From fce01755be56a5716fd635528ea4c8f23f1ebd6c Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 29 Jun 2020 16:26:15 +0200
Subject: [PATCH] empty README and move to wiki pages
---
README.md | 134 +++-----------------------------------------
backend/.env.sample | 1 +
2 files changed, 8 insertions(+), 127 deletions(-)
diff --git a/README.md b/README.md
index c0285ee..0ee7e9c 100644
--- a/README.md
+++ b/README.md
@@ -3,135 +3,15 @@
[](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/dev)
[](https://gitlab.pasteur.fr/metagenomics/metagenedb/commits/dev)
+## The project
+
The main motivation behind MetageneDB is to provide a support for all the analysis that are based on gene catalogs.
It is composed of both an API and a client side for visualization and interaction with the DB.
-----
-
-## Setup the services on your local machine
-
-### Dependencies
-
-The application depends on different services that run independently on docker images and all of this is
-orchestrated by `docker-compose` locally.
-
-Therefore to run the application you need:
-
-* `Docker` : [Install instructions](https://docs.docker.com/install/)
-* `Docker Compose` : [Install instructions](https://docs.docker.com/compose/install/)
-
-### Configuration
-
-For `docker-compose`, you need to create a `.env` file: `touch .env`. An example is available: `.env.sample`.
-
-The settings of the Django server is based on the `backend/.env` file. You can copy the sample file
-(`cp backend/.env.sample backend/.env`) and fill in the variables.
-
-You can of course customize more of the Django server settings in the `settings` module of metagenedb.
-
-Now we will go through the different parts.
-
-#### Secret key
-
-This is the Django `SECRET_KEY` and you need to specify your own. For instance you can use the command
-`openssl rand -base64 32` to generate one by command line.
-
-#### Create your own DB on postgresql
-
-The following variables have the default values:
-
-```bash
-DATABASE_HOST=postgresql
-DATABASE_USER=postgres
-DATABASE_NAME=postgres
-DATABASE_PASSWORD=""
-DATABASE_PORT=5432
-```
-
-It will work if you leave it as it is but you might face security issues having a by default database
-without credentials.
-
-What we recommand is to create your own database. Here is described one way to do it. To do that you need to
-first run the db image and identify its running ID:
-
-```bash
-khillion:~/metagenedb $ docker-compose up postgresql -d # This runs only the postgresql service of your docker-compose in detached mode. You can also detached from you running screen using Ctrl+Z
-Creating postgresql ... done
-khillion:~/metagenedb $ docker ps # List your running docker images
-CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
-5002f210f9d8 postgres:11.4-alpine "docker-entrypoint.s…" 1 minute ago Up 1 minute 0.0.0.0:5433->5432/tcp postgresql
-```
-
-Now that you have the `CONTAINER ID`, here `5002f210f9d8` you can run a `bash` terminal in this container and
-create your own database:
-
-```bash
-khillion:~/metagenedb $ docker exec -it 5002f210f9d8 bash
-bash-5.0# psql --user=postgres
-````
-
-This will open the `SQL` console where you can do what you need:
-
-```psql
-CREATE ROLE metagenedb WITH PASSWORD 'yourawesomepassword';
-ALTER ROLE metagenedb WITH CREATEDB;
-CREATE DATABASE metagenedb WITH OWNER metagenedb;
-exit
-```
-
-Now you have you own database, protected by a password and you need to update your `.env`:
-
-```bash
-DATABASE_HOST=postgresql
-DATABASE_USER=metagenedb
-DATABASE_NAME=metagenedb
-DATABASE_PASSWORD=yourawesomepassword
-DATABASE_PORT=5432
-```
-
-> **Note**: The by default port for postgres is `5432`. In the `docker-compose.yaml` you will notice that this
-port is redirected to `5433` on the `localhost`. This is done in order to not interfere with your local
-postgres if you have one. This means you need to change `DATABASE_HOST` to `localhost` and `DATABASE_POS
-
-### Pre-computed statistics
-
-Some statistics about genes are pre-computed and can be accessed through the `/api/catalog/v1/statistics` endpoint.
-The ID is constructed with the following format: `<statisctics-type>-<gene_source>-<method>-<options>`.
-
-----
-
-## Run the application
-
-For the moment, only the `docker-compose.dev.yaml` is used. To run the application simply run the command:
-
-```bash
-docker-compose up --build
-```
-
-The `--build` option is only necessary during the first usage or when you make changes that need the docker
-container to be built again.
-
-Since directories with source codes are mounted in the containers, changes you make locally should be
-directly reflected on the application.
-
-### Populate the database
-
-You have a set of scripts available that you can list via `manage.py --help`.
-
------
-
-## Dev tips
-
-#### Profiling code
-
-```python
-from metagenedb.common.utils.profiling import profile
+* Graphical interface to browse through the catalog
+* REST API to programmatically query and retrieve information from the database
+* (not implemented) Interface to perform analysis from gene counts present on the catalog
-@profile("/my/file/path")
-def my_function(a, b, c):
- ...
-```
+## Wiki & Documentation
-```bash
-snakeviz /my/file/path
-```
+For more information, please have a look at our [Wiki](https://gitlab.pasteur.fr/metagenomics/metagenedb/-/wikis/MetageneDB)
diff --git a/backend/.env.sample b/backend/.env.sample
index e1d292e..840b355 100644
--- a/backend/.env.sample
+++ b/backend/.env.sample
@@ -6,3 +6,4 @@ DATABASE_NAME=postgres
DATABASE_PASSWORD=""
DATABASE_PORT=5432
SECRET_KEY=YOUR_KEY
+DB_LOG_LEVEL=INFO
--
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