refactor: tweaks IO handling (#3723)

Use BrutIO where possible to improve and simplify stream handling.
Ensure streams are closed when no longer needed.

Some minor formatting tweaks and naming consistency.

No functionality changes.

brut.apktool/apktool-lib/src/main/java/brut/androlib/AaptInvoker.java

@@ -50,7 +50,7 @@ public class AaptInvoker {
         }
     }
 
-    public void invokeAapt(File apkFile, File manifest, File resDir, File rawDir, File assetDir, File[] include)
+    public void invoke(File apkFile, File manifest, File resDir, File rawDir, File assetDir, File[] include)
             throws AndrolibException {
 
         String aaptPath = mConfig.aaptPath;

brut.apktool/apktool-lib/src/main/java/brut/androlib/ApkBuilder.java

@@ -35,7 +35,6 @@ import brut.util.AaptManager;
 import brut.util.BrutIO;
 import brut.util.OS;
 import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
 import org.xml.sax.SAXException;
 
 import javax.xml.parsers.ParserConfigurationException;
@@ -377,7 +376,7 @@ public class ApkBuilder {
 
         try {
             AaptInvoker invoker = new AaptInvoker(mConfig, mApkInfo);
-            invoker.invokeAapt(tmpFile, manifest, resDir, ninePatch, null, getIncludeFiles());
+            invoker.invoke(tmpFile, manifest, resDir, ninePatch, null, getIncludeFiles());
 
             Directory tmpDir = tmpFile.getDirectory();
             tmpDir.copyToDir(outDir, "AndroidManifest.xml");
@@ -417,7 +416,7 @@ public class ApkBuilder {
 
         try {
             AaptInvoker invoker = new AaptInvoker(mConfig, mApkInfo);
-            invoker.invokeAapt(tmpFile, manifest, null, ninePatch, null, getIncludeFiles());
+            invoker.invoke(tmpFile, manifest, null, ninePatch, null, getIncludeFiles());
 
             Directory tmpDir = tmpFile.getDirectory();
             tmpDir.copyToDir(outDir, "AndroidManifest.xml");

brut.apktool/apktool-lib/src/main/java/brut/androlib/apk/ApkInfo.java

@@ -21,7 +21,6 @@ import brut.androlib.exceptions.AndrolibException;
 import brut.androlib.res.data.ResConfigFlags;
 import brut.directory.DirectoryException;
 import brut.directory.ExtFile;
-import brut.directory.FileDirectory;
 
 import java.io.*;
 import java.nio.file.Files;
@@ -212,10 +211,10 @@ public class ApkInfo implements YamlSerializable {
         return apkInfo;
     }
 
-    public static ApkInfo load(File appDir) throws AndrolibException {
+    public static ApkInfo load(ExtFile apkDir) throws AndrolibException {
-        try (InputStream in = new FileDirectory(appDir).getFileInput("apktool.yml")) {
+        try (InputStream in = apkDir.getDirectory().getFileInput("apktool.yml")) {
             ApkInfo apkInfo = ApkInfo.load(in);
-            apkInfo.setApkFile(new ExtFile(appDir));
+            apkInfo.setApkFile(apkDir);
             return apkInfo;
         } catch (DirectoryException | IOException ex) {
             throw new AndrolibException(ex);

brut.apktool/apktool-lib/src/main/java/brut/androlib/res/Framework.java

@@ -22,8 +22,8 @@ import brut.androlib.exceptions.CantFindFrameworkResException;
 import brut.androlib.res.decoder.ARSCDecoder;
 import brut.androlib.res.data.arsc.ARSCData;
 import brut.androlib.res.data.arsc.FlagsOffset;
+import brut.util.BrutIO;
 import brut.util.Jar;
-import org.apache.commons.io.IOUtils;
 
 import java.io.*;
 import java.nio.file.Files;
@@ -50,8 +50,6 @@ public class Framework {
     }
 
     public void installFramework(File frameFile, String tag) throws AndrolibException {
-        InputStream in = null;
-        ZipOutputStream out = null;
         try (ZipFile zip = new ZipFile(frameFile)) {
             ZipEntry entry = zip.getEntry("resources.arsc");
 
@@ -59,9 +57,7 @@ public class Framework {
                 throw new AndrolibException("Can't find resources.arsc file");
             }
 
-            in = zip.getInputStream(entry);
+            byte[] data = BrutIO.readAndClose(zip.getInputStream(entry));
-            byte[] data = IOUtils.toByteArray(in);
-
             ARSCData arsc = ARSCDecoder.decode(new ByteArrayInputStream(data), true, true);
             publicizeResources(data, arsc.getFlagsOffsets());
 
@@ -70,7 +66,7 @@ public class Framework {
                 + (tag == null ? "" : '-' + tag)
                 + ".apk");
 
