pyinaturalist-open-data 0.1.1

Python utilities for working with inaturalist-open-data

pyinaturalist-open-data

This is a work in progress and not yet complete!

pyinaturalist-open-data is a python library and CLI tool for working with inaturalist-open-data. Its goal is to make it easy to import and use this dataset in a python application backed by any SQLAlchemy-compatible database engine (SQLite by default), or simply for local data exploration.

See the CLI in action here or on asciinema:

Installation

Install with pip:

pip install pyinaturalist-open-data

Or for local development:

git clone https://github.com/JWCook/pyinaturalist-open-data.git
cd pyinaturalist-open-data
pip install poetry && poetry install

Usage

This package provides the command pynat. See --help for commands and options:

Usage: pynat [OPTIONS] COMMAND [ARGS]...

  Commands for working with inaturalist open data

Options:
  -v, --verbose  Show more detailed output
  --help         Show this message and exit.

Commands:
  db    Load contents of CSV files into a database
  dl    Download and extract inaturalist open data archive
  init  Just create tables (if they don't already exist) without populating...
  load  Download and load all data into a database.

Run everything

The simplest command is load, which runs all steps:

1. Download and extract the dataset
2. Create database tables and indices
3. Load the data into the database

Options:

Usage: pynat load [OPTIONS]

Options:
  -d, --download-dir TEXT  Alternate path for downloads
  -u, --uri TEXT           Alternate database URI to connect to
  --help                   Show this message and exit.

By default, this will create a new SQLite database. Alternatively, you can provide a URI for any supported database.

Run individual steps

Other commands are available if you only one to run one of those steps at a time.

dl command:

Usage: pynat dl [OPTIONS]

  Download and extract all files in the inaturalist open data archive

Options:
  -d, --download-dir TEXT  Alternate path for downloads
  --help                   Show this message and exit

Note: Both dl and load will reuse local data if already exists and is up to date.

db command:

Usage: pynat db [OPTIONS]

  Load contents of CSV files into a database. Also creates tables and
  indexes, if they don't already exist.

Options:
  -d, --download-dir TEXT         Alternate path for downloads
  -i, --init                      Just initialize the database with tables
                                  + indexes without loading data
  -t, --tables [observation|photo|taxon|user]
                                  Load only these specific tables
  -u, --uri TEXT                  Alternate database URI to connect to

  --help                          Show this message and exit.

Note: This can take a long time to run. Depending on the database type, you will likely get better performance with database-specific bulk loading tools (for example, psql with COPY for PostgreSQL)

Python package

To use as a python package instead of a CLI tool:

from pyinaturalist_open_data import download_metadata, load_all

download_metadata()
load_all()

Full package documentation on readthedocs will be coming soon.

Planned features

Some features I would ideally like to add to this:

• Performance optimizations
• Basic querying features
• Image downloads based on query results
• Integration with iNaturalist API data via pyinaturalist
• Integration with CSV data from the iNaturalist export tool