Browse Source

ApplyCommand: support binary patches

Implement applying binary patches. Handles both literal and delta
patches. Note that C git also runs binary files through the clean
and smudge filters. Implement the same safeguards against corrupted
patches as in C git: require the full OIDs to be present in the patch
file, and apply a binary patch only if both pre- and post-image hashes
match.

Add tests for applying literal and delta patches.

Bug: 371725
Change-Id: I71dc214fe4145d7cc8e4769384fb78c7d0d6c220
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>
tags/v5.12.0.202105261145-m3
Thomas Wolf 3 years ago
parent
commit
10ac449911

+ 2
- 0
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/.gitattributes View File

@@ -1,3 +1,5 @@
*.patch -crlf
*Image -crlf
*.out -crlf
delta* -text
literal* -text

+ 8
- 0
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/delta.patch View File

@@ -0,0 +1,8 @@
diff --git a/delta b/delta
index b4527005bf9e4da2dd1d7185b51bdac623a4218f..8b370bb5f2bc3261b6b62e80d6edd784a61ec225 100644
GIT binary patch
delta 14
ScmZp0Xmwa1z*+$U3j_csN(Dmz

delta 12
TcmZp5XmD5{u!xa=5hEi28?FP4

BIN
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/delta_PostImage View File


BIN
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/delta_PreImage View File


+ 126
- 0
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/literal.patch View File

@@ -0,0 +1,126 @@
diff --git a/literal b/literal
index 799df8578e3cae8a5e979182391b8e9a6a3deded..74e4201af6378ac87bf9e118fbab6553c7fd355c 100644
GIT binary patch
literal 5389
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BIN
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/literal_PostImage View File


BIN
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/literal_PreImage View File


+ 40
- 0
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/literal_add.patch View File

@@ -0,0 +1,40 @@
diff --git a/literal_add b/literal_add
new file mode 100644
index 0000000000000000000000000000000000000000..799df8578e3cae8a5e979182391b8e9a6a3deded
GIT binary patch
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zxoJ3q`BNsdeb*C=&+znTPg(oGZ>TsNm*p6-s^<dE)uQU^{eA!w88Fs9)AywRE_>-~
zo<z<8YO5Qmue&%PLSgx;vV_h7j7ULpIBiX|4d5%!S)|C<QMHv#>5qiMvi`c3fXjnY
z?nzI>n30qgyK(yTm1Cj+ioF{^3@0CWrSO)>rn{c}{@GoeufLXs+vZGT(^C&#7eYib
z@v#)Z=<7IOmIA1i6V}+JBXJIJp`n@GI}ZTx-oB4$Ywcp$iqa857|UG%CfGW821q7=
zq9+APM+z`d>S`Lf|K3fsw_Ssnls$oQ<HruEuZBecMsac?omI_gbs~~-BLDz3)fc$`
z-e1wt-p#TVrMzFUg##aK;af}Q#pw!orcPa&X4EpdpGluTlGk>l&LdL&c>{lV@vUe(
zB{i9~>+T+MNs|1@lU%4xMhqz7rXF{kl4D#XI<rJf|J}hcee;cpJz~<*Mw6VBg4gGb
zooq-lR=Ch_!L_ceK5qAmI2hv|_7ZWTAd$Xz_Z*|K;WE%ypkCQ=fIu+*%<#Kh7hMP!
z=r839ZtBcdRV$IO`b<Y78%j(+fEkbhUvG%-EPj-E3uaPZcZr7cEpa(i)PL^WtF5k7
zKc{_3+6ywu7%f6L4wOU{)g}fo*D?^Jr|{7Sp8?<)H^ESE%sf%~un+ua7rY{J06+}0
zBy8Rps2H|^J|j+2+~rC4Fn?hY0JCP_Lh7i|L+U9?*al+&tkFFXsf0HCR$sKt{%-N*
z3RR6+FmIp}5m(&$ue@g=bLJKRFlTN7-&`_x$UWlocgCh)3Al~C9R)~fZF~*18f4VZ
z7oA&Ukw3@K+7SLg7mjhqTqW}hV+`Lhzc5b6=kLU7I5v9W<&&Sk(HI4gO@x470;o9m
zY+rTyJynfaG+&^Lp59A<M5C)XcqYbh#lf@DF@T<{7x4#s21TzuZbDB++R+zw^S<u0
z;g3DVz_f{JftkB1C;cKAHg^r29JT@cfi7H53U1dZYR<KAsi_ldm7Uv;a`aFYDEI>1
zbX{p6Z2g0st1+xPRr~fQk-nI>L$^#A<JHs;1&T!MQ?sAF12H_pkRrHUeIPC;nNZkA
zAlOSN><5PaL=!6;PSwBuOsthb;@vtaN3H8!fg-Rw7QQgI>Pk?49a|gzM^OzTtUX=(
z<{t+S#TiXq)6|eE-gzSI0rP_+YmYB4y}5I>Ds?yLyvmA{4domX6nRy|Tb{c@gw3Go
zSAy>Q%C;02*syDzNaO$;UaV@p5uVP-xx6jWU($8IpY(BDzOQ7j6qV%)(*@c8YURW;
zzpcp2S4#n^S%{1S+QBwkHC1k7_I_Hk`;+V09uYtc%=Ww#?-e@}G}|!}PU;OD{-Qsp
bU%LDkMDBWX&Ru`<00000NkvXXu0mjfJA@b~

