Dockerized Taxa Tree Generators

Dockerized version of Taxa Tree Generators

Live version available at https://taxon.specifysoftware.org

Installation

Clone the repositories:

git clone https://github.com/specify/taxa_tree_docker
cd taxa_tree_docker
git clone --single-branch --branch gbif https://github.com/specify/taxa_tree ./taxa_tree_gbif
git clone --single-branch --branch itis https://github.com/specify/taxa_tree ./taxa_tree_itis
git clone --single-branch --branch catalogue_of_life_3 https://github.com/specify/taxa_tree ./taxa_tree_col 
git clone --single-branch --branch master https://github.com/specify/taxa_tree_stats ./taxa_tree_stats
git clone --single-branch --branch worms https://github.com/specify/taxa_tree ./taxa_tree_worms
git clone https://github.com/specify/taxa_tree_stats

Install certbot and generate the certificates

sudo certbot certonly -d taxon.specifysoftware.org

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In development, you can generate some test certificates by running these commands inside the taxa_tree_docker dir:

openssl genrsa -out privkey.pem 2048
openssl req -new -key privkey.pem -out localhost.csr
openssl x509 -req -days 365 -in localhost.csr -signkey privkey.pem -out fullchain.pem

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Modify the nginx's volumes section of docker-compose.yml to point to the location of fullchain.pem and privkey.pem

      - './fullchain.pem:/etc/letsencrypt/live/taxon.specifysoftware.org/fullchain.pem:ro'
      - './privkey.pem:/etc/letsencrypt/live/taxon.specifysoftware.org/privkey.pem:ro'

You can configure regular certificate renewal, but that is beyound the scope of this documentation

Config

Find the following line in the ./docker-compose.yml file:

args:
  LINK: 'https://taxon.specifysoftware.org'

Change the LINK variable to an address where the server would be publicly available.

To disable a certain provider, remove it from update-taxa.sh and index.html.

Usage

Start the containers:

docker-compose up

The first startup may take quite some time as the base container images are downloaded, containers are built, taxa trees are downloaded and cache is created.

Copying WoRMS archive

Once you have obtained an archive of WoRMS data, you need to copy it to the correct directory in the back end container to generate the tree.

docker cp /full/path/on/your/system/to/archive.zip taxa_tree_docker-back_end-1:/home/specify/taxa_tree_worms_working_dir/archive.zip

Update data

To begin, you'll need to call the update-taxa shell script file in the back-end container.

To update all sources, you can run this command:

docker exec taxa_tree_docker-back_end-1 ./update-taxa.sh

Catalogue of Life:

docker exec taxa_tree_docker-back_end-1 sh -c "cd /home/specify/taxa_tree_col/back_end/ && /home/specify/venv/bin/python3 refresh_data.py"

GBIF:

docker exec taxa_tree_docker-back_end-1 sh -c "cd /home/specify/taxa_tree_gbif/back_end/ && /home/specify/venv/bin/python3 refresh_data.py"

ITIS:

docker exec taxa_tree_docker-back_end-1 sh -c "cd /home/specify/taxa_tree_itis/back_end/ && /home/specify/venv/bin/python3 refresh_data.py"

WoRMS: (Requires the WoRMS archive in the previous step)

docker exec taxa_tree_docker-back_end-1 sh -c "cd /home/specify/taxa_tree_worms/back_end/ && /home/specify/venv/bin/python3 refresh_data.py"

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Regular updates

It is recommended to also configure a CRON job to check for taxa updates from each provider.

Example crontab:

0 4 * * * docker exec taxa_tree_docker-back_end-1 ./update-taxa.sh >> /home/specify/update-taxa.log 2>&1