Checkpoint: add merkle tree in data table

1 files changed, 352 insertions, 0 deletions

diff --git a/src/table/merkle.rs b/src/table/merkle.rs
new file mode 100644
index 00000000..50cb90d5
--- /dev/null
+++ b/src/table/merkle.rs
@@ -0,0 +1,352 @@
+use std::convert::TryInto;
+use std::sync::Arc;
+use std::time::Duration;
+
+use futures::select;
+use futures_util::future::*;
+use log::{info, warn};
+use serde::{Deserialize, Serialize};
+use sled::transaction::{
+	ConflictableTransactionError, ConflictableTransactionResult, TransactionalTree,
+};
+use tokio::sync::{watch, Notify};
+
+use garage_util::background::BackgroundRunner;
+use garage_util::data::*;
+use garage_util::error::Error;
+
+// This modules partitions the data in 2**16 partitions, based on the top
+// 16 bits (two bytes) of item's partition keys' hashes.
+// It builds one Merkle tree for each of these 2**16 partitions.
+
+pub(crate) struct MerkleUpdater {
+	table_name: String,
+	background: Arc<BackgroundRunner>,
+
+	// Content of the todo tree: items where
+	// - key = the key of an item in the main table, ie hash(partition_key)+sort_key
+	// - value = the hash of the full serialized item, if present,
+	//			 or an empty vec if item is absent (deleted)
+	pub(crate) todo: sled::Tree,
+	pub(crate) todo_notify: Notify,
+
+	// Content of the merkle tree: items where
+	// - key = .bytes() for MerkleNodeKey
+	// - value = serialization of a MerkleNode, assumed to be MerkleNode::empty if not found
+	pub(crate) merkle_tree: sled::Tree,
+	empty_node_hash: Hash,
+}
+
+#[derive(Clone)]
+pub struct MerkleNodeKey {
+	// partition: first 16 bits (two bytes) of the partition_key's hash
+	pub partition: [u8; 2],
+
+	// prefix: a prefix for the hash of full keys, i.e. hash(hash(partition_key)+sort_key)
+	pub prefix: Vec<u8>,
+}
+
+#[derive(PartialEq, Eq, Debug, Serialize, Deserialize)]
+pub enum MerkleNode {
+	// The empty Merkle node
+	Empty,
+
+	// An intermediate Merkle tree node for a prefix
+	// Contains the hashes of the 256 possible next prefixes
+	Intermediate(Vec<(u8, Hash)>),
+
+	// A final node for an item
+	// Contains the full key of the item and the hash of the value
+	Leaf(Vec<u8>, Hash),
+}
+
+impl MerkleUpdater {
+	pub(crate) fn new(
+		table_name: String,
+		background: Arc<BackgroundRunner>,
+		todo: sled::Tree,
+		merkle_tree: sled::Tree,
+	) -> Arc<Self> {
+		let empty_node_hash = blake2sum(&rmp_to_vec_all_named(&MerkleNode::Empty).unwrap()[..]);
+
+		Arc::new(Self {
+			table_name,
+			background,
+			todo,
+			todo_notify: Notify::new(),
+			merkle_tree,
+			empty_node_hash,
+		})
+	}
+
+	pub(crate) fn launch(self: &Arc<Self>) {
+		let self2 = self.clone();
+		self.background.spawn_worker(
+			format!("Merkle tree updater for {}", self.table_name),
+			|must_exit: watch::Receiver<bool>| self2.updater_loop(must_exit),
+		);
+	}
+
+	async fn updater_loop(
+		self: Arc<Self>,
+		mut must_exit: watch::Receiver<bool>,
+	) -> Result<(), Error> {
+		while !*must_exit.borrow() {
+			if let Some(x) = self.todo.iter().next() {
+				match x {
+					Ok((key, valhash)) => {
+						if let Err(e) = self.update_item(&key[..], &valhash[..]) {
+							warn!("Error while updating Merkle tree item: {}", e);
+						}
+					}
+					Err(e) => {
+						warn!("Error while iterating on Merkle todo tree: {}", e);
+						tokio::time::delay_for(Duration::from_secs(10)).await;
+					}
+				}
+			} else {
+				select! {
+					_ = self.todo_notify.notified().fuse() => (),
+					_ = must_exit.recv().fuse() => (),
+				}
+			}
+		}
+		Ok(())
+	}
+
+	fn update_item(&self, k: &[u8], vhash_by: &[u8]) -> Result<(), Error> {
+		let khash = blake2sum(k);
+
+		let new_vhash = if vhash_by.len() == 0 {
+			None
+		} else {
+			let vhash_by: [u8; 32] = vhash_by
+				.try_into()
+				.map_err(|_| Error::Message(format!("Invalid value in Merkle todo table")))?;
+			Some(Hash::from(vhash_by))
+		};
+
+		let key = MerkleNodeKey {
+			partition: k[0..2].try_into().unwrap(),
+			prefix: vec![],
+		};
+		self.merkle_tree
+			.transaction(|tx| self.update_item_rec(tx, k, khash, &key, new_vhash))?;
+
+		let deleted = self
+			.todo
+			.compare_and_swap::<_, _, Vec<u8>>(k, Some(vhash_by), None)?
