BioModelos v2.10.3

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:

• MongoDB Database Service
• BioModelos API Service GitHub Repo
• SQL Database Service

Software

• Ruby version 2.5. It is advisable to use rbenv to install and manage ruby local version.
• Docker version 17.05 or up.
• Git
• Bower

Setup

Download the source code

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

$ git clone git://github.com/LBAB-Humboldt/BioModelos.v2.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 to the BioModelos API service URL and geoserver URL. 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";

Keys and credentials

The app needs the following keys which you can set up in a local_env.yml file under the config folder like this:

SECRET_KEY_BASE: [secret key base]

\# Google Maps API
GOOGLE_MAPS_KEY: [key]

\# Google reCaptcha
RECAPTCHA_SITE_KEY: [site key]
RECAPTCHA_SECRET_KEY: [secret key]

\# Mail Server Gmail
GMAIL_USERNAME: [username]
GMAIL_PASSWORD: [password]

There, you should put information about:

• Rails Application key.
• Google maps key.
• Recaptcha key.
• SMTP credentials.

Run

Install dependencies

gem install bundler

bundle install

bower install --allow-root

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

bundle exec rails s -b 0.0.0.0

Dev env with docker

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

$ docker build -f Dockerfile.dev -t <image name> .

And remember to mount the volumes (or link them) in your source code path

Deploy

Copying static files

First, there are some static .PDF, .PNG and .ZIP files 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.

Building the image

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

$ docker build -t <image name>:<tag> .

Starting the container

Once you have the image, it's recommended to use docker-compose to run the container.

You need to create a docker-compose.yml file and set the volumes according to the models, thumbnails, zip and uploads folders like this:

version: '3'
services:
  biomodelos:
    image: [image name]
    ports:
     - [host port]:[container port]"
    volumes:
     - /path/to/host/methods:/var/www/BioModelos/public/methods
     - /path/to/host/models:/var/www/BioModelos/public/models
     - /path/to/host/thumbs:/var/www/BioModelos/public/thumbs
     - /path/to/host/zip:/var/www/BioModelos/public/zip
     - /path/to/host/uploads:/var/www/BioModelos/public/uploads

Finally, you run the container with the next command:

$ docker-compose up -d

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.