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Introduce the UpdateBuilder and use it in the HTTP routes

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Clément Renault 2020-10-26 20:18:10 +01:00 committed by Kerollmops
parent 5c62fbb6a8
commit 3889d956d9
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8 changed files with 641 additions and 537 deletions
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410
src/indexing/mod.rs
View File

@ -1,410 +0,0 @@
use std::borrow::Cow;
use std::fs::File;
use std::io::{self, Seek, SeekFrom};
use std::sync::mpsc::sync_channel;
use std::time::Instant;
use anyhow::Context;
use bstr::ByteSlice as _;
use grenad::{Writer, Sorter, Merger, Reader, FileFuse, CompressionType};
use heed::types::ByteSlice;
use log::{debug, info, error};
use rayon::prelude::*;
use roaring::RoaringBitmap;
use structopt::StructOpt;
use tempfile::tempfile;
use crate::FieldsIdsMap;
use crate::index::Index;
use self::store::Store;
use self::merge_function::{
main_merge, word_docids_merge, words_pairs_proximities_docids_merge,
docid_word_positions_merge, documents_merge,
};
pub use self::transform::{Transform, TransformOutput};
mod merge_function;
mod store;
mod transform;
#[derive(Debug, Clone, StructOpt)]
pub struct IndexerOpt {
/// The amount of documents to skip before printing
/// a log regarding the indexing advancement.
#[structopt(long, default_value = "1000000")] // 1m
pub log_every_n: usize,
/// MTBL max number of chunks in bytes.
#[structopt(long)]
pub max_nb_chunks: Option<usize>,
/// The maximum amount of memory to use for the MTBL buffer. It is recommended
/// to use something like 80%-90% of the available memory.
///
/// It is automatically split by the number of jobs e.g. if you use 7 jobs
/// and 7 GB of max memory, each thread will use a maximum of 1 GB.
#[structopt(long, default_value = "7516192768")] // 7 GB
pub max_memory: usize,
/// Size of the linked hash map cache when indexing.
/// The bigger it is, the faster the indexing is but the more memory it takes.
#[structopt(long, default_value = "500")]
pub linked_hash_map_size: usize,
/// The name of the compression algorithm to use when compressing intermediate
/// chunks during indexing documents.
///
/// Choosing a fast algorithm will make the indexing faster but may consume more memory.
#[structopt(long, default_value = "snappy", possible_values = &["snappy", "zlib", "lz4", "lz4hc", "zstd"])]
pub chunk_compression_type: CompressionType,
/// The level of compression of the chosen algorithm.
#[structopt(long, requires = "chunk-compression-type")]
pub chunk_compression_level: Option<u32>,
/// The number of bytes to remove from the begining of the chunks while reading/sorting
/// or merging them.
///
/// File fusing must only be enable on file systems that support the `FALLOC_FL_COLLAPSE_RANGE`,
/// (i.e. ext4 and XFS). File fusing will only work if the `enable-chunk-fusing` is set.
#[structopt(long, default_value = "4294967296")] // 4 GB
pub chunk_fusing_shrink_size: u64,
/// Enable the chunk fusing or not, this reduces the amount of disk used by a factor of 2.
#[structopt(long)]
pub enable_chunk_fusing: bool,
/// Number of parallel jobs for indexing, defaults to # of CPUs.
#[structopt(long)]
pub indexing_jobs: Option<usize>,
}
#[derive(Debug, Copy, Clone)]
enum WriteMethod {
Append,
GetMergePut,
}
type MergeFn = for<'a> fn(&[u8], &[Cow<'a, [u8]>]) -> anyhow::Result<Vec<u8>>;
fn create_writer(typ: CompressionType, level: Option<u32>, file: File) -> io::Result<Writer<File>> {
let mut builder = Writer::builder();
builder.compression_type(typ);
if let Some(level) = level {
builder.compression_level(level);
}
builder.build(file)
}
fn create_sorter(
merge: MergeFn,
chunk_compression_type: CompressionType,
chunk_compression_level: Option<u32>,
chunk_fusing_shrink_size: Option<u64>,
max_nb_chunks: Option<usize>,
max_memory: Option<usize>,
) -> Sorter<MergeFn>
{
let mut builder = Sorter::builder(merge);
if let Some(shrink_size) = chunk_fusing_shrink_size {
builder.file_fusing_shrink_size(shrink_size);
}
builder.chunk_compression_type(chunk_compression_type);
if let Some(level) = chunk_compression_level {
builder.chunk_compression_level(level);
}
if let Some(nb_chunks) = max_nb_chunks {
builder.max_nb_chunks(nb_chunks);
}
if let Some(memory) = max_memory {
builder.max_memory(memory);
}
builder.build()
}
fn writer_into_reader(writer: Writer<File>, shrink_size: Option<u64>) -> anyhow::Result<Reader<FileFuse>> {
let mut file = writer.into_inner()?;
file.seek(SeekFrom::Start(0))?;
let file = if let Some(shrink_size) = shrink_size {
FileFuse::builder().shrink_size(shrink_size).build(file)
} else {
FileFuse::new(file)
};
Reader::new(file).map_err(Into::into)
}
fn merge_readers(sources: Vec<Reader<FileFuse>>, merge: MergeFn) -> Merger<FileFuse, MergeFn> {
let mut builder = Merger::builder(merge);
builder.extend(sources);
builder.build()
}
fn merge_into_lmdb_database(
wtxn: &mut heed::RwTxn,
database: heed::PolyDatabase,
sources: Vec<Reader<FileFuse>>,
merge: MergeFn,
method: WriteMethod,
) -> anyhow::Result<()> {
debug!("Merging {} MTBL stores...", sources.len());
let before = Instant::now();
let merger = merge_readers(sources, merge);
let mut in_iter = merger.into_merge_iter()?;
match method {
WriteMethod::Append => {
let mut out_iter = database.iter_mut::<_, ByteSlice, ByteSlice>(wtxn)?;
while let Some((k, v)) = in_iter.next()? {
out_iter.append(k, v).with_context(|| format!("writing {:?} into LMDB", k.as_bstr()))?;
}
},
WriteMethod::GetMergePut => {
while let Some((k, v)) = in_iter.next()? {
match database.get::<_, ByteSlice, ByteSlice>(wtxn, k)? {
Some(old_val) => {
let vals = vec![Cow::Borrowed(old_val), Cow::Borrowed(v)];
let val = merge(k, &vals).expect("merge failed");
database.put::<_, ByteSlice, ByteSlice>(wtxn, k, &val)?
},
None => database.put::<_, ByteSlice, ByteSlice>(wtxn, k, v)?,
}
}
},
}
debug!("MTBL stores merged in {:.02?}!", before.elapsed());
Ok(())
}
fn write_into_lmdb_database(
wtxn: &mut heed::RwTxn,
database: heed::PolyDatabase,
mut reader: Reader<FileFuse>,
merge: MergeFn,
method: WriteMethod,
) -> anyhow::Result<()> {
debug!("Writing MTBL stores...");
let before = Instant::now();
match method {
WriteMethod::Append => {
let mut out_iter = database.iter_mut::<_, ByteSlice, ByteSlice>(wtxn)?;
