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Rework the DocumentsBatchBuilder/Reader to use grenad

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Kerollmops 2022-06-14 16:03:48 +02:00
parent eb63af1f10
commit 419ce3966c
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4 changed files with 218 additions and 356 deletions
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216
milli/src/documents/builder.rs
View File

@ -1,157 +1,159 @@
use std::collections::BTreeMap;
use std::io;
use std::io::{Cursor, Write};
use std::io::{self, Write};
use byteorder::{BigEndian, WriteBytesExt};
use serde::Deserializer;
use serde_json::Value;
use grenad::{CompressionType, WriterBuilder};
use serde_json::{to_writer, Map, Value};
use super::serde_impl::DocumentVisitor;
use super::{ByteCounter, DocumentsBatchIndex, DocumentsMetadata, Error};
use crate::FieldId;
use super::{DocumentsBatchIndex, Error, DOCUMENTS_BATCH_INDEX_KEY};
/// The `DocumentsBatchBuilder` provides a way to build a documents batch in the intermediary
/// format used by milli.
///
/// The writer used by the DocumentBatchBuilder can be read using a `DocumentBatchReader` to
/// iterate over the documents.
/// The writer used by the `DocumentsBatchBuilder` can be read using a `DocumentsBatchReader`
/// to iterate over the documents.
///
/// ## example:
/// ```
/// use milli::documents::DocumentBatchBuilder;
/// use serde_json::json;
/// use std::io::Cursor;
/// use milli::documents::DocumentsBatchBuilder;
///
/// let json = r##"{"id": 1, "name": "foo"}"##;
/// let mut writer = Cursor::new(Vec::new());
/// let mut builder = DocumentBatchBuilder::new(&mut writer).unwrap();
/// builder.extend_from_json(&mut json.as_bytes()).unwrap();
/// builder.finish().unwrap();
/// let json = json!({ "id": 1, "name": "foo" });
///
/// let mut builder = DocumentsBatchBuilder::new(Vec::new());
/// builder.append_json_object(json.as_object().unwrap()).unwrap();
/// let _vector = builder.into_inner().unwrap();
/// ```
pub struct DocumentBatchBuilder<W> {
inner: ByteCounter<W>,
index: DocumentsBatchIndex,
pub struct DocumentsBatchBuilder<W> {
/// The inner grenad writer, the last value must always be the `DocumentsBatchIndex`.
writer: grenad::Writer<W>,
/// A map that creates the relation between field ids and field names.
fields_index: DocumentsBatchIndex,
/// The number of documents that were added to this builder,
/// it doesn't take the primary key of the documents into account at this point.
documents_count: u32,
/// A buffer to store a temporary obkv buffer and avoid reallocating.
obkv_buffer: Vec<u8>,
/// A buffer to serialize the values and avoid reallocating,
/// serialized values are stored in an obkv.
value_buffer: Vec<u8>,
values: BTreeMap<FieldId, Value>,
count: usize,
}
impl<W: io::Write + io::Seek> DocumentBatchBuilder<W> {
pub fn new(writer: W) -> Result<Self, Error> {
let index = DocumentsBatchIndex::default();
let mut writer = ByteCounter::new(writer);
// add space to write the offset of the metadata at the end of the writer
writer.write_u64::<BigEndian>(0)?;
Ok(Self {
inner: writer,
index,
impl<W: Write> DocumentsBatchBuilder<W> {
pub fn new(writer: W) -> DocumentsBatchBuilder<W> {
DocumentsBatchBuilder {
writer: WriterBuilder::new().compression_type(CompressionType::None).build(writer),
fields_index: DocumentsBatchIndex::default(),
documents_count: 0,
obkv_buffer: Vec::new(),
value_buffer: Vec::new(),
values: BTreeMap::new(),
count: 0,
})
}
}
/// Returns the number of documents that have been written to the builder.
pub fn len(&self) -> usize {
self.count
/// Returns the number of documents inserted into this builder.
pub fn documents_count(&self) -> u32 {
self.documents_count
}
/// This method must be called after the document addition is terminated. It will put the
/// metadata at the end of the file, and write the metadata offset at the beginning on the
/// file.
