iridium-db 0.4.0

A high-performance vector-graph hybrid storage and indexing engine
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use crc32c::crc32c;
use std::io::{Cursor, Read, Seek, SeekFrom, Write};
use std::path::Path;

const MAGIC: &[u8; 8] = b"IRSTBL02";
const FENCE_GROUP_SIZE: usize = 64;
const PAGE_SIZE_BYTES: u64 = 8 * 1024;

use crate::core::reactor::Reactor;

#[derive(Debug, Clone, Copy, PartialEq, Eq)]
#[repr(u8)]
pub enum EntryKind {
    FullNode = 0,
    EdgeDelta = 1,
    VectorDelta = 2,
    Tombstone = 3,
}

#[derive(Debug, Clone, PartialEq, Eq)]
pub struct Entry {
    pub key: u64,
    pub version: u64,
    pub kind: EntryKind,
    pub value: Vec<u8>,
}

#[derive(Debug, Clone, PartialEq, Eq)]
pub struct FencePointer {
    pub min_key: u64,
    pub max_key: u64,
    pub offset: u64,
}

#[derive(Debug, Clone)]
pub struct BloomFilter {
    bits: Vec<u8>,
    num_bits: u32,
    num_hashes: u32,
}

impl BloomFilter {
    pub fn new(num_bits: u32, num_hashes: u32) -> Self {
        let byte_len = num_bits.div_ceil(8) as usize;
        Self {
            bits: vec![0u8; byte_len],
            num_bits,
            num_hashes,
        }
    }

    pub fn insert(&mut self, key: u64) {
        for i in 0..self.num_hashes {
            let idx = hash_key(key, i, self.num_bits);
            set_bit(&mut self.bits, idx);
        }
    }

    pub fn may_contain(&self, key: u64) -> bool {
        for i in 0..self.num_hashes {
            let idx = hash_key(key, i, self.num_bits);
            if !get_bit(&self.bits, idx) {
                return false;
            }
        }
        true
    }

    pub fn from_bits(bits: Vec<u8>, num_bits: u32, num_hashes: u32) -> Self {
        Self {
            bits,
            num_bits,
            num_hashes,
        }
    }

    pub fn bits(&self) -> &[u8] {
        &self.bits
    }

    pub fn num_bits(&self) -> u32 {
        self.num_bits
    }

    pub fn num_hashes(&self) -> u32 {
        self.num_hashes
    }
}

#[derive(Debug)]
pub enum SstableError {
    Io(std::io::Error),
    Corrupt(String),
    InvalidInput(String),
}

pub type Result<T> = std::result::Result<T, SstableError>;

impl From<std::io::Error> for SstableError {
    fn from(err: std::io::Error) -> Self {
        Self::Io(err)
    }
}

#[derive(Debug, Clone)]
pub struct Sstable {
    pub entries: Vec<Entry>,
    pub bloom: BloomFilter,
    pub fences: Vec<FencePointer>,
}

pub fn write_sstable(path: &Path, entries: &[Entry]) -> Result<Sstable> {
    write_sstable_with_reactor(path, entries, &crate::core::reactor::SystemReactor)
}

pub fn write_sstable_with_reactor(
    path: &Path,
    entries: &[Entry],
    reactor: &dyn Reactor,
) -> Result<Sstable> {
    if entries.is_empty() {
        return Err(SstableError::InvalidInput(
            "entries must not be empty".to_string(),
        ));
    }

    let mut sorted = entries.to_vec();
    sorted.sort_by(|a, b| (a.key, a.version).cmp(&(b.key, b.version)));

    let num_bits = (sorted.len() as u32).saturating_mul(12).max(128);
    let num_hashes = 7u32;
    let mut bloom = BloomFilter::new(num_bits, num_hashes);
    for entry in &sorted {
        bloom.insert(entry.key);
    }

    let mut fences = Vec::new();
    let mut offset = header_len() as u64;

