forked from filipg/gonito
209 lines
8.7 KiB
Markdown
209 lines
8.7 KiB
Markdown
Gonito platform
|
||
===============
|
||
|
||
[Gonito](https://gonito.net) (pronounced _ɡɔ̃ˈɲitɔ_) is a Kaggle-like
|
||
platform for machine learning competitions (disclaimer: Gonito is
|
||
neither affiliated with nor endorsed by [Kaggle](https://www.kaggle.com)).
|
||
|
||
|
||
What's so special about Gonito:
|
||
|
||
* free & open-source (GPL), you can use it your own, in your
|
||
company, at your university, etc.
|
||
* git-based (challenges and solutions are submitted only with git).
|
||
|
||
See the home page (and an instance of Gonito) at https://gonito.net .
|
||
|
||
Installation
|
||
------------
|
||
|
||
## For development
|
||
|
||
[Gonito](https://gonito.net) is written in [Haskell](https://www.haskell.org) and uses
|
||
[Yesod Web Framework](http://www.yesodweb.com/), but all you need is
|
||
just [the Stack tool](https://github.com/commercialhaskell/stack). See https://github.com/commercialhaskell/stack
|
||
for instruction how to install Stack on your computer.
|
||
|
||
By default, Gonito uses [Postgresql](http://www.postgresql.org/), so it needs to be installed and running at your computer.
|
||
|
||
After installing Stack:
|
||
|
||
createdb -E utf8 gonito # Postgres needs to be configured
|
||
git clone --recurse-submodules git://gonito.net/gonito
|
||
cd gonito
|
||
stack setup
|
||
# before starting the build you might need some non-Haskell dependencies, e.g. in Ubuntu:
|
||
# sudo apt-get install libbz2-dev liblzma-dev libpcre3-dev libcairo-dev libfcgi-dev
|
||
stack build
|
||
stack exec yesod devel
|
||
|
||
The last command will start the Web server with Gonito (go to
|
||
http://127.0.0.1:3000 in your browser).
|
||
|
||
## With docker-compose
|
||
|
||
The easiest way to run Gonito is with docker-compose.
|
||
|
||
git clone --recurse-submodules https://gitlab.com/filipg/gonito
|
||
cd gonito
|
||
cp sample.env .env
|
||
# now you need to edit .env manually,
|
||
# in particular, you need to set up the administrator's
|
||
# password and paths to volumes for the volumes,
|
||
# cloned data ("arena"), certificates and SSH data;
|
||
# also you need to set up your certificate
|
||
# here is an easy way to do it just for local
|
||
# testing
|
||
mkdir certs
|
||
cd certs
|
||
# generating certificates for HTTPS, remember to
|
||
# set the `NGINX_CERTIFICATE_DIR` variable in `.env`
|
||
# so that it would point to `certs` here
|
||
openssl req -x509 -newkey rsa:4096 -keyout privkey.pem -out fullchain.pem -days 365 -nodes
|
||
cd ..
|
||
docker-compose up
|
||
|
||
Gonito will be available at <https://127.0.0.1/>. Of course, your
|
||
browser will complain about "Potential Security Risk" as these are
|
||
local certificates.
|
||
|
||
Gonito as backend
|
||
-----------------
|
||
|
||
On the one hand, Gonito is a monolithic Web application without front-
|
||
and back-end separated. On the other, some features are provided as
|
||
end-points, so that Gonito could be used with whatever front-end. The
|
||
documentation in the Swagger format is provided at `/static/swagger-ui/index.html`.
|
||
(see <https://gonito.net/static/swagger-ui/index.html> for this at the main instance).
|
||
|
||
Keycloak is assumed as the identity provider here for those end-points that
|
||
require authorization.
|
||
|
||
Integration with Keycloak
|
||
-------------------------
|
||
|
||
Gonito can be easily integrated with Keycloak for the back-end
|
||
end-points (but not yet for signing in Gonito as the monolithic Web
|
||
application, this feature is on the way).
|
||
|
||
1. Let's assume that you have a Keycloak instance. A simple way to run
|
||
for development and testing is: `docker run -e KEYCLOAK_USER=admin -e KEYCLOAK_PASSWORD=admin -p 8080:8080 jboss/keycloak`.
|
||
|
||
2. You need to set up the JWK key from your Keycloak instance.
|
||
Go to `https://<KEYCLOAK-HOST>/auth/realms/<KEYCLOAK-REALM>/protocol/openid-connect/certs`
|
||
and copy the contents of the key from the JSON the (key/0 element
|
||
not the whole JSON!).
|
||
|
||
3. Create `gonito` client in Keycloak (_Clients_ / _Create_).
|
||
|
||
4. Set _Valid Redirect URIs_ for the `gonito` client in Keycloak (e.g. simply add `*` there).
|
||
|
||
5. Set _Web Origin_ for the `gonito` client in Keycloak (e.g. simply add `*` there).
|
||
|
||
6. Set `JSON_WEB_KEY` variable to the content of the JWK key (or `GONITO_JSON_WEB_KEY` when using docker-compose)
|
||
and run Gonito.
