Add optional deletion of corrupted chunks and region files

Signed-off-by: trivernis <trivernis@protonmail.com>

Cargo.lock

@@ -307,7 +307,7 @@ dependencies = [
 
 [[package]]
 name = "minecraft-regions-tool"
-version = "0.4.1"
+version = "0.5.0"
 dependencies = [
  "byteorder",
  "colored",

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "minecraft-regions-tool"
-version = "0.4.1"
+version = "0.5.0"
 authors = ["trivernis <trivernis@protonmail.com>"]
 edition = "2018"
 license = "GPL-3.0"

src/chunk.rs

@@ -11,6 +11,7 @@ type IOResult<T> = io::Result<T>;
 const TAG_LEVEL: &str = "Level";
 const TAG_X_POS: &str = "xPos";
 const TAG_Z_POS: &str = "zPos";
+const TAG_SECTIONS: &str = "Sections";
 
 #[derive(Debug)]
 pub struct Chunk {
@@ -54,8 +55,15 @@ impl Chunk {
                     Err(ChunkScanError::MissingTag(TAG_X_POS))
                 } else if !lvl_data.contains_key(TAG_Z_POS) {
                     Err(ChunkScanError::MissingTag(TAG_Z_POS))
+                } else if !lvl_data.contains_key(TAG_SECTIONS) {
+                    Err(ChunkScanError::MissingTag(TAG_SECTIONS))
                 } else {
+                    let sections = &lvl_data[TAG_SECTIONS];
+                    if let NBTValue::List(_) = sections {
                         Ok(())
+                    } else {
+                        Err(ChunkScanError::InvalidFormat(TAG_SECTIONS))
+                    }
                 }
             } else {
                 Err(ChunkScanError::InvalidFormat(TAG_LEVEL))

src/lib.rs

@@ -2,4 +2,5 @@ pub mod chunk;
 pub mod nbt;
 pub mod region_file;
 pub mod scan;
+pub mod utils;
 pub mod world_folder;

src/main.rs

@@ -1,6 +1,7 @@
 use colored::*;
 use env_logger::Env;
 use log::Level;
+use minecraft_regions_tool::scan::ScanOptions;
 use minecraft_regions_tool::world_folder::WorldFolder;
 use std::path::PathBuf;
 use structopt::StructOpt;
@@ -26,14 +27,19 @@ enum SubCommand {
     Count,
 
     /// Scan for errors in the region files and optionally fix them
-    Scan(ScanOptions),
+    Scan(ScanArgs),
 }
 
 #[derive(StructOpt, Debug)]
 #[structopt()]
-struct ScanOptions {
+struct ScanArgs {
+    /// Fixes errors that can be fixed without problems
     #[structopt(short, long)]
     fix: bool,
+
+    /// Deletes corrupted data
+    #[structopt(short, long)]
+    delete: bool,
 }
 
 fn main() {
@@ -47,7 +53,12 @@ fn main() {
                 log::info!("Fixing fixable errors.");
             }
             log::info!("Scanning Region files for errors...");
-            log::info!("Scan Results:\n{}", world.scan_files(opt.fix).unwrap())
+            log::info!(
+                "Scan Results:\n{}",
+                world
+                    .scan_files(ScanOptions::new().fix(opt.fix).fix_delete(opt.delete))
+                    .unwrap()
+            )
         }
     }
 }

src/nbt.rs

@@ -1,13 +1,14 @@
+use crate::utils::ByteArrayCache;
 use byteorder::{BigEndian, ReadBytesExt};
 use std::collections::HashMap;
 use std::error::Error;
 use std::fmt::{self, Display, Formatter};
-use std::io::{self, Read};
+use std::io::{self};
 
 const MAX_RECURSION: u64 = 100;
 
 pub struct NBTReader<R> {
-    inner: Box<R>,
+    inner: R,
     recursion: u64,
 }
 
@@ -19,7 +20,7 @@ where
 {
     pub fn new(inner: R) -> Self {
         Self {
-            inner: Box::new(inner),
+            inner,
             recursion: 0,
         }
     }
@@ -73,13 +74,14 @@ where
     }
 