    for chunk in sorted.chunks(FENCE_GROUP_SIZE) {
        let min_key = chunk.first().unwrap().key;
        let max_key = chunk.last().unwrap().key;
        fences.push(FencePointer {
            min_key,
            max_key,
            offset,
        });
        for entry in chunk {
            offset += entry_len(entry) as u64;
        }
    }

    let bloom_offset = align_offset(offset, PAGE_SIZE_BYTES);
    let fence_offset = align_offset(bloom_offset + bloom.bits().len() as u64, PAGE_SIZE_BYTES);

    let mut buffer = Vec::new();
    {
        let mut cursor = Cursor::new(&mut buffer);
        write_header(
            &mut cursor,
            sorted.len() as u32,
            bloom.num_bits(),
            bloom.num_hashes(),
            fences.len() as u32,
            bloom_offset,
            fence_offset,
        )?;

        for entry in &sorted {
            write_entry(&mut cursor, entry)?;
        }

        let entries_end = cursor.stream_position()?;
        if entries_end < bloom_offset {
            write_padding(&mut cursor, (bloom_offset - entries_end) as usize)?;
        }

        cursor.write_all(bloom.bits())?;
        let bloom_end = cursor.stream_position()?;
        if bloom_end < fence_offset {
            write_padding(&mut cursor, (fence_offset - bloom_end) as usize)?;
        }

        for fence in &fences {
            cursor.write_all(&fence.min_key.to_le_bytes())?;
            cursor.write_all(&fence.max_key.to_le_bytes())?;
            cursor.write_all(&fence.offset.to_le_bytes())?;
        }

        let file_end = cursor.stream_position()?;
        let padded_end = align_offset(file_end, PAGE_SIZE_BYTES);
        if padded_end > file_end {
            write_padding(&mut cursor, (padded_end - file_end) as usize)?;
        }
    }
    reactor.write_file(path, &buffer)?;

    Ok(Sstable {
        entries: sorted,
        bloom,
        fences,
    })
}

pub fn read_sstable(path: &Path) -> Result<Sstable> {
    read_sstable_with_reactor(path, &crate::core::reactor::SystemReactor)
}

pub fn read_sstable_with_reactor(path: &Path, reactor: &dyn Reactor) -> Result<Sstable> {
    let buffer = reactor.read_file(path)?;
    let mut cursor = Cursor::new(buffer);
    let header = read_header(&mut cursor)?;
    let total_len = cursor.get_ref().len() as u64;
    if header.bloom_offset % PAGE_SIZE_BYTES != 0 || header.fence_offset % PAGE_SIZE_BYTES != 0 {
        return Err(SstableError::Corrupt(
            "unaligned section offsets".to_string(),
        ));
    }
    if header.bloom_offset > total_len || header.fence_offset > total_len {
        return Err(SstableError::Corrupt(
            "section offset out of bounds".to_string(),
        ));
    }
    let bloom_end = header.bloom_offset.saturating_add(header.bloom_len as u64);
    if bloom_end > total_len {
        return Err(SstableError::Corrupt(
            "bloom block out of bounds".to_string(),
        ));
    }
    if header.fence_offset < bloom_end {
        return Err(SstableError::Corrupt(
            "fence offset before bloom end".to_string(),
        ));
    }

    let mut entries = Vec::with_capacity(header.entry_count as usize);
    for _ in 0..header.entry_count {
        entries.push(read_entry(&mut cursor)?);
    }
    cursor.seek(SeekFrom::Start(header.bloom_offset))?;
    let mut bloom_bits = vec![0u8; header.bloom_len as usize];
    cursor.read_exact(&mut bloom_bits)?;
    let bloom = BloomFilter::from_bits(bloom_bits, header.bloom_bits, header.bloom_hashes);

    let mut fences = Vec::with_capacity(header.fence_count as usize);
    cursor.seek(SeekFrom::Start(header.fence_offset))?;
    for _ in 0..header.fence_count {
        fences.push(read_fence(&mut cursor)?);
    }

