def test_catalogue_of_life(tmpdir):
data = fixtures('data_providers', 'catalogueoflife')
id_ = '9249d9473aac5c8e99fb9d758ced91ec'
repos = create_repos(tmpdir)
with patch('pytsammalex.util.requests',
MockRequests(content=data['identify'])):
prov = CatalogueOfLife(Path(repos))
assert (prov.identify('x') == id_)
with patch('pytsammalex.util.requests',
MockRequests(content=data['metadata'])):
prov = CatalogueOfLife(Path(repos))
md = prov.cached_metadata('test', id_)
taxon = {}
prov.update(taxon, md)
assert (
taxon ==
{
'catalogueoflife_url': 'http://www.catalogueoflife.org/col/'
'browse/tree/id/'
'9249d9473aac5c8e99fb9d758ced91ec',
'class': 'Mammalia',
'family': 'Felidae',
'kingdom': 'Animalia',
'order': 'Carnivora',
'phylum': 'Chordata'})
def _provider_img_data(cls):
prov = cls(None)
return (prov,
Staged_images.fromdict({
'id': prov.__example__[0],
'taxa__id': 'abc'
}), fixtures('image_providers', prov.__class__.__name__.lower()))
def test_catalogue_of_life(tmpdir):
data = fixtures('data_providers', 'catalogueoflife')
id_ = '9249d9473aac5c8e99fb9d758ced91ec'
repos = create_repos(tmpdir)
with patch('pytsammalex.util.requests',
MockRequests(content=data['identify'])):
prov = CatalogueOfLife(Path(repos))
assert (prov.identify('x') == id_)
with patch('pytsammalex.util.requests',
MockRequests(content=data['metadata'])):
prov = CatalogueOfLife(Path(repos))
md = prov.cached_metadata('test', id_)
taxon = {}
prov.update(taxon, md)
assert (taxon == {
'catalogueoflife_url':
'http://www.catalogueoflife.org/col/'
'browse/tree/id/'
'9249d9473aac5c8e99fb9d758ced91ec',
'class':
'Mammalia',
'family':
'Felidae',
'kingdom':
'Animalia',
'order':
'Carnivora',
'phylum':
'Chordata'
})
def test_Eol(self):
from pytsammalex.data_providers.eol import EOL
data = fixtures('data_providers', 'eol')
with patch(
'pytsammalex.util.requests',
MockRequests(json=[
data['identify'], data['metadata'], data['hierarchy']
])):
prov = EOL(create_repos(self.tmp_path()))
taxon = {'id': 'pantheraleo', 'name': 'Panthera leo'}
prov.update_taxon(taxon)
self.assertEqual(
taxon, {
'eol_id': 328672,
'english_name': 'Asian lion',
'id': 'pantheraleo',
'name': 'Panthera leo',
'class': 'Mammalia',
'family': 'Felidae',
'genus': 'Panthera',
'kingdom': 'Animalia',
'order': 'Carnivora',
'phylum': 'Chordata',
'taxonRank': 'species'
})
def test_Catalogueoflife(self):
from pytsammalex.data_providers.catalogueoflife import CatalogueOfLife
data = fixtures('data_providers', 'catalogueoflife')
id_ = '9249d9473aac5c8e99fb9d758ced91ec'
repos = create_repos(self.tmp_path())
with patch('pytsammalex.util.requests',
MockRequests(content=data['identify'])):
prov = CatalogueOfLife(repos)
self.assertEqual(prov.identify('x'), id_)
with patch('pytsammalex.util.requests',
MockRequests(content=data['metadata'])):
prov = CatalogueOfLife(repos)
md = prov.cached_metadata('test', id_)
taxon = {}
prov.update(taxon, md)
self.assertEqual(
taxon, {
'catalogueoflife_url':
'http://www.catalogueoflife.org/col/browse/tree/id/9249d9473aac5c8e99fb9d758ced91ec',
'class': 'Mammalia',
'family': 'Felidae',
'kingdom': 'Animalia',
'order': 'Carnivora',
'phylum': 'Chordata'
})
def test_gbif(tmpdir):
data = fixtures('data_providers', 'gbif')
with patch('pytsammalex.util.requests',
MockRequests(json=[data['identify'], data['metadata']])):
prov = GBIF(Path(create_repos(tmpdir)))
taxon = {'id': 'pantheraleo', 'name': 'Panthera leo'}
prov.update_taxon(taxon)
assert (taxon == {
'gbif_id': 5219404,
'id': 'pantheraleo',
'name': 'Panthera leo',
'class': 'Mammalia',
'family': 'Felidae',
'genus': 'Panthera',
'kingdom': 'Animalia',
'order': 'Carnivora',
'phylum': 'Chordata',
'taxonRank': 'species'
})
def test_gbif(tmpdir):
data = fixtures('data_providers', 'gbif')
with patch(
'pytsammalex.util.requests',
MockRequests(json=[data['identify'], data['metadata']])):
prov = GBIF(Path(create_repos(tmpdir)))
taxon = {'id': 'pantheraleo', 'name': 'Panthera leo'}
prov.update_taxon(taxon)
assert (
taxon ==
{
'gbif_id': 5219404,
'id': 'pantheraleo',
'name': 'Panthera leo',
'class': 'Mammalia',
'family': 'Felidae',
'genus': 'Panthera',
'kingdom': 'Animalia',
'order': 'Carnivora',
'phylum': 'Chordata',
'taxonRank': 'species'})
def test_Gbif(self):
from pytsammalex.data_providers.gbif import GBIF
data = fixtures('data_providers', 'gbif')
with patch('pytsammalex.util.requests',
MockRequests(json=[data['identify'], data['metadata']])):
prov = GBIF(create_repos(self.tmp_path()))
taxon = {'id': 'pantheraleo', 'name': 'Panthera leo'}
prov.update_taxon(taxon)
self.assertEqual(
taxon, {
'gbif_id': 5219404,
'id': 'pantheraleo',
'name': 'Panthera leo',
'class': 'Mammalia',
'family': 'Felidae',
'genus': 'Panthera',
'kingdom': 'Animalia',
'order': 'Carnivora',
'phylum': 'Chordata',
'taxonRank': 'species'
})
def test_eol(tmpdir):
data = fixtures('data_providers', 'eol')
with patch(
'pytsammalex.util.requests',
MockRequests(
json=[data['identify'], data['metadata'], data['hierarchy']])
):
prov = EOL(Path(create_repos(tmpdir)))
taxon = {'id': 'pantheraleo', 'name': 'Panthera leo'}
prov.update_taxon(taxon)
assert (
taxon ==
{
'eol_id': 328672,
'english_name': 'Asian lion',
'id': 'pantheraleo',
'name': 'Panthera leo',
'class': 'Mammalia',
'family': 'Felidae',
'genus': 'Panthera',
'kingdom': 'Animalia',
'order': 'Carnivora',
'phylum': 'Chordata',
'taxonRank': 'species'})
def _provider_img_data(cls):
prov = cls(None)
return (
prov,
Staged_images.fromdict({'id': prov.__example__[0], 'taxa__id': 'abc'}),
fixtures('image_providers', prov.__class__.__name__.lower()))