+			.is_ok();
+
+		if !deleted {
+			info!(
+				"Item not deleted from Merkle todo because it changed: {:?}",
+				k
+			);
+		}
+		Ok(())
+	}
+
+	fn update_item_rec(
+		&self,
+		tx: &TransactionalTree,
+		k: &[u8],
+		khash: Hash,
+		key: &MerkleNodeKey,
+		new_vhash: Option<Hash>,
+	) -> ConflictableTransactionResult<Option<Hash>, Error> {
+		let i = key.prefix.len();
+		let mutate = match self.read_node_txn(tx, &key)? {
+			MerkleNode::Empty => {
+				if let Some(vhv) = new_vhash {
+					Some(MerkleNode::Leaf(k.to_vec(), vhv))
+				} else {
+					None
+				}
+			}
+			MerkleNode::Intermediate(mut children) => {
+				let key2 = key.next_key(khash);
+				if let Some(subhash) = self.update_item_rec(tx, k, khash, &key2, new_vhash)? {
+					if subhash == self.empty_node_hash {
+						intermediate_rm_child(&mut children, key2.prefix[i]);
+					} else {
+						intermediate_set_child(&mut children, key2.prefix[i], subhash);
+					}
+					if children.len() == 0 {
+						// should not happen
+						warn!("Replacing intermediate node with empty node, should not happen.");
+						Some(MerkleNode::Empty)
+					} else if children.len() == 1 {
+						// move node down to this level
+						let key_sub = key.add_byte(children[0].0);
+						let subnode = self.read_node_txn(tx, &key_sub)?;
+						tx.remove(key_sub.encode())?;
+						Some(subnode)
+					} else {
+						Some(MerkleNode::Intermediate(children))
+					}
+				} else {
+					None
+				}
+			}
+			MerkleNode::Leaf(exlf_key, exlf_hash) => {
+				if exlf_key == k {
+					match new_vhash {
+						Some(vhv) if vhv == exlf_hash => None,
+						Some(vhv) => Some(MerkleNode::Leaf(k.to_vec(), vhv)),
+						None => Some(MerkleNode::Empty),
+					}
+				} else {
+					if let Some(vhv) = new_vhash {
+						// Create two sub-nodes and replace by intermediary node
+						let (pos1, h1) = {
+							let key2 = key.next_key(blake2sum(&exlf_key[..]));
+							let subhash =
+								self.put_node_txn(tx, &key2, &MerkleNode::Leaf(exlf_key, exlf_hash))?;
+							(key2.prefix[i], subhash)
+						};
+						let (pos2, h2) = {
+							let key2 = key.next_key(khash);
+							let subhash =
+								self.put_node_txn(tx, &key2, &MerkleNode::Leaf(k.to_vec(), vhv))?;
+							(key2.prefix[i], subhash)
+						};
+						let mut int = vec![];
+						intermediate_set_child(&mut int, pos1, h1);
+						intermediate_set_child(&mut int, pos2, h2);
+						Some(MerkleNode::Intermediate(int))
+					} else {
+						None
+					}
+				}
+			}
+		};
+
+		if let Some(new_node) = mutate {
+			let hash = self.put_node_txn(tx, &key, &new_node)?;
+			Ok(Some(hash))
+		} else {
+			Ok(None)
+		}
+	}
+
+	// Merkle tree node manipulation
+
+	fn read_node_txn(
+		&self,
+		tx: &TransactionalTree,
+		k: &MerkleNodeKey,
+	) -> ConflictableTransactionResult<MerkleNode, Error> {
+		let ent = tx.get(k.encode())?;
+		match ent {
+			None => Ok(MerkleNode::Empty),
+			Some(v) => Ok(rmp_serde::decode::from_read_ref::<_, MerkleNode>(&v[..])