pub fn finish(self) -> Result<usize, Error> {
let Self { inner: ByteCounter { mut writer, count: offset }, index, count, .. } = self;
/// Appends a new JSON object into the batch and updates the `DocumentsBatchIndex` accordingly.
pub fn append_json_object(&mut self, object: &Map<String, Value>) -> io::Result<()> {
// Make sure that we insert the fields ids in order as the obkv writer has this requirement.
let mut fields_ids: Vec<_> = object.keys().map(|k| self.fields_index.insert(&k)).collect();
fields_ids.sort_unstable();
let meta = DocumentsMetadata { count, index };
self.obkv_buffer.clear();
let mut writer = obkv::KvWriter::new(&mut self.obkv_buffer);
for field_id in fields_ids {
let key = self.fields_index.name(field_id).unwrap();
self.value_buffer.clear();
to_writer(&mut self.value_buffer, &object[key])?;
writer.insert(field_id, &self.value_buffer)?;
}
bincode::serialize_into(&mut writer, &meta)?;
let internal_id = self.documents_count.to_be_bytes();
let document_bytes = writer.into_inner()?;
self.writer.insert(internal_id, &document_bytes)?;
self.documents_count += 1;
writer.seek(io::SeekFrom::Start(0))?;
writer.write_u64::<BigEndian>(offset as u64)?;
writer.flush()?;
Ok(count)
Ok(())
}
/// Extends the builder with json documents from a reader.
pub fn extend_from_json<R: io::Read>(&mut self, reader: R) -> Result<(), Error> {
let mut de = serde_json::Deserializer::from_reader(reader);
let mut visitor = DocumentVisitor {
inner: &mut self.inner,
index: &mut self.index,
obkv_buffer: &mut self.obkv_buffer,
value_buffer: &mut self.value_buffer,
values: &mut self.values,
count: &mut self.count,
};
de.deserialize_any(&mut visitor).map_err(Error::JsonError)?
}
/// Creates a builder from a reader of CSV documents.
///
/// Since all fields in a csv documents are guaranteed to be ordered, we are able to perform
/// optimisations, and extending from another CSV is not allowed.
pub fn from_csv<R: io::Read>(reader: R, writer: W) -> Result<Self, Error> {
let mut this = Self::new(writer)?;
// Ensure that this is the first and only addition made with this builder
debug_assert!(this.index.is_empty());
let mut records = csv::Reader::from_reader(reader);
let headers = records
/// Appends a new CSV file into the batch and updates the `DocumentsBatchIndex` accordingly.
pub fn append_csv<R: io::Read>(&mut self, mut reader: csv::Reader<R>) -> Result<(), Error> {
// Make sure that we insert the fields ids in order as the obkv writer has this requirement.
let mut typed_fields_ids: Vec<_> = reader
.headers()?
.into_iter()
.map(parse_csv_header)
.map(|(k, t)| (this.index.insert(k), t))
.collect::<BTreeMap<_, _>>();
.map(|(k, t)| (self.fields_index.insert(k), t))
.enumerate()
.collect();
typed_fields_ids.sort_unstable_by_key(|(_, (fid, _))| *fid);
for (i, record) in records.into_records().enumerate() {
let record = record?;
this.obkv_buffer.clear();
let mut writer = obkv::KvWriter::new(&mut this.obkv_buffer);
for (value, (fid, ty)) in record.into_iter().zip(headers.iter()) {
let value = match ty {
let mut record = csv::StringRecord::new();
let mut line = 0;
while reader.read_record(&mut record)? {
// We increment here and not at the end of the while loop to take
// the header offset into account.
line += 1;
self.obkv_buffer.clear();
let mut writer = obkv::KvWriter::new(&mut self.obkv_buffer);
for (i, (field_id, type_)) in typed_fields_ids.iter() {
self.value_buffer.clear();
let value = &record[*i];
match type_ {
AllowedType::Number => {
if value.trim().is_empty() {
Value::Null
to_writer(&mut self.value_buffer, &Value::Null)?;
} else {
value.trim().parse::<f64>().map(Value::from).map_err(|error| {
Error::ParseFloat {
error,
// +1 for the header offset.
line: i + 1,
value: value.to_string(),
match value.trim().parse::<f64>() {
Ok(float) => {
to_writer(&mut self.value_buffer, &float)?;
}
})?