    Ok(Sstable {
        entries,
        bloom,
        fences,
    })
}

pub fn sstable_iterator(path: &Path) -> Result<Vec<Entry>> {
    Ok(read_sstable(path)?.entries)
}

pub fn read_entries_for_key(path: &Path, key: u64) -> Result<Vec<Entry>> {
    read_entries_for_key_with_reactor(path, key, &crate::core::reactor::SystemReactor)
}

pub fn read_entries_for_key_with_reactor(
    path: &Path,
    key: u64,
    reactor: &dyn Reactor,
) -> Result<Vec<Entry>> {
    let table = read_sstable_with_reactor(path, reactor)?;
    Ok(read_entries_for_key_in_table(&table, key))
}

pub fn read_entries_for_key_in_table(table: &Sstable, key: u64) -> Vec<Entry> {
    if !table.bloom.may_contain(key) {
        return Vec::new();
    }

    let mut in_fence = false;
    for fence in &table.fences {
        if key >= fence.min_key && key <= fence.max_key {
            in_fence = true;
            break;
        }
    }
    if !in_fence {
        return Vec::new();
    }
    if table.entries.is_empty() {
        return Vec::new();
    }
    let start = table.entries.partition_point(|entry| entry.key < key);
    if start >= table.entries.len() || table.entries[start].key != key {
        return Vec::new();
    }
    let end = start + table.entries[start..].partition_point(|entry| entry.key == key);
    table.entries[start..end].to_vec()
}

struct Header {
    entry_count: u32,
    bloom_bits: u32,
    bloom_hashes: u32,
    bloom_len: u32,
    fence_count: u32,
    bloom_offset: u64,
    fence_offset: u64,
}

fn header_len() -> usize {
    8 + 4 * 5 + 8 * 2
}

fn write_header(
    file: &mut impl Write,
    entry_count: u32,
    bloom_bits: u32,
    bloom_hashes: u32,
    fence_count: u32,
    bloom_offset: u64,
    fence_offset: u64,
) -> Result<()> {
    let bloom_len = bloom_bits.div_ceil(8);
    file.write_all(MAGIC)?;
    file.write_all(&entry_count.to_le_bytes())?;
    file.write_all(&bloom_bits.to_le_bytes())?;
    file.write_all(&bloom_hashes.to_le_bytes())?;
    file.write_all(&bloom_len.to_le_bytes())?;
    file.write_all(&fence_count.to_le_bytes())?;
    file.write_all(&bloom_offset.to_le_bytes())?;
    file.write_all(&fence_offset.to_le_bytes())?;
    Ok(())
}

fn read_header(file: &mut impl Read) -> Result<Header> {
    let mut magic = [0u8; 8];
    file.read_exact(&mut magic)?;
    if &magic != MAGIC {
        return Err(SstableError::Corrupt("invalid magic".to_string()));
    }

    let entry_count = read_u32(file)?;
    let bloom_bits = read_u32(file)?;
    let bloom_hashes = read_u32(file)?;
    let bloom_len = read_u32(file)?;
    let fence_count = read_u32(file)?;
    let bloom_offset = read_u64(file)?;
    let fence_offset = read_u64(file)?;

    Ok(Header {
        entry_count,
        bloom_bits,
        bloom_hashes,
        bloom_len,
        fence_count,
        bloom_offset,
        fence_offset,
    })
}

fn read_fence(file: &mut impl Read) -> Result<FencePointer> {
    Ok(FencePointer {
        min_key: read_u64(file)?,
        max_key: read_u64(file)?,
        offset: read_u64(file)?,
    })
}

fn write_entry(file: &mut impl Write, entry: &Entry) -> Result<()> {
    let key_bytes = entry.key.to_le_bytes();
    let version_bytes = entry.version.to_le_bytes();
    let len = entry.value.len() as u32;
    let len_bytes = len.to_le_bytes();
    file.write_all(&key_bytes)?;
    file.write_all(&version_bytes)?;
    file.write_all(&[entry.kind as u8])?;
    file.write_all(&len_bytes)?;
    file.write_all(&entry.value)?;
    let checksum = entry_checksum(
        &key_bytes,
        &version_bytes,
        entry.kind as u8,
        &len_bytes,
        &entry.value,
    );
    file.write_all(&checksum.to_le_bytes())?;
    Ok(())
}

