Risteys

The project is based on the Phoenix web framework. This framework is written in elixir, which is also used to do data pre-processing and import into the database. The front-end interactions are using Vue.js. Communication between Vue.js and the backend is done using Phoenix Channels (which runs on Websockets).

Setting up a development environment

Requirements

• elixir

• node.js

• PostgreSQL database

Configuration

Some configuration files contain secret credentials, therefore are not present in this public GitHub repository. Risteys developer can get them by requesting access to the GitLab repository "risteys/risteys_secrets".

Create a file dev.secret.exs in the config/ directory, with the following content and replacing the <VAR>:

dev.secret.exs

use Mix.Config

# Configure your database
config :risteys, Risteys.Repo,
  username: "<USER>",
  password: "<PASSWORD>",
  database: "<DBNAME>",
  hostname: "<HOSTNAME>",
  pool_size: 10

Tips to find needed information:

• Open a psql console in a terminal by running psql postgres (\q to quit).

• List existing users by \du. If you don’t have postrgesql user (other than superuser), create a user with the ability to create a database.

  • create user: CREATE USER <username> WITH PASSWORD <password>;

  • grant permission to create a database: ALTER USER <username> CREATEDB;

• get database name: \conninfo

• get hostname:
  SELECT boot_val,reset_val
FROM pg_settings
WHERE name='listen_addresses';;

Create a file config.secret.exs in the config/ directory, with the below content and replacing the <INSERT KEY HERE> with key with a random key given by Vincent. (For a working project, a random key can be made by using a command mix phx.gen.secret 64).

config.secret.exs

use Mix.Config

# Configures the endpoint
config :risteys, RisteysWeb.Endpoint,
  url: [host: "localhost"],
  secret_key_base: "<INSERT KEY HERE>",
  render_errors: [view: RisteysWeb.ErrorView, accepts: ~w(html json)],
  pubsub: [name: Risteys.PubSub, adapter: Phoenix.PubSub.PG2]

First-time dependency initialization

From a terminal in the project root directory (i.e. risteys_elixir), run:

• mix deps.get to get the Elixir dependencies

• mix ecto.setup to create the DB and apply the migrations

• change directory to assets/ and then npm install to install the Javascript dependencies listed in the assets\package.json

  • if the command directs to some other file than assets\package.json and is not installing dependencies listed in that file, but gives an error instead, remove node_modules and package-lock.json and run again.

Running

change directory back to risteys_elixir and connect to the server: mix phx.server

You can now access Risteys from http://localhost:4000

Importing data

Import files are in risteys_elixir and they should be run in that directory: mix run import_icd9.exs <path-to-input-file>.
Input files are listed at the beginning of import_ files.

Import scripts should be run in this order:

1. import_icd10.exs

2. import_icd9.exs

3. import_endpoint_csv.exs

4. import_ontology.exs

5. import_aggregated_stats.exs

6. import_coxhr.exs