-            out = new ZipOutputStream(Files.newOutputStream(outFile.toPath()));
+            try (ZipOutputStream out = new ZipOutputStream(Files.newOutputStream(outFile.toPath()))) {
                 out.setMethod(ZipOutputStream.STORED);
                 CRC32 crc = new CRC32();
                 crc.update(data);
@@ -82,11 +78,10 @@ public class Framework {
                 out.write(data);
                 out.closeEntry();
 
-            //Write fake AndroidManifest.xml file to support original aapt
+                // write fake AndroidManifest.xml file to support original aapt
                 entry = zip.getEntry("AndroidManifest.xml");
                 if (entry != null) {
-                in = zip.getInputStream(entry);
+                    byte[] manifest = BrutIO.readAndClose(zip.getInputStream(entry));
-                byte[] manifest = IOUtils.toByteArray(in);
                     CRC32 manifestCrc = new CRC32();
                     manifestCrc.update(manifest);
                     entry.setSize(manifest.length);
@@ -96,13 +91,11 @@ public class Framework {
                     out.write(manifest);
                     out.closeEntry();
                 }
+            }
 
             LOGGER.info("Framework installed to: " + outFile);
         } catch (IOException ex) {
             throw new AndrolibException(ex);
-        } finally {
-            IOUtils.closeQuietly(in);
-            IOUtils.closeQuietly(out);
         }
     }
 
@@ -212,15 +205,12 @@ public class Framework {
         }
 
         if (id == 1) {
-            try (
+            try {
-                InputStream in = getAndroidFrameworkResourcesAsStream();
+                BrutIO.copyAndClose(getAndroidFrameworkResourcesAsStream(), Files.newOutputStream(apk.toPath()));
-                OutputStream out = Files.newOutputStream(apk.toPath())
-            ) {
-                IOUtils.copy(in, out);
-                return apk;
             } catch (IOException ex) {
                 throw new AndrolibException(ex);
             }
+            return apk;
         }
 
         throw new CantFindFrameworkResException(id);

brut.apktool/apktool-lib/src/main/java/brut/androlib/res/ResourcesDecoder.java

@@ -25,9 +25,8 @@ import brut.androlib.res.xml.ResValuesXmlSerializable;
 import brut.androlib.res.xml.ResXmlPatcher;
 import brut.directory.Directory;
 import brut.directory.DirectoryException;
-import brut.directory.FileDirectory;
+import brut.directory.ExtFile;
 import brut.xmlpull.MXSerializer;
-import org.apache.commons.io.IOUtils;
 import org.xmlpull.v1.XmlSerializer;
 
 import java.io.*;
@@ -77,27 +76,25 @@ public class ResourcesDecoder {
         XmlSerializer xmlSerializer = newXmlSerializer();
         ResStreamDecoder fileDecoder = new AndroidManifestPullStreamDecoder(axmlParser, xmlSerializer);
 
-        Directory inApk, out;
+        Directory in, out;
-        InputStream inputStream = null;
-        OutputStream outputStream = null;
         try {
-            inApk = mApkInfo.getApkFile().getDirectory();
+            in = mApkInfo.getApkFile().getDirectory();
-            out = new FileDirectory(outDir);
+            out = new ExtFile(outDir).getDirectory();
 
             if (mApkInfo.hasResources()) {
                 LOGGER.info("Decoding AndroidManifest.xml with resources...");
             } else {
                 LOGGER.info("Decoding AndroidManifest.xml with only framework resources...");
             }
-            inputStream = inApk.getFileInput("AndroidManifest.xml");
-            outputStream = out.getFileOutput("AndroidManifest.xml");
-            fileDecoder.decode(inputStream, outputStream);
 
-        } catch (DirectoryException ex) {
+            try (
+                InputStream is = in.getFileInput("AndroidManifest.xml");
+                OutputStream os = out.getFileOutput("AndroidManifest.xml")
+            ) {
+                fileDecoder.decode(is, os);
+            }
+        } catch (DirectoryException | IOException ex) {
             throw new AndrolibException(ex);
-        } finally {
-            IOUtils.closeQuietly(inputStream);
-            IOUtils.closeQuietly(outputStream);
         }
 
         File manifest = new File(outDir, "AndroidManifest.xml");
@@ -171,25 +168,24 @@ public class ResourcesDecoder {
         Directory in, out, outRes;
 
         try {
-            out = new FileDirectory(outDir);
             in = mApkInfo.getApkFile().getDirectory();
-            outRes = out.createDir("res");
+            out = new ExtFile(outDir).getDirectory().createDir("res");
         } catch (DirectoryException ex) {
             throw new AndrolibException(ex);
         }
 
         for (ResPackage pkg : mResTable.listMainPackages()) {
-
             LOGGER.info("Decoding file-resources...");
             for (ResResource res : pkg.listFiles()) {
-                fileDecoder.decode(res, in, outRes, mResFileMapping);
+                fileDecoder.decode(res, in, out, mResFileMapping);
             }
 