fn entry_checksum(
    key_bytes: &[u8],
    version_bytes: &[u8],
    kind: u8,
    len_bytes: &[u8],
    value: &[u8],
) -> u32 {
    let mut buf = Vec::with_capacity(8 + 8 + 1 + 4 + value.len());
    buf.extend_from_slice(key_bytes);
    buf.extend_from_slice(version_bytes);
    buf.push(kind);
    buf.extend_from_slice(len_bytes);
    buf.extend_from_slice(value);
    crc32c(&buf)
}

fn read_entry(file: &mut impl Read) -> Result<Entry> {
    let key = read_u64(file)?;
    let version = read_u64(file)?;
    let mut kind_byte = [0u8; 1];
    file.read_exact(&mut kind_byte)?;
    let len = read_u32(file)?;
    let mut value = vec![0u8; len as usize];
    file.read_exact(&mut value)?;
    let stored = read_u32(file)?;
    let expected = entry_checksum(
        &key.to_le_bytes(),
        &version.to_le_bytes(),
        kind_byte[0],
        &len.to_le_bytes(),
        &value,
    );
    if stored != expected {
        return Err(SstableError::Corrupt(format!(
            "entry checksum mismatch: stored={stored}, computed={expected}"
        )));
    }
    let kind = match kind_byte[0] {
        0 => EntryKind::FullNode,
        1 => EntryKind::EdgeDelta,
        2 => EntryKind::VectorDelta,
        3 => EntryKind::Tombstone,
        other => {
            return Err(SstableError::Corrupt(format!(
                "invalid entry kind {}",
                other
            )))
        }
    };
    Ok(Entry {
        key,
        version,
        kind,
        value,
    })
}

fn read_u32(file: &mut impl Read) -> Result<u32> {
    let mut buf = [0u8; 4];
    file.read_exact(&mut buf)?;
    Ok(u32::from_le_bytes(buf))
}

fn read_u64(file: &mut impl Read) -> Result<u64> {
    let mut buf = [0u8; 8];
    file.read_exact(&mut buf)?;
    Ok(u64::from_le_bytes(buf))
}

fn entry_len(entry: &Entry) -> usize {
    8 + 8 + 1 + 4 + entry.value.len() + 4
}

fn align_offset(offset: u64, alignment: u64) -> u64 {
    if alignment == 0 {
        return offset;
    }
    let rem = offset % alignment;
    if rem == 0 {
        offset
    } else {
        offset + (alignment - rem)
    }
}

fn write_padding(file: &mut impl Write, len: usize) -> Result<()> {
    if len == 0 {
        return Ok(());
    }
    let padding = vec![0u8; len];
    file.write_all(&padding)?;
    Ok(())
}

fn hash_key(key: u64, seed: u32, num_bits: u32) -> u32 {
    let mut bytes = [0u8; 12];
    bytes[..8].copy_from_slice(&key.to_le_bytes());
    bytes[8..12].copy_from_slice(&seed.to_le_bytes());
    let hash = crc32c(&bytes);
    if num_bits == 0 {
        0
    } else {
        hash % num_bits
    }
}

fn set_bit(bits: &mut [u8], idx: u32) {
    let byte = (idx / 8) as usize;
    let bit = idx % 8;
    if let Some(slot) = bits.get_mut(byte) {
        *slot |= 1u8 << bit;
    }
}

fn get_bit(bits: &[u8], idx: u32) -> bool {
    let byte = (idx / 8) as usize;
    let bit = idx % 8;
    bits.get(byte)
        .is_some_and(|slot| (slot & (1u8 << bit)) != 0)
}

#[cfg(test)]
mod tests;