BioModelos v2.12.7

BioModelos is a web app that facilitates the generation, validation and consultation of hypothesis of species distribution for the continental biodiversity of Colombia. As such, it provides tools to (1) improve existing species distribution models (SDMs) by integrating expert's opinion, (2) generate expert maps and (3) publish SDMs. Our objective is to provide freely and openly access to the most up to date information on species distributions, validated by a large network of researchers, to support national environmental decision making processes and research.

Requirements

Services

Deploy these services before setting up the app:

• BioModelos API Service GitHub Repo
• PosgresSQL Database Service v.17

Software

• Ruby version 3.1.6. It is advisable to use rbenv to install and manage ruby local version.
• Docker version 17.05 or up.
• Git.
• npm version 10.8.2.
• Yarn classic version 1.22.22. Install it using npm.

Setup

Download the source code

Clone the repository to the server where you are deploying the app:

$ git clone https://github.com/PEM-Humboldt/biomodelos-website.git

Web app database

To build the database according to the schema file using the SQL Service, you should follow the next steps:

1. Create a database.yml file with the configuration of your SQL Service and add it to the /config/ path. Use database_template.yml as a template which is located at /config/ folder
2. Once you have the Docker container running, you may execute the migrations /db/migrate/ following this guide.

Configuration

Some files and paths in BioModelos need to be configured in order for the app to work as intended.

Files

• Models folder with raster files.
• Thumbnails folder with thumbnails image files.
• Zip folder with zip files of the models.

Connection to other BioModelos services

You need to setup a path for the BioModelos API service URL and geoserver URL, then, you must create a new file url.rb under the /config/initializers/ folder and setup the next env vars:

BASE_URI = "http://localhost:3000/v2";
GEOSERVER_URI = "http://localhost:8080/geoserver";

Credentials and Keys

You need to configure the secret credentials in an encrypted file such as ENVIRONMENT.yml.enc, where ENVIRONMENT must be: production, development or test.

There are more Information about how to setup the credentials.

These credentials files require the master key file (ENVIRONMENT.key) to decrypt and modify the keys according to your specific requirements.

In this file you should put information about:

• Google maps key.
• Recaptcha keys (Version 2 and 3).
• SMTP credentials.

Content file example:

# Rails Secret Key
SECRET_KEY_BASE: "secret key"

# Google Maps API
google_maps:
  GOOGLE_MAPS_KEY: "secret key"

# Google reCaptcha
recaptcha:
  RECAPTCHA_SITE_KEY_V2: "secret key"
  RECAPTCHA_SECRET_KEY_V2: "secret key"
  RECAPTCHA_SITE_KEY_V3: "secret key"
  RECAPTCHA_SECRET_KEY_V3: "secret key"

# Mail Server Gmail
mail_server:
  GMAIL_USERNAME: "secret email"
  GMAIL_PASSWORD: "secret password"

For Humboldt organization, you must copy the encrypted files and the master keys from the internal repository to config/credentials.

Run

Important: You should have installed previously Ruby 3.1.6.

Install dependencies using these commands in your terminal

$ gem install bundler -v 2.6.5

$ bundle install

$ yarn

Run the following command to execute the app in your local env terminal

$ bundle exec rails s -b 0.0.0.0

Extra configuration are at the internal repository.

Dockerization

Environment variables

To run the application in Docker, you need to configure the environment variables in the .env file, as in this example. This file contains environment variables for the rails application and configuration variables for the docker container.

Dev env with docker

You can create a docker container for development purposes, just build the image with the docker-compose.dev.yml file:

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

And remember to configure the volumes in the .env file

Deploy

Copying static files

First, there are some static .PDF, .PNG and .ZIP files that you need to copy to the /public/ folder. Those files are part of the guides and graphic pieces to advertise BioModelos and are not part of our repo.

Environment variables

Configure the .env file according to the example.

You must modify the .env file and configure the volumes according to the methods, models, thumbs, zip, uploads and credentials folders.

Running the container

It's recommended to use docker-compose to build the image and run the container.

The production docker-compose file is included in the repository.

On the root path of the rails app you enter this command to build the image and run the container:

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

LICENSE

The MIT License (MIT) 2018 - Instituto de Investigación de Recursos Biológicos Alexander von Humboldt. Please have a look at the LICENSE.md file for more details.