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from __future__ import print_function, unicode_literals
import os
from tsammalexdata.util import data_file, csv_items, jsondump, jsonload, DataProvider
class GBIF(DataProvider):
host = 'api.gbif.org'
def get_id(self, name):
res = self.get('v1/species/match', name=name)
if 'rank' not in res:
return
rank = res['rank'].lower()
if rank in ['subspecies', 'variety'] and rank + 'Key' not in res:
rank = 'species'
try:
return res[rank + 'Key']
except KeyError:
return
def get_info(self, id):
kw = dict(
taxonKey=id,
basisOfRecord='HUMAN_OBSERVATION',
hasCoordinate='true',
limit=100)
return self.get('v1/occurrence/search', **kw)
def update(self, taxon, data):
if data.get('results'):
result = data['results'][0]
for key in 'kingdom phylum class order genus family'.split():
if result.get(key):
taxon[key] = result[key]
if 'taxonRank' in result:
taxon['taxonRank'] = result['taxonRank'].lower()
def save_occurrences(sid, sname):
api = GBIF()
out = data_file('external', 'gbif', '%s.json' % sid)
if not os.path.exists(out):
try:
res = api.get_info(api.get_id(sname))
jsondump(res, out)
print('%s: %s occurrences' % (sname, min([res['count'], res['limit']])))
except:
# we'll have to try again next time!
res = None
else:
try:
res = jsonload(out)
except:
os.remove(out)
res = None
return res
if __name__ == '__main__':
for item in csv_items('taxa.csv'):
save_occurrences(item['id'], item['scientific_name'])
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