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Overview

New research from the University of Notre Dame will be used to generate maps that provide time-sensitive estimates of mosquito densities, human birth rates and Zika transmission activity across Latin America and the Caribbean. The model outputs will be available online to provide users with the ability to find reported cases and estimated incidences by location to improve disease transmission and prevalence forecasts, which is critical to making accurate predictions and translating results into effective public health strategies.

The study is being conducted by Alex Perkins, Eck Family Assistant Professor of Biological Sciences and Eck Institute for Global Health affiliated faculty member, who received a rapid response grant (RAPID) from the National Science Foundation’s (NSF) Division of Environmental Biology’s Ecology and Evolution of Infectious Diseases Program for his research proposal that focuses on enabling estimation and forecasting of Zika virus transmission. NSF created these RAPID awards in order to specifically understand the rate of spread, number of infected people and the likely persistence of Zika as a public health threat, and to help prepare for the next outbreak.

Results from the project will benefit the Zika public health emergency response, as researchers will have tools in place to share quality data and forecasts both during the study and after the project concludes. This will be a valuable asset for policymakers as they continue to make decisions surrounding this disease.

#System requirements

This Django project has been tested on Windows 10 x64, MAC OS 10.7 and CentOS 7

  • Django 1.10
  • Python 3.4
  • PostgreSQL 9.4
  • Apache 2.4

Project documentation

Project documentation, including meeting minutes is on Google Drive - https://drive.google.com/drive/folders/0BwiQpgfLBcI1aVVtQ2VoVnBoMHc

#Quick Start Guide

  1. Create database structures ./manage.py migrate

  2. Check if there are database migrations by reviewing the list of known migrations: ./manage.py migrate --list

  3. Create an admin user ./manage.py createsuperuser

  4. Upload simulation data Click the 'Upload Simulation' link. Select this file: website/apps/simulation/data/data_cases_combo_new.csv Click Upload. There will now be data to visualize in charts and maps.

Using docker-compose

Run docker-compose up in the project's root directory to quickly start development without having to setup a specific dev environment first.

By default, the web interface is reachable at 'http://127.0.0.1:8001', while the database is listening on port 5433.

#Using Vagrant

  1. Create Virtualbox VM vagrant up. It may take a while when starting VM for the first time

  2. Login to VM using vagrant ssh command or your favorite ssh client. Login: vagrant, password vagrant

  3. Switch to /vagrant directory cd /vagrant

  4. Start django server python manage.py runserver 0.0.0.0:8000 Note you have to use 0.0.0.0 as server address, otherwise port forwarding may not work

You can edit files in your project directory, and changes will be visible to the virtual machine (in /vagrant directory)

Credentials

SSH Login: vagrant, password vagrant

PostgreSQL Database: zika, Login: zika, Password: zika

Note: To utilize the PostgreSQL database, create a settings_local.py file containing the following:

DATABASES = {
    'default': {
        'ENGINE': 'django.db.backends.postgresql_psycopg2',
        'NAME': 'zika',
        'USER': 'zika',
        'PASSWORD': 'zika',
        'HOST': '127.0.0.1',
        'PORT': '5432',
    }
}

Specifying settings file

  1. By default, website.settings.dev is used for manage.py and website.settings.prod is used in wsgi.py It is typically required to change default settings file used in manage.py in production and qa enviroments

  2. Exporting DJANGO_SETTINGS_MODULE variable

This method works well on the command line, but it doesn't seem to work with apache - SetEnv doesn't seem to have any effect when mod_wsgi is initalizing wsgi application object.

  1. Creating config_local.py in the root folder (next to wsgi.py and manage.py)

Note if DJANGO_SETTINGS_MODULE is defined, it takes precedence over settings_module in config_local.py

Example:

settings_module = "website.settings.qa"

Check wsgi.py and manage.py to see how it works - they are different from default versions generated by Django.

Production deployment checklist

  1. Copy config_local_example.py to config_local.py

  2. Generate new SECRET_KEY in settings_local.py

  3. Enable VecNet SSO

  4. Make sure web server has write access to media and logs directories

sudo chown avyushko:www-data logs
sudo chmod -R g+rw logs
sudo chown avyushko:www-data media
sudo chmod -R g+rw media
sudo chmod g+rwx media/simulation_files

Enable VecNet SSO

  1. Install django-auth-pubtkt package pip install django-auth-pubtkt

  2. Copy public key for validating pubtkt tickets to /etc/httpd/conf/sso/tkt_pubkey_dsa.pem

  3. Enable DjangoAuthPubtkt middleware - put snippet below to website/settings_local.py Order is important - if you choose to keep standard Django authentication backends, then django_auth_pubtkt.DjangoAuthPubtkt should be after them.

    'django.middleware.common.CommonMiddleware',
    'django.contrib.sessions.middleware.SessionMiddleware',
    'django.middleware.csrf.CsrfViewMiddleware',
    'django_auth_pubtkt.DjangoAuthPubtkt',
    'django.contrib.messages.middleware.MessageMiddleware',
) ```

4. Set configuration options below (in website/settings_local.py)
```from django_auth_pubtkt.views import redirect_to_sso
from django.conf.urls import url
LOGIN_URL = "/sso/"
TKT_AUTH_LOGIN_URL = "https://www.vecnet.org/index.php/sso-login"
TKT_AUTH_PUBLIC_KEY = '/etc/httpd/conf/sso/tkt_pubkey_dsa.pem'
SSO_URLS = [url(r'^sso/', redirect_to_sso),]