publish

PhyloPic: Publisher

Publishing scripts for PhyloPic builds.

Setting up

See instructions in the PhyloPic project README for setting up the monorepo project.

Prerequisites

Make sure you have the following installed on your system and reachable via the system path:

• AWS CLI (v2.4.20 or higher)
• Image Magick (v7.1 or higher)
• Inkscape (v1.1 or higher)
• Node.js (v16 or higher)
• potrace (v1.16 or higher)
• Yarn (v1.22 or higher)

Environment variables

The following environment variables are required. They may be stored in .env in the root of this project.

Variable Name	Description
API_CLOUDFRONT_DISTRIBUTION_ID	Distribution ID of the Amazon Web Services CloudFront distribution that serves as a CDN for the API
PGHOST	Postgres host
PGPASSWORD	Postgres password
PGUSER	Postgres user
REVALIDATE_KEY	Key for revalidating the main website pages
S3_ACCESS_KEY_ID	Amazon Web Services S3 access key ID
S3_REGION	Amazon Web Services S3 region
S3_SECRET_ACCESS_KEY	Amazon Web Services S3 secret access key
WWW_URL	Root URL of the main website (https://www.phylopic.org)

The following environment variables are optional:

Variable Name	Description
EOL_API_KEY	Encyclopedia of Life API key
PGPORT	Postgres port (default: 5432)

Running scripts

Release a new build

This will build and release a new build of the website, created from the files in the source-images.phylopic.org bucket and data in the phylopic-source database.

yarn make

Autolink externals

These commands will pull data from external APIs and try to match them to nodes in the phylopic-source database.

yarn autolink eol
yarn autolink gbif
yarn autolink otol
yarn autolink pbdb

Normalize names

Node names should be normalized already, but to ensure nothing got missed, they can all be normalized by running:

yarn normalize

Report silhouette coverage

This command will report coverage statistics for nodes (number of silhouettes per number of terminal nodes, as reported by the Open Tree of Life).

yarn coverage <UUID> <UUID> ...