             LOGGER.info("Decoding values */* XMLs...");
             for (ResValuesFile valuesFile : pkg.listValuesFiles()) {
-                generateValuesFile(valuesFile, outRes, xmlSerializer);
+                generateValuesFile(valuesFile, out, xmlSerializer);
             }
-            generatePublicXml(pkg, outRes, xmlSerializer);
+
+            generatePublicXml(pkg, out, xmlSerializer);
         }
 
         AndrolibException decodeError = axmlParser.getFirstError();

brut.apktool/apktool-lib/src/main/java/brut/androlib/res/decoder/ResFileDecoder.java

@@ -22,9 +22,9 @@ import brut.androlib.exceptions.RawXmlEncounteredException;
 import brut.androlib.res.data.ResResource;
 import brut.androlib.res.data.value.ResBoolValue;
 import brut.androlib.res.data.value.ResFileValue;
-import brut.directory.DirUtil;
 import brut.directory.Directory;
 import brut.directory.DirectoryException;
+import brut.directory.DirUtil;
 import brut.util.BrutIO;
 
 import java.io.*;

brut.apktool/apktool-lib/src/main/java/brut/androlib/res/decoder/ResRawStreamDecoder.java

@@ -23,8 +23,7 @@ import java.io.*;
 
 public class ResRawStreamDecoder implements ResStreamDecoder {
     @Override
-    public void decode(InputStream in, OutputStream out)
+    public void decode(InputStream in, OutputStream out) throws AndrolibException {
-            throws AndrolibException {
         try {
             IOUtils.copy(in, out);
         } catch (IOException ex) {

brut.j.dir/src/main/java/brut/directory/DirUtil.java

@@ -52,16 +52,16 @@ public class DirUtil {
         copyToDir(in, out, fileName, fileName);
     }
 
-    public static void copyToDir(Directory in, Directory out, String inFile, String outFile)
+    public static void copyToDir(Directory in, Directory out, String inFileName, String outFileName)
             throws DirectoryException {
         try {
-            if (in.containsDir(inFile)) {
+            if (in.containsDir(inFileName)) {
-                in.getDir(inFile).copyToDir(out.createDir(outFile));
+                in.getDir(inFileName).copyToDir(out.createDir(outFileName));
             } else {
-                BrutIO.copyAndClose(in.getFileInput(inFile), out.getFileOutput(outFile));
+                BrutIO.copyAndClose(in.getFileInput(inFileName), out.getFileOutput(outFileName));
             }
         } catch (IOException ex) {
-            throw new DirectoryException("Error copying file: " + inFile, ex);
+            throw new DirectoryException("Error copying file: " + inFileName, ex);
         }
     }
 
@@ -81,28 +81,33 @@ public class DirUtil {
 
     public static void copyToDir(Directory in, File out, String fileName)
             throws DirectoryException {
+        copyToDir(in, out, fileName, fileName);
+    }
+
+    public static void copyToDir(Directory in, File out, String inFileName, String outFileName)
+            throws DirectoryException {
         try {
-            if (in.containsDir(fileName)) {
+            if (in.containsDir(inFileName)) {
-                File outDir = new File(out, fileName);
+                File outDir = new File(out, outFileName);
                 OS.rmdir(outDir);
-                in.getDir(fileName).copyToDir(outDir);
+                in.getDir(inFileName).copyToDir(outDir);
-            } else if (in.containsFile(fileName)) {
+            } else if (in.containsFile(inFileName)) {
-                String validFileName = BrutIO.sanitizePath(out, fileName);
+                outFileName = BrutIO.sanitizePath(out, outFileName);
-                if (!validFileName.isEmpty()) {
+                if (!outFileName.isEmpty()) {
-                    File outFile = new File(out, validFileName);
+                    File outFile = new File(out, outFileName);
                     //noinspection ResultOfMethodCallIgnored
                     outFile.getParentFile().mkdirs();
-                    BrutIO.copyAndClose(in.getFileInput(fileName), Files.newOutputStream(outFile.toPath()));
+                    BrutIO.copyAndClose(in.getFileInput(inFileName), Files.newOutputStream(outFile.toPath()));
                 }
             } else {
                 // Skip if directory/file not found
             }
         } catch (FileSystemException ex) {
-            LOGGER.warning(String.format("Skipping file %s (%s)", fileName, ex.getReason()));
+            LOGGER.warning(String.format("Skipping file %s (%s)", inFileName, ex.getReason()));
         } catch (RootUnknownFileException | InvalidUnknownFileException | TraversalUnknownFileException | IOException ex) {
-            LOGGER.warning(String.format("Skipping file %s (%s)", fileName, ex.getMessage()));
+            LOGGER.warning(String.format("Skipping file %s (%s)", inFileName, ex.getMessage()));
         } catch (BrutException ex) {
-            throw new DirectoryException("Error copying file: " + fileName, ex);
+            throw new DirectoryException("Error copying file: " + inFileName, ex);
         }
     }
 }

