Fix for core.autocrlf=input resulting in modified file

This version does not attempt to unsmudge, unlike the first attempt
in Idafad150553df14827eccfde2e3b95760e16a8b6.

Bug: 372834
Change-Id: I9300e735cb16d6208e1df963abb1ff69f688155d
Also-by: Robin Stocker <robin@nibor.org>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Signed-off-by: Robin Stocker <robin@nibor.org>

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java

@@ -68,9 +68,11 @@ import org.eclipse.jgit.dircache.DirCacheEditor;
 import org.eclipse.jgit.dircache.DirCacheEditor.PathEdit;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.CoreConfig.AutoCRLF;
 import org.eclipse.jgit.lib.IndexDiff.StageState;
 import org.eclipse.jgit.merge.MergeStrategy;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
 import org.eclipse.jgit.util.IO;
 import org.junit.Test;
@@ -576,6 +578,35 @@ public class IndexDiffTest extends RepositoryTestCase {
 		assertTrue(StageState.BOTH_ADDED.hasTheirs());
 	}
 
+	@Test
+	public void testAutoCRLFInput() throws Exception {
+		Git git = new Git(db);
+		FileBasedConfig config = db.getConfig();
+
+		// Make sure core.autocrlf is false before adding
+		config.setEnum(ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_AUTOCRLF, AutoCRLF.FALSE);
+		config.save();
+
+		// File is already in repository with CRLF
+		writeTrashFile("crlf.txt", "this\r\ncontains\r\ncrlf\r\n");
+		git.add().addFilepattern("crlf.txt").call();
+		git.commit().setMessage("Add crlf.txt").call();
+
+		// Now set core.autocrlf to input
+		config.setEnum(ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_AUTOCRLF, AutoCRLF.INPUT);
+		config.save();
+
+		FileTreeIterator iterator = new FileTreeIterator(db);
+		IndexDiff diff = new IndexDiff(db, Constants.HEAD, iterator);
+		diff.diff();
+
+		assertTrue(
+				"Expected no modified files, but there were: "
+						+ diff.getModified(), diff.getModified().isEmpty());
+	}
+
 	private void verifyStageState(StageState expected, int... stages)
 			throws IOException {
 		DirCacheBuilder builder = db.lockDirCache().builder();

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java

@@ -223,7 +223,9 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 		ObjectId fromRaw = ObjectId.fromRaw(fti.idBuffer(), fti.idOffset());
 		assertEquals("6b584e8ece562ebffc15d38808cd6b98fc3d97ea",
 				fromRaw.getName());
-		assertFalse(fti.isModified(dce, false));
+		ObjectReader objectReader = db.newObjectReader();
+		assertFalse(fti.isModified(dce, false, objectReader));
+		objectReader.release();
 	}
 
 	@Test
@@ -242,7 +244,9 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 				.getConfig().get(WorkingTreeOptions.KEY));
 		while (!fti.getEntryPathString().equals("symlink"))
 			fti.next(1);
-		assertFalse(fti.isModified(dce, false));
+		ObjectReader objectReader = db.newObjectReader();
+		assertFalse(fti.isModified(dce, false, objectReader));
+		objectReader.release();
 	}
 
 	@Test
@@ -265,7 +269,9 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 		// If the rounding trick does not work we could skip the compareMetaData
 		// test and hope that we are usually testing the intended code path.
 		assertEquals(MetadataDiff.SMUDGED, fti.compareMetadata(dce));
-		assertTrue(fti.isModified(dce, false));
+		ObjectReader objectReader = db.newObjectReader();
+		assertTrue(fti.isModified(dce, false, objectReader));
+		objectReader.release();
 	}
 
