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""" |
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Functionality to retrieve information from the Catalogue of Life Web Service |
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.. seealso:: http://webservice.catalogueoflife.org/col/webservice |
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""" |
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from __future__ import print_function, unicode_literals, absolute_import, division |
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import sys |
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import os |
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from tsammalexdata.util import data_file, jsonload, jsondump, csv_items, DataProvider, unique |
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def text(e, ee): |
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ee = e.find(ee) |
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return (ee.text if ee is not None else '') or '' |
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class CatalogueOfLife(DataProvider): |
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host = 'www.catalogueoflife.org' |
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def _get(self, **kw): |
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try: |
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return self.get('col/webservice', type='xml', **kw).find('result') |
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except: |
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return None |
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def get_id(self, name): |
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result = self._get(name=name) |
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if result: |
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if text(result, 'name_status') == 'accepted name': |
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return text(result, 'id') |
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if result.find('accepted_name'): |
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return text(result.find('accepted_name'), 'id') |
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def get_info(self, id_): |
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result = self._get(id=id_, response='full') |
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if result: |
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res = {k: text(result, k) for k in 'genus species author url'.split()} |
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res['distribution'] = unique( |
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region.split()[0] for region in |
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text(result, 'distribution').split('; ') if region) |
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if result.find('classification'): |
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res['classification'] = { |
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t.rank.lower(): t.as_dict() for t in |
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[Taxon(e) for e in result.find('classification').findall('taxon')]} |
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if result.find('synonyms'): |
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res['synonyms'] = filter( |
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None, |
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[text(e, 'name') for e in result.find('synonyms').findall('synonym')]) |
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return {k: v for k, v in res.items() if v} |
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def update(self, taxon, data): |
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if 'distribution' in data: |
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taxon['tdwgregions'] = unique(data['distribution']) |
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classification = data.get('classification', {}) |
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for key in 'kingdom phylum class order genus family'.split(): |
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if classification.get(key): |
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taxon[key] = classification[key]['name'] |
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taxon[self.name + '_url'] = data['url'] |
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if 'author' in data: |
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taxon['description'] = data['author'] |
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class Taxon(object): |
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def __init__(self, e): |
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for attr in 'id name rank url'.split(): |
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setattr(self, attr, text(e, attr)) |
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def as_dict(self): |
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return dict(id=self.id, name=self.name, url=self.url) |
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if __name__ == '__main__': |
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api = CatalogueOfLife() |
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if sys.argv[1:]: |
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print(api.cli(sys.argv[1])) |
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