literal 0
HcmV?d00001

BIN
org.eclipse.jgit.test/tst-rsrc/org/eclipse/jgit/diff/literal_add_PostImage View File


+ 41
- 0
org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ApplyCommandTest.java View File

@@ -9,6 +9,7 @@
*/
package org.eclipse.jgit.api;

import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
@@ -19,6 +20,7 @@ import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.Files;

import org.eclipse.jgit.api.errors.PatchApplyException;
import org.eclipse.jgit.api.errors.PatchFormatException;
@@ -29,6 +31,7 @@ import org.eclipse.jgit.diff.RawText;
import org.eclipse.jgit.junit.RepositoryTestCase;
import org.eclipse.jgit.lib.Config;
import org.eclipse.jgit.lib.ConfigConstants;
import org.eclipse.jgit.util.IO;
import org.junit.Test;

public class ApplyCommandTest extends RepositoryTestCase {
@@ -246,6 +249,44 @@ public class ApplyCommandTest extends RepositoryTestCase {
}
}

private void checkBinary(String name, boolean hasPreImage)
throws Exception {
try (Git git = new Git(db)) {
byte[] post = IO
.readWholeStream(getTestResource(name + "_PostImage"), 0)
.array();
File f = new File(db.getWorkTree(), name);
if (hasPreImage) {
byte[] pre = IO
.readWholeStream(getTestResource(name + "_PreImage"), 0)
.array();
Files.write(f.toPath(), pre);
git.add().addFilepattern(name).call();
git.commit().setMessage("PreImage").call();
}
ApplyResult result = git.apply()
.setPatch(getTestResource(name + ".patch")).call();
assertEquals(1, result.getUpdatedFiles().size());
assertEquals(f, result.getUpdatedFiles().get(0));
assertArrayEquals(post, Files.readAllBytes(f.toPath()));
}
}

@Test
public void testBinaryDelta() throws Exception {
checkBinary("delta", true);
}

@Test
public void testBinaryLiteral() throws Exception {
checkBinary("literal", true);
}

@Test
public void testBinaryLiteralAdd() throws Exception {
checkBinary("literal_add", false);
}

@Test
public void testAddA1() throws Exception {
ApplyResult result = init("A1", false, true);

+ 3
- 0
org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties View File

@@ -13,6 +13,9 @@ ambiguousObjectAbbreviation=Object abbreviation {0} is ambiguous
aNewObjectIdIsRequired=A NewObjectId is required.
anExceptionOccurredWhileTryingToAddTheIdOfHEAD=An exception occurred while trying to add the Id of HEAD
anSSHSessionHasBeenAlreadyCreated=An SSH session has been already created
applyBinaryBaseOidWrong=Cannot apply binary patch; OID for file {0} does not match
applyBinaryOidTooShort=Binary patch for file {0} does not have full IDs
applyBinaryResultOidWrong=Result of binary patch for file {0} has wrong OID.
applyingCommit=Applying {0}
archiveFormatAlreadyAbsent=Archive format already absent: {0}
archiveFormatAlreadyRegistered=Archive format already registered with different implementation: {0}

+ 244
- 30
org.eclipse.jgit/src/org/eclipse/jgit/api/ApplyCommand.java View File

@@ -9,7 +9,9 @@
*/
package org.eclipse.jgit.api;

import java.io.BufferedInputStream;
import java.io.BufferedWriter;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
@@ -25,6 +27,7 @@ import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.zip.InflaterInputStream;