Err(error) => {
return Err(Error::ParseFloat {
error,
line,
value: value.to_string(),
});
}
}
}
}
AllowedType::String => {
if value.is_empty() {
Value::Null
to_writer(&mut self.value_buffer, &Value::Null)?;
} else {
Value::String(value.to_string())
to_writer(&mut self.value_buffer, value)?;
}
}
};
}
this.value_buffer.clear();
serde_json::to_writer(Cursor::new(&mut this.value_buffer), &value)?;
writer.insert(*fid, &this.value_buffer)?;
// We insert into the obkv writer the value buffer that has been filled just above.
writer.insert(*field_id, &self.value_buffer)?;
}
this.inner.write_u32::<BigEndian>(this.obkv_buffer.len() as u32)?;
this.inner.write_all(&this.obkv_buffer)?;
this.count += 1;
let internal_id = self.documents_count.to_be_bytes();
let document_bytes = writer.into_inner()?;
self.writer.insert(internal_id, &document_bytes)?;
self.documents_count += 1;
}
Ok(this)
Ok(())
}
/// Flushes the content on disk and stores the final version of the `DocumentsBatchIndex`.
pub fn into_inner(mut self) -> io::Result<W> {
let DocumentsBatchBuilder { mut writer, fields_index, .. } = self;
// We serialize and insert the `DocumentsBatchIndex` as the last key of the grenad writer.
self.value_buffer.clear();
to_writer(&mut self.value_buffer, &fields_index)?;
writer.insert(DOCUMENTS_BATCH_INDEX_KEY, &self.value_buffer)?;
writer.into_inner()
}
}

107
milli/src/documents/mod.rs
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@ -1,24 +1,22 @@
mod builder;
/// The documents module defines an intermediary document format that milli uses for indexation, and
/// provides an API to easily build and read such documents.
///
/// The `DocumentBatchBuilder` interface allows to write batches of documents to a writer, that can
/// later be read by milli using the `DocumentBatchReader` interface.
mod reader;
mod serde_impl;
use std::fmt::{self, Debug};
use std::io;
use bimap::BiHashMap;
pub use builder::DocumentBatchBuilder;
pub use reader::DocumentBatchReader;
pub use builder::DocumentsBatchBuilder;
pub use reader::{DocumentsBatchCursor, DocumentsBatchReader};
use serde::{Deserialize, Serialize};
use crate::FieldId;
/// The key that is used to store the `DocumentsBatchIndex` datastructure,
/// it is the absolute last key of the list.
const DOCUMENTS_BATCH_INDEX_KEY: [u8; 8] = u64::MAX.to_be_bytes();
/// A bidirectional map that links field ids to their name in a document batch.
#[derive(Default, Debug, Serialize, Deserialize)]
#[derive(Default, Clone, Debug, Serialize, Deserialize)]
pub struct DocumentsBatchIndex(pub BiHashMap<FieldId, String>);
impl DocumentsBatchIndex {
@ -46,8 +44,8 @@ impl DocumentsBatchIndex {
self.0.iter()
}
pub fn name(&self, id: FieldId) -> Option<&String> {
self.0.get_by_left(&id)
pub fn name(&self, id: FieldId) -> Option<&str> {
self.0.get_by_left(&id).map(AsRef::as_ref)
}
pub fn recreate_json(
@ -69,50 +67,20 @@ impl DocumentsBatchIndex {
}
}
#[derive(Debug, Serialize, Deserialize)]
struct DocumentsMetadata {
count: usize,
index: DocumentsBatchIndex,
}
pub struct ByteCounter<W> {
count: usize,
writer: W,
}
impl<W> ByteCounter<W> {
fn new(writer: W) -> Self {
Self { count: 0, writer }
}
}
impl<W: io::Write> io::Write for ByteCounter<W> {
fn write(&mut self, buf: &[u8]) -> io::Result<usize> {
let count = self.writer.write(buf)?;
self.count += count;
Ok(count)
}
fn flush(&mut self) -> io::Result<()> {
self.writer.flush()
}
}
#[derive(Debug)]
pub enum Error {
ParseFloat { error: std::num::ParseFloatError, line: usize, value: String },
InvalidDocumentFormat,
Custom(String),
JsonError(serde_json::Error),
CsvError(csv::Error),
Serialize(bincode::Error),
Csv(csv::Error),
Json(serde_json::Error),
Serialize(serde_json::Error),
Grenad(grenad::Error),
Io(io::Error),
DocumentTooLarge,
