ecoregions_for_species.py

"""
Python 2.7 script to determine WWF Ecoregions in which a given species has been observed.

Assumes you have downloaded the WWF Ecoregions shapefile.

Usage:

    $ python ecoregions_for_species.py "Ursus maritimus"
    PA1101 Arctic desert
    NA0616 Southern Hudson Bay taiga
    NA1113 Kalaallit Nunaat low arctic tundra
    NA1112 Kalaallit Nunaat high arctic tundra
"""
import sys

import fiona
from shapely.geometry import shape, Point
import requests



def gbif_api(path, **params):
    return requests.get('http://api.gbif.org/v1/' + path, params=params).json()


def occurrences(species):
    kw = dict(
        taxonKey=gbif_api('species/match', name=species)['speciesKey'],
        basisOfRecord='HUMAN_OBSERVATION',
        hasCoordinate='true',
        limit=100)
    return gbif_api('occurrence/search', **kw)['results']


def get_ecoregions(species):
    with fiona.collection('wwf_terr_ecos.shp', "r") as source:
        ecoregions = [
            (feature['properties'], shape(feature['geometry']))
            for feature in source if feature['geometry']]

    eco_codes = {}
    for oc in occurrences(species):
        point = Point(oc['decimalLongitude'], oc['decimalLatitude'])
        for props, er in ecoregions:
            eco_code = props['eco_code']
            try:
                if er.contains(point):
                    if eco_code not in eco_codes:
                        eco_codes[eco_code] = props['ECO_NAME']
                        break
            except:
                pass
    return eco_codes


if __name__ == "__main__":
    for code, name in get_ecoregions(sys.argv[1]).items():
        print code, name