while let Some((k, v)) = reader.next()? {
out_iter.append(k, v).with_context(|| format!("writing {:?} into LMDB", k.as_bstr()))?;
}
},
WriteMethod::GetMergePut => {
while let Some((k, v)) = reader.next()? {
match database.get::<_, ByteSlice, ByteSlice>(wtxn, k)? {
Some(old_val) => {
let vals = vec![Cow::Borrowed(old_val), Cow::Borrowed(v)];
let val = merge(k, &vals).expect("merge failed");
database.put::<_, ByteSlice, ByteSlice>(wtxn, k, &val)?
},
None => database.put::<_, ByteSlice, ByteSlice>(wtxn, k, v)?,
}
}
}
}
debug!("MTBL stores merged in {:.02?}!", before.elapsed());
Ok(())
}
pub fn run<F>(
env: &heed::Env,
index: &Index,
opt: &IndexerOpt,
fields_ids_map: FieldsIdsMap,
users_ids_documents_ids: fst::Map<Vec<u8>>,
new_documents_ids: RoaringBitmap,
documents: grenad::Reader<&[u8]>,
documents_count: u32,
progress_callback: F,
) -> anyhow::Result<()>
where F: Fn(u32, u32) + Sync + Send,
{
let jobs = opt.indexing_jobs.unwrap_or(0);
let pool = rayon::ThreadPoolBuilder::new().num_threads(jobs).build()?;
pool.install(|| {
run_intern(
env,
index,
opt,
fields_ids_map,
users_ids_documents_ids,
new_documents_ids,
documents,
documents_count,
progress_callback,
)
})
}
fn run_intern<F>(
env: &heed::Env,
index: &Index,
opt: &IndexerOpt,
fields_ids_map: FieldsIdsMap,
users_ids_documents_ids: fst::Map<Vec<u8>>,
new_documents_ids: RoaringBitmap,
documents: grenad::Reader<&[u8]>,
documents_count: u32,
progress_callback: F,
) -> anyhow::Result<()>
where F: Fn(u32, u32) + Sync + Send,
{
let before_indexing = Instant::now();
let num_threads = rayon::current_num_threads();
let linked_hash_map_size = opt.linked_hash_map_size;
let max_nb_chunks = opt.max_nb_chunks;
let max_memory_by_job = opt.max_memory / num_threads;
let chunk_compression_type = opt.chunk_compression_type;
let chunk_compression_level = opt.chunk_compression_level;
let log_every_n = opt.log_every_n;
let chunk_fusing_shrink_size = if opt.enable_chunk_fusing {
Some(opt.chunk_fusing_shrink_size)
} else {
None
};
let readers = rayon::iter::repeatn(documents, num_threads)
.enumerate()
.map(|(i, documents)| {
let store = Store::new(
linked_hash_map_size,
max_nb_chunks,
Some(max_memory_by_job),
chunk_compression_type,
chunk_compression_level,
chunk_fusing_shrink_size,
)?;
store.index(documents, documents_count, i, num_threads, log_every_n, &progress_callback)
})
.collect::<Result<Vec<_>, _>>()?;
let mut main_readers = Vec::with_capacity(readers.len());
let mut word_docids_readers = Vec::with_capacity(readers.len());
let mut docid_word_positions_readers = Vec::with_capacity(readers.len());
let mut words_pairs_proximities_docids_readers = Vec::with_capacity(readers.len());
let mut documents_readers = Vec::with_capacity(readers.len());
readers.into_iter().for_each(|readers| {
main_readers.push(readers.main);
word_docids_readers.push(readers.word_docids);
docid_word_positions_readers.push(readers.docid_word_positions);
words_pairs_proximities_docids_readers.push(readers.words_pairs_proximities_docids);
documents_readers.push(readers.documents);
});
// This is the function that merge the readers
// by using the given merge function.
let merge_readers = move |readers, merge| {
let mut writer = tempfile().and_then(|f| {
create_writer(chunk_compression_type, chunk_compression_level, f)
})?;
let merger = merge_readers(readers, merge);
merger.write_into(&mut writer)?;
writer_into_reader(writer, chunk_fusing_shrink_size)
};
// The enum and the channel which is used to transfert
// the readers merges potentially done on another thread.
enum DatabaseType { Main, WordDocids, WordsPairsProximitiesDocids };
let (sender, receiver) = sync_channel(3);
debug!("Merging the main, word docids and words pairs proximity docids in parallel...");
rayon::spawn(move || {
vec![
(DatabaseType::Main, main_readers, main_merge as MergeFn),
(DatabaseType::WordDocids, word_docids_readers, word_docids_merge),
(
DatabaseType::WordsPairsProximitiesDocids,
words_pairs_proximities_docids_readers,
words_pairs_proximities_docids_merge,
),
]
.into_par_iter()
.for_each(|(dbtype, readers, merge)| {
let result = merge_readers(readers, merge);
if let Err(e) = sender.send((dbtype, result)) {
error!("sender error: {}", e);
}
});
});
// We create the write transaction of this update.
// TODO we must get this transaction as an argument to be able
// to first delete the replaced documents for example.
let mut wtxn = env.write_txn()?;
let mut documents_ids = index.documents_ids(&wtxn)?;
let contains_documents = !documents_ids.is_empty();
let write_method = if contains_documents {
WriteMethod::GetMergePut
} else {
WriteMethod::Append
};
// We write the fields ids map into the main database
index.put_fields_ids_map(&mut wtxn, &fields_ids_map)?;
// We write the users_ids_documents_ids into the main database.
index.put_users_ids_documents_ids(&mut wtxn, &users_ids_documents_ids)?;
// We merge the new documents ids with the existing ones.
documents_ids.union_with(&new_documents_ids);
index.put_documents_ids(&mut wtxn, &documents_ids)?;
debug!("Writing the docid word positions into LMDB on disk...");
merge_into_lmdb_database(
&mut wtxn,
*index.docid_word_positions.as_polymorph(),
docid_word_positions_readers,
docid_word_positions_merge,
write_method
)?;
debug!("Writing the documents into LMDB on disk...");
merge_into_lmdb_database(
&mut wtxn,
*index.documents.as_polymorph(),
documents_readers,
documents_merge,
write_method
)?;
for (db_type, result) in receiver {
let content = result?;
match db_type {
DatabaseType::Main => {
debug!("Writing the main elements into LMDB on disk...");
write_into_lmdb_database(&mut wtxn, index.main, content, main_merge, write_method)?;
},
DatabaseType::WordDocids => {
debug!("Writing the words docids into LMDB on disk...");
let db = *index.word_docids.as_polymorph();
write_into_lmdb_database(&mut wtxn, db, content, word_docids_merge, write_method)?;
},
DatabaseType::WordsPairsProximitiesDocids => {
debug!("Writing the words pairs proximities docids into LMDB on disk...");
let db = *index.word_pair_proximity_docids.as_polymorph();
write_into_lmdb_database(
&mut wtxn,
db,
content,
words_pairs_proximities_docids_merge,
write_method,
)?;
},
}
}
wtxn.commit()?;
info!("Update processed in {:.02?}", before_indexing.elapsed());
Ok(())
}