import org.eclipse.jgit.api.errors.FilterFailedException;
import org.eclipse.jgit.api.errors.GitAPIException;
@@ -44,10 +47,13 @@ import org.eclipse.jgit.internal.JGitText;
import org.eclipse.jgit.lib.Constants;
import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
import org.eclipse.jgit.lib.FileMode;
import org.eclipse.jgit.lib.ObjectId;
import org.eclipse.jgit.lib.ObjectLoader;
import org.eclipse.jgit.lib.ObjectStream;
import org.eclipse.jgit.lib.Repository;
import org.eclipse.jgit.patch.BinaryHunk;
import org.eclipse.jgit.patch.FileHeader;
import org.eclipse.jgit.patch.FileHeader.PatchType;
import org.eclipse.jgit.patch.HunkHeader;
import org.eclipse.jgit.patch.Patch;
import org.eclipse.jgit.treewalk.FileTreeIterator;
@@ -57,14 +63,17 @@ import org.eclipse.jgit.treewalk.filter.AndTreeFilter;
import org.eclipse.jgit.treewalk.filter.NotIgnoredFilter;
import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
import org.eclipse.jgit.util.FS;
import org.eclipse.jgit.util.FS.ExecutionResult;
import org.eclipse.jgit.util.FileUtils;
import org.eclipse.jgit.util.IO;
import org.eclipse.jgit.util.RawParseUtils;
import org.eclipse.jgit.util.StringUtils;
import org.eclipse.jgit.util.TemporaryBuffer;
import org.eclipse.jgit.util.FS.ExecutionResult;
import org.eclipse.jgit.util.TemporaryBuffer.LocalFile;
import org.eclipse.jgit.util.io.BinaryDeltaInputStream;
import org.eclipse.jgit.util.io.BinaryHunkInputStream;
import org.eclipse.jgit.util.io.EolStreamTypeUtil;
import org.eclipse.jgit.util.sha1.SHA1;

/**
* Apply a patch to files and/or to the index.
@@ -191,6 +200,9 @@ public class ApplyCommand extends GitCommand<ApplyResult> {

private void apply(Repository repository, String path, DirCache cache,
File f, FileHeader fh) throws IOException, PatchApplyException {
if (PatchType.BINARY.equals(fh.getPatchType())) {
return;
}
boolean convertCrLf = needsCrLfConversion(f, fh);
// Use a TreeWalk with a DirCacheIterator to pick up the correct
// clean/smudge filters. CR-LF handling is completely determined by
@@ -217,16 +229,23 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
FileTreeIterator file = walk.getTree(fileIdx,
FileTreeIterator.class);
if (file != null) {
command = walk
.getFilterCommand(Constants.ATTR_FILTER_TYPE_CLEAN);
RawText raw;
// Can't use file.openEntryStream() as it would do CR-LF
// conversion as usual, not as wanted by us.
try (InputStream input = filterClean(repository, path,
new FileInputStream(f), convertCrLf, command)) {
raw = new RawText(IO.readWholeStream(input, 0).array());
if (PatchType.GIT_BINARY.equals(fh.getPatchType())) {
applyBinary(repository, path, f, fh,
file::openEntryStream, file.getEntryObjectId(),
checkOut);
} else {
command = walk.getFilterCommand(
Constants.ATTR_FILTER_TYPE_CLEAN);
RawText raw;
// Can't use file.openEntryStream() as it would do CR-LF
// conversion as usual, not as wanted by us.
try (InputStream input = filterClean(repository, path,
new FileInputStream(f), convertCrLf, command)) {
raw = new RawText(
IO.readWholeStream(input, 0).array());
}
applyText(repository, path, raw, f, fh, checkOut);
}
apply(repository, path, raw, f, fh, checkOut);
return;
}
}
@@ -234,21 +253,30 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
// File ignored?
RawText raw;
CheckoutMetadata checkOut;
if (convertCrLf) {
try (InputStream input = EolStreamTypeUtil.wrapInputStream(
new FileInputStream(f), EolStreamType.TEXT_LF)) {
raw = new RawText(IO.readWholeStream(input, 0).array());
}
checkOut = new CheckoutMetadata(EolStreamType.TEXT_CRLF, null);
} else {
raw = new RawText(f);
if (PatchType.GIT_BINARY.equals(fh.getPatchType())) {
checkOut = new CheckoutMetadata(EolStreamType.DIRECT, null);
applyBinary(repository, path, f, fh, () -> new FileInputStream(f),
null, checkOut);
} else {
if (convertCrLf) {
try (InputStream input = EolStreamTypeUtil.wrapInputStream(
new FileInputStream(f), EolStreamType.TEXT_LF)) {
raw = new RawText(IO.readWholeStream(input, 0).array());
}
checkOut = new CheckoutMetadata(EolStreamType.TEXT_CRLF, null);
} else {
raw = new RawText(f);
checkOut = new CheckoutMetadata(EolStreamType.DIRECT, null);
}
applyText(repository, path, raw, f, fh, checkOut);
}
apply(repository, path, raw, f, fh, checkOut);
}

