From 6ef9ae141cf221bc2c76502b5d1235b93a558519 Mon Sep 17 00:00:00 2001
From: Mick Jordan <mick.jordan@oracle.com>
Date: Sat, 17 Sep 2016 14:25:20 -0700
Subject: [PATCH] implement bzip2 decompression internally
---
.../truffle/r/runtime/RCompression.java | 73 +++++++------------
1 file changed, 27 insertions(+), 46 deletions(-)
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java
index e284889c96..e53f11fdad 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RCompression.java
@@ -35,6 +35,7 @@ import java.util.zip.GZIPInputStream;
import com.oracle.truffle.r.runtime.conn.GZIPConnections.GZIPRConnection;
import com.oracle.truffle.r.runtime.ffi.RFFIFactory;
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
import org.tukaani.xz.LZMA2InputStream;
import org.tukaani.xz.XZInputStream;
@@ -179,64 +180,44 @@ public class RCompression {
}
}
- /**
- * This is used by {@link GZIPRConnection}.
- */
+ @FunctionalInterface
+ private interface CreateInStream<T extends InputStream> {
+ InputStream create(InputStream base) throws IOException;
+ }
+
public static byte[] lzmaUncompressFromFile(String path) {
try {
- byte[] data = Files.readAllBytes(Paths.get(path));
- byte[] buffer = new byte[data.length * 4];
- try (XZInputStream lzmaStream = new XZInputStream(new ByteArrayInputStream(data))) {
- int totalRead = 0;
- int n;
- while ((n = lzmaStream.read(buffer, totalRead, buffer.length - totalRead)) > 0) {
- totalRead += n;
- if (totalRead == buffer.length) {
- byte[] newbuffer = new byte[buffer.length * 2];
- System.arraycopy(buffer, 0, newbuffer, 0, buffer.length);
- buffer = newbuffer;
- }
- }
- byte[] result = new byte[totalRead];
- System.arraycopy(buffer, 0, result, 0, totalRead);
- return result;
- }
-
+ return genericUncompressFromFile(path, (is) -> new XZInputStream(is));
} catch (IOException ex) {
throw RInternalError.shouldNotReachHere(ex);
}
}
public static byte[] bzipUncompressFromFile(String path) {
- return genericUncompressFromFile(new String[]{"bzip2", "-dc", path});
- }
-
- private static byte[] genericUncompressFromFile(String[] command) {
- int rc;
- ProcessBuilder pb = new ProcessBuilder(command);
- pb.redirectError(Redirect.INHERIT);
try {
- Process p = pb.start();
- InputStream is = p.getInputStream();
- ProcessOutputManager.OutputThreadVariable readThread = new ProcessOutputManager.OutputThreadVariable(command[0], is);
- readThread.start();
- rc = p.waitFor();
- if (rc == 0) {
- readThread.join();
- return readThread.getData();
- }
- } catch (InterruptedException | IOException ex) {
- // fall through
+ return genericUncompressFromFile(path, (is) -> new BZip2CompressorInputStream(is));
+ } catch (IOException ex) {
+ throw RInternalError.shouldNotReachHere(ex);
}
- throw RInternalError.shouldNotReachHere(join(command));
}
- private static String join(String[] args) {
- StringBuilder sb = new StringBuilder();
- for (String s : args) {
- sb.append(s);
- sb.append(' ');
+ private static <T extends InputStream> byte[] genericUncompressFromFile(String path, CreateInStream<T> creator) throws IOException {
+ byte[] data = Files.readAllBytes(Paths.get(path));
+ byte[] buffer = new byte[data.length * 4];
+ try (InputStream in = creator.create(new ByteArrayInputStream(data))) {
+ int totalRead = 0;
+ int n;
+ while ((n = in.read(buffer, totalRead, buffer.length - totalRead)) > 0) {
+ totalRead += n;
+ if (totalRead == buffer.length) {
+ byte[] newbuffer = new byte[buffer.length * 2];
+ System.arraycopy(buffer, 0, newbuffer, 0, buffer.length);
+ buffer = newbuffer;
+ }
+ }
+ byte[] result = new byte[totalRead];
+ System.arraycopy(buffer, 0, result, 0, totalRead);
+ return result;
}
- return sb.toString();
}
}
--
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