1
src/lib.rs
View File

@ -1,7 +1,6 @@
mod criterion;
mod fields_ids_map;
mod index;
mod indexing;
mod mdfs;
mod query_tokens;
mod search;

146
src/subcommand/serve.rs
View File

@ -11,6 +11,7 @@ use askama_warp::Template;
use flate2::read::GzDecoder;
use futures::stream;
use futures::{FutureExt, StreamExt};
use grenad::CompressionType;
use heed::EnvOpenOptions;
use indexmap::IndexMap;
use serde::{Serialize, Deserialize};
@ -21,9 +22,8 @@ use tokio::sync::broadcast;
use warp::filters::ws::Message;
use warp::{Filter, http::Response};
use crate::indexing::{self, IndexerOpt, Transform, TransformOutput};
use crate::tokenizer::{simple_tokenizer, TokenType};
use crate::update::AvailableDocumentsIds;
use crate::update::{UpdateBuilder, IndexDocumentsMethod};
use crate::{Index, UpdateStore, SearchResult};
#[derive(Debug, StructOpt)]
@ -60,6 +60,58 @@ pub struct Opt {
indexer: IndexerOpt,
}
#[derive(Debug, Clone, StructOpt)]
pub struct IndexerOpt {
/// The amount of documents to skip before printing
/// a log regarding the indexing advancement.
#[structopt(long, default_value = "1000000")] // 1m
pub log_every_n: usize,
/// MTBL max number of chunks in bytes.
#[structopt(long)]
pub max_nb_chunks: Option<usize>,
/// The maximum amount of memory to use for the MTBL buffer. It is recommended
/// to use something like 80%-90% of the available memory.
///
/// It is automatically split by the number of jobs e.g. if you use 7 jobs
/// and 7 GB of max memory, each thread will use a maximum of 1 GB.
#[structopt(long, default_value = "7516192768")] // 7 GB
pub max_memory: usize,
/// Size of the linked hash map cache when indexing.
/// The bigger it is, the faster the indexing is but the more memory it takes.
#[structopt(long, default_value = "500")]
pub linked_hash_map_size: usize,
/// The name of the compression algorithm to use when compressing intermediate
/// chunks during indexing documents.
///
/// Choosing a fast algorithm will make the indexing faster but may consume more memory.
#[structopt(long, default_value = "snappy", possible_values = &["snappy", "zlib", "lz4", "lz4hc", "zstd"])]
pub chunk_compression_type: CompressionType,
/// The level of compression of the chosen algorithm.
#[structopt(long, requires = "chunk-compression-type")]
pub chunk_compression_level: Option<u32>,
/// The number of bytes to remove from the begining of the chunks while reading/sorting
/// or merging them.
///
/// File fusing must only be enable on file systems that support the `FALLOC_FL_COLLAPSE_RANGE`,
/// (i.e. ext4 and XFS). File fusing will only work if the `enable-chunk-fusing` is set.
#[structopt(long, default_value = "4294967296")] // 4 GB
pub chunk_fusing_shrink_size: u64,
/// Enable the chunk fusing or not, this reduces the amount of disk used by a factor of 2.
#[structopt(long)]
pub enable_chunk_fusing: bool,
/// Number of parallel jobs for indexing, defaults to # of CPUs.
#[structopt(long)]
pub indexing_jobs: Option<usize>,
}
fn highlight_record(record: &mut IndexMap<String, String>, words: &HashSet<String>) {
for (_key, value) in record.iter_mut() {
let old_value = mem::take(value);
@ -152,25 +204,36 @@ pub fn run(opt: Opt) -> anyhow::Result<()> {
update_store_options,
update_store_path,
move |update_id, meta, content| {
let result = match meta {
// We prepare the update by using the update builder.
let mut update_builder = UpdateBuilder::new();
if let Some(max_nb_chunks) = indexer_opt_cloned.max_nb_chunks {
update_builder.max_nb_chunks(max_nb_chunks);
}
if let Some(chunk_compression_level) = indexer_opt_cloned.chunk_compression_level {
update_builder.chunk_compression_level(chunk_compression_level);
}
if let Some(indexing_jobs) = indexer_opt_cloned.indexing_jobs {
update_builder.indexing_jobs(indexing_jobs);
}
update_builder.log_every_n(indexer_opt_cloned.log_every_n);
update_builder.max_memory(indexer_opt_cloned.max_memory);
update_builder.linked_hash_map_size(indexer_opt_cloned.linked_hash_map_size);
update_builder.chunk_compression_type(indexer_opt_cloned.chunk_compression_type);
update_builder.chunk_fusing_shrink_size(indexer_opt_cloned.chunk_fusing_shrink_size);
// we extract the update type and execute the update itself.
let result: anyhow::Result<()> = match meta {
UpdateMeta::DocumentsAddition => {
// We must use the write transaction of the update here.
let rtxn = env_cloned.read_txn()?;
let fields_ids_map = index_cloned.fields_ids_map(&rtxn)?;
let documents_ids = index_cloned.documents_ids(&rtxn)?;
let available_documents_ids = AvailableDocumentsIds::from_documents_ids(&documents_ids);
let users_ids_documents_ids = index_cloned.users_ids_documents_ids(&rtxn).unwrap();
let mut wtxn = env_cloned.write_txn()?;
let mut builder = update_builder.index_documents(&mut wtxn, &index_cloned);
let transform = Transform {
fields_ids_map,
available_documents_ids,
users_ids_documents_ids,
chunk_compression_type: indexer_opt_cloned.chunk_compression_type,
chunk_compression_level: indexer_opt_cloned.chunk_compression_level,
chunk_fusing_shrink_size: Some(indexer_opt_cloned.chunk_fusing_shrink_size),
max_nb_chunks: indexer_opt_cloned.max_nb_chunks,
max_memory: Some(indexer_opt_cloned.max_memory),
};
let replace_documents = true;
if replace_documents {
builder.index_documents_method(IndexDocumentsMethod::ReplaceDocuments);
} else {
builder.index_documents_method(IndexDocumentsMethod::UpdateDocuments);
}
let gzipped = false;
let reader = if gzipped {
@ -179,41 +242,22 @@ pub fn run(opt: Opt) -> anyhow::Result<()> {
Box::new(content) as Box<dyn io::Read>
};
let TransformOutput {
fields_ids_map,
users_ids_documents_ids,
new_documents_ids,
replaced_documents_ids,
documents_count,
documents_file,
} = transform.from_csv(reader).unwrap();
let result = builder.execute(reader, |count, total| {
let _ = update_status_sender_cloned.send(UpdateStatus::Progressing {
update_id,
meta: UpdateMetaProgress::DocumentsAddition {
processed_number_of_documents: count,
total_number_of_documents: Some(total),
}
});
});
drop(rtxn);
let mmap = unsafe { memmap::Mmap::map(&documents_file)? };
let documents = grenad::Reader::new(mmap.as_ref()).unwrap();
indexing::run(
&env_cloned,
&index_cloned,
&indexer_opt_cloned,
fields_ids_map,
users_ids_documents_ids,
new_documents_ids,
documents,
documents_count as u32,
|count, total| {
// We send progress status...
let meta = UpdateMetaProgress::DocumentsAddition {
processed_number_of_documents: count as usize,
total_number_of_documents: Some(total as usize),
};
let progress = UpdateStatus::Progressing { update_id, meta };
let _ = update_status_sender_cloned.send(progress);
match result {
Ok(()) => wtxn.commit().map_err(Into::into),
Err(e) => Err(e.into())
}
},
)
},
UpdateMeta::DocumentsAdditionFromPath { path } => {
UpdateMeta::DocumentsAdditionFromPath { path: _ } => {
todo!()
}
};

