diff --git a/documentation/README.md b/documentation/README.md deleted file mode 100644 index cb312ec..0000000 --- a/documentation/README.md +++ /dev/null @@ -1,27 +0,0 @@ -# Project Documentation - -This project's documentation is generated using [asciidoctor-web-pdf](https://github.com/ggrossetie/asciidoctor-web-pdf), a tool that converts AsciiDoc content to a styled PDF using web technologies. - -## Prerequisites - -Ensure you have [Node.js](https://nodejs.org/) and [npm](https://www.npmjs.com/) installed on your machine. - -## Setup - -1. **Install Dependencies**: - - Before generating the documentation, you need to install the necessary dependencies. Navigate to the project directory and run: - - ```shell - npm install - ``` - -2. **Generate Documentation**: - - Once the dependencies are installed, you can generate the documentation using the provided script: - - ```shell - npm run generate-doc - ``` - -After executing the script, the generated documentation will be available in the specified output directory. \ No newline at end of file diff --git a/documentation/custom.css b/documentation/custom.css deleted file mode 100644 index 94eb358..0000000 --- a/documentation/custom.css +++ /dev/null @@ -1,4 +0,0 @@ -.center-image img { - display:block; - margin: 0 auto; -} \ No newline at end of file diff --git a/documentation/package-lock.json b/documentation/package-lock.json deleted file mode 100644 index ed22520..0000000 --- a/documentation/package-lock.json +++ /dev/null @@ -1,1609 +0,0 @@ -{ - "name": "documentation", - "version": "1.0.0", - "lockfileVersion": 3, - "requires": true, - "packages": { - "": { - "name": "documentation", - "version": "1.0.0", - "license": "ISC", - "devDependencies": { - "@asciidoctor/core": "^3.0.2", - "asciidoctor-kroki": "^0.17.0", - "asciidoctor-pdf": "^1.0.0-alpha.16" - } - }, - "node_modules/@asciidoctor/cli": { - "version": "3.5.0", - "resolved": "https://registry.npmjs.org/@asciidoctor/cli/-/cli-3.5.0.tgz", - "integrity": "sha512-/VMHXcZBnZ9vgWfmqk9Hu0x0gMjPLup0YGq/xA8qCQuk11kUIZNMVQwgSsIUzOEwJqIUD7CgncJdtfwv1Ndxuw==", - "dev": true, - "dependencies": { - "yargs": "16.2.0" - }, - "bin": { - "asciidoctor": "bin/asciidoctor", - "asciidoctorjs": "bin/asciidoctor" - }, - "engines": { - "node": ">=8.11", - "npm": ">=5.0.0" - }, - "peerDependencies": { - "@asciidoctor/core": "^2.0.0-rc.1" - } - }, - "node_modules/@asciidoctor/cli/node_modules/yargs": { - "version": "16.2.0", - "resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz", - "integrity": "sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw==", - "dev": true, - "dependencies": { - "cliui": "^7.0.2", - "escalade": "^3.1.1", - "get-caller-file": "^2.0.5", - "require-directory": "^2.1.1", - "string-width": "^4.2.0", - "y18n": "^5.0.5", - "yargs-parser": "^20.2.2" - }, - "engines": { - "node": ">=10" - } - }, - "node_modules/@asciidoctor/cli/node_modules/yargs-parser": { - "version": "20.2.9", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz", - "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==", - "dev": true, - "engines": { - "node": ">=10" - } - }, - "node_modules/@asciidoctor/core": { - "version": "3.0.2", - "resolved": "https://registry.npmjs.org/@asciidoctor/core/-/core-3.0.2.tgz", - "integrity": "sha512-GbQWpqLlM/kN+90QrlLYISdU/vbGkUSeHsBQR9BzYNmVHDd6CEb/xfQZIFUo//EtT7e+QS3Sv3yYDzgjr96TbA==", - "dev": true, - "dependencies": { - "@asciidoctor/opal-runtime": "3.0.1", - "unxhr": "1.2.0" - }, - "engines": { - "node": ">=16", - "npm": ">=8" - } - }, - "node_modules/@asciidoctor/opal-runtime": { - "version": "3.0.1", - "resolved": "https://registry.npmjs.org/@asciidoctor/opal-runtime/-/opal-runtime-3.0.1.tgz", - "integrity": "sha512-iW7ACahOG0zZft4A/4CqDcc7JX+fWRNjV5tFAVkNCzwZD+EnFolPaUOPYt8jzadc0+Bgd80cQTtRMQnaaV1kkg==", - "dev": true, - "dependencies": { - "glob": "8.1.0", - "unxhr": "1.2.0" - }, - "engines": { - "node": ">=16" - } - }, - "node_modules/@babel/polyfill": { - "version": "7.12.1", - "resolved": "https://registry.npmjs.org/@babel/polyfill/-/polyfill-7.12.1.tgz", - "integrity": "sha512-X0pi0V6gxLi6lFZpGmeNa4zxtwEmCs42isWLNjZZDE0Y8yVfgu0T2OAHlzBbdYlqbW/YXVvoBHpATEM+goCj8g==", - "deprecated": "🚨 This package has been deprecated in favor of separate inclusion of a polyfill and regenerator-runtime (when needed). 