| from __future__ import print_function, unicode_literals | |
| import os | |
| from io import open | |
| from shapely.geometry import shape, Point | |
| from shapely.geos import PredicateError, TopologicalError | |
| from tsammalexdata.util import data_file, jsonload, unique | |
| INVALID_ECO_CODES = {'AA0803', 'Lake', 'AT1202', 'IM1303', 'AA0803'} | |
| DATA_FILE = data_file('distribution.csv') | |
| def format_ids(iterable): | |
| return ';'.join(unique(iterable)) | |
| def main(): | |
| res = {} | |
| with open(DATA_FILE, encoding='utf8') as fp: | |
| for line in fp.read().split('\n'): | |
| if line: | |
| cols = line.split(',') | |
| res[cols[0]] = cols[1:] | |
| ecoregions = [ | |
| (er['properties']['eco_code'], shape(er['geometry'])) | |
| for er in jsonload(data_file('ecoregions.json'))['features'] | |
| if er['geometry'] and er['properties']['eco_code'] not in INVALID_ECO_CODES] | |
| for fname in os.listdir(data_file('external', 'gbif')): | |
| sid = fname.split('.')[0] | |
| v = res.get(sid, ['', '']) | |
| if len(v) == 1: | |
| v.append('') | |
| if not v[0] or not v[1]: | |
| occurrences = jsonload( | |
| data_file('external', 'gbif', fname)).get('results', []) | |
| if not v[0]: | |
| v[0] = format_ids(match(occurrences, ecoregions)) | |
| if not v[1]: | |
| v[1] = format_ids(r.get('countryCode') for r in occurrences) | |
| res[sid] = v | |
| with open(DATA_FILE, 'w', encoding='utf8') as fp: | |
| for key in sorted(res.keys()): | |
| fp.write('%s,%s\r\n' % (key, ','.join(res[key]))) | |
| def match(occurrences, ecoregions): | |
| for oc in occurrences: | |
| point = Point(oc['decimalLongitude'], oc['decimalLatitude']) | |
| for eco_code, er in ecoregions: | |
| try: | |
| if er.contains(point): | |
| yield eco_code | |
| except (PredicateError, TopologicalError): | |
| print('--error--: ', eco_code) | |
| pass | |
| if __name__ == '__main__': | |
| main() | |