pygbif 0.2.0

Python client for GBIF

pygbif

Python client for the GBIF API

Source on GitHub at sckott/pygbif

Other GBIF clients:

• R: rgbif, ropensci/rgbif

Installation

Stable from pypi

pip install pygbif

Development version

[sudo] pip install git+git://github.com/sckott/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

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

Note that GBIF maps API is not included in pygbif.

Registry module

registry module API:

• organizations

• nodes

• networks

• installations

• datasets

• dataset_metrics

• dataset_suggest

• dataset_search

Example usage:

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:

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

Occurrences module

registry 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

Example usage:

from pygbif import occurrences as occ
occ.search(taxonKey = 3329049)
occ.get(key = 252408386)
occ.count(isGeoreferenced = True)
occ.download('basisOfRecord = LITERATURE')
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")

Contributors

• Scott Chamberlain

• Robert Forkel

• Jan Legind

• Stijn Van Hoey

• Peter Desmet

Meta

• License: MIT, see LICENSE file

• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Changelog

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