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Python client for the iNaturalist APIs

Project description

pyinaturalist

Build status Documentation Status (stable) Documentation Status (latest) Coverage Status PyPI PyPI - Python Versions PyPI - Format

Pyinaturalist is an iNaturalist API client for python. See full project documentation at https://pyinaturalist.readthedocs.io.

Features

iNaturalist is a rich source of biodiversity data, and offers an extensive API to interact with nearly every aspect of its platform.

If you want to explore or analyze these data using python, then pyinaturalist can help. It adds a number of python-specific conveniences, including:

  • Requests: Simplified usage with python types and data structures rather than raw request parameter strings
  • Responses: Type conversions from JSON primitives to things you would expect in python
  • Typing: Complete parameter definitions with type annotations, which significantly enhances usability within an IDE, Jupyter notebook, or any other environment with type checking & autocompletion
  • Messages: Improved error handling, which means less time spent figuring out why an API call failed
  • Docs: Thorough documentation with example requests and responses
  • Security: Keyring integration for secure credential storage
  • Testing: A dry-run mode to preview your requests before potentially modifying data

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

  • Searching for:
    • controlled terms
    • observations
    • observation fields
    • observation species counts
    • places
    • projects
    • species
  • Text search autocompletion for:
    • places
    • species
  • Creating and updating:
    • observations
    • observation fields
    • observation photos

See Endpoints for a complete list of implemented endpoints, and see Reference to skip straight to the API docs.

Installation

Install the latest stable version with pip:

$ pip install pyinaturalist

Or, if you would like to use the latest development (pre-release) version:

$ pip install --pre pyinaturalist

To install with minimal dependencies (which disables some optional features):

$ pip install --no-deps pyinaturalist
$ pip install python-dateutil requests

See Contributing for details on setup for local development.

Development Status

Pyinaturalist is under active development. More endpoints and features will continue to be added as they are needed or requested.

  • See History for details on past and current releases
  • See Issues for planned & proposed features
  • Create an issue if there is an endpoint or feature you would like to have added
  • PRs are welcome!

Usage Examples

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

Also see the examples/ folder for some more detailed examples.

Observations

Search observations

There are numerous fields you can search on. An obvious search to start with would be getting all of your own observations:

from pyinaturalist.node_api import get_all_observations
obs = get_all_observations(user_id='my_username')

Get an access token

For authenticated API calls (creating/updating/deleting data), you first need to obtain an access token. This requires creating an iNaturalist app.

from pyinaturalist.auth import get_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 additional authentication options, including environment variables and keyring services.

Create a new observation

from pyinaturalist.rest_api import create_observation
from datetime import datetime

response = create_observation(
    taxon_id=54327,  # Vespa Crabro
    observed_on_string=datetime.now().isoformat(),
    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, # meters,
    # sets vespawatch_id (an observation field whose ID is 9613) to the value '100'.
    observation_fields={9613: 100},
    access_token=token,
)
new_observation_id = response[0]['id']

Upload a picture for this observation

from pyinaturalist.rest_api import add_photo_to_observation

add_photo_to_observation(
    new_observation_id,
    access_token=token,
    photo='/Users/nicolasnoe/vespa.jpg',
)

Update an existing observation

from pyinaturalist.rest_api import update_observation

update_observation(
    17932425,
    access_token=token,
    description='updated description !',
)

Get a list of all (globally available) observation fields

from pyinaturalist.rest_api import get_all_observation_fields
response = get_all_observation_fields(search_query="DNA")

Set an observation field on an existing observation

Observation Fields are a way to add extra information to your observations. They are similar to tags, but with a typed value.

from pyinaturalist.rest_api import get_observation_fields, put_observation_field_values

# First find an observation field by name, if the ID is unknown
response = get_observation_fields('vespawatch_id')
observation_field_id = response[0]['id']

put_observation_field_values(
    observation_id=7345179,
    observation_field_id=observation_field_id,
    value=250,
    access_token=token,
)

Get observation data in alternative formats

A separate endpoint can provide other data formats, including Darwin Core, KML, and CSV:

from pyinaturalist.rest_api import get_observations
obs = get_observations(user_id='niconoe', response_format='dwc')

Get observation species counts

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

from pyinaturalist.node_api import get_observation_species_counts
obs_counts = get_observation_species_counts(user_id='my_username', quality_grade='research')

