29 Jan 2020 Update: Amphibian Disease portal is migrating! Read more in our blog announcement here. This repo is frozen at the moment during our transition. Look forward to new stability and functionality!
Please refer to AmphibiaWebDiseasePortal 2.0
See the documentation over at https://amphibian-disease-tracker.readthedocs.org/en/latest
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
- 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
- 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
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
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.
- 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
yarn installto install local dependencies.
- Blackbox You can install Blackbox by runing
brew install blackbox
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
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