16
src/indexing/merge_function.rs → src/update/index_documents/merge_function.rs
View File

@ -69,3 +69,19 @@ pub fn words_pairs_proximities_docids_merge(_key: &[u8], values: &[Cow<[u8]>]) -
pub fn documents_merge(key: &[u8], _values: &[Cow<[u8]>]) -> anyhow::Result<Vec<u8>> {
bail!("merging documents is an error ({:?})", key.as_bstr())
}
pub fn merge_two_obkv(base: obkv::KvReader, update: obkv::KvReader, buffer: &mut Vec<u8>) {
use itertools::merge_join_by;
use itertools::EitherOrBoth::{Both, Left, Right};
buffer.clear();
let mut writer = obkv::KvWriter::new(buffer);
for eob in merge_join_by(base.iter(), update.iter(), |(b, _), (u, _)| b.cmp(u)) {
match eob {
Both(_, (k, v)) | Left((k, v)) | Right((k, v)) => writer.insert(k, v).unwrap(),
}
}
writer.finish().unwrap();
}

446
src/update/index_documents/mod.rs
View File

@ -1,4 +1,161 @@
use crate::Index;
use std::borrow::Cow;
use std::fs::File;
use std::io::{self, Seek, SeekFrom};
use std::sync::mpsc::sync_channel;
use std::time::Instant;
use anyhow::Context;
use bstr::ByteSlice as _;
use grenad::{Writer, Sorter, Merger, Reader, FileFuse, CompressionType};
use heed::types::ByteSlice;
use log::{debug, info, error};
use rayon::prelude::*;
use crate::index::Index;
use self::store::Store;
use self::merge_function::{
main_merge, word_docids_merge, words_pairs_proximities_docids_merge,
docid_word_positions_merge, documents_merge,
};
pub use self::transform::{Transform, TransformOutput};
use super::UpdateBuilder;
mod merge_function;
mod store;
mod transform;
#[derive(Debug, Copy, Clone)]
enum WriteMethod {
Append,
GetMergePut,
}
type MergeFn = for<'a> fn(&[u8], &[Cow<'a, [u8]>]) -> anyhow::Result<Vec<u8>>;
fn create_writer(typ: CompressionType, level: Option<u32>, file: File) -> io::Result<Writer<File>> {
let mut builder = Writer::builder();
builder.compression_type(typ);
if let Some(level) = level {
builder.compression_level(level);
}
builder.build(file)
}
fn create_sorter(
merge: MergeFn,
chunk_compression_type: CompressionType,
chunk_compression_level: Option<u32>,
chunk_fusing_shrink_size: Option<u64>,
max_nb_chunks: Option<usize>,
max_memory: Option<usize>,
) -> Sorter<MergeFn>
{
let mut builder = Sorter::builder(merge);
if let Some(shrink_size) = chunk_fusing_shrink_size {
builder.file_fusing_shrink_size(shrink_size);
}
builder.chunk_compression_type(chunk_compression_type);
if let Some(level) = chunk_compression_level {
builder.chunk_compression_level(level);
}
if let Some(nb_chunks) = max_nb_chunks {
builder.max_nb_chunks(nb_chunks);
}
if let Some(memory) = max_memory {
builder.max_memory(memory);
}
builder.build()
}
fn writer_into_reader(writer: Writer<File>, shrink_size: Option<u64>) -> anyhow::Result<Reader<FileFuse>> {
let mut file = writer.into_inner()?;
file.seek(SeekFrom::Start(0))?;
let file = if let Some(shrink_size) = shrink_size {
FileFuse::builder().shrink_size(shrink_size).build(file)
} else {
FileFuse::new(file)
};
Reader::new(file).map_err(Into::into)
}
fn merge_readers(sources: Vec<Reader<FileFuse>>, merge: MergeFn) -> Merger<FileFuse, MergeFn> {
let mut builder = Merger::builder(merge);
builder.extend(sources);
builder.build()
}
fn merge_into_lmdb_database(
wtxn: &mut heed::RwTxn,
database: heed::PolyDatabase,
sources: Vec<Reader<FileFuse>>,
merge: MergeFn,
method: WriteMethod,
) -> anyhow::Result<()> {
debug!("Merging {} MTBL stores...", sources.len());
let before = Instant::now();
let merger = merge_readers(sources, merge);
let mut in_iter = merger.into_merge_iter()?;
match method {
WriteMethod::Append => {
let mut out_iter = database.iter_mut::<_, ByteSlice, ByteSlice>(wtxn)?;
while let Some((k, v)) = in_iter.next()? {
out_iter.append(k, v).with_context(|| format!("writing {:?} into LMDB", k.as_bstr()))?;
}
},
WriteMethod::GetMergePut => {
while let Some((k, v)) = in_iter.next()? {
match database.get::<_, ByteSlice, ByteSlice>(wtxn, k)? {
Some(old_val) => {
let vals = vec![Cow::Borrowed(old_val), Cow::Borrowed(v)];
let val = merge(k, &vals).expect("merge failed");
database.put::<_, ByteSlice, ByteSlice>(wtxn, k, &val)?
},
None => database.put::<_, ByteSlice, ByteSlice>(wtxn, k, v)?,
}
}
},
}
debug!("MTBL stores merged in {:.02?}!", before.elapsed());
Ok(())
}
fn write_into_lmdb_database(
wtxn: &mut heed::RwTxn,
database: heed::PolyDatabase,
mut reader: Reader<FileFuse>,
merge: MergeFn,
method: WriteMethod,
) -> anyhow::Result<()> {
debug!("Writing MTBL stores...");
let before = Instant::now();
match method {
WriteMethod::Append => {
let mut out_iter = database.iter_mut::<_, ByteSlice, ByteSlice>(wtxn)?;
while let Some((k, v)) = reader.next()? {
out_iter.append(k, v).with_context(|| format!("writing {:?} into LMDB", k.as_bstr()))?;
}
},
WriteMethod::GetMergePut => {
