OneZoom Tree Building repo

This repository contains everything that is needed to build the OneZoom tree and all the other files needed by the backend. It also contains scripting libraries for harvesting information from wikidata and images from wikimedia commons that can be used to populate a running OneZoom instance.

Setting up the environment

The first step to using this repo is to create a Python virtual environment and activate it:

# From the root of the repo, create a Python environment and activate it
python -m venv .venv
source .venv/bin/activate

# Install it
pip install -e .

After the first time, you just need to run the source .venv/bin/activate each time you want to activate it in a new shell.

If you want to run the test suite, make sure the test requirements are also installed, with:

pip install -e '.[test]'

Testing

Assuming you have installed the test requirements, you shoule be able to run

python -m pytest --conf-file tests/appconfig.ini

Here we have used a basic conf file to create a fake OneZoom database. However, if you wish to test using the real OneZoom database, you can specify a different path to an appconfig.ini file, or omit the --conf-file option entirely, in which case the test suite will look for ../OZtree/private/appconfig.ini, which assumes hat this repository is a sibling to a non-live OZtree installation, and that the database used by this OZtree installation is active.

python -m pytest  # Uses the "real" OneZoom database - take care!

This uses mocked APIs. You can also run with the real APIs using the --real-apis swithc, in whcih case you will need a valid Azure Image cropping key in your appconfig.ini.

Building the latest tree from OpenTree

Setup

We assume that you want to build a OneZoom tree based on the most recent online OpenTree version. You can check the most recent version of both the synthetic tree (synth_id) and the taxonomy (taxonomy_version) via the API e.g. by running curl -X POST https://api.opentreeoflife.org/v3/tree_of_life/about. Later in the build, we use specific environment variables set to these version numbers. Assuming you are in a bash shell or similar, you can set them as follows:

OT_VERSION=14_9 #or whatever your OpenTree version is
OT_TAXONOMY_VERSION=3.6
OT_TAXONOMY_EXTRA=draft1 #optional - the draft for this version, e.g. `draft1` if the taxonomy_version is 3.6draft1

Download

Constructing the full tree of life requires various files downloaded from the internet. They should be placed within the appropriate directories in the data directory, as documented here.

Building the tree

Once data files are downloaded, you should be set up to actually build the tree and other backend files, by following these instructions.