Merge pull request #14 from FlintMC/fix/bad-stream-read

Fix/bad stream read

Author: zortax

src/main/java/net/flintmc/gradle/environment/DeobfuscationEnvironment.java

@@ -42,12 +42,13 @@ static DeobfuscationEnvironment createFor(EnvironmentInput input) {
   String name();
 
   /**
-   * Runs the deobfuscation on the given client and server artifacts. One of the 2 artifacts may
-   * be null, but never both at the same time.
+   * Runs the deobfuscation on the given client and server artifacts. One of the 2 artifacts may be null, but never both
+   * at the same time.
    *
    * @param clientPom The client artifact, may be null if serverPom is not null
    * @param serverPom The client artifact, may be null if clientPom is not null
    * @param utilities Various utilities useful during deobfuscation
+   * @throws DeobfuscationException If the deobfuscation fails
    */
   void runDeobfuscation(MavenPom clientPom, MavenPom serverPom, DeobfuscationUtilities utilities)
       throws DeobfuscationException;

src/main/java/net/flintmc/gradle/environment/mcp/ModCoderPackEnvironment.java

@@ -296,12 +296,6 @@ public void runDeobfuscation(MavenPom clientPom, MavenPom serverPom, Deobfuscati
     }
   }
 
-  /**
-   * {@inheritDoc}
-   *
-   * @param client
-   * @param server
-   */
   @Override
   public Collection<MavenArtifact> getCompileArtifacts(MavenArtifact client, MavenArtifact server) {
     String version = getVersion(client, server);
@@ -311,12 +305,6 @@ public Collection<MavenArtifact> getCompileArtifacts(MavenArtifact client, Maven
     return Collections.singletonList(getJoinedArtifact(version));
   }
 
-  /**
-   * {@inheritDoc}
-   *
-   * @param client
-   * @param server
-   */
   @Override
   public Collection<MavenArtifact> getRuntimeArtifacts(MavenArtifact client, MavenArtifact server) {
     String version = getVersion(client, server);

src/main/java/net/flintmc/gradle/environment/mcp/function/InjectFunction.java

@@ -38,6 +38,7 @@ public class InjectFunction extends MCPFunction {
    *
    * @param name   The name of the function
    * @param output The output of the function
+   * @param input  The input of the function
    */
   public InjectFunction(String name, Path input, Path output) {
     super(name, output);
@@ -49,14 +50,14 @@ public InjectFunction(String name, Path input, Path output) {
    */
   @Override
   public void execute(DeobfuscationUtilities utilities) throws DeobfuscationException {
-    try (
+    try(
         ZipInputStream inputStream = new ZipInputStream(Files.newInputStream(input));
         ZipOutputStream outputStream = new ZipOutputStream(Files.newOutputStream(output))
     ) {
       ZipEntry entry;
 
       // Iterate over every entry
-      while ((entry = inputStream.getNextEntry()) != null) {
+      while((entry = inputStream.getNextEntry()) != null) {
         // Copy the entry one to one
         outputStream.putNextEntry(entry);
         Util.copyStream(inputStream, outputStream);
@@ -69,7 +70,7 @@ public void execute(DeobfuscationUtilities utilities) throws DeobfuscationExcept
       entry = new ZipEntry(".mcp-processed");
       outputStream.putNextEntry(entry);
       outputStream.closeEntry();
-    } catch (IOException e) {
+    } catch(IOException e) {
       throw new DeobfuscationException("Failed to execute inject function named " + name, e);
     }
   }

src/main/java/net/flintmc/gradle/environment/mcp/function/JavaExecutionFunction.java

@@ -43,8 +43,12 @@ public class JavaExecutionFunction extends MCPFunction {
   /**
    * Constructs a new java execution function with the given name, input and output.
    *
-   * @param name   The name of the function
-   * @param output The output of the function
+   * @param name               The name of the function
+   * @param output             The output of the function
+   * @param executionArtifact  The artifact to execute
+   * @param artifactRepository The repository to retrieve the artifact from if it is missing
+   * @param args               The arguments to pass to the executable
+   * @param jvmArgs            The arguments to pass to the JVM executing the executable
    */
   public JavaExecutionFunction(
       String name,
@@ -67,31 +71,31 @@ public JavaExecutionFunction(
   @Override
   public void prepare(DeobfuscationUtilities utilities) throws DeobfuscationException {
     SimpleMavenRepository localRepository = utilities.getInternalRepository();
-    if (!localRepository.isInstalled(executionArtifact)) {
+    if(!localRepository.isInstalled(executionArtifact)) {
       // Retrieve utilities
       MavenArtifactDownloader downloader = utilities.getDownloader();
 
       // The artifact is not installed already, install it
-      if (artifactRepository == null) {
+      if(artifactRepository == null) {
         // Can't download anything in offline mode
         throw new DeobfuscationException("Missing artifact " + executionArtifact + " in local repository, " +
             "but working in offline mode");
       }
 
       boolean setupSource = !downloader.hasSource(artifactRepository);
-      if (setupSource) {
+      if(setupSource) {
         // The download has the source not set already, add it now
         downloader.addSource(artifactRepository);
       }
 
       try {
         // Install the artifact including dependencies
         downloader.installAll(executionArtifact, localRepository, true);
-      } catch (IOException | MavenResolveException e) {
+      } catch(IOException | MavenResolveException e) {
         throw new DeobfuscationException("Failed to install execution artifact", e);
       }
 
