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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

Python client for the iNaturalist APIs. See full documentation at https://pyinaturalist.readthedocs.io.

Installation

Install the latest stable version with pip:

$ pip install pyinaturalist

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

$ pip install --pre pyinaturalist

To set up for local development (preferably in a new virtualenv):

$ git clone https://github.com/niconoe/pyinaturalist.git
$ cd pyinaturalist
$ pip install -Ue ".[dev]"

Development Status

Pyinaturalist is under active development. Currently, a handful of the most relevant API endpoints are implemented, including:

  • Searching, creating, and updating observations and observation fields
  • Searching for places, projects, species, and species counts
  • Text search autocompletion for species and places

See below for some examples, see Endpoints for a complete list of implemented endpoints, and see Issues for planned & proposed features.

More endpoints will continue to be added as they are needed. Please create an issue if there is an endpoint you would like to have added, and PRs are welcome!

Note:

The two iNaturalist APIs expose a combined total of 103 endpoints*. Some of these are generally useful and could potentially be added to pyinaturalist, but many others are primarily for internal use by the iNaturalist web application and mobile apps, and are unlikely to be added unless there are specific use cases for them.

*As of 2020-10-01: 37 in REST API, 65 in Node API, and 1 undocumented

Examples

Observations

Search observations

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

See available parameters

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.rest_api import get_access_token
token = get_access_token(
    username='<your_inaturalist_username>',
    password='<your_inaturalist_password>',
    app_id='<your_inaturalist_app_id>',
    app_secret='<your_inaturalist_app_secret>',
)

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_field_values_attributes=[
        {'observation_field_id': 9613,'value': 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

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

Update an existing observation of yours

from pyinaturalist.rest_api import update_observation

r = 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
r = get_all_observation_fields(search_query="DNA")

Set an observation field value on an existing observation

from pyinaturalist.rest_api import put_observation_field_values

put_observation_field_values(
    observation_id=7345179,
    observation_field_id=9613,
    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')

See available parameters and formats

Get observation species counts

There is an additional endpoint to 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')

Taxonomy

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

History

0.11.0 (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

0.10.0 (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)

0.9.0 (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()

0.8.0 (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.

0.7.0 (2019-05-08)

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

0.6.0 (2018-11-15)

  • New function: rest_api.delete_observation()

0.5.0 (2018-11-05)

  • New function: node_api.get_observation()

0.4.0 (2018-11-05)

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

0.3.0 (2018-11-05)

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

0.2.0 (2018-10-31)

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

0.1.0 (2018-10-10)

  • First release on PyPI.

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