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GBIF Download Standalone

Description of folders:

  • 01_prepare_checklist: code to preprocess species checklists and fetch GBIF taxonomic data
  • 02_preprocess_dwca: code to preprocess the Darwin Core Archive files, to be used by subsequent download code.
  • 03_download_images: code to download GBIF images.
  • species_checklists: original checklists provided by CEH, as well as their preprocessed versions.
  • data_stats_files: csv files containing an "n_imgs" column specifying how many images we have downloaded for a given species checklist.
  • helper_files: miscellaneous helper files.
  • helper_scripts: miscellaneous helper scripts for code development, debugging, testing, etc.

Setting up the environment

The repository uses conda to manage the environment and packages which are specified in the environment.yml file.

For first time use, create a new conda environment using:

source ~/miniforge3/bin/activate
conda create -p ../conda_envs/gbif_download_standalone

The -p argument should be the full path to the location of the environment.

Run conda activate gbif_download_standalone.

Update the environment with packages specified in environment.yml: conda env update --file environment.yml --prune

On basekerville you can skip straight to:

conda activate gbif_download_standalone

Pre-commits

Pre-commits are specified in the .pre-commit-config.yaml file.

For first time use, run pre-commit install --install-hooks.

Note various exceptions for flake8 specified in file .flake8

Sequence of steps to take:

  1. Prepare the species checklist file for each region. This will be used to download GBIF images. See 01_prepare_checklist for further instructions.
  2. Preprocess the Darwin Core Archive file. The Darwin Core Archive (dwca) file for the checklist needs to be extracted and preprocessed. See 02_preprocess_dwca for further instructions. This step does not need to be run every time.
  3. Download GBIF images. Using the dwca files and the checklist, get images from GBIF. Then, calculate a summary file documenting how many images we have for the checklist. See 03_download_images for further instructions.

License and authorship

The code in this repository is adapted and modified from RolnickLab Species Trainer repository.

See the LICENSE file.