Species

Search species and other taxa

Let's say you partially remember either a genus or family name that started with 'vespi'-something:

>>> from pyinaturalist.node_api import get_taxa
>>>
>>> response = get_taxa(q="vespi", rank=["genus", "family"])
>>> print({taxon["id"]: taxon["name"] for taxon in response["results"]})
{52747: "Vespidae", 84737: "Vespina", 92786: "Vespicula", 646195: "Vespiodes", ...}

Oh, that's right, it was 'Vespidae'! Now let's find all of its subfamilies using its taxon ID from the results above:

>>> response = get_taxa(parent_id=52747)
>>> print({taxon["id"]: taxon["name"] for taxon in response["results"]})
{343248: "Polistinae", 84738: "Vespinae", 119344: "Eumeninae", 121511: "Masarinae", ...}

Get a species by ID

Let's find out more about this 'Polistinae' genus. We could search for it by name or by ID, but since we already know the ID from the previous search, let's use that:

>>> from pyinaturalist.node_api import get_taxa_by_id
>>> response = get_taxa_by_id(343248)

There is a lot of info in there, but let's just get the basics for now:

>>> basic_fields = ["preferred_common_name", "observations_count", "wikipedia_url", "wikipedia_summary"]
>>> print({f: response["results"][0][f] for f in basic_fields})
{
    "preferred_common_name": "Paper Wasps",
    "observations_count": 69728,
    "wikipedia_url": "http://en.wikipedia.org/wiki/Polistinae",
    "wikipedia_summary": "The Polistinae are eusocial wasps closely related to the more familiar yellow jackets...",
}

Taxon autocomplete

This is a text search-optimized endpoint that provides autocompletion in the Naturalist web UI:

Taxon autocompletion in the iNaturalist web UI

This one is a bit more niche, but it provides a fast way to search the iNaturalist taxonomy database. Here is an example that will run searches from console input:

from pyinaturalist.node_api import get_taxa_autocomplete

while True:
    query = input("> ")
    response = get_taxa_autocomplete(q=query, minify=True)
    print("\n".join(response["results"]))

Example usage:

> opilio
527573:     Genus Opilio
47367:      Order Opiliones (Harvestmen)
84644:      Species Phalangium opilio (European Harvestman)
527419:     Subfamily Opilioninae
...
> coleo
372759:     Subclass Coleoidea (Coleoids)
47208:      Order Coleoptera (Beetles)
359229:     Species Coleotechnites florae (Coleotechnites Flower Moth)
53502:      Genus Brickellia (brickellbushes)
...
<Ctrl-C>

If you get unexpected matches, the search likely matched a synonym, either in the form of a common name or an alternative classification. Check the matched_term property for more info. For example:

>>> first_result = get_taxa_autocomplete(q='zygoca')['results'][0]
>>> first_result["name"]
"Schlumbergera truncata"
>>> first_result["matched_term"]
"Zygocactus truncatus"  # An older synonym for Schlumbergera

...And much more!

Check out the Reference section to see what else you can do with pyinaturalist.

Feedback

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

Note: pyinaturalist is not directly affiliated with iNaturalist.org or the California Academy of Sciences. If you have non-python-specific questions about iNaturalist, the iNaturalist Community Forum is going to be your best resource.

History

0.12 (2021-02-02)

See all Issues & PRs

New Endpoints

  • Added new function for Observation Histogram endpoint: get_observation_histogram()
  • Added new function for Observers endpoint: get_observation_observers()
  • Added new function for Identifiers endpoint: get_observation_identifiers()
  • Added new function for Controlled Terms endpoints: get_controlled_terms()
    • Wraps both GET /controlled_terms and /controlled_terms/for_taxon endpoints

Modified Endpoints

  • Added conversion from date/time strings to timezone-aware python datetime objects. This applies to the following functions:
    • node_api.get_observation()
    • node_api.get_observations()
    • node_api.get_all_observation()
    • node_api.get_projects()
    • node_api.get_projects_by_id()
    • node_api.get_taxa()
    • node_api.get_taxa_by_id()
    • rest_api.get_observation()
    • rest_api.get_observation_fields()
    • rest_api.get_all_observation_fields()
  • Added conversion for an additional location field in observation responses

Authentication

  • Added support for providing credentials via environment variables
  • Added integration with system keyring for credentials storage
  • Added documentation & examples for authentication options

