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