Abstract database behind generic interface and implement alternative drivers (#322)

- [x] Design interface
- [x] Implement Sled backend
  - [x] Re-implement the SledCountedTree hack ~~on Sled backend~~ on all backends (i.e. over the abstraction)
- [x] Convert Garage code to use generic interface
- [x] Proof-read converted Garage code
- [ ] Test everything well
- [x] Implement sqlite backend
- [x] Implement LMDB backend
- [ ] (Implement Persy backend?)
- [ ] (Implement other backends? (like RocksDB, ...))
- [x] Implement backend choice in config file and garage server module
- [x] Add CLI for converting between DB formats
- Exploit the new interface to put more things in transactions
  - [x] `.updated()` trigger on Garage tables

Fix #284

**Bugs**

- [x] When exporting sqlite, trees iterate empty??
- [x] LMDB doesn't work

**Known issues for various back-ends**

- Sled:
  - Eats all my RAM and also all my disk space
  - `.len()` has to traverse the whole table
  - Is actually quite slow on some operations
  - And is actually pretty bad code...
- Sqlite:
  - Requires a lock to be taken on all operations. The lock is also taken when iterating on a table with `.iter()`, and the lock isn't released until the iterator is dropped. This means that we must be VERY carefull to not do anything else inside a `.iter()` loop or else we will have a deadlock! Most such cases have been eliminated from the Garage codebase, but there might still be some that remain. If your Garage-over-Sqlite seems to hang/freeze, this is the reason.
  - (adapter uses a bunch of unsafe code)
- Heed (LMDB):
  - Not suited for 32-bit machines as it has to map the whole DB in memory.
  - (adpater uses a tiny bit of unsafe code)

**My recommendation:** avoid 32-bit machines and use LMDB as much as possible.

**Converting databases** is actually quite easy. For example from Sled to LMDB:

```bash
cd src/db
cargo run --features cli --bin convert -- -i path/to/garage/meta/db -a sled -o path/to/garage/meta/db.lmdb -b lmdb
```

Then, just add this to your `config.toml`:

```toml
db_engine = "lmdb"
```

Co-authored-by: Alex Auvolat <alex@adnab.me>
Reviewed-on: https://git.deuxfleurs.fr/Deuxfleurs/garage/pulls/322
Co-authored-by: Alex <alex@adnab.me>
Co-committed-by: Alex <alex@adnab.me>

src/table/data.rs

@@ -3,12 +3,13 @@ use std::convert::TryInto;
 use std::sync::Arc;
 
 use serde_bytes::ByteBuf;
-use sled::{IVec, Transactional};
 use tokio::sync::Notify;
 
+use garage_db as db;
+use garage_db::counted_tree_hack::CountedTree;
+
 use garage_util::data::*;
 use garage_util::error::*;
-use garage_util::sled_counter::SledCountedTree;
 
 use garage_rpc::system::System;
 
@@ -25,12 +26,12 @@ pub struct TableData<F: TableSchema, R: TableReplication> {
 	pub instance: F,
 	pub replication: R,
 
-	pub store: sled::Tree,
+	pub store: db::Tree,
 
-	pub(crate) merkle_tree: sled::Tree,
-	pub(crate) merkle_todo: sled::Tree,
+	pub(crate) merkle_tree: db::Tree,
+	pub(crate) merkle_todo: db::Tree,
 	pub(crate) merkle_todo_notify: Notify,
-	pub(crate) gc_todo: SledCountedTree,
+	pub(crate) gc_todo: CountedTree,
 
 	pub(crate) metrics: TableMetrics,
 }
@@ -40,7 +41,7 @@ where
 	F: TableSchema,
 	R: TableReplication,
 {
-	pub fn new(system: Arc<System>, instance: F, replication: R, db: &sled::Db) -> Arc<Self> {
+	pub fn new(system: Arc<System>, instance: F, replication: R, db: &db::Db) -> Arc<Self> {
 		let store = db
 			.open_tree(&format!("{}:table", F::TABLE_NAME))
 			.expect("Unable to open DB tree");
@@ -55,7 +56,7 @@ where
 		let gc_todo = db
 			.open_tree(&format!("{}:gc_todo_v2", F::TABLE_NAME))
 			.expect("Unable to open DB tree");
-		let gc_todo = SledCountedTree::new(gc_todo);
+		let gc_todo = CountedTree::new(gc_todo).expect("Cannot count gc_todo_v2");
 
 		let metrics = TableMetrics::new(F::TABLE_NAME, merkle_todo.clone(), gc_todo.clone());
 