private boolean needsCrLfConversion(File f, FileHeader fileHeader)
throws IOException {
if (PatchType.GIT_BINARY.equals(fileHeader.getPatchType())) {
return false;
}
if (!hasCrLf(fileHeader)) {
try (InputStream input = new FileInputStream(f)) {
return RawText.isCrLfText(input);
@@ -258,7 +286,7 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
}

private static boolean hasCrLf(FileHeader fileHeader) {
if (fileHeader == null) {
if (PatchType.GIT_BINARY.equals(fileHeader.getPatchType())) {
return false;
}
for (HunkHeader header : fileHeader.getHunks()) {
@@ -330,19 +358,30 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
return result.getStdout().openInputStreamWithAutoDestroy();
}

/**
* Something that can supply an {@link InputStream}.
*/
private interface StreamSupplier {
InputStream load() throws IOException;
}

/**
* We write the patch result to a {@link TemporaryBuffer} and then use
* {@link DirCacheCheckout}.getContent() to run the result through the CR-LF
* and smudge filters. DirCacheCheckout needs an ObjectLoader, not a
* TemporaryBuffer, so this class bridges between the two, making the
* TemporaryBuffer look like an ordinary git blob to DirCacheCheckout.
* TemporaryBuffer, so this class bridges between the two, making any Stream
* provided by a {@link StreamSupplier} look like an ordinary git blob to
* DirCacheCheckout.
*/
private static class BufferLoader extends ObjectLoader {
private static class StreamLoader extends ObjectLoader {

private TemporaryBuffer data;
private StreamSupplier data;

BufferLoader(TemporaryBuffer data) {
private long size;

StreamLoader(StreamSupplier data, long length) {
this.data = data;
this.size = length;
}

@Override
@@ -352,7 +391,7 @@ public class ApplyCommand extends GitCommand<ApplyResult> {

@Override
public long getSize() {
return data.length();
return size;
}

@Override
@@ -369,12 +408,146 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
public ObjectStream openStream()
throws MissingObjectException, IOException {
return new ObjectStream.Filter(getType(), getSize(),
data.openInputStream());
new BufferedInputStream(data.load()));
}
}

private void apply(Repository repository, String path, RawText rt, File f,
FileHeader fh, CheckoutMetadata checkOut)
private void initHash(SHA1 hash, long size) {
hash.update(Constants.encodedTypeString(Constants.OBJ_BLOB));
hash.update((byte) ' ');
hash.update(Constants.encodeASCII(size));
hash.update((byte) 0);
}

private ObjectId hash(File f) throws IOException {
SHA1 hash = SHA1.newInstance();
initHash(hash, f.length());
try (InputStream input = new FileInputStream(f)) {
byte[] buf = new byte[8192];
int n;
while ((n = input.read(buf)) >= 0) {
hash.update(buf, 0, n);
}
}
return hash.toObjectId();
}

private void checkOid(ObjectId baseId, ObjectId id, ChangeType type, File f,
String path)
throws PatchApplyException, IOException {
boolean hashOk = false;
if (id != null) {
hashOk = baseId.equals(id);
if (!hashOk && ChangeType.ADD.equals(type)
&& ObjectId.zeroId().equals(baseId)) {
// We create the file first. The OID of an empty file is not the
// zero id!
hashOk = Constants.EMPTY_BLOB_ID.equals(id);
}
} else {
if (ObjectId.zeroId().equals(baseId)) {
// File empty is OK.
hashOk = !f.exists() || f.length() == 0;
} else {
hashOk = baseId.equals(hash(f));
}
}
if (!hashOk) {
throw new PatchApplyException(MessageFormat
.format(JGitText.get().applyBinaryBaseOidWrong, path));
}
}