}
impl From<csv::Error> for Error {
fn from(e: csv::Error) -> Self {
Self::CsvError(e)
Self::Csv(e)
}
}
@ -122,15 +90,15 @@ impl From<io::Error> for Error {
}
}
impl From<bincode::Error> for Error {
fn from(other: bincode::Error) -> Self {
Self::Serialize(other)
impl From<serde_json::Error> for Error {
fn from(other: serde_json::Error) -> Self {
Self::Json(other)
}
}
impl From<serde_json::Error> for Error {
fn from(other: serde_json::Error) -> Self {
Self::JsonError(other)
impl From<grenad::Error> for Error {
fn from(other: grenad::Error) -> Self {
Self::Grenad(other)
}
}
@ -140,13 +108,14 @@ impl fmt::Display for Error {
Error::ParseFloat { error, line, value } => {
write!(f, "Error parsing number {:?} at line {}: {}", value, line, error)
}
Error::Custom(s) => write!(f, "Unexpected serialization error: {}", s),
Error::InvalidDocumentFormat => f.write_str("Invalid document addition format."),
Error::JsonError(err) => write!(f, "Couldn't serialize document value: {}", err),
Error::InvalidDocumentFormat => {
f.write_str("Invalid document addition format, missing the documents batch index.")
}
Error::Io(e) => write!(f, "{}", e),
Error::DocumentTooLarge => f.write_str("Provided document is too large (>2Gib)"),
Error::Serialize(e) => write!(f, "{}", e),
Error::CsvError(e) => write!(f, "{}", e),
Error::Grenad(e) => write!(f, "{}", e),
Error::Csv(e) => write!(f, "{}", e),
Error::Json(e) => write!(f, "{}", e),
}
}
}
@ -158,15 +127,25 @@ impl std::error::Error for Error {}
macro_rules! documents {
($data:tt) => {{
let documents = serde_json::json!($data);
let mut writer = std::io::Cursor::new(Vec::new());
let mut builder = crate::documents::DocumentBatchBuilder::new(&mut writer).unwrap();
let documents = serde_json::to_vec(&documents).unwrap();
builder.extend_from_json(std::io::Cursor::new(documents)).unwrap();
builder.finish().unwrap();
let documents = match documents {
object @ serde_json::Value::Object(_) => vec![object],
serde_json::Value::Array(objects) => objects,
invalid => {
panic!("an array of objects must be specified, {:#?} is not an array", invalid)
}
};
writer.set_position(0);
let mut builder = crate::documents::DocumentsBatchBuilder::new(Vec::new());
for document in documents {
let object = match document {
serde_json::Value::Object(object) => object,
invalid => panic!("an object must be specified, {:#?} is not an object", invalid),
};
builder.append_json_object(&object).unwrap();
}
crate::documents::DocumentBatchReader::from_reader(writer).unwrap()
let vector = builder.into_inner().unwrap();
crate::documents::DocumentsBatchReader::from_reader(std::io::Cursor::new(vector)).unwrap()
}};
}

117
milli/src/documents/reader.rs
View File

@ -1,11 +1,9 @@
use std::convert::TryInto;
use std::io;
use std::io::{BufReader, Read};
use std::mem::size_of;
use byteorder::{BigEndian, ReadBytesExt};
use obkv::KvReader;
use super::{DocumentsBatchIndex, DocumentsMetadata, Error};
use super::{DocumentsBatchIndex, Error, DOCUMENTS_BATCH_INDEX_KEY};
use crate::FieldId;
/// The `DocumentsBatchReader` provides a way to iterate over documents that have been created with
@ -13,63 +11,80 @@ use crate::FieldId;
///
/// The documents are returned in the form of `obkv::Reader` where each field is identified with a
/// `FieldId`. The mapping between the field ids and the field names is done thanks to the index.
pub struct DocumentBatchReader<R> {
reader: BufReader<R>,
metadata: DocumentsMetadata,
buffer: Vec<u8>,
seen_documents: usize,
pub struct DocumentsBatchReader<R> {
cursor: grenad::ReaderCursor<R>,
fields_index: DocumentsBatchIndex,
}
impl<R: io::Read + io::Seek> DocumentBatchReader<R> {
impl<R: io::Read + io::Seek> DocumentsBatchReader<R> {
/// Construct a `DocumentsReader` from a reader.