while let Some((k, v)) = reader.next()? {
match database.get::<_, ByteSlice, ByteSlice>(wtxn, k)? {
Some(old_val) => {
let vals = vec![Cow::Borrowed(old_val), Cow::Borrowed(v)];
let val = merge(k, &vals).expect("merge failed");
database.put::<_, ByteSlice, ByteSlice>(wtxn, k, &val)?
},
None => database.put::<_, ByteSlice, ByteSlice>(wtxn, k, v)?,
}
}
}
}
debug!("MTBL stores merged in {:.02?}!", before.elapsed());
Ok(())
}
#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
pub enum IndexDocumentsMethod {
@ -14,12 +171,72 @@ pub enum IndexDocumentsMethod {
pub struct IndexDocuments<'t, 'u, 'i> {
wtxn: &'t mut heed::RwTxn<'u>,
index: &'i Index,
log_every_n: Option<usize>,
max_nb_chunks: Option<usize>,
max_memory: Option<usize>,
linked_hash_map_size: Option<usize>,
chunk_compression_type: CompressionType,
chunk_compression_level: Option<u32>,
chunk_fusing_shrink_size: Option<u64>,
indexing_jobs: Option<usize>,
update_method: IndexDocumentsMethod,
}
impl<'t, 'u, 'i> IndexDocuments<'t, 'u, 'i> {
pub fn new(wtxn: &'t mut heed::RwTxn<'u>, index: &'i Index) -> IndexDocuments<'t, 'u, 'i> {
IndexDocuments { wtxn, index, update_method: IndexDocumentsMethod::ReplaceDocuments }
IndexDocuments {
wtxn,
index,
log_every_n: None,
max_nb_chunks: None,
max_memory: None,
linked_hash_map_size: None,
chunk_compression_type: CompressionType::None,
chunk_compression_level: None,
chunk_fusing_shrink_size: None,
indexing_jobs: None,
update_method: IndexDocumentsMethod::ReplaceDocuments
}
}
pub(crate) fn log_every_n(&mut self, log_every_n: usize) -> &mut Self {
self.log_every_n = Some(log_every_n);
self
}
pub(crate) fn max_nb_chunks(&mut self, max_nb_chunks: usize) -> &mut Self {
self.max_nb_chunks = Some(max_nb_chunks);
self
}
pub(crate) fn max_memory(&mut self, max_memory: usize) -> &mut Self {
self.max_memory = Some(max_memory);
self
}
pub(crate) fn linked_hash_map_size(&mut self, linked_hash_map_size: usize) -> &mut Self {
self.linked_hash_map_size = Some(linked_hash_map_size);
self
}
pub(crate) fn chunk_compression_type(&mut self, chunk_compression_type: CompressionType) -> &mut Self {
self.chunk_compression_type = chunk_compression_type;
self
}
pub(crate) fn chunk_compression_level(&mut self, chunk_compression_level: u32) -> &mut Self {
self.chunk_compression_level = Some(chunk_compression_level);
self
}
pub(crate) fn chunk_fusing_shrink_size(&mut self, chunk_fusing_shrink_size: u64) -> &mut Self {
self.chunk_fusing_shrink_size = Some(chunk_fusing_shrink_size);
self
}
pub(crate) fn indexing_jobs(&mut self, indexing_jobs: usize) -> &mut Self {
self.indexing_jobs = Some(indexing_jobs);
self
}
pub fn index_documents_method(&mut self, method: IndexDocumentsMethod) -> &mut Self {
@ -27,7 +244,228 @@ impl<'t, 'u, 'i> IndexDocuments<'t, 'u, 'i> {
self
}
pub fn execute(self) -> anyhow::Result<()> {
todo!()
pub fn execute<R, F>(self, reader: R, progress_callback: F) -> anyhow::Result<()>
where
R: io::Read,
F: Fn(usize, usize) + Sync,
{
let before_indexing = Instant::now();
let transform = Transform {
rtxn: &self.wtxn,
index: self.index,
chunk_compression_type: self.chunk_compression_type,
chunk_compression_level: self.chunk_compression_level,
chunk_fusing_shrink_size: self.chunk_fusing_shrink_size,
max_nb_chunks: self.max_nb_chunks,
max_memory: self.max_memory,
index_documents_method: self.update_method,
};
let TransformOutput {
fields_ids_map,
users_ids_documents_ids,
new_documents_ids,
replaced_documents_ids,
documents_count,
documents_file,
} = transform.from_csv(reader)?;
// We delete the documents that this document addition replaces. This way we are
// able to simply insert all the documents even if they already exist in the database.
if !replaced_documents_ids.is_empty() {
let update_builder = UpdateBuilder {
log_every_n: self.log_every_n,
max_nb_chunks: self.max_nb_chunks,
max_memory: self.max_memory,
linked_hash_map_size: self.linked_hash_map_size,
chunk_compression_type: self.chunk_compression_type,
chunk_compression_level: self.chunk_compression_level,
chunk_fusing_shrink_size: self.chunk_fusing_shrink_size,
indexing_jobs: self.indexing_jobs,
};
let mut deletion_builder = update_builder.delete_documents(self.wtxn, self.index)?;
deletion_builder.delete_documents(&replaced_documents_ids);
let _deleted_documents_count = deletion_builder.execute()?;
}
let mmap = unsafe {
memmap::Mmap::map(&documents_file).context("mmaping the transform documents file")?
};
let documents = grenad::Reader::new(mmap.as_ref())?;
// The enum which indicates the type of the readers
// merges that are potentially done on different threads.
enum DatabaseType {
Main,
WordDocids,
WordsPairsProximitiesDocids,
}
let linked_hash_map_size = self.linked_hash_map_size;