     /// Parses an array of bytes
-    fn parse_byte_array(&mut self) -> NBTResult<Vec<u8>> {
+    fn parse_byte_array(&mut self) -> NBTResult<ByteArrayCache> {
         let length = self.inner.read_u32::<BigEndian>()?;
-        for _ in 0..length {
+        let mut cache = ByteArrayCache::new();
-            self.inner.read_u8()?;
+        let mut buf = vec![0u8; length as usize];
-        }
+        self.inner.read_exact(&mut buf)?;
+        cache.write(&buf[..])?;
 
-        Ok(Vec::with_capacity(0))
+        Ok(cache)
     }
 
     /// Parses a string value
@@ -155,7 +157,7 @@ pub enum NBTValue {
     Long(i64),
     Float(f32),
     Double(f64),
-    ByteArray(Vec<u8>),
+    ByteArray(ByteArrayCache),
     String(String),
     List(Vec<NBTValue>),
     Compound(HashMap<String, NBTValue>),

src/region_file.rs

@@ -1,9 +1,12 @@
 use crate::chunk::{Chunk, ChunkScanError};
+use crate::scan::ScanOptions;
 use crate::scan::ScanStatistics;
 use byteorder::{BigEndian, ByteOrder, WriteBytesExt};
+use std::cmp::Ordering;
 use std::fs::{File, OpenOptions};
 use std::io::{BufReader, BufWriter, Read, Result, Seek, SeekFrom, Write};
 use std::path::PathBuf;
+use std::sync::Arc;
 
 pub const BLOCK_SIZE: usize = 4096;
 
@@ -37,28 +40,66 @@ impl RegionFile {
 
     /// Returns the number of chunks in the file
     pub fn count_chunks(&self) -> usize {
-        return self.locations.valid_entries().len();
+        return self.locations.valid_entries_enumerate().len();
     }
 
     /// Scans the chunk entries for possible errors
-    pub fn scan_chunks(&mut self, fix: bool) -> Result<ScanStatistics> {
+    pub fn scan_chunks(&mut self, options: &Arc<ScanOptions>) -> Result<ScanStatistics> {
         let mut statistic = ScanStatistics::new();
 
-        let entries = self.locations.valid_entries();
+        let mut entries = self.locations.valid_entries_enumerate();
-        let mut corrected_entries = Vec::new();
+        entries.sort_by(|(_, (a, _)), (_, (b, _))| {
+            if a > b {
+                Ordering::Greater
+            } else if a < b {
+                Ordering::Less
+            } else {
+                Ordering::Equal
+            }
+        });
         statistic.total_chunks = entries.len() as u64;
 
-        for (offset, sections) in &entries {
+        for (index, (offset, sections)) in entries {
-            let reader_offset = *offset as u64 * BLOCK_SIZE as u64;
+            let reader_offset = offset as u64 * BLOCK_SIZE as u64;
             self.reader.seek(SeekFrom::Start(reader_offset))?;
 
             match Chunk::from_buf_reader(&mut self.reader) {
-                Ok(mut chunk) => {
+                Ok(chunk) => {
+                    self.scan_chunk(index, offset, sections, chunk, &mut statistic, options)?;
+                }
+                Err(e) => {
+                    statistic.failed_to_read += 1;
+                    log::error!("Failed to read chunk at {}: {}", offset, e);
+                }
+            }
+        }
+
+        if options.fix || options.fix_delete {
+            self.writer.seek(SeekFrom::Start(0))?;
+            self.writer
+                .write_all(self.locations.to_bytes().as_slice())?;
+            self.writer.flush()?;
+        }
+
+        Ok(statistic)
+    }
+
+    /// Scans a single chunk for errors
+    fn scan_chunk(
+        &mut self,
+        index: usize,
+        offset: u32,
+        sections: u8,
+        mut chunk: Chunk,
+        statistic: &mut ScanStatistics,
+        options: &Arc<ScanOptions>,
+    ) -> Result<()> {
         let chunk_sections = ((chunk.length + 4) as f64 / BLOCK_SIZE as f64).ceil();
+        let reader_offset = offset as u64 * BLOCK_SIZE as u64;
 
