pygbif

pygbif

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Python client for the GBIF API <https://www.gbif.org/developer/summary>_

Source on GitHub at gbif/pygbif <https://github.com/gbif/pygbif>_

Other GBIF clients:

• R: rgbif, ropensci/rgbif <https://github.com/ropensci/rgbif>_
• Ruby: gbifrb, sckott/gbifrb <https://github.com/sckott/gbifrb>_
• PHP: php-gbif, restelae/php-gbif <https://gitlab.res-telae.cat/restelae/php-gbif>_

Contributing: CONTRIBUTING.md <https://github.com/gbif/pygbif/blob/master/.github/CONTRIBUTING.md>_

Installation

Stable from pypi

.. code-block:: console

pip install pygbif

Development version

.. code-block:: console

[sudo] pip install git+git://github.com/gbif/pygbif.git#egg=pygbif

pygbif is split up into modules for each of the major groups of API methods.

• Registry - Datasets, Nodes, Installations, Networks, Organizations
• Species - Taxonomic names
• Occurrences - Occurrence data, including the download API
• Maps - Maps, get raster maps from GBIF as png or mvt

You can import the entire library, or each module individually as needed.

In addition there is a utils module, currently with one method: wkt_rewind, and a caching method to manage whether HTTP requests are cached or not. See ?pygbif.caching.

Registry module

registry module API:

• organizations
• nodes
• networks
• installations
• datasets
• dataset_metrics
• dataset_suggest
• dataset_search

Example usage:

.. code-block:: python

from pygbif import registry
registry.dataset_metrics(uuid='3f8a1297-3259-4700-91fc-acc4170b27ce')

Species module

species module API:

• name_backbone
• name_suggest
• name_usage
• name_lookup
• name_parser

Example usage:

.. code-block:: python

from pygbif import species
species.name_suggest(q='Puma concolor')

Occurrences module

occurrences module API:

• search
• get
• get_verbatim
• get_fragment
• count
• count_basisofrecord
• count_year
• count_datasets
• count_countries
• count_schema
• count_publishingcountries
• download
• download_meta
• download_list
• download_get
• download_citation
• download_describe
• download_sql

Example usage:

.. code-block:: python

from pygbif import occurrences as occ
occ.search(taxonKey = 3329049)
occ.get(key = 252408386)
occ.count(isGeoreferenced = True)
occ.download('basisOfRecord = PRESERVED_SPECIMEN')
occ.download('taxonKey = 3119195')
occ.download('decimalLatitude > 50')
occ.download_list(user = "sckott", limit = 5)
occ.download_meta(key = "0000099-140929101555934")
occ.download_get("0000066-140928181241064")
occ.download_citation("0002526-241107131044228")
occ.download_describe("simpleCsv")
occ.download_sql("SELECT gbifid,countryCode FROM occurrence WHERE genusKey = 2435098")

Maps module

maps module API:

• map

Example usage:

.. code-block:: python

from pygbif import maps
out = maps.map(taxonKey = 212, year = 1998, bin = "hex",
       hexPerTile = 30, style = "classic-noborder.poly")
out.response
out.path
out.img
out.plot()

.. image:: https://github.com/gbif/pygbif/raw/master/gbif_map.png :width: 25%

utils module

utils module API:

• wkt_rewind

Example usage:

.. code-block:: python

from pygbif import utils
x = 'POLYGON((144.6 13.2, 144.6 13.6, 144.9 13.6, 144.9 13.2, 144.6 13.2))'
utils.wkt_rewind(x)

Contributors

• Scott Chamberlain <https://github.com/sckott>_
• Robert Forkel <https://github.com/xrotwang>_
• Jan Legind <https://github.com/jlegind>_
• Stijn Van Hoey <https://github.com/stijnvanhoey>_
• Peter Desmet <https://github.com/peterdesmet>_
• Nicolas Noé <https://github.com/niconoe>_

Meta

• License: MIT, see LICENSE file <LICENSE>_
• Please note that this project is released with a Contributor Code of Conduct <CONDUCT.md>_. By participating in this project you agree to abide by its terms.