let max_nb_chunks = self.max_nb_chunks;
let max_memory = self.max_memory;
let chunk_compression_type = self.chunk_compression_type;
let chunk_compression_level = self.chunk_compression_level;
let log_every_n = self.log_every_n;
let chunk_fusing_shrink_size = self.chunk_fusing_shrink_size;
let jobs = self.indexing_jobs.unwrap_or(0);
let pool = rayon::ThreadPoolBuilder::new().num_threads(jobs).build()?;
let (receiver, docid_word_positions_readers, documents_readers) = pool.install(|| {
let num_threads = rayon::current_num_threads();
let max_memory_by_job = max_memory.map(|mm| mm / num_threads);
let readers = rayon::iter::repeatn(documents, num_threads)
.enumerate()
.map(|(i, documents)| {
let store = Store::new(
linked_hash_map_size,
max_nb_chunks,
max_memory_by_job,
chunk_compression_type,
chunk_compression_level,
chunk_fusing_shrink_size,
)?;
store.index(
documents,
documents_count,
i,
num_threads,
log_every_n,
&progress_callback,
)
})
.collect::<Result<Vec<_>, _>>()?;
let mut main_readers = Vec::with_capacity(readers.len());
let mut word_docids_readers = Vec::with_capacity(readers.len());
let mut docid_word_positions_readers = Vec::with_capacity(readers.len());
let mut words_pairs_proximities_docids_readers = Vec::with_capacity(readers.len());
let mut documents_readers = Vec::with_capacity(readers.len());
readers.into_iter().for_each(|readers| {
main_readers.push(readers.main);
word_docids_readers.push(readers.word_docids);
docid_word_positions_readers.push(readers.docid_word_positions);
words_pairs_proximities_docids_readers.push(readers.words_pairs_proximities_docids);
documents_readers.push(readers.documents);
});
// This is the function that merge the readers
// by using the given merge function.
let merge_readers = move |readers, merge| {
let mut writer = tempfile::tempfile().and_then(|f| {
create_writer(chunk_compression_type, chunk_compression_level, f)
})?;
let merger = merge_readers(readers, merge);
merger.write_into(&mut writer)?;
writer_into_reader(writer, chunk_fusing_shrink_size)
};
// The enum and the channel which is used to transfert
// the readers merges potentially done on another thread.
let (sender, receiver) = sync_channel(3);
debug!("Merging the main, word docids and words pairs proximity docids in parallel...");
rayon::spawn(move || {
vec![
(DatabaseType::Main, main_readers, main_merge as MergeFn),
(DatabaseType::WordDocids, word_docids_readers, word_docids_merge),
(
DatabaseType::WordsPairsProximitiesDocids,
words_pairs_proximities_docids_readers,
words_pairs_proximities_docids_merge,
),
]
.into_par_iter()
.for_each(|(dbtype, readers, merge)| {
let result = merge_readers(readers, merge);
if let Err(e) = sender.send((dbtype, result)) {
error!("sender error: {}", e);
}
});
});
Ok((receiver, docid_word_positions_readers, documents_readers)) as anyhow::Result<_>
})?;
let mut documents_ids = self.index.documents_ids(self.wtxn)?;
let contains_documents = !documents_ids.is_empty();
let write_method = if contains_documents {
WriteMethod::GetMergePut
} else {
WriteMethod::Append
};
// We write the fields ids map into the main database
self.index.put_fields_ids_map(self.wtxn, &fields_ids_map)?;
// We write the users_ids_documents_ids into the main database.
self.index.put_users_ids_documents_ids(self.wtxn, &users_ids_documents_ids)?;
// We merge the new documents ids with the existing ones.
documents_ids.union_with(&new_documents_ids);
self.index.put_documents_ids(self.wtxn, &documents_ids)?;
debug!("Writing the docid word positions into LMDB on disk...");
merge_into_lmdb_database(
self.wtxn,
*self.index.docid_word_positions.as_polymorph(),
docid_word_positions_readers,
docid_word_positions_merge,
write_method
)?;
debug!("Writing the documents into LMDB on disk...");
merge_into_lmdb_database(
self.wtxn,
*self.index.documents.as_polymorph(),
documents_readers,
documents_merge,
write_method
)?;
for (db_type, result) in receiver {
let content = result?;
match db_type {
DatabaseType::Main => {
debug!("Writing the main elements into LMDB on disk...");
write_into_lmdb_database(
self.wtxn,
self.index.main,
content,
main_merge,
write_method,
)?;
},
DatabaseType::WordDocids => {
debug!("Writing the words docids into LMDB on disk...");
let db = *self.index.word_docids.as_polymorph();
write_into_lmdb_database(
self.wtxn,
db,
content,
word_docids_merge,
write_method,
)?;
},
DatabaseType::WordsPairsProximitiesDocids => {
debug!("Writing the words pairs proximities docids into LMDB on disk...");
let db = *self.index.word_pair_proximity_docids.as_polymorph();
write_into_lmdb_database(
self.wtxn,
db,
content,
words_pairs_proximities_docids_merge,
write_method,
)?;
},
}
}
info!("Update processed in {:.02?}", before_indexing.elapsed());
Ok(())
}
}