@@ -98,30 +99,30 @@ where
 					None => partition_hash.to_vec(),
 					Some(sk) => self.tree_key(partition_key, sk),
 				};
-				let range = self.store.range(first_key..);
+				let range = self.store.range(first_key..)?;
 				self.read_range_aux(partition_hash, range, filter, limit)
 			}
 			EnumerationOrder::Reverse => match start {
 				Some(sk) => {
 					let last_key = self.tree_key(partition_key, sk);
-					let range = self.store.range(..=last_key).rev();
+					let range = self.store.range_rev(..=last_key)?;
 					self.read_range_aux(partition_hash, range, filter, limit)
 				}
 				None => {
 					let mut last_key = partition_hash.to_vec();
 					let lower = u128::from_be_bytes(last_key[16..32].try_into().unwrap());
 					last_key[16..32].copy_from_slice(&u128::to_be_bytes(lower + 1));
-					let range = self.store.range(..last_key).rev();
+					let range = self.store.range_rev(..last_key)?;
 					self.read_range_aux(partition_hash, range, filter, limit)
 				}
 			},
 		}
 	}
 
-	fn read_range_aux(
+	fn read_range_aux<'a>(
 		&self,
 		partition_hash: Hash,
-		range: impl Iterator<Item = sled::Result<(IVec, IVec)>>,
+		range: db::ValueIter<'a>,
 		filter: &Option<F::Filter>,
 		limit: usize,
 	) -> Result<Vec<Arc<ByteBuf>>, Error> {
@@ -139,7 +140,7 @@ where
 				}
 			};
 			if keep {
-				ret.push(Arc::new(ByteBuf::from(value.as_ref())));
+				ret.push(Arc::new(ByteBuf::from(value)));
 			}
 			if ret.len() >= limit {
 				break;
@@ -183,12 +184,10 @@ where
 		tree_key: &[u8],
 		f: impl Fn(Option<F::E>) -> F::E,
 	) -> Result<Option<F::E>, Error> {
-		let changed = (&self.store, &self.merkle_todo).transaction(|(store, mkl_todo)| {
-			let (old_entry, old_bytes, new_entry) = match store.get(tree_key)? {
+		let changed = self.store.db().transaction(|mut tx| {
+			let (old_entry, old_bytes, new_entry) = match tx.get(&self.store, tree_key)? {
 				Some(old_bytes) => {
-					let old_entry = self
-						.decode_entry(&old_bytes)
-						.map_err(sled::transaction::ConflictableTransactionError::Abort)?;
+					let old_entry = self.decode_entry(&old_bytes).map_err(db::TxError::Abort)?;
 					let new_entry = f(Some(old_entry.clone()));
 					(Some(old_entry), Some(old_bytes), new_entry)
 				}
@@ -204,24 +203,28 @@ where
 			// the associated Merkle tree entry.
 			let new_bytes = rmp_to_vec_all_named(&new_entry)
 				.map_err(Error::RmpEncode)
-				.map_err(sled::transaction::ConflictableTransactionError::Abort)?;
+				.map_err(db::TxError::Abort)?;
 			let encoding_changed = Some(&new_bytes[..]) != old_bytes.as_ref().map(|x| &x[..]);
+			drop(old_bytes);
 
 			if value_changed || encoding_changed {
 				let new_bytes_hash = blake2sum(&new_bytes[..]);
-				mkl_todo.insert(tree_key.to_vec(), new_bytes_hash.as_slice())?;
-				store.insert(tree_key.to_vec(), new_bytes)?;
-				Ok(Some((old_entry, new_entry, new_bytes_hash)))
+				tx.insert(&self.merkle_todo, tree_key, new_bytes_hash.as_slice())?;
+				tx.insert(&self.store, tree_key, new_bytes)?;
+
+				self.instance
+					.updated(&mut tx, old_entry.as_ref(), Some(&new_entry))?;
+
+				Ok(Some((new_entry, new_bytes_hash)))
 			} else {
 				Ok(None)
 			}
 		})?;
 