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"author": "", - "license": "ISC", - "devDependencies": { - "@asciidoctor/core": "^3.0.2", - "asciidoctor-pdf": "^1.0.0-alpha.16", - "asciidoctor-kroki": "^0.17.0" - } -} diff --git a/documentation/specification.adoc b/documentation/specification.adoc deleted file mode 100644 index e5343b3..0000000 --- a/documentation/specification.adoc +++ /dev/null @@ -1,437 +0,0 @@ -= Besu Bonsaï like storage: Specification -:doctype: book -:toc: -:sectnums: -:kroki-fetch-diagram: -:center-image: style="display:block; margin: 0 auto;" - - -== Introduction - -=== Scope of the document - -This specification is the entrypoint for developers to contribute to the project and provides all the guidelines to organize the work efficiently. This document should be enough to work as a team with all the necessary explanations and overview of the whole project. This document will evolve over time. - -=== Target of the document - -This document should be a starting point and a reference for all the developers that contribute and a high level source of documentation about the project. - -A technical expertise in Rust is required to understand the interfaces. The rest of the document is readable with limited knowledge of the technical principles involved. - -=== Concepts and Vocabulary - -==== Besu Bonsai storage - -Besu Bonsai storage is an advanced storage management system developed by HyperLedger for their Ethereum client, Besu. -For a detailed specification, follow this link:https://hackmd.io/@kt2am/BktBblIL3[link]. - -==== Trie - -Unlike a conventional tree, a trie is designed so that each node (except the root) represents a byte. Each path descending the trie can symbolize a key in the form of a byte array. Each key is associated to an arbitrary value, making the trie a key-value data structure. -To better understand, consider the following illustration: - -image:https://upload.wikimedia.org/wikipedia/commons/b/be/Trie_example.svg[Tree structure,200,role="center-image"] - -In this trie, connected nodes form keys by appending the key byte they represent. For instance, the trie contains keys like **A** - with a value of 15, **to** - 7, **tea** - 3, and so on. However, **t** or **te** aren't keys but merely prefixes. - -For a deeper dive into tries, follow this link:https://en.wikipedia.org/wiki/Trie[link]. The advantages of the trie data structure are detailed link:https://www.geeksforgeeks.org/advantages-trie-data-structure/[here]. - -==== Radix trie - -Also known as a radix tree, compact prefix tree or compressed trie, a radix trie is data structure that represents a space-optimized trie in which each node that is the only child is merged with its parent. Here's a visual representation: - -image:https://upload.wikimedia.org/wikipedia/commons/a/ae/Patricia_trie.svg[Radix trie,250,role="center-image"] - -In this trie, the nodes **om**, **ub**, **ulus** ... are merged into a single node, as they are the only children of their parent. Instead of needing 7 nodes to represent the key **romulus**, each letter having its node, this space-optimized representation only needs 3, **r**, **om** and **ulus**. - -For a deeper dive into radix tries, follow this link:https://en.wikipedia.org/wiki/Radix_tree[link]. - -==== PATRICIA tree - -A PATRICIA tree, which stands for Practical Algorithm to Retrieve Information Coded in Alphanumeric, is a special variant of the radix trie where the radix is equal to 2. This implies that each node carries a 1-bit portion of the key and has at most two children (child 0 and child 1). - -For a deeper explanation of the difference between PATRICIA tree and radix trie, you can explore link:https://cs.stackexchange.com/a/63060[here]. - -The