15
src/indexing/store.rs → src/update/index_documents/store.rs
View File

@ -56,7 +56,7 @@ pub struct Store {
impl Store {
pub fn new(
linked_hash_map_size: usize,
linked_hash_map_size: Option<usize>,
max_nb_chunks: Option<usize>,
max_memory: Option<usize>,
chunk_compression_type: CompressionType,
@ -66,6 +66,7 @@ impl Store {
{
// We divide the max memory by the number of sorter the Store have.
let max_memory = max_memory.map(|mm| cmp::max(ONE_KILOBYTE, mm / 3));
let linked_hash_map_size = linked_hash_map_size.unwrap_or(500);
let main_sorter = create_sorter(
main_merge,
@ -280,13 +281,13 @@ impl Store {
pub fn index<F>(
mut self,
mut documents: grenad::Reader<&[u8]>,
documents_count: u32,
documents_count: usize,
thread_index: usize,
num_threads: usize,
log_every_n: usize,
log_every_n: Option<usize>,
mut progress_callback: F,
) -> anyhow::Result<Readers>
where F: FnMut(u32, u32),
where F: FnMut(usize, usize),
{
debug!("{:?}: Indexing in a Store...", thread_index);
@ -301,9 +302,9 @@ impl Store {
// We skip documents that must not be indexed by this thread.
if count % num_threads == thread_index {
// This is a log routine that we do every `log_every_n` documents.
if count % log_every_n == 0 {
if log_every_n.map_or(false, |len| count % len == 0) {
info!("We have seen {} documents so far ({:.02?}).", format_count(count), before.elapsed());
progress_callback(count as u32, documents_count);
progress_callback(count, documents_count);
before = Instant::now();
}
@ -325,7 +326,7 @@ impl Store {
count = count + 1;
}
progress_callback(count as u32, documents_count);
progress_callback(count, documents_count);
let readers = self.finish()?;
debug!("{:?}: Store created!", thread_index);

60
src/indexing/transform.rs → src/update/index_documents/transform.rs
View File

@ -8,9 +8,10 @@ use fst::{IntoStreamer, Streamer};
use grenad::CompressionType;
use roaring::RoaringBitmap;
use crate::FieldsIdsMap;
use crate::{BEU32, Index, FieldsIdsMap};
use crate::update::AvailableDocumentsIds;
use super::{create_writer, create_sorter};
use super::merge_function::merge_two_obkv;
use super::{create_writer, create_sorter, IndexDocumentsMethod};
pub struct TransformOutput {
pub fields_ids_map: FieldsIdsMap,
@ -21,41 +22,30 @@ pub struct TransformOutput {
pub documents_file: File,
}
pub struct Transform<A> {
pub fields_ids_map: FieldsIdsMap,
pub available_documents_ids: AvailableDocumentsIds,
pub users_ids_documents_ids: fst::Map<A>,
pub struct Transform<'t, 'i> {
pub rtxn: &'t heed::RoTxn,
pub index: &'i Index,
pub chunk_compression_type: CompressionType,
pub chunk_compression_level: Option<u32>,
pub chunk_fusing_shrink_size: Option<u64>,
pub max_nb_chunks: Option<usize>,
pub max_memory: Option<usize>,
pub index_documents_method: IndexDocumentsMethod,
}
fn merge_two_obkv(base: obkv::KvReader, update: obkv::KvReader, buffer: &mut Vec<u8>) {
use itertools::merge_join_by;
use itertools::EitherOrBoth::{Both, Left, Right};
buffer.clear();
let mut writer = obkv::KvWriter::new(buffer);
for eob in merge_join_by(base.iter(), update.iter(), |(b, _), (u, _)| b.cmp(u)) {
match eob {
Both(_, (k, v)) | Left((k, v)) | Right((k, v)) => writer.insert(k, v).unwrap(),
}
}
writer.finish().unwrap();
}
impl<A: AsRef<[u8]>> Transform<A> {
impl Transform<'_, '_> {
/// Extract the users ids, deduplicate and compute the new internal documents ids
/// and fields ids, writing all the documents under their internal ids into a final file.
///
/// Outputs the new `FieldsIdsMap`, the new `UsersIdsDocumentsIds` map, the new documents ids,
/// the replaced documents ids, the number of documents in this update and the file
/// containing all those documents.
pub fn from_csv<R: Read>(mut self, reader: R) -> anyhow::Result<TransformOutput> {
pub fn from_csv<R: Read>(self, reader: R) -> anyhow::Result<TransformOutput> {
let mut fields_ids_map = self.index.fields_ids_map(self.rtxn)?;
let documents_ids = self.index.documents_ids(self.rtxn)?;
let mut available_documents_ids = AvailableDocumentsIds::from_documents_ids(&documents_ids);
let users_ids_documents_ids = self.index.users_ids_documents_ids(self.rtxn).unwrap();
let mut csv = csv::Reader::from_reader(reader);
let headers = csv.headers()?.clone();
let user_id_pos = headers.iter().position(|h| h == "id").context(r#"missing "id" header"#)?;
@ -63,7 +53,7 @@ impl<A: AsRef<[u8]>> Transform<A> {
// Generate the new fields ids based on the current fields ids and this CSV headers.
let mut fields_ids = Vec::new();
for header in headers.iter() {
let id = self.fields_ids_map.insert(header)
let id = fields_ids_map.insert(header)
.context("impossible to generate a field id (limit reached)")?;
fields_ids.push(id);
}
@ -120,7 +110,7 @@ impl<A: AsRef<[u8]>> Transform<A> {
let mut iter = sorter.into_iter()?;
while let Some((user_id, update_obkv)) = iter.next()? {
let (docid, obkv) = match self.users_ids_documents_ids.get(user_id) {
let (docid, obkv) = match users_ids_documents_ids.get(user_id) {
Some(docid) => {
// If we find the user id in the current users ids documents ids map
// we use it and insert it in the list of replaced documents.
@ -129,20 +119,22 @@ impl<A: AsRef<[u8]>> Transform<A> {
// Depending on the update indexing method we will merge
// the document update with the current document or not.
let must_merge_documents = false;
if must_merge_documents {
let base_obkv = todo!();
match self.index_documents_method {
IndexDocumentsMethod::ReplaceDocuments => (docid, update_obkv),
IndexDocumentsMethod::UpdateDocuments => {
let key = BEU32::new(docid);
let base_obkv = self.index.documents.get(&self.rtxn, &key)?
.context("document not found")?;
let update_obkv = obkv::KvReader::new(update_obkv);
merge_two_obkv(base_obkv, update_obkv, &mut obkv_buffer);
(docid, obkv_buffer.as_slice())
} else {
(docid, update_obkv)
}
}
},
None => {
// If this user id is new we add it to the users ids documents ids map
// for new ids and into the list of new documents.
let new_docid = self.available_documents_ids.next()
let new_docid = available_documents_ids.next()
.context("no more available documents ids")?;
new_users_ids_documents_ids_builder.insert(user_id, new_docid as u64)?;
new_documents_ids.insert(new_docid);
@ -163,7 +155,7 @@ impl<A: AsRef<[u8]>> Transform<A> {
// We create the union between the existing users ids documents ids with the new ones.
let new_users_ids_documents_ids = new_users_ids_documents_ids_builder.into_map();
let union_ = fst::map::OpBuilder::new()
.add(&self.users_ids_documents_ids)
.add(&users_ids_documents_ids)
.add(&new_users_ids_documents_ids)
.r#union();
@ -176,7 +168,7 @@ impl<A: AsRef<[u8]>> Transform<A> {
}
Ok(TransformOutput {
fields_ids_map: self.fields_ids_map,
fields_ids_map,
users_ids_documents_ids: users_ids_documents_ids_builder.into_map(),
new_documents_ids,
replaced_documents_ids,

