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NeuroScout web app and API

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# neuroscout

[![Build Status](https://travis-ci.com/PsychoinformaticsLab/neuroscout.svg?token=mytABRBRnBitJJpBpMxh&branch=master)](https://travis-ci.com/PsychoinformaticsLab/neuroscout)
[![codecov](https://codecov.io/gh/neuroscout/neuroscout/branch/master/graph/badge.svg)](https://codecov.io/gh/neuroscout/neuroscout)
[![DOI](https://zenodo.org/badge/68325864.svg)](https://zenodo.org/badge/latestdoi/68325864)

This is the repository for the neuroscout server.

Requirements: Docker and docker-compose.

## Configuration
First, set up the main environment variables in `.env` (see: `.env.example`).
Set `DATASET_DIR`, `KEY_DIR`, and `FILE_DATA` to folders on the host machine.

Optionally, set up pliers API keys for feature extraction in `.pliersenv` (see: `.pliersenv.example`).
[More information on pliers API keys](http://tyarkoni.github.io/pliers/installation.html#api-keys)

Next, set up the Flask server's environment variables by modifying `neuroscout/config/example_app.py`
and saving as `neuroscout/config/app.py`.

Finally, set up the frontend's env variables by modifying `neuroscout/frontend/src/config.ts.example`
and saving as `neuroscout/frontend/src/config.ts`.

For single sign on using Google, a [sign-in project](https://developers.google.com/identity/sign-in/web/sign-in) is needed.

## Initalizing backend
Build the containers and start services using the development configuration:

docker-compose -f docker-compose.yml -f docker-compose.dev.yml build
    docker-compose -f docker-compose.yml -f docker-compose.dev.yml up -d

The server should now be running at http://localhost/

Next, initialize, migrate and upgrade the database migrations.
If you have a database file, load it using `pg_restore`. Otherwise, delete the migrations folder,
initalize the database and add a test user.

docker-compose exec neuroscout bash
    rm -rf /migrations/migrations
    python manage.py db init
    python manage.py db migrate
    python manage.py db upgrade
    python manage.py add_user useremail password

### Staging & production server

For the staging server, you can trigger a manual build as follows:

docker-compose -f docker-compose.yml -f docker-compose.build.yml build
    docker-compose -f docker-compose.yml -f docker-compose.build.yml up -d

For the staging or production server, you can trigger pull a pre-built image from GHCR:
First set the variable `IMAGE_TAG` to the apprioriate image tag

docker-compose -f docker-compose.yml -f docker-compose.image.yml build
    docker-compose -f docker-compose.yml -f docker-compose.image.yml up -d

## Setting up front end
The frontend dependencies are managed using `yarn`

Enter the neuroscout image, and install all the necessary libraries like so:

docker-compose exec neuroscout bash
    cd frontend
    yarn

You can then start a development server:

yarn start

Or make a production build:

yarn build

## Ingesting datasets and extracting features
You can use `manage.py` commands to ingest data into the database.
Run the following commands inside docker: `docker-compose exec neuroscout bash`

To add BIDS datasets

python manage.py add_task bids_directory_path task_name

For example for dataset ds009

python manage.py add_task /datasets/ds009 emotionalregulation

Finally, once having added a dataset to the database, you can extract features
  using pliers into the database as follows:

python manage.py extract_features bids_directory_path task_name graph_json

For example:

python manage.py extract_features /datasets/ds009 emotionalregulation graph.json

Even easier, is to use a preconfigured dataset config file, such as:

docker-compose exec neuroscout python manage.py ingest_from_json /neuroscout/config/ds009.json

## Maintaining docker image and db
If you make a change to /neuroscout, you should be able to simply restart the server.

docker-compose restart neuroscout

If you need to upgrade the db after changing any models:

docker-compose exec neuroscout python manage.py db migrate
    docker-compose exec neuroscout python manage.py db upgrade

To inspect the database using psql:

docker-compose run postgres psql -U postgres -h postgres

## API
Once the server is up and running, you can access the API however you'd like.

The API is document using Swagger UI at:

http://localhost/swagger-ui

### Authorization
To authorize API requests, we use JSON Web Tokens using Flask-JWT. Simply navigate to localhost:5000/auth and post the following

{
        "username": "user@example.com",
        "password": "string"
    }

You will receive an authorization token in return, such as:

{
        "access_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6MSwiaWF0IjoxNDQ0OTE3NjQwLCJuYmYiOjE0NDQ5MTc2NDAsImV4cCI6MTQ0NDkxNzk0MH0.KPmI6WSjRjlpzecPvs3q_T3cJQvAgJvaQAPtk1abC_E"
    }

You can then insert this token into the header to authorize API requests:

GET /protected HTTP/1.1
    Authorization: JWT eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6MSwiaWF0IjoxNDQ0OTE3NjQwLCJuYmYiOjE0NDQ5MTc2NDAsImV4cCI6MTQ0NDkxNzk0MH0.KPmI6WSjRjlpzecPvs3q_T3cJQvAgJvaQAPtk1abC_E

Note that in order to use any protected routes, you must confirm the email on your account. Confusingly, you can get a valid token without confirming your account, but protected routes will not function until confirmation.

## Running backend tests
To run tests, after starting services, create a test database:

docker-compose exec postgres psql -h postgres -U postgres -c "create database scout_test"

and execute:

docker-compose run -e "APP_SETTINGS=neuroscout.config.app.DockerTestConfig" --rm -w /neuroscout neuroscout python -m pytest neuroscout/tests

or run them interactively:
    docker.compose exec neuroscout bash
    APP_SETTINGS=neuroscout.config.app.DockerTestConfig python -m pytest neuroscout/tests/ --pdb

To run frontend tests run:

docker-compose run --rm -w /neuroscout/neuroscout/frontend neuroscout npm test

## Running frontened tests
To run frontend tests, have Cypress 6.0 or greater installed locally.
First, ensure neurscout is running:

docker-compose -f docker-compose.yml -f docker-compose.dev.yml up -d

Next, set up the test environment:

docker-compose exec neuroscout bash
    export APP_SETTINGS=neuroscout.config.app.DockerTestConfig
    bash setup_frontend_tests.sh

In a separate window, you can run cypress:

cd neuroscout/frontend
   cypress open

Once done, kill the first command, and run the following to tear down the test db

docker-compose exec -e APP_SETTINGS=neuroscout.config.app.DockerTestConfig neuroscout python manage.py teardown_test_db

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