PATRICIA tree in Ethereum also provides optimizations on the trie format that are detailed link:https://ethereum.org/en/developers/docs/data-structures-and-encoding/patricia-merkle-trie/#optimization[here]. - -==== Merkle Tree - -A Merkle Tree is a specialized tree where every "leaf" or node is labeled with the cryptographic hash of a data block. Conversely, every non-leaf node, often referred to as a branch, inner node, or inode, carries the cryptographic hash of its child nodes' labels. Here's a visual representation: - -image:https://upload.wikimedia.org/wikipedia/commons/9/95/Hash_Tree.svg[Merkle Tree,400,role="center-image"] - -In this depiction, hashes 0-0 and 0-1 represent the hash values of data blocks L1 and L2, respectively. Meanwhile, hash 0 is derived from the combined hashes 0-0 and 0-1. - -For comprehensive information on the Merkle Tree, visit link:https://en.wikipedia.org/wiki/Merkle_tree[here]. The benefits of the Merkle Tree data structure are outlined link:https://www.geeksforgeeks.org/blockchain-merkle-trees/#Advantages%20of%20Merkle%20Tree:~:text=longest%2C%20valid%20blockchain.-,Advantages%20of%20Merkle%20Tree,-Efficient%20verification%3A[here]. - -One important feature of Merkle Trees is that they allow exhibiting compact proofs of existence of an element in the tree. The proof size is logarithmic in the number of elements in the tree. - -==== Merkle-Patricia Trie -A Merkle-Patricia Trie (MPT) is a combination of a Merkle Tree and a Patricia Tree. This data structure is famous because it is being used by Ethereum to store the state of an Ethereum blockchain. The Ethereum version of the MPT is composed of 3 types of nodes: - -* **Branch:** A node with up to 16 child links, each corresponding to a hex character. -* **Extension:** A node storing a key segment with a common prefix and a link to the next node. -* **Leaf:** An end-node holding the key's final segment and its value. - -Here's a visual representation: - -image:https://i.stack.imgur.com/YZGxe.png[Patricia Merkle Trie in Ethereum,450,role="center-image"] - -In this depiction, the key a77d397, having the value of 0.12 ETH, is stored using 5 nodes (a7 - extension node, 7 - branch node, d3 extension node, 9 - branch node, 7 - leaf node). - -=== External Resources - -Substrate:: link:https://github.com/paritytech/polkadot-sdk/tree/master/substrate[Substrate] is a Rust framework developed by ParityTech, designed to facilitate the creation of blockchain nodes. - -=== Versions -[%header,cols="1,1,1,3"] -|=== -| Version | Date | Author | Description -| 0.1 | 2023-11-16 | Aurélien FOUCAULT | Initial version - -| 0.2 | 2023-11-20 | Aurélien FOUCAULT | Rework interfaces -|=== - -== Function Description - -=== Actors - -==== Caller - -The library is designed for callers who need a key-value data structure with efficient data management operations for retrieval, storage and deletion, while maintaining a global fingerprint (hash) of the whole structure that allows for compact proofs of element existence. Callers can either use the library directly or through another intermediary library. The primary advantage is that callers can utilize the library without delving into its underlying implementation and can choose a database implementation that suits their needs. - -==== High-Level Interface - -This interface serves as the library's main entry point and the primary interface for callers. It simplifies interactions with the library, ensuring that the caller only engages with this interface, abstracting away the complexities of the underlying processes. - -==== Accumulator - -The accumulator plays a pivotal role in the management of the state of the data structure. It facilitates the addition of new states and retrieves states at specific point in time. The high-level interface leverages the accumulator for these tasks. - -==== Trie - -Trie is the chosen data structure for data storage within the library. Both the accumulator and the high-level interface utilize the Trie for data operations. - -==== Trie