCH_SECTION, null,
 				ConfigConstants.CONFIG_KEY_AUTOSETUPREBASE,
 				ConfigConstants.CONFIG_KEY_ALWAYS);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java
index 83181eea23..2a2a6ba1bc 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitOnlyTest.java
@@ -1295,9 +1295,15 @@ public class CommitOnlyTest extends RepositoryTestCase {
 		try {
 			final Repository repo = git.getRepository();
 			final ObjectId headId = repo.resolve(Constants.HEAD + "^{commit}");
+			if (headId == null) {
+				return "";
+			}
 			try (RevWalk rw = new RevWalk(repo)) {
 				final TreeWalk tw = TreeWalk.forPath(repo, path,
 						rw.parseTree(headId));
+				if (tw == null) {
+					return "";
+				}
 				return new String(tw.getObjectReader().open(tw.getObjectId(0))
 						.getBytes(), UTF_8);
 			}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java
index 6fa35d64b0..35f4fcba9b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java
@@ -62,6 +62,7 @@ import java.time.Instant;
 import java.util.ArrayList;
 import java.util.concurrent.TimeUnit;
 
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FS.FileStoreAttributes;
 import org.eclipse.jgit.util.FileUtils;
@@ -84,6 +85,7 @@ public class FileSnapshotTest {
 
 	@Before
 	public void setUp() throws Exception {
+		SystemReader.setInstance(new MockSystemReader());
 		trash = Files.createTempDirectory("tmp_");
 		// measure timer resolution before the test to avoid time critical tests
 		// are affected by time needed for measurement
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java
index d5a07e02fa..cafec04f7c 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java
@@ -80,6 +80,7 @@ public class LocalDiskRefTreeDatabaseTest extends LocalDiskRepositoryTestCase {
 	@Override
 	@Before
 	public void setUp() throws Exception {
+		super.setUp();
 		FileRepository init = createWorkRepository();
 		FileBasedConfig cfg = init.getConfig();
 		cfg.setInt("core", null, "repositoryformatversion", 1);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
index 43648206f0..5100d258d7 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
@@ -56,9 +56,11 @@ import java.nio.file.StandardOpenOption;
 import java.util.StringTokenizer;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.IO;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
@@ -90,6 +92,7 @@ public class FileBasedConfigTest {
 
 	@Before
 	public void setUp() throws Exception {
+		SystemReader.setInstance(new MockSystemReader());
 		trash = Files.createTempDirectory("tmp_");
 		FS.getFileStoreAttributes(trash.getParent());
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
index 99d435100b..89a2fc44c7 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
@@ -67,6 +67,7 @@ import java.util.Set;
 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.errors.CommandFailedException;
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.RepositoryCache;
 import org.junit.After;
@@ -79,6 +80,7 @@ public class FSTest {
 
 	@Before
 	public void setUp() throws Exception {
+		SystemReader.setInstance(new MockSystemReader());
 		trash = File.createTempFile("tmp_", "");
 		trash.delete();
 		assertTrue("mkdir " + trash, trash.mkdir());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FS_POSIXTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FS_POSIXTest.java
new file mode 100644
index 0000000000..87349a25a4
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FS_POSIXTest.java
@@ -0,0 +1,139 @@
+/*
+ * Copyright (C) 2019, Vishal Devgire <vishaldevgire@gmail.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package org.eclipse.jgit.util;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.eclipse.jgit.junit.MockSystemReader;
+import org.eclipse.jgit.lib.ConfigConstants;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class FS_POSIXTest {
+	private SystemReader originalSystemReaderInstance;
+
+	private FileBasedConfig systemConfig;
+
+	private FileBasedConfig userConfig;
+
+	private Path tmp;
+
+	@Before
+	public void setUp() throws Exception {
+		tmp = Files.createTempDirectory("jgit_test_");
+		MockSystemReader mockSystemReader = new MockSystemReader();
+		SystemReader.setInstance(mockSystemReader);
+
+		// Measure timer resolution before the test to avoid time critical tests
+		// are affected by time needed for measurement.
+		// The MockSystemReader must be configured first since we need to use
+		// the same one here
+		FS.getFileStoreAttributes(tmp.getParent());
+		systemConfig = new FileBasedConfig(
+				new File(tmp.toFile(), "systemgitconfig"), FS.DETECTED);
+		userConfig = new FileBasedConfig(systemConfig,
+				new File(tmp.toFile(), "usergitconfig"), FS.DETECTED);
+		// We have to set autoDetach to false for tests, because tests expect to
+		// be able to clean up by recursively removing the repository, and
+		// background GC might be in the middle of writing or deleting files,
+		// which would disrupt this.
+		userConfig.setBoolean(ConfigConstants.CONFIG_GC_SECTION, null,
+				ConfigConstants.CONFIG_KEY_AUTODETACH, false);
+		userConfig.save();
+		mockSystemReader.setSystemGitConfig(systemConfig);
+		mockSystemReader.setUserGitConfig(userConfig);
+
+		originalSystemReaderInstance = SystemReader.getInstance();
+		SystemReader.setInstance(mockSystemReader);
+	}
+
+	@After
+	public void tearDown() throws IOException {
+		SystemReader.setInstance(originalSystemReaderInstance);
+		FileUtils.delete(tmp.toFile(), FileUtils.RECURSIVE | FileUtils.RETRY);
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnSupportedAsDefault() {
+		assertTrue(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnTrueIfFlagIsSetInUserConfig() {
+		setAtomicCreateCreationFlag(userConfig, "true");
+		assertTrue(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnTrueIfFlagIsSetInSystemConfig() {
+		setAtomicCreateCreationFlag(systemConfig, "true");
+		assertTrue(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnFalseIfFlagUnsetInUserConfig() {
+		setAtomicCreateCreationFlag(userConfig, "false");
+		assertFalse(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnFalseIfFlagUnsetInSystemConfig() {
+		setAtomicCreateCreationFlag(systemConfig, "false");
+		assertFalse(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	private void setAtomicCreateCreationFlag(FileBasedConfig config,
+			String value) {
+		config.setString(ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_SUPPORTSATOMICFILECREATION, value);
+	}
+}