         if chunk.compression_type > 3 {
             statistic.invalid_compression_method += 1;
-                        if fix {
+            if options.fix {
                 self.writer.seek(SeekFrom::Start(reader_offset + 4))?;
                 self.writer.write_u8(1)?;
             }
@@ -67,11 +108,7 @@ impl RegionFile {
             if let Err(e) = chunk.validate_nbt_data(&mut self.reader) {
                 match e {
                     ChunkScanError::IO(e) => {
-                                    log::debug!(
+                        log::debug!("Compression error at chunk {}: {}", offset, e);
-                                        "Compression error when reading chunk {}: {}",
-                                        offset,
-                                        e
-                                    );
                         statistic.corrupted_compression += 1;
                     }
                     ChunkScanError::NBTError(e) => {
@@ -83,32 +120,44 @@ impl RegionFile {
                         statistic.missing_nbt += 1;
                     }
                 }
+                self.delete_chunk(index)?;
             }
         }
 
-                    if *sections != chunk_sections as u8 || chunk.length >= 1_048_576 {
+        if sections != chunk_sections as u8 || chunk.length >= 1_048_576 {
             statistic.invalid_length += 1;
-                        corrected_entries.push((*offset, chunk_sections as u8));
+            self.locations
-                    } else {
+                .replace_entry_unchecked(index, (offset, chunk_sections as u8));
-                        corrected_entries.push((*offset, *sections));
-                    }
-                }
-                Err(e) => {
-                    statistic.failed_to_read += 1;
-                    log::error!("Failed to read chunk at {}: {}", offset, e);
-                }
         }
+
+        Ok(())
     }
-        self.locations.set_entries(corrected_entries);
 
-        if fix {
+    /// Deletes a chunk and shifts all other chunks
-            self.writer.seek(SeekFrom::Start(0))?;
+    pub fn delete_chunk(&mut self, index: usize) -> Result<()> {
+        let (offset, sections) = self.locations.get_chunk_entry_unchecked(index);
+        self.reader.seek(SeekFrom::Start(
+            (offset as usize * BLOCK_SIZE + sections as usize * BLOCK_SIZE) as u64,
+        ))?;
         self.writer
-                .write_all(self.locations.to_bytes().as_slice())?;
+            .seek(SeekFrom::Start((offset as usize * BLOCK_SIZE) as u64))?;
-            self.writer.flush()?;
+        log::debug!(
+            "Shifting chunk entries starting from {} by {} to the left",
+            offset,
+            sections as u32
+        );
+        loop {
+            let mut buf = [0u8; BLOCK_SIZE];
+            let read = self.reader.read(&mut buf)?;
+            self.writer.write(&buf)?;
+            if read < BLOCK_SIZE {
+                break;
             }
+        }
+        self.locations.delete_chunk_entry_unchecked(index);
+        self.locations.shift_entries(offset, -(sections as i32));
 
-        Ok(statistic)
+        Ok(())
     }
 }
 
@@ -158,16 +207,55 @@ impl Locations {
     }
 
     /// Returns chunk entry list
-    pub fn valid_entries(&self) -> Vec<(u32, u8)> {
+    pub fn valid_entries_enumerate(&self) -> Vec<(usize, (u32, u8))> {
         self.inner
             .iter()
-            .filter_map(|e| if (*e).0 >= 2 { Some(*e) } else { None })
+            .enumerate()
+            .filter_map(|e| {
+                if (*e.1).0 >= 2 {
+                    Some((e.0, *e.1))
+                } else {
+                    None
+                }
+            })
             .collect()
     }
 
-    /// Replaces the entry list with a new one
+    /// Replaces an entry with a new one. Panics if the index doesn't exist
-    pub fn set_entries(&mut self, entries: Vec<(u32, u8)>) {
+    pub fn replace_entry_unchecked(&mut self, index: usize, entry: (u32, u8)) {
-        self.inner = entries;
+        self.inner[index] = entry;
+    }
+
+    /// Returns a chunk entry for an index. Panics if it doesn't exist.
+    pub fn get_chunk_entry_unchecked(&self, index: usize) -> (u32, u8) {
+        self.inner[index]
+    }
+
+    /// Sets a chunk entry to not generated. Panics if the index doesn't exists
+    pub fn delete_chunk_entry_unchecked(&mut self, index: usize) {
+        self.inner[index] = (0, 0);
+    }
+
+    /// Shifts all entries starting from `start_index` by `amount`
+    pub fn shift_entries(&mut self, start_offset: u32, amount: i32) {
+        log::debug!(
+            "Shifting location entries starting from {} by {}",
+            start_offset,
+            amount
+        );
+        self.inner = self
+            .inner
+            .iter()
+            .map(|e| {
+                let mut entry = *e;
+
+                if e.0 >= start_offset {
+                    entry.0 = (entry.0 as i32 + amount) as u32;
+                }
+
+                entry
+            })
+            .collect();
     }
 }
 

