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ITIS to CoLDP Conversion Tool

Using Docker Compose, this data pipeline automatically converts ITIS.gov's monthly MySQL export to CoLDP format for publishing in ChecklistBank. The utility checks for an update from ITIS, downloads the update, imports it into a docker MySQL database, converts the data to CoLDP format and then exports the data as tab-delimited text files in the coldp directory.

Use

  1. Clone the repository:
git clone https://github.com/catalogueoflife/data-itis.git

  1. The ITIS database does not provide extinct statuses so ask for an updated list of extinct TSNs from ITIS and update the raw/extinct.tsv

  2. Run the docker conversion container (replacing DATABASE_PASSWORD with any password you want):

DATABASE_PASSWORD=password COL_USER=user COL_PASS=pass COL_API=api_host COL_DATASET_ID=2144 docker-compose run conversion

If the optional environment variables COL_USER, COL_PASS, COL_API, and COL_DATASET_ID are provided, the dataset will be automatically uploaded into ChecklistBank.