Other Changes

  • Added a Dockerfile and docker-compose.yml for a Jupyter notebook containing pyinaturalist + other relevant packages
  • Added some more detailed usage examples under examples/
  • Improved performance for large paginated queries
  • Fixed bug that dropped request parameter values of 0 as if they were None
  • Dropped support for python 3.5
  • Removed request parameters that were deprecated in 0.11

0.11 (2020-11-04)

See all Issues & PRs

New Endpoints

  • Added new functions for Node API Places endpoints:
    • get_places_by_id()
    • get_places_nearby()
    • get_places_autocomplete()
  • Added new functions for Node API Projects endpoints:
    • get_projects()
    • get_projects_by_id()
  • Added new function for an additional Node API Observation endpoint:
    • get_observation_species_counts()
    • get_all_observation_species_counts()

Modified Endpoints

  • Added support for simplified observation field syntax (observation_fields={id: value}) for create_observations() and update_observation()
  • Updated node_api.get_taxa_by_id() to accept multiple IDs
  • Updated rest_api.get_observations() with type conversion from strings to floats for response lat/long coordinates. Only applies to JSON response format.
  • Updated node_api.get_taxa_autocomplete() with optional min_rank and max_rank parameters, for consistency with get_taxa()
  • Using the params positional argument for the handful of functions that used it will raise a DeprecationWarning, but will otherwise still be functional until 0.12
  • Renamed search_query argument to q to be consistent with API request parameters
  • Using the search_query argument for rest_api.get_observation_fields() and rest_api.get_all_observation_fields() will raise a DeprecationWarning, but will otherwise still be functional until 0.12
  • Renamed create_observations() to create_observation(), as this only supports creating a single observation per call. This is aliased to create_observations() for backwards-compatibility, but will raise a DeprecationWarning.

Documentation & Usability

  • Added example response data to docs all endpoints
  • Added links to official API reference to docs for all endpoints
  • Added full API request parameters to all API functions, in the form of keyword arguments with type annotations and docstrings
  • Added complete table of iNaturalist API endpoints and endpoints implemented by pyinaturalist
  • Added and improved usage examples
  • Numerous other documentation improvements
  • Made all API function signatures consistent by taking request params as keyword arguments

Other Changes

  • Dropped testing & support for python 3.4
  • Added testing & support for python 3.9
  • Added parameter validation for multiple-choice request parameters

0.10 (2020-06-16)

See all Issues & PRs

New Endpoints

  • Added new Observation endpoint: rest_api.get_observations(), with 6 additional observation response formats, including GeoJSON, Darwin Core, and others

Modified Endpoints

  • Added minify option to node_api.get_taxa_autocomplete()

Other Changes

  • Added more info & examples to README for taxa endpoints, and other documentation improvements
  • Added conversion for all date and datetime parameters to timezone-aware ISO 8601 timestamps
  • Added a dry-run mode to mock out API requests for testing
  • Set up pre-release builds for latest development version

0.9.1 (2020-05-26)

  • Bugfix: proper support for boolean and integer list parameters (Issue #17)

0.9 (2020-05-06)

New Endpoints

  • Added new functions for Node API Taxa endpoints:

    • node_api.get_taxa()
    • node_api.get_taxa_autocomplete()
    • node_api.get_taxa_by_id()

0.8 (2019-07-11)

  • All functions now take an optional user-agent <https://en.wikipedia.org/wiki/User_agent>_ parameter in order to identify yourself to iNaturalist. If not set, Pyinaturalist/<VERSION> will be used.

0.7 (2019-05-08)

  • rest_api.delete_observation() now raises ObservationNotFound if the observation doesn't exist
  • minor dependencies update for security reasons

0.6 (2018-11-15)

  • New function: rest_api.delete_observation()

0.5 (2018-11-05)

  • New function: node_api.get_observation()

0.4 (2018-11-05)

  • create_observation() now raises exceptions in case of errors.

0.3 (2018-11-05)

  • update_observation() now raises exceptions in case of errors.

0.2 (2018-10-31)

  • Better infrastructure (type annotations, documentation, ...)
  • Dropped support for Python 2.
  • New function: update_observation()
  • rest_api.AuthenticationError is now exceptions.AuthenticationError

0.1 (2018-10-10)

  • First release on PyPI.

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