Logs - -Trie logs capture batches of modifications, detailing every change made during the processing of a "commit" which is an atomic batch of modifications that can for example represent the changes caused by the execution of block in a blockchain. These log are required to the accumulator when it needs to roll back or roll forward to a particular state. - -==== Database Interface - -Serving as the underlying persistent storage mechanism, the database ensures data longevity by saving it to the disk. While various library components rely on the database for low-level data management, its interface is implemented by the caller. This design choice maximizes abstraction and portability, allowing the library to be adaptable across different database implementations. - -=== Diagrams - -==== Use case - -[plantuml, format="svg", id="use-case", width="100%", pdfwidth="100%"] ----- -@startuml -left to right direction -skinparam actorStyle awesome - -actor Caller as caller - -package "Trie" as t { - usecase "CRUD data" as t_crud - usecase "Commit" as t_commit -} - -package "Database Interface" as dbi { - usecase "CRUD key/value" as dbi_crudKV - usecase "Add a trielog" as dbi_addTrieLog - usecase "Get trielogs" as dbi_getTrieLog -} - -package "Trie Log" as tl { - usecase "Save to databse" as tl_save2DB - usecase "Save modifications" as tl_saveModification -} - -package "BonsaiStorage" as a { - usecase "Go to state at CommitID X" as a_getStateAtX - usecase "Get Root hash" as a_getRootHash - usecase "CRUD data" as a_crud - usecase "Commit" as a_commit -} - -caller --> a_getRootHash - -caller --> a_getStateAtX -a_getStateAtX --> dbi_getTrieLog - -caller --> a_crud -a_crud --> t_crud -a_crud --> tl_saveModification -caller --> a_commit -a_commit --> t_commit -a_commit --> tl_save2DB -t_commit --> dbi_crudKV - - -tl_save2DB --> dbi_addTrieLog -@enduml ----- - -=== Sequence - -[plantuml, format="svg", id="sequence-diagram", width="100%", pdfwidth="100%"] ----- -@startuml -participant Caller as Caller -participant Interface as Interface -participant Trie as Trie -participant TrieLog as TrieLog -participant BonsaiStorage as BonsaiStorage -participant Database as Database - -== Processign a commit == - -autonumber 1 -Caller -> Interface : New commit of changes to save -Interface -> Trie : Modify the trie and save in the DB -Trie -> Database : Fetch the nodes -Database -> Trie : Return the nodes -Trie -> Database : Save all modifications to DB -Trie -> TrieLog : Save modifications in the Trie Logs -TrieLog -> Database : Save the Trie Logs in the database -TrieLog -> BonsaiStorage : Save the Trie Logs to the BonsaiStorage -BonsaiStorage -> Database : Save a snapshot every N batches -Trie -> Caller : Result of the modifications -autonumber stop - -== Asking for a specific state at a certain CommitID == - - -autonumber 1 -Caller -> Interface : Ask for a state X -Interface -> BonsaiStorage : Ask for the state -BonsaiStorage -> BonsaiStorage : Is it my current state ? -BonsaiStorage -[#green]> Caller : Return the state -autonumber stop -autonumber 4 1 -BonsaiStorage -[#red]> BonsaiStorage : Can we go to this state using the Trie Logs -BonsaiStorage -[#green]> BonsaiStorage : If yes, apply them -BonsaiStorage -> Caller : Return the state -autonumber stop -autonumber 5 1 -BonsaiStorage -[#red]> Database : Ask for the closest snapshot -Database -> BonsaiStorage : Return the closest snapshot -BonsaiStorage -> BonsaiStorage : Is the closest snapshot exactly at the asked state ? -BonsaiStorage -[#green]> Caller : Return the snapshot state -autonumber stop -autonumber 8 1 -BonsaiStorage -[#red]> Database : Ask for the trie logs to derive the asked state \n from the snapshot -Database -> BonsaiStorage : Return the trie logs -BonsaiStorage -> BonsaiStorage : Apply the trie logs -BonsaiStorage -> Caller : Return the state (or an error) -@enduml ----- - -== Technical Description - -=== Trie - -The Trie is the central component of the Besu storage system. To avoid reimplementing a