Build & run

Table of Contents

• Introduction
• Quick start
• Docker containers

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Introduction

Before setting up SciNote server, you are advised to read the Technical overview section to get a general idea about the SciNote architecture, and what are the options for setting up SciNote.

Development mode

This section describes the setup of SciNote server in development mode. If you want to setup SciNote server in a production mode, please visit the Production mode section.

Prerequisites

Please make sure to also read the Prerequisites section before proceeding with the SciNote setup below.

Quick start

Assuming the prerequisites are met, the following are the minimal steps neccesary to start SciNote server in development mode:

1. Clone SciNote Git repository onto your development machine

git clone https://github.com/biosistemika/scinote-web.git

2. Configure the server

To setup the basic configuration of SciNote server, create a file config/application.yml in the root SciNote directory.

Populate it with mandatory environmental variables, as described in the environmental variables section.

The configuration file is used to store the configuration environmental variables in YAML format - basically, it acts as a simple key-value store for variables, which are loaded into the process environment at a run-time.

3. Build the local Docker images

In SciNote root folder, run the following command:

make docker

This command will build the neccesary SciNote Docker image locally.

This process can take a while, since the Ruby image needs to be pulled from the Internet.

After this is done, run the following command when inside the SciNote root folder:

make run

This command is generally used to start the SciNote server, but at this specific timepoint it is used to build the PostgreSQL Docker image locally. Once the SciNote server starts (it is not yet functional), you should see something similar to this in the console output:

[1] * Preloading application
[1] * Listening on tcp://0.0.0.0:3000
[1] Use Ctrl-C to stop
[1] - Worker 0 (pid: xx) booted, phase: 0
[1] - Worker 1 (pid: yy) booted, phase: 0

Press Ctrl + C to shutdown the server.

4. Initialize the database

To enter the SciNote container, run the following command when inside the SciNote root folder:

make cli

Once inside the container, run the following sequence of commands:

rails db:drop
rails db:create
rails db:migrate
rails db:seed

This sequence of commands will drop the database, create it, migrate the data schema, and seed the initial data into the PostgreSQL database.

5. Load the front-end dependencies

While still inside the container, run the following 2 commands:

yarn
rails webpacker:compile

This will load & bundle the front-end dependencies (JavaScript, CSS assets).

If yarn command doesn't work, try npm install.

Exit the Docker container by typing exit.

6. Start the server

To finally start the SciNote server, run the following command from the SciNote root folder:

make run

This command will start the SciNote server (web workers), and print the output to the terminal. Wait until the server starts listening on port 3000.

To also start the background worker process, you should navigate to SciNote root folder in another terminal window, and run the following command:

make worker

The background worker process is used by SciNote for a lot of demanding tasks.

That's it! Open your favourite browser and navigate to http://localhost:3000. Use the seeded administrator account from seeds.rb (or different admin credentials set up using environmental variables) to login, or sign up for a new account.

Docker containers

SciNote server in development mode uses the following Docker containers:

1. scinote_development_postgres (persistent) hosts all database engine files, and is placed by default into /var/lib/docker/volumes folder on the host system;
2. scinote_development_files (persistent) stores all generated & uploaded files when SciNote is configured to use local filesystem for storage (PAPERCLIP_STORAGE is set to 'filesystem'); it is mapped to the public/system folder within the SciNote root folder;
3. scinote_db_development (non-persistent) hosts the database engine process;
4. Job worker container (non-persistent) hosts the background worker process;
5. scinote_web_development (non-persistent) hosts the web application process.

These Docker containers were introduced to SciNote in version 1.10.0; previous versions had a different containers set.