|
||
|
||
If you create a new user, you need to run `/api/add-info` GET
|
||
end-point. No parameters are needed it just read the user's data from
|
||
the token and adds a record to the Gonito database.
|
||
|
||
You can simulate a front-end by going to `/static/test-gonito-as-backend.html`.
|
||
|
||
Gonito & git
|
||
------------
|
||
|
||
Gonito uses git in an inherent manner:
|
||
|
||
* challenges (data sets) are provided as git repositories,
|
||
* submissions are uploaded via git repositories, they are referred to with
|
||
git commit hashes.
|
||
|
||
Advantages:
|
||
|
||
* great flexibility as far as where you want to keep your challenges
|
||
and submissions (could be external, well-known services such as
|
||
GitHub or GitLab, your local git server, let's say gitolite or Gogs, or
|
||
just a disk accessible in a Gonito instance),
|
||
* even if Gonito ceases to exist, the challenges and submissions are still available
|
||
in a standard manner, provided that git repositories (be it external or local) are
|
||
accessible,
|
||
* data sets can be easily downloaded using the command line
|
||
(e.g. `git clone git://gonito.net/paranormal-or-skeptic`), without
|
||
even clicking anything in the Web browser,
|
||
* facilitates experiment repeatability and reproducibility (at worst
|
||
the system output is easily available via git)
|
||
* tools that were used to generate the output could be linked as git subrepositories
|
||
* some challenge/submission metadata are tracked in a Gonito-independent way
|
||
(within git commits),
|
||
* copying data can be avoided with git mechanisms (e.g. when the challenge is already
|
||
cloned, downloading specific submissions should be much quicker),
|
||
* large data sets and models could be stored if needed using mechanisms such as git-annex (see below).
|
||
|
||
### Commit structure
|
||
|
||
The following flow of git commits is recommended (though not required):
|
||
|
||
* the challenge without hidden data for main test sets (i.e. files such as `test-A/expected.tsv`)
|
||
should be pushed to the `master` branch
|
||
* the hidden files (`test-A/expected.tsv`) should be added in a
|
||
subsequent commit and pushed either to the `dont-peek` branch or a
|
||
`master` branch of a separate repository (if access to the hidden
|
||
data must be more strict),
|
||
* the submissions should be committed with the `master` branch as the
|
||
parent (or at least ancestor) commit and pushed to the same
|
||
repository as the challenge data (in some user-specific branch) or any other
|
||
repository (could be user-owned repositories)
|
||
* any subsequent submissions could be derived in a natural way from other git commits
|
||
(e.g. when a submission is improved, or even two approaches are merged)
|
||
* new versions of the challenge can be committed (a challenge can be updated at Gonito)
|
||
to the `master` (and `dont-peek`) branches
|
||
|
||
See also the following picture:
|
||
|
||
|
||
|
||
### git-annex
|
||
|
||
In some cases, you don't want to store challenge/submissions files simply in git:
|
||
|
||
* very large data files, textual files (e.g. `train/in.tsv` even if
|
||
compressed as `train/in.tsv.xz`)
|
||
* binary training/testing data (PDF files, images, movies, recordings)
|
||
* data sensitive due to privacy/security concerns (a scenario where it's OK to store
|
||
metadata and some files in a widely accessible repository, but some files require
|
||
limited access)
|
||
* large ML models (note that Gonito does not require models for evaluation, but still
|
||
it might be a good practice to commit them along with output files and scripts)
|
||
|
||
Such cases can be handled in a natural manner using git-annex, a git
|
||
extension for handling files and their metadata without commiting
|
||
their content to the repository. The contents can be stored at a wide
|
||
range of [special
|
||
remotes](https://git-annex.branchable.com/special_remotes/), e.g. S3
|
||
buckets, WebDAV, rsync servers.
|
||
|
||
It's up to you which files are stored in git in a regular manner and
|
||
which are added with `git annex add`, but note that if a
|
||
challenge/submission file must be stored via git-annex and are required
|
||
for evaluation (e.g. `expected.tsv` files for the challenge or
|
||
`out.tsv` files for submissions), the git-annex special remote must be
|
||
given when a challenge is created or a submission is done and the
|
||
Gonito server must have access to such a special remote.
|
||
|
||
Authors
|
||
-------
|
||
|
||
* Filip Graliński
|
||
|
||
References
|
||
----------
|
||
|
||
@inproceedings{gralinski:2016:gonito,
|
||
title="{Gonito.net - Open Platform for Research Competition, Cooperation and Reproducibility}",
|
||
author={Grali{\'n}ski, Filip and Jaworski, Rafa{\l} and Borchmann, {\L}ukasz and Wierzcho{\'n}, Piotr},
|
||
booktitle="{Branco, Ant{\'o}nio and Nicoletta Calzolari and Khalid Choukri (eds.), Proceedings of the 4REAL Workshop: Workshop on Research Results Reproducibility and Resources Citation in Science and Technology of Language}",
|
||
pages={13--20},
|
||
year=2016,
|
||
url="http://4real.di.fc.ul.pt/wp-content/uploads/2016/04/4REALWorkshopProceedings.pdf"
|
||
}
|