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----
-
-title: Durable persistent trees and parser combinators - building a database
-
-date: 2020-11-12
-
-updated_at: 2021-02-09
-
-layout: post
-
-lang: en
-
-ref: durable-persistent-trees-and-parser-combinators-building-a-database
-
-eu_categories: mediator
-
----
-
-I've received with certain frequency messages from people wanting to know if
-I've made any progress on the database project
-[I've written about]({% link _articles/2020-08-31-the-database-i-wish-i-had.md %}).
-
-There are a few areas where I've made progress, and here's a public post on it.
-
-## Proof-of-concept: DAG log
-
-The main thing I wanted to validate with a concrete implementation was the
-concept of modeling a DAG on a sequence of datoms.
-
-The notion of a *datom* is a rip-off from Datomic, which models data with time
-aware *facts*, which come from RDF. RDF's fact is a triple of
-subject-predicate-object, and Datomic's datoms add a time component to it:
-subject-predicate-object-time, A.K.A. entity-attribute-value-transaction:
-
-```clojure
-[[person :likes "pizza" 0 true]
- [person :likes "bread" 1 true]
- [person :likes "pizza" 1 false]]
-```
-
-The above datoms say:
-- at time 0, `person` like pizza;
-- at time 1, `person` stopped liking pizza, and started to like bread.
-
-Datomic ensures total consistency of this ever growing log by having a single
-writer, the transactor, that will enforce it when writing.
-
-In order to support disconnected clients, I needed a way to allow multiple
-writers, and I chose to do it by making the log not a list, but a
-directed acyclic graph (DAG):
-
-```clojure
-[[person :likes  "pizza"  0 true]
- [0      :parent :db/root 0 true]
- [person :likes  "bread"  1 true]
- [person :likes  "pizza"  1 false]
- [1      :parent 0        1 true]]
-```
-
-The extra datoms above add more information to build the directionality to the
-log, and instead of a single consistent log, the DAG could have multiple leaves
-that coexist, much like how different Git branches can have different "latest"
-commits.
-
-In order to validate this idea, I started with a Clojure implementation. The
-goal was not to write the actual final code, but to make a proof-of-concept that
-would allow me to test and stretch the idea itself.
-
-This code [already exists][clj-poc], but is yet fairly incomplete:
-
-- the building of the index isn't done yet (with some
-  [commented code][clj-poc-index] on the next step to be implemented)
-- the indexing is extremely inefficient, with [more][clj-poc-o2-0]
-  [than][clj-poc-o2-1] [one][clj-poc-o2-2] occurrence of `O²` functions;
-- no query support yet.
-
-[clj-poc]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n1
-[clj-poc-index]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n295
-[clj-poc-o2-0]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n130
-[clj-poc-o2-1]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n146
-[clj-poc-o2-2]: https://euandre.org/git/mediator/tree/src/core/clojure/src/mediator.clj?id=db4a727bc24b54b50158827b34502de21dbf8948#n253
-
-## Top-down *and* bottom-up
-
-However, as time passed and I started looking at what the final implementation
-would look like, I started to consider keeping the PoC around.
-
-The top-down approach (Clojure PoC) was in fact helping guide me with the
-bottom-up, and I now have "promoted" the Clojure PoC into a "reference
-implementation". It should now be a finished implementation that says what the
-expected behaviour is, and the actual code should match the behaviour.
-
-The good thing about a reference implementation is that it has no performance of
-resources boundary, so if it ends up being 1000x slower and using 500× more
-memory, it should be find. The code can be also 10x or 100x simpler, too.
-
-## Top-down: durable persistent trees
-
-In promoting the PoC into a reference implementation, this top-down approach now
-needs to go beyond doing everything in memory, and the index data structure now
-needs to be disk-based.
-
-Roughly speaking, most storage engines out there are based either on B-Trees or
-LSM Trees, or some variations of those.
-
-But when building an immutable database, update-in-place B-Trees aren't an
-option, as it doesn't accommodate keeping historical views of the tree. LSM Trees
-may seem a better alternative, but duplication on the files with compaction are
-also ways to delete old data which is indeed useful for a historical view.
-
-I think the thing I'm after is a mix of a Copy-on-Write B-Tree, which would keep
-historical versions with the write IO cost amortization of memtables of LSM
-Trees. I don't know of any B-Tree variant out there that resembles this, so I'll
-call it "Flushing Copy-on-Write B-Tree".
-
-I haven't written any code for this yet, so all I have is a high-level view of
-what it will look like:
-
-1. like Copy-on-Write B-Trees, changing a leaf involves creating a new leaf and
-  building a new path from root to the leaf. The upside is that writes a lock
-  free, and no coordination is needed between readers and writers, ever;
-
-1. the downside is that a single leaf update means at least `H` new nodes that
-  will have to be flushed to disk, where `H` is the height of the tree. To avoid
-  that, the writer creates these nodes exclusively on the in-memory memtable, to
-  avoid flushing to disk on every leaf update;
-
-1. a background job will consolidate the memtable data every time it hits X MB,
-  and persist it to disk, amortizing the cost of the Copy-on-Write B-Tree;
-
-1. readers than will have the extra job of getting the latest relevant
-  disk-resident value and merge it with the memtable data.
