AmphibianDisease.org - ARCHIVE ONLY

29 Jan 2020 Update: Amphibian Disease portal has migrated! Read more in our blog announcement here. This repo is frozen at the moment during our transition.

Please refer to our current repo at AmphibiaWebDiseasePortal 2.0

Visit the new site at AmphibianDisease.org

Quick Links

• Project Site
• Project Dashboard
• Project Contribution Page
• AmphibianDisease.org Code
• AmphibianDisease.org API

Documentation

See the documentation over at https://amphibian-disease-tracker.readthedocs.org/en/latest

Features

TODO

Data Storage

You can view a CSON representation of the data storage of the system at ./meta/data-storage.coffee

There is no equivalent to BD-Maps' following fields:

• Global ID: Redundant to sample ID
• Country / Continent / Region: Redundant and derivable from coordinate bounding boxes
• Elevation: Lookup-able from sample coordinates
• Accuracy: Should be built in to radius field.
• Coordinate source: Is the model of GPS actually relevant?
• Developmental stage: Per-sample, should be included in raw data. At a high level, redundant to sampled_species_detail[N].sampled_life_stages
• Method of detection: Since this may vary on a per-sample basis, this is relegated to the raw data.
• Abnormalities: Problems in data are encapsulated in disease_no_confidence, problems with animals belong with the raw data.
• All individual sample data (eg, spore count, genbank ID, etc): Belongs in raw data

Configuration Data

This data is encrypted using BlackBox. If you want access to the configuration, please ask to have your credentials added, or add it yourself in a clone and push the changes. Once you let an administrator know, you can be added to the keyring and gain decryption privledges.

Building the application

Dependencies

This writeup assumes you have access to a Linux-like environment. If you run Windows, set up Bash on Ubuntu on Windows (WSL) for best results.

Your life will also be a lot easier if you have Homebrew or LinuxBrew installed.

Build dependencies

• Yarn You can install Yarn by running brew install yarn
• Grunt. You can install Grunt from the command line by running yarn global add grunt-cli.
• Recommended: Coffeescript and Less. They're included locally but often behave better globally via yarn global add coffee-script less
• Run yarn install to install local dependencies.

Deploy dependencies

• Blackbox You can install Blackbox by runing brew install blackbox

Deploying

You can update the whole application, with dependencies, by running grunt build at the root directory.

If you don't need to update dependencies, just run grunt qbuild.

Installation

Configuration Files

If you're part of the project, your PGP public key should already be registered in the application. If you need to make changes, do:

blackbox_edit_start PATH/TO/FILE.ext.gpg
# Edit your file
blackbox_edit_end PATH/TO/FILE.ext

The two primary configuration files are CONFIG.php.gpg and admin/CONFIG.php.gpg