private void applyBinary(Repository repository, String path, File f,
FileHeader fh, StreamSupplier loader, ObjectId id,
CheckoutMetadata checkOut)
throws PatchApplyException, IOException {
if (!fh.getOldId().isComplete() || !fh.getNewId().isComplete()) {
throw new PatchApplyException(MessageFormat
.format(JGitText.get().applyBinaryOidTooShort, path));
}
BinaryHunk hunk = fh.getForwardBinaryHunk();
// A BinaryHunk has the start at the "literal" or "delta" token. Data
// starts on the next line.
int start = RawParseUtils.nextLF(hunk.getBuffer(),
hunk.getStartOffset());
int length = hunk.getEndOffset() - start;
SHA1 hash = SHA1.newInstance();
// Write to a buffer and copy to the file only if everything was fine
TemporaryBuffer buffer = new TemporaryBuffer.LocalFile(null);
try {
switch (hunk.getType()) {
case LITERAL_DEFLATED:
// This just overwrites the file. We need to check the hash of
// the base.
checkOid(fh.getOldId().toObjectId(), id, fh.getChangeType(), f,
path);
initHash(hash, hunk.getSize());
try (OutputStream out = buffer;
InputStream inflated = new SHA1InputStream(hash,
new InflaterInputStream(
new BinaryHunkInputStream(
new ByteArrayInputStream(
hunk.getBuffer(), start,
length))))) {
DirCacheCheckout.getContent(repository, path, checkOut,
new StreamLoader(() -> inflated, hunk.getSize()),
null, out);
if (!fh.getNewId().toObjectId().equals(hash.toObjectId())) {
throw new PatchApplyException(MessageFormat.format(
JGitText.get().applyBinaryResultOidWrong,
path));
}
}
try (InputStream bufIn = buffer.openInputStream()) {
Files.copy(bufIn, f.toPath(),
StandardCopyOption.REPLACE_EXISTING);
}
break;
case DELTA_DEFLATED:
// Unfortunately delta application needs random access to the
// base to construct the result.
byte[] base;
try (InputStream input = loader.load()) {
base = IO.readWholeStream(input, 0).array();
}
// At least stream the result!
try (BinaryDeltaInputStream input = new BinaryDeltaInputStream(
base,
new InflaterInputStream(new BinaryHunkInputStream(
new ByteArrayInputStream(hunk.getBuffer(),
start, length))))) {
long finalSize = input.getExpectedResultSize();
initHash(hash, finalSize);
try (OutputStream out = buffer;
SHA1InputStream hashed = new SHA1InputStream(hash,
input)) {
DirCacheCheckout.getContent(repository, path, checkOut,
new StreamLoader(() -> hashed, finalSize), null,
out);
if (!fh.getNewId().toObjectId()
.equals(hash.toObjectId())) {
throw new PatchApplyException(MessageFormat.format(
JGitText.get().applyBinaryResultOidWrong,
path));
}
}
}
try (InputStream bufIn = buffer.openInputStream()) {
Files.copy(bufIn, f.toPath(),
StandardCopyOption.REPLACE_EXISTING);
}
break;
default:
break;
}
} finally {
buffer.destroy();
}
}

private void applyText(Repository repository, String path, RawText rt,
File f, FileHeader fh, CheckoutMetadata checkOut)
throws IOException, PatchApplyException {
List<String> oldLines = new ArrayList<>(rt.size());
for (int i = 0; i < rt.size(); i++) {
@@ -514,7 +687,9 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
}
try (OutputStream output = new FileOutputStream(f)) {
DirCacheCheckout.getContent(repository, path, checkOut,
new BufferLoader(buffer), null, output);
new StreamLoader(buffer::openInputStream,
buffer.length()),
null, output);
}
} finally {
buffer.destroy();
@@ -565,4 +740,43 @@ public class ApplyCommand extends GitCommand<ApplyResult> {
return lhrt.getString(lhrt.size() - 1)
.equals("\\ No newline at end of file"); //$NON-NLS-1$
}

/**
* An {@link InputStream} that updates a {@link SHA1} on every byte read.
* The hash is supposed to have been initialized before reading starts.
*/
private static class SHA1InputStream extends InputStream {

private final SHA1 hash;

private final InputStream in;

SHA1InputStream(SHA1 hash, InputStream in) {
this.hash = hash;
this.in = in;
}

@Override
public int read() throws IOException {
int b = in.read();
if (b >= 0) {
hash.update((byte) b);
}
return b;
}

@Override
public int read(byte[] b, int off, int len) throws IOException {
int n = in.read(b, off, len);
if (n > 0) {
hash.update(b, off, n);
}
return n;
}

@Override
public void close() throws IOException {
in.close();
}
}
}

+ 3
- 0
org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java View File

@@ -41,6 +41,9 @@ public class JGitText extends TranslationBundle {
/***/ public String aNewObjectIdIsRequired;
/***/ public String anExceptionOccurredWhileTryingToAddTheIdOfHEAD;
/***/ public String anSSHSessionHasBeenAlreadyCreated;
/***/ public String applyBinaryBaseOidWrong;
/***/ public String applyBinaryOidTooShort;
/***/ public String applyBinaryResultOidWrong;
/***/ public String applyingCommit;
/***/ public String archiveFormatAlreadyAbsent;
/***/ public String archiveFormatAlreadyRegistered;

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