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iNaturalist API client for python

Project description

pyinaturalist

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Introduction

iNaturalist is a community science platform that helps people get involved in the natural world by observing and identifying the living things around them. Collectively, the community produces a rich source of global biodiversity data that can be valuable to anyone from hobbyists to scientists.

pyinaturalist is a client for the iNaturalist API that makes these data easily accessible in the python programming language.

Features

  • ➡️ Easier requests: Simplified request formats, easy pagination, and complete request parameter type annotations for better IDE integration
  • ⬅️ Convenient responses: Type conversions to the things you would expect in python, and an optional object-oriented inteface for response data
  • 🔒 Security: Keyring integration for secure credential storage
  • 📗 Docs: Example requests, responses, scripts, and Jupyter notebooks to help get you started
  • 💚 Responsible use: Follows the API Recommended Practices by default, so you can be nice to the iNaturalist servers and not worry about rate-limiting errors
  • 🧪 Testing: A dry-run testing mode to preview your requests before potentially modifying data

Supported Endpoints

Many of the most relevant API endpoints are supported, including:

  • 📝 Annotations and observation fields
  • 🆔 Identifications
  • 💬 Messages
  • 👀 Observations (multiple formats)
  • 📷 Observation photos + sounds
  • 📊 Observation observers, identifiers, histograms, life lists, and species counts
  • 📍 Places
  • 👥 Projects
  • 🐦Species
  • 👤 Users

Quickstart

Here are usage examples for some of the most commonly used features.

First, install with pip:

pip install pyinaturalist

Then, import the main API functions:

from pyinaturalist import *

Search observations

Let's start by searching for all your own observations. There are numerous fields you can search on, but we'll just use user_id for now:

>>> observations = get_observations(user_id='my_username')

The full response will be in JSON format, but we can use pyinaturalist.pprint() to print out a summary:

>>> for obs in observations['results']:
>>>    pprint(obs)
ID         Taxon                               Observed on   User     Location
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
117585709  Genus: Hyoscyamus (henbanes)        May 18, 2022  niconoe  Calvi, France
117464920  Genus: Omophlus                     May 17, 2022  niconoe  Galéria, France
117464393  Genus: Briza (Rattlesnake Grasses)  May 17, 2022  niconoe  Galéria, France
...

You can also get observation counts by species. On iNaturalist.org, this information can be found on the 'Species' tab of search results. For example, to get species counts of all your own research-grade observations:

>>> counts = get_observation_species_counts(user_id='my_username', quality_grade='research')
>>> pprint(counts)
 ID     Rank      Scientific name               Common name             Count
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
47934   species   🐛 Libellula luctuosa         Widow Skimmer           7
48627   species   🌻 Echinacea purpurea         Purple Coneflower       6
504060  species   🍄 Pleurotus citrinopileatus  Golden Oyster Mushroom  6
...

Another useful format is the observation histogram, which shows the number of observations over a given interval. The default is month_of_year:

>>> histogram = get_observation_histogram(user_id='my_username')
>>> print(histogram)
{
    1: 8,  # January
    2: 1,  # February
    3: 19, # March
    ...,   # etc.
}

Create and update observations

To create or modify observations, you will first need to log in. This requires creating an iNaturalist app, which will be used to get an access token.

token = get_access_token(
    username='my_username',
    password='my_password',
    app_id='my_app_id',
    app_secret='my_app_secret',
)

See Authentication for more options including environment variables, keyrings, and password managers.

Now we can create a new observation:

from datetime import datetime

response = create_observation(
    taxon_id=54327,  # Vespa Crabro
    observed_on_string=datetime.now(),
    time_zone='Brussels',
    description='This is a free text comment for the observation',
    tag_list='wasp, Belgium',
    latitude=50.647143,
    longitude=4.360216,
    positional_accuracy=50,  # GPS accuracy in meters
    access_token=token,
    photos=['~/observations/wasp1.jpg', '~/observations/wasp2.jpg'],
)

# Save the new observation ID
new_observation_id = response[0]['id']

We can then update the observation information, photos, or sounds:

update_observation(
    17932425,
    access_token=token,
    description='updated description !',
    photos='~/observations/wasp_nest.jpg',
    sounds='~/observations/wasp_nest.mp3',
)

Search species

Let's say you partially remember either a genus or family name that started with 'vespi'-something. The taxa endpoint can be used to search by name, rank, and several other criteria

>>> response = get_taxa(q='vespi', rank=['genus', 'family'])

As with observations, there is a lot of information in the response, but we'll print just a few basic details:

>>> pprint(response)
[52747] Family: Vespidae (Hornets, Paper Wasps, Potter Wasps, and Allies)
[92786] Genus: Vespicula
[84737] Genus: Vespina
...

Next Steps

For more information, see:

  • User Guide: introduction and general features that apply to most endpoints
  • Endpoint Summary: a complete list of endpoints wrapped by pyinaturalist
  • Examples: data visualizations and other examples of things to do with iNaturalist data
  • Reference: Detailed API documentation
  • Contributing Guide: development details for anyone interested in contributing to pyinaturalist
  • History: details on past and current releases
  • Issues: planned & proposed features

Feedback

If you have any problems, suggestions, or questions about pyinaturalist, please let us know! Just create an issue. Also, PRs are welcome!

Note: pyinaturalist is developed by members of the iNaturalist community, and is not endorsed by iNaturalist.org or the California Academy of Sciences. If you have non-python-specific questions about the iNaturalist API or iNaturalist in general, the iNaturalist Community Forum is the best place to start.

Related Projects

Other python projects related to iNaturalist:

  • naturtag: A desktop application for tagging image files with iNaturalist taxonomy & observation metadata
  • pyinaturalist-convert: Tools to convert observation data to and from a variety of useful formats
  • pyinaturalist-notebook: Jupyter notebook Docker image for pyinaturalist
  • dronefly: A Discord bot with iNaturalist integration, used by the iNaturalist Discord server.

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