PMT, we use the crate link:https://github.com/paritytech/trie[Trie from paritytech] which provides a standard PMT. This choice was made for multiple reasons: - -- It avoids re-implementing a PMT. -- It provides the flexibility to create Tries formatted for different blockchains. -- The code has a lot of generics and gives us the possibility to make modifications to the PMT structure easily. - -We only use the sub-crate `trie-db` and override its keys, database, and layout implementations. -However, this sub-crate only solves part of the problem: -- In a Bonsai Trie, we store nodes directly by their location, while the Trie crate stores them by hash -- The Trie crate does not allow the implementation of trie logs, which require some modifications to the crate code - -Given those constraints, we forked the Trie crate while minimizing the changes to the code. -Our modifications make the crate more generic and are being proposed to the maintainers as an upstream PR. - -==== Attributes - -No attributes need to be defined. All traits are detailed below. - -==== Traits/Implementations - -===== Trie interface - -The `TrieDBMut` structure of the `trie` crate is used. Definition can be found link:https://docs.rs/trie-db/latest/trie_db/triedbmut/struct.TrieDBMut.html[here] - -==== Database trait - -The Trie crate from paritytech already provides a database trait described link:https://github.com/paritytech/trie/blob/1645fddec8e5461d5aca7dd880303042b8527465/hash-db/src/lib.rs#L128[here]. We reuse the same trait for this part of the project. - -==== Child encoding - -In the sub-crate `trie-db`, the children of a branch node are either inline or referenced by hash. In a Bonsai Trie, as the nodes are stored by their locations, we still want to save the hash to have it cached when parent hashes need to be computed (up to the trie root hash). - -==== Node encoding - -The sub-crate `reference-trie`` gives the implementations of `trait NodeCodec` (that manages the serialization/deserialization of nodes to store them in DB) with the same behavior as the one used on Substrate. We re-use it as it corresponds to our needs and gives us more compatibility with existing Substrate code. - -=== Accumulator - -The accumulator is an optimization component that is used to register all the reads and changes made to provide optimizations for future actions. For example when reading a value, in a second thread, the path in the trie will be loaded in the accumulator in case the value is modified in the same batch of changes - -=== Trie logs - -Trie logs store a batch of modifications to the trie to be applied to a state. - -==== Attribute - -- In each trie log, we should save all keys/values that are modified within `HashMap>, Option>)>`. The value is represented as `Vec<(Option>, Option>` to be able to hold the old value (if existed) and the new one (if we are not in a remove operation) for each key. -- An ID - -==== Traits/Implementations - -[source,rust] ----- -impl TrieLog -where: - CommitID: Id { - // Initialize a trie log with a batch of modifications - fn new(id: CommitID, modifications: Vec<(Option>, Option>)>) -> Self - - // Get the associated CommitID - fn get_commit_id(&self) -> CommitID; -} ----- - -=== Database - -The database implementation is generic on the underlying database. We provide a first implementation of the database using RocksDB. - -All methods take an optional transaction type that allows making transactional modifications to the database if the database type allows it. If the transaction object is provided, we don't update the DB directly but accumulate the changes into the provided TX, and commit it afterwards. - -==== Attributes - -- A connector to the database - -==== Traits/Implementations - -[source,rust] ----- -pub enum DatabaseError { - // All errors related to the db, omitted here -} - -pub trait BonsaiDatabase { - fn new(path_to_database: &str) -> Self - - // Insert an entry in the trie - fn insert(&mut self, key: &[u8], value: &[u8]) -> Result<(), DatabaseError>; - - // Remove