def get_taxon_with_ancestors(taxon_id: int) -> list[dict]:
"""Get a taxon with all its parents"""
logger.info(f'API: Fetching parents of taxon {taxon_id}')
results = get_taxa_by_id(taxon_id).get('results', [])
if not results:
logger.info(f'API: taxon {taxon_id} not found')
return []
taxon = results[0]
logger.info(f'API: {len(taxon["ancestors"])} parent taxa found')
return taxon['ancestors'] + [taxon]
def test_get_taxa_by_id(requests_mock):
taxon_id = 70118
requests_mock.get(
f'{API_V1_BASE_URL}/taxa/{taxon_id}',
json=load_sample_data('get_taxa_by_id.json'),
status_code=200,
)
response = get_taxa_by_id(taxon_id)
result = response['results'][0]
assert response['total_results'] == len(response['results']) == 1
assert result['id'] == taxon_id
assert result['name'] == 'Nicrophorus vespilloides'
assert result['rank'] == 'species'
assert result['is_active'] is True
assert len(result['ancestors']) == 12
def get_observation_from_metadata(metadata) -> tuple[dict, dict]:
if not metadata.observation_id:
logger.info('API: No observation ID specified')
return None, None
observation = get_observation(metadata.observation_id)
taxon = None
taxon_id = observation.get('taxon', {}).get('id')
# Handle observation with no taxon ID (e.g., not yet identified)
if taxon_id:
taxon = get_taxa_by_id(taxon_id).get('results', [None])[0]
logger.info(
f'API: Found observation {metadata.observation_id} and taxon {taxon_id}'
)
else:
logger.warning(
f'API: Observation {metadata.observation_id} is unidentified')
return taxon, observation
def from_id(cls, id: int) -> 'Taxon':
"""Lookup and create a new Taxon object by ID"""
from pyinaturalist.v1 import get_taxa_by_id
r = get_taxa_by_id(id)
return cls.from_json(r['results'][0])
def test_get_taxa_by_id__invalid_inputs(taxon_id):
with pytest.raises(ValueError):
get_taxa_by_id(taxon_id)