brut.j.util/src/main/java/brut/util/BrutIO.java

@@ -26,6 +26,14 @@ import java.io.*;
 import java.util.zip.CRC32;
 
 public class BrutIO {
+    public static byte[] readAndClose(InputStream in) throws IOException {
+        try {
+            return IOUtils.toByteArray(in);
+        } finally {
+            IOUtils.closeQuietly(in);
+        }
+    }
+
     public static void copyAndClose(InputStream in, OutputStream out) throws IOException {
         try {
             IOUtils.copy(in, out);
@@ -60,11 +68,11 @@ public class BrutIO {
         return modified;
     }
 
-    public static CRC32 calculateCrc(InputStream input) throws IOException {
+    public static CRC32 calculateCrc(InputStream in) throws IOException {
         CRC32 crc = new CRC32();
         int bytesRead;
         byte[] buffer = new byte[8192];
-        while ((bytesRead = input.read(buffer)) != -1) {
+        while ((bytesRead = in.read(buffer)) != -1) {
             crc.update(buffer, 0, bytesRead);
         }
         return crc;

brut.j.util/src/main/java/brut/util/ExtCountingDataInput.java

@@ -24,6 +24,8 @@ import java.io.IOException;
 import java.util.logging.Logger;
 
 public class ExtCountingDataInput extends ExtDataInput {
+    private static final Logger LOGGER = Logger.getLogger(ExtCountingDataInput.class.getName());
+
     private final CountingInputStream mCountIn;
 
     public ExtCountingDataInput(LittleEndianDataInputStream in) {
@@ -67,6 +69,4 @@ public class ExtCountingDataInput extends ExtDataInput {
         }
         return array;
     }
-
-    private static final Logger LOGGER = Logger.getLogger(ExtCountingDataInput.class.getName());
 }

brut.j.util/src/main/java/brut/util/Jar.java

@@ -17,6 +17,7 @@
 package brut.util;
 
 import brut.common.BrutException;
+import brut.util.BrutIO;
 import org.apache.commons.io.IOUtils;
 
 import java.io.*;
@@ -42,8 +43,9 @@ public abstract class Jar {
     }
 
     public static File extractToTmp(String resourcePath, String tmpPrefix, Class<?> clazz) throws BrutException {
+        InputStream in = null;
         try {
-            InputStream in = clazz.getResourceAsStream(resourcePath);
+            in = clazz.getResourceAsStream(resourcePath);
             if (in == null) {
                 throw new FileNotFoundException(resourcePath);
             }
@@ -52,14 +54,13 @@ public abstract class Jar {
             File fileOut = File.createTempFile(tmpPrefix, suffix + ".tmp");
             fileOut.deleteOnExit();
 
-            OutputStream out = Files.newOutputStream(fileOut.toPath());
+            BrutIO.copyAndClose(in, Files.newOutputStream(fileOut.toPath()));
-            IOUtils.copy(in, out);
-            in.close();
-            out.close();
 
             return fileOut;
         } catch (IOException ex) {
             throw new BrutException("Could not extract resource: " + resourcePath, ex);
+        } finally {
+            IOUtils.closeQuietly(in);
         }
     }
 }

brut.j.util/src/main/java/brut/util/OS.java

@@ -17,7 +17,7 @@
 package brut.util;
 
 import brut.common.BrutException;
-import org.apache.commons.io.IOUtils;
+import brut.util.BrutIO;
 
 import java.io.*;
 import java.nio.file.Files;
@@ -28,7 +28,6 @@ import java.util.concurrent.TimeUnit;
 import java.util.logging.Logger;
 
 public class OS {
-
     private static final Logger LOGGER = Logger.getLogger("");
 
     public static void rmdir(File dir) throws BrutException {
@@ -77,11 +76,7 @@ public class OS {
                 continue;
             }
             try {
-                try (InputStream in = Files.newInputStream(file.toPath())) {
+                BrutIO.copyAndClose(Files.newInputStream(file.toPath()), Files.newOutputStream(destFile.toPath()));
-                    try (OutputStream out = Files.newOutputStream(destFile.toPath())) {
-                        IOUtils.copy(in, out);
-                    }
-                }
             } catch (IOException ex) {
                 throw new BrutException("Could not copy file: " + file, ex);
             }