src/scan.rs

@@ -64,3 +64,30 @@ impl Display for ScanStatistics {
         )
     }
 }
+
+#[derive(Clone, Debug)]
+pub struct ScanOptions {
+    pub fix: bool,
+    pub fix_delete: bool,
+}
+
+impl ScanOptions {
+    pub fn new() -> Self {
+        ScanOptions {
+            fix: false,
+            fix_delete: false,
+        }
+    }
+
+    pub fn fix(mut self, fix: bool) -> Self {
+        self.fix = fix;
+
+        self
+    }
+
+    pub fn fix_delete(mut self, fix_delete: bool) -> Self {
+        self.fix_delete = fix_delete;
+
+        self
+    }
+}

src/utils.rs

@@ -0,0 +1,45 @@
+use flate2::read::ZlibEncoder;
+use flate2::Compression;
+use std::io::{Read, Result};
+
+#[derive(Clone, Debug)]
+pub struct ByteArrayCache {
+    inner: Vec<u8>,
+    position: usize,
+}
+
+impl ByteArrayCache {
+    /// Creates a new byte array cache
+    pub fn new() -> Self {
+        Self {
+            inner: Vec::new(),
+            position: 0,
+        }
+    }
+
+    /// Creates a new byte array cache with capacity
+    pub fn with_capacity(capacity: usize) -> Self {
+        Self {
+            inner: Vec::with_capacity(capacity),
+            position: 0,
+        }
+    }
+
+    pub fn write<R: Read>(&mut self, reader: R) -> Result<()> {
+        let mut encoder = ZlibEncoder::new(reader, Compression::default());
+        let mut buffer = Vec::new();
+        encoder.read_to_end(&mut buffer)?;
+        self.inner.append(&mut buffer);
+
+        Ok(())
+    }
+}
+
+impl Read for ByteArrayCache {
+    fn read(&mut self, buf: &mut [u8]) -> Result<usize> {
+        let read = (&self.inner[self.position..]).read(buf)?;
+        self.position += read;
+
+        Ok(read)
+    }
+}

src/world_folder.rs

@@ -1,4 +1,5 @@
 use crate::region_file::RegionFile;
+use crate::scan::ScanOptions;
 use crate::scan::ScanStatistics;
 use indicatif::{ProgressBar, ProgressDrawTarget, ProgressStyle};
 use log::LevelFilter;
@@ -7,6 +8,7 @@ use std::fs;
 use std::io;
 use std::ops::Add;
 use std::path::PathBuf;
+use std::sync::Arc;
 
 pub struct WorldFolder {
     path: PathBuf,
@@ -29,9 +31,11 @@ impl WorldFolder {
         Ok(count)
     }
 
-    pub fn scan_files(&self, fix: bool) -> io::Result<ScanStatistics> {
+    /// Scans all region files for potential errors
+    pub fn scan_files(&self, options: ScanOptions) -> io::Result<ScanStatistics> {
         let paths = self.region_file_paths();
         let bar = ProgressBar::new(paths.len() as u64);
+        let options = Arc::new(options);
         bar.set_style(
             ProgressStyle::default_bar().template("\r[{eta_precise}] {wide_bar} {pos}/{len} "),
         );
@@ -46,13 +50,18 @@ impl WorldFolder {
                 log::debug!("Opening and scanning region file {:?}", path);
                 let mut region_file = RegionFile::new(path)
                     .map_err(|e| {
-                        log::error!("Failed to open region file {:?}: {}", path, e);
+                        log::error!("Failed to open region file {:?}: {}\n", path, e);
+                        if options.fix_delete {
+                            if let Err(e) = fs::remove_file(path) {
+                                return e;
+                            }
+                        }
 
                         e
                     })
                     .ok()?;
 
-                let result = region_file.scan_chunks(fix).ok()?;
+                let result = region_file.scan_chunks(&options).ok()?;
                 bar.inc(1);
                 log::debug!("Statistics for {:?}:\n{}", path, result);