78
src/update/update_builder.rs
View File

@ -1,35 +1,37 @@
use std::borrow::Cow;
use std::convert::TryFrom;
use fst::{IntoStreamer, Streamer};
use grenad::CompressionType;
use itertools::Itertools;
use roaring::RoaringBitmap;
use crate::{Index, BEU32};
use crate::Index;
use super::clear_documents::ClearDocuments;
use super::delete_documents::DeleteDocuments;
use super::index_documents::IndexDocuments;
pub struct UpdateBuilder {
log_every_n: usize,
max_nb_chunks: Option<usize>,
max_memory: usize,
linked_hash_map_size: usize,
chunk_compression_type: CompressionType,
chunk_compression_level: Option<u32>,
chunk_fusing_shrink_size: u64,
enable_chunk_fusing: bool,
indexing_jobs: Option<usize>,
pub(crate) log_every_n: Option<usize>,
pub(crate) max_nb_chunks: Option<usize>,
pub(crate) max_memory: Option<usize>,
pub(crate) linked_hash_map_size: Option<usize>,
pub(crate) chunk_compression_type: CompressionType,
pub(crate) chunk_compression_level: Option<u32>,
pub(crate) chunk_fusing_shrink_size: Option<u64>,
pub(crate) indexing_jobs: Option<usize>,
}
impl UpdateBuilder {
pub fn new() -> UpdateBuilder {
todo!()
UpdateBuilder {
log_every_n: None,
max_nb_chunks: None,
max_memory: None,
linked_hash_map_size: None,
chunk_compression_type: CompressionType::None,
chunk_compression_level: None,
chunk_fusing_shrink_size: None,
indexing_jobs: None,
}
}
pub fn log_every_n(&mut self, log_every_n: usize) -> &mut Self {
self.log_every_n = log_every_n;
self.log_every_n = Some(log_every_n);
self
}
@ -39,12 +41,12 @@ impl UpdateBuilder {
}
pub fn max_memory(&mut self, max_memory: usize) -> &mut Self {
self.max_memory = max_memory;
self.max_memory = Some(max_memory);
self
}
pub fn linked_hash_map_size(&mut self, linked_hash_map_size: usize) -> &mut Self {
self.linked_hash_map_size = linked_hash_map_size;
self.linked_hash_map_size = Some(linked_hash_map_size);
self
}
@ -59,12 +61,7 @@ impl UpdateBuilder {
}
pub fn chunk_fusing_shrink_size(&mut self, chunk_fusing_shrink_size: u64) -> &mut Self {
self.chunk_fusing_shrink_size = chunk_fusing_shrink_size;
self
}
pub fn enable_chunk_fusing(&mut self, enable_chunk_fusing: bool) -> &mut Self {
self.enable_chunk_fusing = enable_chunk_fusing;
self.chunk_fusing_shrink_size = Some(chunk_fusing_shrink_size);
self
}
@ -97,6 +94,33 @@ impl UpdateBuilder {
index: &'i Index,
) -> IndexDocuments<'t, 'u, 'i>
{
IndexDocuments::new(wtxn, index)
let mut builder = IndexDocuments::new(wtxn, index);
if let Some(log_every_n) = self.log_every_n {
builder.log_every_n(log_every_n);
}
if let Some(max_nb_chunks) = self.max_nb_chunks {
builder.max_nb_chunks(max_nb_chunks);
}
if let Some(max_memory) = self.max_memory {
builder.max_memory(max_memory);
}
if let Some(linked_hash_map_size) = self.linked_hash_map_size {
builder.linked_hash_map_size(linked_hash_map_size);
}
builder.chunk_compression_type(self.chunk_compression_type);
if let Some(chunk_compression_level) = self.chunk_compression_level {
builder.chunk_compression_level(chunk_compression_level);
}
if let Some(chunk_fusing_shrink_size) = self.chunk_fusing_shrink_size {
builder.chunk_fusing_shrink_size(chunk_fusing_shrink_size);
}
if let Some(indexing_jobs) = self.indexing_jobs {
builder.indexing_jobs(indexing_jobs);
}
builder
}
}