 	@Test

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java

@@ -326,7 +326,8 @@ public class DirCacheCheckout {
 						m.getEntryFileMode());
 			} else if (i.getDirCacheEntry() != null) {
 				// The index contains a file (and not a folder)
-				if (f.isModified(i.getDirCacheEntry(), true)
+				if (f.isModified(i.getDirCacheEntry(), true,
+						this.walk.getObjectReader())
 						|| i.getDirCacheEntry().getStage() != 0)
 					// The working tree file is dirty or the index contains a
 					// conflict
@@ -660,7 +661,9 @@ public class DirCacheCheckout {
 				break;
 			case 0xFFD: // 12 13 14
 				if (equalIdAndMode(hId, hMode, iId, iMode))
-					if (f == null || f.isModified(dce, true))
+					if (f == null
+							|| f.isModified(dce, true,
+									this.walk.getObjectReader()))
 						conflict(name, dce, h, m);
 					else
 						remove(name);
@@ -774,7 +777,8 @@ public class DirCacheCheckout {
 						// Nothing in Head
 						// Something in Index
 						if (dce != null
-								&& (f == null || f.isModified(dce, true)))
+								&& (f == null || f.isModified(dce, true,
+										this.walk.getObjectReader())))
 							// No file or file is dirty
 							// Nothing in Merge and current path is part of
 							// File/Folder conflict
@@ -841,7 +845,9 @@ public class DirCacheCheckout {
 						// Something different from a submodule in Index
 						// Nothing in Merge
 						// Something in Head
-						if (f == null || f.isModified(dce, true))
+						if (f == null
+								|| f.isModified(dce, true,
+										this.walk.getObjectReader()))
 							// file is dirty
 							// Index contains the same as Head
 							// Something different from a submodule in Index
@@ -904,7 +910,8 @@ public class DirCacheCheckout {
 						// file content
 						update(name, mId, mMode);
 					} else if (dce != null
-							&& (f == null || f.isModified(dce, true))) {
+							&& (f == null || f.isModified(dce, true,
+									this.walk.getObjectReader()))) {
 						// File doesn't exist or is dirty
 						// Head and Index don't contain a submodule
 						// Head contains the same as Index. Merge differs
@@ -1041,7 +1048,8 @@ public class DirCacheCheckout {
 			wtIt = tw.getTree(1, WorkingTreeIterator.class);
 			if (dcIt == null || wtIt == null)
 				return true;
-			if (wtIt.isModified(dcIt.getDirCacheEntry(), true)) {
+			if (wtIt.isModified(dcIt.getDirCacheEntry(), true,
+					this.walk.getObjectReader())) {
 				return true;
 			}
 		}

org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java

@@ -440,7 +440,8 @@ public class IndexDiff {
 					missing.add(treeWalk.getPathString());
 				} else {
 					if (workingTreeIterator.isModified(
-							dirCacheIterator.getDirCacheEntry(), true)) {
+							dirCacheIterator.getDirCacheEntry(), true,
+							treeWalk.getObjectReader())) {
 						// in index, in workdir, content differs => modified
 						modified.add(treeWalk.getPathString());
 					}

org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java

@@ -73,10 +73,12 @@ import org.eclipse.jgit.ignore.IgnoreRule;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.CoreConfig;
+import org.eclipse.jgit.lib.CoreConfig.CheckStat;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ObjectLoader;
+import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.lib.CoreConfig.CheckStat;
 import org.eclipse.jgit.submodule.SubmoduleWalk;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.IO;
@@ -796,22 +798,46 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 	 *            True if the actual file content should be checked if
 	 *            modification time differs.
 	 * @return true if content is most likely different.
+	 * @deprecated Use {@link #isModified(DirCacheEntry, boolean, ObjectReader)}
 	 */
 	public boolean isModified(DirCacheEntry entry, boolean forceContentCheck) {
+		return isModified(entry, false, null);
+	}
+
+	/**
+	 * Checks whether this entry differs from a given entry from the
+	 * {@link DirCache}.
+	 *
+	 * File status information is used and if status is same we consider the
+	 * file identical to the state in the working directory. Native git uses
+	 * more stat fields than we have accessible in Java.
+	 *
+	 * @param entry
+	 *            the entry from the dircache we want to compare against
+	 * @param forceContentCheck
+	 *            True if the actual file content should be checked if
+	 *            modification time differs.
+	 * @param reader
+	 *            access to repository objects if necessary. Should not be null.
+	 * @return true if content is most likely different.
+	 * @since 3.3
+	 */
+	public boolean isModified(DirCacheEntry entry, boolean forceContentCheck,
+			ObjectReader reader) {
 		MetadataDiff diff = compareMetadata(entry);
 		switch (diff) {
 		case DIFFER_BY_TIMESTAMP:
 			if (forceContentCheck)
 				// But we are told to look at content even though timestamps
 				// tell us about modification
-				return contentCheck(entry);
+				return contentCheck(entry, reader);
 			else
 				// We are told to assume a modification if timestamps differs
 				return true;
 		case SMUDGED:
 			// The file is clean by timestamps but the entry was smudged.
 			// Lets do a content check
-			return contentCheck(entry);
+			return contentCheck(entry, reader);
 		case EQUAL:
 			return false;
 		case DIFFER_BY_METADATA:
@@ -854,10 +880,12 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 	 *
 	 * @param entry
 	 *            the entry to be checked
-	 * @return <code>true</code> if the content matches, <code>false</code>
+	 * @param reader
-	 *         otherwise
+	 *            acccess to repository data if necessary
+	 * @return <code>true</code> if the content doesn't match,
+	 *         <code>false</code> if it matches
 	 */
-	private boolean contentCheck(DirCacheEntry entry) {
+	private boolean contentCheck(DirCacheEntry entry, ObjectReader reader) {
 		if (getEntryObjectId().equals(entry.getObjectId())) {
 			// Content has not changed
 