-
-The key difference to existing Copy-on-Write B-Trees is that the new trees
-are only periodically written to disk, and the intermediate values are kept in
-memory. Since no node is ever updated, the page utilization is maximum as it
-doesn't need to keep space for future inserts and updates.
-
-And the key difference to existing LSM Trees is that no compaction is run:
-intermediate values are still relevant as the database grows. So this leaves out
-tombstones and value duplication done for write performance.
-
-One can delete intermediate index values to reclaim space, but no data is lost
-on the process, only old B-Tree values. And if the database ever comes back to
-that point (like when doing a historical query), the B-Tree will have to be
-rebuilt from a previous value. After all, the database *is* a set of datoms, and
-everything else is just derived data.
-
-Right now I'm still reading about other data structures that storage engines
-use, and I'll start implementing the "Flushing Copy-on-Write B-Tree" as I learn
-more[^learn-more-db] and mature it more.
-
-[^learn-more-db]: If you are interested in learning more about this too, the
-    very best two resources on this subject are Andy Pavlo's
-    "[Intro to Database Systems](https://www.youtube.com/playlist?list=PLSE8ODhjZXjbohkNBWQs_otTrBTrjyohi)"
-    course and Alex Petrov's "[Database Internals](https://www.databass.dev/)" book.
-
-## Bottom-up: parser combinators and FFI
-
-I chose Rust as it has the best WebAssembly tooling support.
-
-My goal is not to build a Rust database, but a database that happens to be in
-Rust. In order to reach client platforms, the primary API is the FFI one.
-
-I'm not very happy with current tools for exposing Rust code via FFI to the
-external world: they either mix C with C++, which I don't want to do, or provide
-no access to the intermediate representation of the FFI, which would be useful
-for generating binding for any language that speaks FFI.
-
-I like better the path that the author of [cbindgen][cbindgen-crate]
-crate [proposes][rust-ffi]: emitting an data representation of the Rust C API
-(the author calls is a `ffi.json` file), and than building transformers from the
-data representation to the target language. This way you could generate a C API
-*and* the node-ffi bindings for JavaScript automatically from the Rust code.
-
-So the first thing to be done before moving on is an FFI exporter that doesn't
-mix C and C++, and generates said `ffi.json`, and than build a few transformers
-that take this `ffi.json` and generate the language bindings, be it C, C++,
-JavaScript, TypeScript, Kotlin, Swift, Dart, *etc*[^ffi-langs].
-
-[^ffi-langs]: Those are, specifically, the languages I'm more interested on. My
-    goal is supporting client applications, and those languages are the most
-    relevant for doing so: C for GTK, C++ for Qt, JavaScript and TypeScript for
-    Node.js and browser, Kotlin for Android and Swing, Swift for iOS, and Dart
-    for Flutter.
-
-I think the best way to get there is by taking the existing code for cbindgen,
-which uses the [syn][syn-crate] crate to parse the Rust code[^rust-syn], and
-adapt it to emit the metadata.
-
-[^rust-syn]: The fact that syn is an external crate to the Rust compiler points
-    to a big warning: procedural macros are not first class in Rust. They are
-    just like Babel plugins in JavaScript land, with the extra shortcoming that
-    there is no specification for the Rust syntax, unlike JavaScript.
-
-    As flawed as this may be, it seems to be generally acceptable and adopted,
-    which works against building a solid ecosystem for Rust.
-
-    The alternative that rust-ffi implements relies on internals of the Rust
-    compiler, which isn't actually worst, just less common and less accepted.
-
-I've started a fork of cbindgen: ~~x-bindgen~~[^x-bindgen]. Right now it is
-just a copy of cbindgen verbatim, and I plan to remove all C and C++ emitting
-code from it, and add a IR emitting code instead.
-
-[^x-bindgen]: *EDIT*: now archived, the experimentation was fun. I've started to move more towards C, so this effort became deprecated.
-
-When starting working on x-bindgen, I realized I didn't know what to look for in
-a header file, as I haven't written any C code in many years. So as I was
-writing [libedn][libedn-repo], I didn't know how to build a good C API to
-expose. So I tried porting the code to C, and right now I'm working on building
-a *good* C API for a JSON parser using parser combinators:
-~~ParsecC~~ [^parsecc].
-
-[^parsecc]: *EDIT*: now also archived.
-
-After "finishing" ParsecC I'll have a good notion of what a good C API is, and
-I'll have a better direction towards how to expose code from libedn to other
-languages, and work on x-bindgen then.
-
-What both libedn and ParsecC are missing right now are proper error reporting,
-and property-based testing for libedn.
-
-[cbindgen-crate]: https://github.com/eqrion/cbindgen
-[syn-crate]: https://github.com/dtolnay/syn
-[rust-ffi]: https://blog.eqrion.net/future-directions-for-cbindgen/
-[libedn-repo]: https://euandre.org/git/libedn/
-
-## Conclusion
-
-I've learned a lot already, and I feel the journey I'm on is worth going
-through.
-
-If any of those topics interest you, message me to discuss more or contribute!
-Patches welcome!