alice-annotation-tool's Introduction

ALICE Annotation Tool

How to set up dev (no docker-compose)

Run postgres on 5432

docker run -p 5432:5432 -d -e POSTGRES_PASSWORD=pwd postgres

Run redis on 6379

docker run --name some-redis -d -p 6379:6379 redis

Go through readme.md from backend

How to set up dev

Create a docker network if not created

docker network create reverse-proxy

Set up .env files.

cp back/.env.sample back/.env
cp postgres/.env.sample postgres/.env

For production change secret key in back/.env and postgres password in postgres/.env.

First start up

Build docker-compose. You need at least 8 Gb RAM for the build

docker-compose build

First, we need to init postgres db

docker-compose up postgres

After initialization is done exit docker-compose and start all the containers

docker-compose up

If everything is fine you can run it in the background mode

docker-compose up -d

Updating

Use a regular docker-compose command sequence

docker-compose down
docker-compose build
docker-compose up -d

Set up dev db

docker exec -it eeg-ic-annotation_back_1 /bin/bash

# then inside the container
cd drf_backend
python manage.py init_dev_db
python manage.py update_component_plots --dataset test_dataset
python manage.py update_links --dataset test_dataset
python manage.py update_plots --dataset test_dataset

You can login as admin/admin

How to set up prod

Set up proper .env files

TODO - adding admin user

Db dump

pg_dump --host localhost --port 5433 -U postgres postgres > eeg_ica_dump

psql --host=localhost --port 5433 -U postgres postgres_2 < eeg_ica_dump

alice-annotation-tool's People

Watchers

alice-annotation-tool's Issues

Add new mechanics to store images

Add new method for image generation

Add flag that image is calculated

Paths for images

MEDIA_ROOT/topomaps/dataset_name/subject_id/ic_id.png
MEDIA_ROOT/spectrum/dataset_name/subject_id/ic_id.png
MEDIA_ROOT/epochs_image/dataset_name/subject_id/ic_id.png

Get rid of odd layers

Merge short similar RUN instructions into single command
Change ADD by COPY

Add monitoring

We struggle with consequent errors.

Idea - add custom error handler with notification to TG chat

Stack all-in-one

Gather all services within single docker-compose stack.

Add PosgreSQL service next to the others, e.g. services: postgres:
Substitute host network by docker's one, e.g. network: annotation-network
Parameterize mount points from host machine by environment variables, e.g. volumes: $MEDIA_DATA:/django_media