@@ -873,7 +901,50 @@ public abstract class WorkingTreeIterator extends AbstractTreeIterator {
 
 			return false;
 		} else {
-			// Content differs: that's a real change!
+			// Content differs: that's a real change, perhaps
+			if (reader == null) // deprecated use, do no further checks
+				return true;
+			switch (getOptions().getAutoCRLF()) {
+			case INPUT:
+			case TRUE:
+				InputStream dcIn = null;
+				try {
+					ObjectLoader loader = reader.open(entry.getObjectId());
+					if (loader == null)
+						return true;
+
+					// We need to compute the length, but only if it is not
+					// a binary stream.
+					dcIn = new EolCanonicalizingInputStream(
+							loader.openStream(), true, true /* abort if binary */);
+					long dcInLen;
+					try {
+						dcInLen = computeLength(dcIn);
+					} catch (EolCanonicalizingInputStream.IsBinaryException e) {
+						return true;
+					} finally {
+						dcIn.close();
+					}
+
+					dcIn = new EolCanonicalizingInputStream(
+							loader.openStream(), true);
+					byte[] autoCrLfHash = computeHash(dcIn, dcInLen);
+					boolean changed = getEntryObjectId().compareTo(
+							autoCrLfHash, 0) != 0;
+					return changed;
+				} catch (IOException e) {
+					return true;
+				} finally {
+					if (dcIn != null)
+						try {
+							dcIn.close();
+						} catch (IOException e) {
+							// empty
+						}
+				}
+			case FALSE:
+				break;
+			}
 			return true;
 		}
 	}

org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/IndexDiffFilter.java

@@ -53,6 +53,7 @@ import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.lib.FileMode;
+import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.WorkingTreeIterator;
 
@@ -72,7 +73,7 @@ import org.eclipse.jgit.treewalk.WorkingTreeIterator;
  * <p>
  * If no difference is found then we have to compare index and working-tree as
  * the last step. By making use of
- * {@link WorkingTreeIterator#isModified(org.eclipse.jgit.dircache.DirCacheEntry, boolean)}
+ * {@link WorkingTreeIterator#isModified(org.eclipse.jgit.dircache.DirCacheEntry, boolean, ObjectReader)}
  * we can avoid the computation of the content id if the file is not dirty.
  * <p>
  * Instances of this filter should not be used for multiple {@link TreeWalk}s.
@@ -219,7 +220,7 @@ public class IndexDiffFilter extends TreeFilter {
 		// Only one chance left to detect a diff: between index and working
 		// tree. Make use of the WorkingTreeIterator#isModified() method to
 		// avoid computing SHA1 on filesystem content if not really needed.
-		return wi.isModified(di.getDirCacheEntry(), true);
+		return wi.isModified(di.getDirCacheEntry(), true, tw.getObjectReader());
 	}
 
 	/**

org.eclipse.jgit/src/org/eclipse/jgit/util/io/EolCanonicalizingInputStream.java

@@ -70,6 +70,23 @@ public class EolCanonicalizingInputStream extends InputStream {
 
 	private boolean detectBinary;
 
+	private boolean abortIfBinary;
+
+	/**
+	 * A special exception thrown when {@link EolCanonicalizingInputStream} is
+	 * told to throw an exception when attempting to read a binary file. The
+	 * exception may be thrown at any stage during reading.
+	 *
+	 * @since 3.3
+	 */
+	public static class IsBinaryException extends IOException {
+		private static final long serialVersionUID = 1L;
+
+		IsBinaryException() {
+			super();
+		}
+	}
+
 	/**
 	 * Creates a new InputStream, wrapping the specified stream
 	 *
@@ -80,8 +97,25 @@ public class EolCanonicalizingInputStream extends InputStream {
 	 * @since 2.0
 	 */
 	public EolCanonicalizingInputStream(InputStream in, boolean detectBinary) {
+		this(in, detectBinary, false);
+	}
+
+	/**
+	 * Creates a new InputStream, wrapping the specified stream
+	 *
+	 * @param in
+	 *            raw input stream
+	 * @param detectBinary
+	 *            whether binaries should be detected
+	 * @param abortIfBinary
+	 *            throw an IOException if the file is binary
+	 * @since 3.3
+	 */
+	public EolCanonicalizingInputStream(InputStream in, boolean detectBinary,
+			boolean abortIfBinary) {
 		this.in = in;
 		this.detectBinary = detectBinary;
+		this.abortIfBinary = abortIfBinary;
 	}
 
 	@Override
@@ -128,6 +162,14 @@ public class EolCanonicalizingInputStream extends InputStream {
 		return i == off ? -1 : i - off;
 	}
 
+	/**
+	 * @return true if the stream has detected as a binary so far
+	 * @since 3.3
+	 */
+	public boolean isBinary() {
+		return isBinary;
+	}
+
 	@Override
 	public void close() throws IOException {
 		in.close();
@@ -140,6 +182,8 @@ public class EolCanonicalizingInputStream extends InputStream {
 		if (detectBinary) {
 			isBinary = RawText.isBinary(buf, cnt);
 			detectBinary = false;
+			if (isBinary && abortIfBinary)
+				throw new IsBinaryException();
 		}
 		ptr = 0;
 		return true;