///
/// It first retrieves the index, then moves to the first document. Subsequent calls to
/// `next_document` advance the document reader until all the documents have been read.
pub fn from_reader(mut reader: R) -> Result<Self, Error> {
let mut buffer = Vec::new();
/// It first retrieves the index, then moves to the first document. Use the `into_cursor`
/// method to iterator over the documents, from the first to the last.
pub fn from_reader(reader: R) -> Result<Self, Error> {
let reader = grenad::Reader::new(reader)?;
let mut cursor = reader.into_cursor()?;
let meta_offset = reader.read_u64::<BigEndian>()?;
reader.seek(io::SeekFrom::Start(meta_offset))?;
reader.read_to_end(&mut buffer)?;
let metadata: DocumentsMetadata = bincode::deserialize(&buffer)?;
let fields_index = match cursor.move_on_key_equal_to(DOCUMENTS_BATCH_INDEX_KEY)? {
Some((_, value)) => serde_json::from_slice(value).map_err(Error::Serialize)?,
None => return Err(Error::InvalidDocumentFormat),
};
reader.seek(io::SeekFrom::Start(size_of::<u64>() as u64))?;
buffer.clear();
let reader = BufReader::new(reader);
Ok(Self { reader, metadata, buffer, seen_documents: 0 })
Ok(DocumentsBatchReader { cursor, fields_index })
}
/// Returns the next document in the reader, and wraps it in an `obkv::KvReader`, along with a
/// reference to the addition index.
pub fn next_document_with_index<'a>(
&'a mut self,
) -> io::Result<Option<(&'a DocumentsBatchIndex, KvReader<'a, FieldId>)>> {
if self.seen_documents < self.metadata.count {
let doc_len = self.reader.read_u32::<BigEndian>()?;
self.buffer.resize(doc_len as usize, 0);
self.reader.read_exact(&mut self.buffer)?;
self.seen_documents += 1;
let reader = KvReader::new(&self.buffer);
Ok(Some((&self.metadata.index, reader)))
} else {
Ok(None)
}
}
/// Return the fields index for the documents batch.
pub fn index(&self) -> &DocumentsBatchIndex {
&self.metadata.index
}
/// Returns the number of documents in the reader.
pub fn len(&self) -> usize {
self.metadata.count
pub fn documents_count(&self) -> u32 {
self.cursor.len().saturating_sub(1).try_into().expect("Invalid number of documents")
}
pub fn is_empty(&self) -> bool {
self.len() == 0
self.cursor.len().saturating_sub(1) == 0
}
pub fn documents_batch_index(&self) -> &DocumentsBatchIndex {
&self.fields_index
}
/// This method returns a forward cursor over the documents.
pub fn into_cursor(self) -> DocumentsBatchCursor<R> {
let DocumentsBatchReader { cursor, fields_index } = self;
let mut cursor = DocumentsBatchCursor { cursor, fields_index };
cursor.reset();
cursor
}
}
/// A forward cursor over the documents in a `DocumentsBatchReader`.
pub struct DocumentsBatchCursor<R> {
cursor: grenad::ReaderCursor<R>,
fields_index: DocumentsBatchIndex,
}
impl<R> DocumentsBatchCursor<R> {
pub fn into_reader(self) -> DocumentsBatchReader<R> {
let DocumentsBatchCursor { cursor, fields_index, .. } = self;
DocumentsBatchReader { cursor, fields_index }
}
pub fn documents_batch_index(&self) -> &DocumentsBatchIndex {
&self.fields_index
}
/// Resets the cursor to be able to read from the start again.
pub fn reset(&mut self) {
self.cursor.reset();
}
}
impl<R: io::Read + io::Seek> DocumentsBatchCursor<R> {
/// Returns the next document, starting from the first one. Subsequent calls to
/// `next_document` advance the document reader until all the documents have been read.