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Changelog

0.6.5 (2024-10-28)

• added support for occurrences.download_citation 158
• added support for occurrences.download_sql 157
• added support for occurrences.download_describe 142
• added support for literature.search 149

0.6.4 (2024-03-12)

• fixed a bug in building the documentation with readthedocs 138, 129
• tests now run against live GBIF APIs 101, 128
• updated caching.py since the remove_expired_responses method is deprecated. 126

0.6.3 (2023-05-25)

• added support for predicates: isNull, isNotNull, in and not 92, 102 and 103
• added support for nested queries/dictionaries 104
• deprecated the add_predicate function and added add_pred_dict to accomodate for newly supported predicates to ensure that the arguments that are sent are added in the payload function 108
• added support for multiple download formats 105
• updated operators and look-up tables 107
• included documentation on newly supported predicates and dictionaries 106

0.6.2 (2023-01-24)

• update to fix requesting GBIF downloads
• minor documentation updates 95 and 99

0.6.1 (2022-06-23)

• update to fix broken dependencies 93
• minor documentation updates

0.6.0 (2021-07-08)

• Fix for occurrences.download when giving geometry as a string rather than using add_geometry; predicates were being split on whitespace, which doesn't work for WKT 81 84
• Moved to using the logging module instead of print() for giving information on occurrence download methods 78
• Clarify that occurrences.count for length 1 inputs only; see occurrences.search for > 1 value 75 77
• Improved documentation for species.name_usage method, mostly for the language parameter 68
• Gains download method download_cancel for cancelling/deleting a download request 59

0.5.0 (2020-09-29)

• occurrences.search now supports recordedByID and identifiedByID search parameters 62
• clean up the Contributing file, thanks @niconoe 64
• clean up internal imports in the library, thanks @niconoe 65
• fix usage of is and ==, was using them inappropriately sometimes (via https://realpython.com/python-is-identity-vs-equality/), 69
• remove redundant parameter in a doc string, thanks @faroit 71
• make a test for internal fxn gbif_GET_write more general to avoid errors if GBIF changes content type response header slightly 72

0.4.0 (2019-11-20)

• changed base url to https for all requests; was already https for maps and downloads in previous versions
• occurrences, species, and registry modules gain docstrings with brief summary of each method
• pygbif gains ability to cache http requests. caching is off by default. See ?pygbif.caching for all the details 52 56 via @nleguillarme
• made note in docs that if you are trying to get the same behavior as the GBIF website for name searching, species.name_backbone is likely what you want 55 thanks @qgroom
• for parameters that expect a bool, convert them to lowercase strings internally before doing HTTP requests

0.3.0 (2019-01-25)

• pygbif is Python 3 only now 19
• Gains maps module with maps.map method for working with the GBIF maps API 41 49
• Gains new module utils with one method wkt_rewind 46 thanks @aubreymoore for the inspiration
• Fixed bug in registry.installations: typo in one of the parameters identifierTyp instead of identifierType 48 thanks @data-biodiversity-aq
• Link to GitHub issues from Changelog 🎉
• Fix a occurrence download test 47
• Much more thorough docs 25

0.2.0 (2016-10-18)

• Download methods much improved 16 27 thanks @jlegind @stijnvanhoey @peterdesmet !
• MULTIPOLYGON now supported in geometry parameter 35
• Fixed docs for occurrences.get, and occurrences.get_verbatim, occurrences.get_fragment and demo that used occurrence keys that no longer exist in GBIF 39
• Added organizations method to registry module 12
• Added remainder of datasets methods: registry.dataset_search (including faceting support 37) and registry.dataset_suggest, for the /dataset/search and /dataset/suggest routes, respectively 40
• Added remainder of species methods: species.name_lookup (including faceting support 38) and species.name_usage, for the /species/search and /species routes, respectively 18
• Added more tests to cover new methods
• Changed species.name_suggest to give back data stucture as received from GBIF. We used to parse out the classification data, but for simplicity and speed, that is left up to the user now.
• start parameter in species.name_suggest, occurrences.download_list, registry.organizations, registry.nodes, registry.networks, and registry.installations, changed to offset to match GBIF API and match usage throughout remainder of pygbif

0.1.5.4 (2016-10-01)

• Added many new occurrence.search parameters, including repatriated, kingdomKey, phylumKey, classKey, orderKey, familyKey, genusKey, subgenusKey, establishmentMeans, facet, facetMincount, facetMultiselect, and support for facet paging via **kwargs 30 34
• Fixes to **kwargs in occurrence.search so that facet parameters can be parsed correctly and requests GET request options are collected correctly 36
• Added spellCheck parameter to occurrence.search that goes along with the q parameter to optionally spell check full text searches 31

0.1.4 (2016-06-04)

• Added variable types throughout docs
• Changed default limit value to 300 for occurrences.search method
• tox now included, via @xrotwang 20
• Added more registry methods 11
• Started occurrence download methods 16
• Added more names methods 18
• All requests now send user-agent headers with requests and pygbif versions 13
• Bug fix for occurrences.download_get 23
• Fixed bad example for occurrences.get 22
• Fixed wheel to be universal for 2 and 3 10
• Improved documentation a lot, autodoc methods now

0.1.1 (2015-11-03)

• Fixed distribution for pypi

0.1.0 (2015-11-02)

• First release