-		if let Some((old_entry, new_entry, new_bytes_hash)) = changed {
+		if let Some((new_entry, new_bytes_hash)) = changed {
 			self.metrics.internal_update_counter.add(1);
 
 			let is_tombstone = new_entry.is_tombstone();
-			self.instance.updated(old_entry.as_ref(), Some(&new_entry));
 			self.merkle_todo_notify.notify_one();
 			if is_tombstone {
 				// We are only responsible for GC'ing this item if we are the
@@ -244,22 +247,23 @@ where
 	}
 
 	pub(crate) fn delete_if_equal(self: &Arc<Self>, k: &[u8], v: &[u8]) -> Result<bool, Error> {
-		let removed = (&self.store, &self.merkle_todo).transaction(|(store, mkl_todo)| {
-			if let Some(cur_v) = store.get(k)? {
-				if cur_v == v {
-					store.remove(k)?;
-					mkl_todo.insert(k, vec![])?;
-					return Ok(true);
+		let removed = self
+			.store
+			.db()
+			.transaction(|mut tx| match tx.get(&self.store, k)? {
+				Some(cur_v) if cur_v == v => {
+					tx.remove(&self.store, k)?;
+					tx.insert(&self.merkle_todo, k, vec![])?;
+
+					let old_entry = self.decode_entry(v).map_err(db::TxError::Abort)?;
+					self.instance.updated(&mut tx, Some(&old_entry), None)?;
+					Ok(true)
 				}
-			}
-			Ok(false)
-		})?;
+				_ => Ok(false),
+			})?;
 
 		if removed {
 			self.metrics.internal_delete_counter.add(1);
-
-			let old_entry = self.decode_entry(v)?;
-			self.instance.updated(Some(&old_entry), None);
 			self.merkle_todo_notify.notify_one();
 		}
 		Ok(removed)
@@ -270,25 +274,26 @@ where
 		k: &[u8],
 		vhash: Hash,
 	) -> Result<bool, Error> {
-		let removed = (&self.store, &self.merkle_todo).transaction(|(store, mkl_todo)| {
-			if let Some(cur_v) = store.get(k)? {
-				if blake2sum(&cur_v[..]) == vhash {
-					store.remove(k)?;
-					mkl_todo.insert(k, vec![])?;
-					return Ok(Some(cur_v));
-				}
-			}
-			Ok(None)
-		})?;
+		let removed = self
+			.store
+			.db()
+			.transaction(|mut tx| match tx.get(&self.store, k)? {
+				Some(cur_v) if blake2sum(&cur_v[..]) == vhash => {
+					tx.remove(&self.store, k)?;
+					tx.insert(&self.merkle_todo, k, vec![])?;
 
-		if let Some(old_v) = removed {
-			let old_entry = self.decode_entry(&old_v[..])?;
-			self.instance.updated(Some(&old_entry), None);
+					let old_entry = self.decode_entry(&cur_v[..]).map_err(db::TxError::Abort)?;
+					self.instance.updated(&mut tx, Some(&old_entry), None)?;
+					Ok(true)
+				}
+				_ => Ok(false),
+			})?;
+
+		if removed {
+			self.metrics.internal_delete_counter.add(1);
 			self.merkle_todo_notify.notify_one();
-			Ok(true)
-		} else {
-			Ok(false)
 		}
+		Ok(removed)
 	}
 
 	// ---- Utility functions ----
@@ -315,7 +320,7 @@ where
 		}
 	}
 
-	pub fn gc_todo_len(&self) -> usize {
-		self.gc_todo.len()
+	pub fn gc_todo_len(&self) -> Result<usize, Error> {
+		Ok(self.gc_todo.len())
 	}
 }