pub fn next_document(&mut self) -> Result<Option<KvReader<FieldId>>, grenad::Error> {
match self.cursor.move_on_next()? {
Some((key, value)) if key != DOCUMENTS_BATCH_INDEX_KEY => {
Ok(Some(KvReader::new(value)))
}
_otherwise => Ok(None),
}
}
}

134
milli/src/documents/serde_impl.rs
View File

@ -1,134 +0,0 @@
use std::collections::BTreeMap;
use std::fmt;
use std::io::{Cursor, Write};
use byteorder::WriteBytesExt;
use serde::de::{DeserializeSeed, MapAccess, SeqAccess, Visitor};
use serde::Deserialize;
use serde_json::Value;
use super::{ByteCounter, DocumentsBatchIndex, Error};
use crate::FieldId;
macro_rules! tri {
($e:expr) => {
match $e {
Ok(r) => r,
Err(e) => return Ok(Err(e.into())),
}
};
}
struct FieldIdResolver<'a>(&'a mut DocumentsBatchIndex);
impl<'a, 'de> DeserializeSeed<'de> for FieldIdResolver<'a> {
type Value = FieldId;
fn deserialize<D>(self, deserializer: D) -> Result<Self::Value, D::Error>
where
D: serde::Deserializer<'de>,
{
deserializer.deserialize_str(self)
}
}
impl<'a, 'de> Visitor<'de> for FieldIdResolver<'a> {
type Value = FieldId;
fn visit_str<E>(self, v: &str) -> Result<Self::Value, E>
where
E: serde::de::Error,
{
Ok(self.0.insert(v))
}
fn expecting(&self, f: &mut fmt::Formatter) -> fmt::Result {
write!(f, "a string")
}
}
struct ValueDeserializer;
impl<'de> DeserializeSeed<'de> for ValueDeserializer {
type Value = serde_json::Value;
fn deserialize<D>(self, deserializer: D) -> Result<Self::Value, D::Error>
where
D: serde::Deserializer<'de>,
{
serde_json::Value::deserialize(deserializer)
}
}
pub struct DocumentVisitor<'a, W> {
pub inner: &'a mut ByteCounter<W>,
pub index: &'a mut DocumentsBatchIndex,
pub obkv_buffer: &'a mut Vec<u8>,
pub value_buffer: &'a mut Vec<u8>,
pub values: &'a mut BTreeMap<FieldId, Value>,
pub count: &'a mut usize,
}
impl<'a, 'de, W: Write> Visitor<'de> for &mut DocumentVisitor<'a, W> {
/// This Visitor value is nothing, since it write the value to a file.
type Value = Result<(), Error>;
fn visit_seq<A>(self, mut seq: A) -> Result<Self::Value, A::Error>
where
A: SeqAccess<'de>,
{
while let Some(v) = seq.next_element_seed(&mut *self)? {
tri!(v)
}
Ok(Ok(()))
}
fn visit_map<A>(self, mut map: A) -> Result<Self::Value, A::Error>
where
A: MapAccess<'de>,
{
while let Some((key, value)) =
map.next_entry_seed(FieldIdResolver(&mut *self.index), ValueDeserializer)?
{
self.values.insert(key, value);
}
self.obkv_buffer.clear();
let mut obkv = obkv::KvWriter::new(Cursor::new(&mut *self.obkv_buffer));
for (key, value) in self.values.iter() {
self.value_buffer.clear();
// This is guaranteed to work
tri!(serde_json::to_writer(Cursor::new(&mut *self.value_buffer), value));
tri!(obkv.insert(*key, &self.value_buffer));
}
let reader = tri!(obkv.into_inner()).into_inner();
tri!(self.inner.write_u32::<byteorder::BigEndian>(reader.len() as u32));
tri!(self.inner.write_all(reader));
*self.count += 1;
self.values.clear();
Ok(Ok(()))
}
fn expecting(&self, f: &mut fmt::Formatter) -> fmt::Result {
write!(f, "a documents, or a sequence of documents.")
}
}
impl<'a, 'de, W> DeserializeSeed<'de> for &mut DocumentVisitor<'a, W>
where
W: Write,
{
type Value = Result<(), Error>;
fn deserialize<D>(self, deserializer: D) -> Result<Self::Value, D::Error>
where
D: serde::Deserializer<'de>,
{
deserializer.deserialize_map(self)
}
}