-      if (setupSource) {
+      if(setupSource) {
         // We added the source, clean up afterwards
         downloader.removeSource(artifactRepository);
       }
@@ -118,18 +122,18 @@ public void execute(DeobfuscationUtilities utilities) throws DeobfuscationExcept
           args,
           jvmArgs
       );
-    } catch (IOException e) {
+    } catch(IOException e) {
       // This happens if the execution fails, but has nothing to do with the exit code
       throw new DeobfuscationException("Failed to execute java process for function " + name);
     }
 
-    if (result.getExitCode() != 0) {
+    if(result.getExitCode() != 0) {
       // The process failed to execute properly
       Path standardOutput;
       try {
         // Try to save the standard output
         standardOutput = saveOutput("stdout", result.getStdout());
-      } catch (IOException e) {
+      } catch(IOException e) {
         throw new DeobfuscationException("Failed to save standard output after process failed, " +
             "some is very wrong", e);
       }
@@ -138,7 +142,7 @@ public void execute(DeobfuscationUtilities utilities) throws DeobfuscationExcept
       try {
         // Try to save the standard error
         standardError = saveOutput("stderr", result.getStderr());
-      } catch (IOException e) {
+      } catch(IOException e) {
         throw new DeobfuscationException("Failed to save standard error after process failed, " +
             "some is very wrong", e);
       }

src/main/java/net/flintmc/gradle/environment/mcp/function/PatchFunction.java

@@ -45,8 +45,10 @@ public class PatchFunction extends MCPFunction {
   /**
    * Constructs a new Patch function with the given name and output.
    *
-   * @param name   The name of the function
-   * @param output The output of the function
+   * @param name    The name of the function
+   * @param output  The output of the function
+   * @param input   The input of the function
+   * @param patches The path to the patches to apply
    */
   public PatchFunction(String name, Path input, Path output, Path patches) {
     super(name, output);
@@ -74,7 +76,7 @@ public void prepare(DeobfuscationUtilities utilities) throws DeobfuscationExcept
                 .replace("\\", "/");
             indexedPatches.put(relativePath, patchPath);
           });
-    } catch (IOException e) {
+    } catch(IOException e) {
       throw new DeobfuscationException("IO error occurred while collecting patch files", e);
     }
   }
@@ -84,17 +86,17 @@ public void prepare(DeobfuscationUtilities utilities) throws DeobfuscationExcept
    */
   @Override
   public void execute(DeobfuscationUtilities utilities) throws DeobfuscationException {
-    try (
+    try(
         ZipInputStream inputStream = new ZipInputStream(Files.newInputStream(input));
         ZipOutputStream outputStream = new ZipOutputStream(Files.newOutputStream(output))
     ) {
       ZipEntry entry;
       // Iterate all entries
-      while ((entry = inputStream.getNextEntry()) != null) {
+      while((entry = inputStream.getNextEntry()) != null) {
         outputStream.putNextEntry(entry);
 
         // Check if there is a patch for the entry if it is not a directory
-        if (!entry.isDirectory() && indexedPatches.containsKey(entry.getName())) {
+        if(!entry.isDirectory() && indexedPatches.containsKey(entry.getName())) {
           // Parse the patch file (unified diff format)
           Patch<String> patch =
               UnifiedDiffUtils.parseUnifiedDiff(Files.readAllLines(indexedPatches.get(entry.getName())));
@@ -104,7 +106,7 @@ public void execute(DeobfuscationUtilities utilities) throws DeobfuscationExcept
 
           try {
             patchedLines = DiffUtils.patch(originalLines, patch);
-          } catch (PatchFailedException e) {
+          } catch(PatchFailedException e) {
             throw new DeobfuscationException("Failed to patch file " + entry.getName(), e);
           }
 
@@ -117,7 +119,7 @@ public void execute(DeobfuscationUtilities utilities) throws DeobfuscationExcept
         // Make sure to close the entry
         outputStream.closeEntry();
       }
-    } catch (IOException e) {
+    } catch(IOException e) {
       throw new DeobfuscationException("IO error occurred while patching", e);
     }
   }

src/main/java/net/flintmc/gradle/extension/FlintStaticFileDescription.java

@@ -62,6 +62,7 @@ public FlintStaticFileDescription(Project project, String name) {
    * Sets the source this static file should be obtained from.
    *
    * @param source The source of this static file
+   * @throws URISyntaxException If source is not a valid URL
    */
   public void from(Object source) throws URISyntaxException {
     if(source instanceof URI) {

src/main/java/net/flintmc/gradle/manifest/tasks/GenerateStaticFileChecksumsTask.java

@@ -19,15 +19,12 @@
 
 package net.flintmc.gradle.manifest.tasks;
 
-import net.flintmc.gradle.FlintGradleException;
 import net.flintmc.gradle.manifest.cache.StaticFileChecksums;
 import net.flintmc.gradle.manifest.data.ManifestStaticFile;
 import net.flintmc.gradle.manifest.data.ManifestStaticFileInput;
 import net.flintmc.gradle.util.MaybeNull;
 import net.flintmc.gradle.util.Util;
 import okhttp3.OkHttpClient;
-import okhttp3.Request;
-import okhttp3.Response;
 import org.gradle.api.DefaultTask;
 import org.gradle.api.tasks.Input;
 import org.gradle.api.tasks.InputFiles;
@@ -139,7 +136,7 @@ public void generate() throws IOException {
       for(URI remoteFile : getRemoteFiles()) {
         // Calculate the checksum
         try(InputStream stream = Util.getURLStream(httpClient, remoteFile)) {
-          checksums.add(remoteFile, Util.md5Hex(Util.toByteArray(stream)));
+          checksums.add(remoteFile, Util.md5Hex(Util.readAllAsBytes(stream)));
         }
       }
     } else {