an entry from the trie - fn remove(&mut self, key: &[u8]) -> Result<(), DatabaseError>; - - // Get a value in trie - fn get(&self, key: &[u8]) -> Result, DatabaseError>; - - // Check if the key is in trie - fn contains(&self, key: &[u8]) -> Result; - - // PUT operation in TRIE_LOG column - fn put_trie_log(&mut self, key: &[u8], value: &[u8]) -> Result<(), DatabaseError>; - - // GET operation in TRIE_LOG column - fn get_trie_log(&self, key: &[u8]) -> Result, DatabaseError>; - - // Generate a snapshot - fn generate_snapshot(&mut self) -> Result - - // Get a snapshot - fn get_snapshot(&self, snapshot_id: u64) -> Result -} ----- - -=== User-facing interface - -This is the main interface that the Caller interacts with. - -==== Definition - -[source,rust] ----- -// Error type for the interface (elided) -pub enum BonsaiStorageError {} - -// Configuration -// None = unlimited -pub struct BonsaiStorageConfig { - pub max_trie_log_size: Option, - pub max_snapshot_saved: Option, - pub max_trie_logs_in_memory: Option, - pub snapshot_interval: usize, -} - -pub trait BonsaiStorage<'a, CommitID> -where: - CommitID: Id { - // Create a new bonsai storage instance - fn new(db: &'a mut KeyValueDB, root: &'a mut BonsaiTrieHash, config: BonsaiStorageConfig) -> Self; - - // Insert a new key/value in the trie, overwriting the previous value if it exists - // If the value already exists it will overwrite it and return the previous value if any - fn insert(&mut self, key: &[u8], value: &[u8]) -> Result<(), BonsaiStorageError>; - - // Remove a key/value in the trie - // If the value doesn't exist it will do nothing - fn remove(&mut self, key: &[u8]) -> Result<(), BonsaiStorageError>; - - // Commit all the changes to the trie - // This is in charge of saving the in-memory `insert`/`remove` operations in the database otherwise - fn commit(&mut self, id: CommitID) -> Result<(), BonsaiStorageError>; - - // Get a value in the trie - fn get(&self, key: &[u8]) -> Result>, BonsaiStorageError>; - - // contains checks if the key exists - fn contains(&self, key: &[u8]) -> Result; - - // Go to a specific commit ID using trie logs and snapshots. - // If insert/remove is called between the last `commit()` and a call to this function, - // the in-memory changes will be discarded - fn go_to(&mut self, commit_id: CommitID) -> Result<(), BonsaiStorageError>; - - // Get the root hash of the trie, at the state of the latest commit - fn root_hash(&self) -> Hash; -} ----- - -==== Usage example - -For example you will be able to use the interface like this: - -[source,rust] ----- -fn main() { - let mut db = KeyValueDB::::new(RocksDB::new("./rocksdb")); // add empty node - let mut root = BonsaiTrieHash::default(); - let mut bonsai_storage = BonsaiStorage::new(&mut db, &mut root, BonsaiStorageConfig::default()); - let mut id_builder = BasicIdBuilder::new(); - bonsai_storage.insert(&[1, 2, 3, 4, 5, 6], &[4, 5, 6]); - bonsai_storage.insert(&[1, 2, 3, 4, 5, 7], &[4, 5, 8]); - bonsai_storage.commit(id_builder.new_id()); - bonsai_storage.insert(&[1, 2, 2], &[7, 5, 6]); - let go_to_id = id_builder.new_id(); - bonsai_storage.commit(go_to_id); - bonsai_storage.remove(&[1, 2, 2]); - bonsai_storage.commit(id_builder.new_id()); - println!("root hash: {:#?}", bonsai_storage.root()); - println!( - "value for key [1, 2, 3, 4, 5, 6]: {:#?}", - bonsai_storage.get(&[1, 2, 3, 4, 5, 6]).unwrap() - ); - bonsai_storage.go_to(go_to_id).unwrap(); - println!("root hash: {:#?}", bonsai_storage.root()); - println!("value for key [1, 2, 2]: {:#?}", bonsai_storage.get(&[1, 2, 2]).unwrap()); -} ----- - -=== Tests - -We provide the following tests: - -- A test with a simple set of key/value -- A test with a big set of key/value -- A test with different types of `TrieValue` -- A test with behavior closest to the one of Madara. diff --git a/documentation/specification.pdf b/documentation/specification.pdf deleted file mode 100644 index 3751c77..0000000 Binary files a/documentation/specification.pdf and /dev/null differ