+				.map_err(|e| ConflictableTransactionError::Abort(e.into()))?),
+		}
+	}
+
+	fn put_node_txn(
+		&self,
+		tx: &TransactionalTree,
+		k: &MerkleNodeKey,
+		v: &MerkleNode,
+	) -> ConflictableTransactionResult<Hash, Error> {
+		if *v == MerkleNode::Empty {
+			tx.remove(k.encode())?;
+			Ok(self.empty_node_hash)
+		} else {
+			let vby = rmp_to_vec_all_named(v)
+				.map_err(|e| ConflictableTransactionError::Abort(e.into()))?;
+			let rethash = blake2sum(&vby[..]);
+			tx.insert(k.encode(), vby)?;
+			Ok(rethash)
+		}
+	}
+
+	pub(crate) fn read_node(
+		&self,
+		k: &MerkleNodeKey,
+	) -> Result<MerkleNode, Error> {
+		let ent = self.merkle_tree.get(k.encode())?;
+		match ent {
+			None => Ok(MerkleNode::Empty),
+			Some(v) => Ok(rmp_serde::decode::from_read_ref::<_, MerkleNode>(&v[..])?)
+		}
+	}
+}
+
+impl MerkleNodeKey {
+	fn encode(&self) -> Vec<u8> {
+		let mut ret = Vec::with_capacity(2 + self.prefix.len());
+		ret.extend(&self.partition[..]);
+		ret.extend(&self.prefix[..]);
+		ret
+	}
+
+	pub fn next_key(&self, h: Hash) -> Self {
+		assert!(&h.as_slice()[0..self.prefix.len()] == &self.prefix[..]);
+		let mut s2 = self.clone();
+		s2.prefix.push(h.as_slice()[self.prefix.len()]);
+		s2
+	}
+
+	pub fn add_byte(&self, b: u8) -> Self {
+		let mut s2 = self.clone();
+		s2.prefix.push(b);
+		s2
+	}
+}
+
+fn intermediate_set_child(ch: &mut Vec<(u8, Hash)>, pos: u8, v: Hash) {
+	for i in 0..ch.len() {
+		if ch[i].0 == pos {
+			ch[i].1 = v;
+			return;
+		} else if ch[i].0 > pos {
+			ch.insert(i, (pos, v));
+			return;
+		}
+	}
+	ch.insert(ch.len(), (pos, v));
+}
+
+fn intermediate_rm_child(ch: &mut Vec<(u8, Hash)>, pos: u8) {
+	for i in 0..ch.len() {
+		if ch[i].0 == pos {
+			ch.remove(i);
+			return;
+		}
+	}
+}
+
+#[test]
+fn test_intermediate_aux() {
+	let mut v = vec![];
+	
+	intermediate_set_child(&mut v, 12u8, [12u8; 32].into());
+	assert!(v == vec![(12u8, [12u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 42u8, [42u8; 32].into());
+	assert!(v == vec![(12u8, [12u8; 32].into()), (42u8, [42u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 4u8, [4u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (12u8, [12u8; 32].into()), (42u8, [42u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 12u8, [8u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (12u8, [8u8; 32].into()), (42u8, [42u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 6u8, [6u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [6u8; 32].into()), (12u8, [8u8; 32].into()), (42u8, [42u8; 32].into())]);
+
+	intermediate_rm_child(&mut v, 42u8);
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [6u8; 32].into()), (12u8, [8u8; 32].into())]);
+
+	intermediate_rm_child(&mut v, 11u8);
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [6u8; 32].into()), (12u8, [8u8; 32].into())]);
+
+	intermediate_rm_child(&mut v, 6u8);
+	assert!(v == vec![(4u8, [4u8; 32].into()), (12u8, [8u8; 32].into())]);
+	
+	intermediate_set_child(&mut v, 6u8, [7u8; 32].into());
+	assert!(v == vec![(4u8, [4u8; 32].into()), (6u8, [7u8; 32].into()), (12u8, [8u8; 32].into())]);
+}