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_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_senckenberg():
prov, img, data = _provider_img_data(Senckenberg)
with patch('pytsammalex.util.requests',
MockRequests(text=data['metadata'])):
assert (prov.metadata(img)['source_url'] ==
'http://www.westafricanplants.senckenberg.de/images/pictures/'
'ficus_polita_img_04024_ralfbiechele_722_fc6e25.jpg')
def test_zimbabweflora():
prov, img, data = _provider_img_data(Zimbabweflora)
with patch('pytsammalex.util.requests',
MockRequests(text=data['metadata'])):
assert (prov.metadata(img)['source_url'] ==
'http://www.zimbabweflora.co.zw/speciesdata/images/'
'10/100760-2.jpg')
def test_ImageProvider_retrieve(self):
from pytsammalex.image_providers.base import ImageProvider
repos = create_repos(self.tmp_path())
fname = self.tmp_path('test')
media = self.tmp_path(('media.json'))
with fname.open('w', encoding='utf8') as fp:
fp.write('test')
class P(ImageProvider):
def __init__(self, md):
self._md = md
ImageProvider.__init__(self, repos)
def metadata(self, item):
return self._md
self.assertIsNone(P({}).retrieve(None, None, None, None))
staged_image = Staged_images.fromdict({'id': 'abc', 'taxa__id': 'abc'})
prov = P({'source_url': fname})
with self.assertRaises(ValueError):
prov.retrieve(staged_image, None, [md5(fname)], None)
cdstar = MagicMock(
create=MagicMock(return_value=[(None, None, MOCK_CDSTAR_OBJECT)]))
prov = P({'source_url': 'x'})
with patch('pytsammalex.util.requests', MockRequests()):
with MediaCatalog(media.name, repos=repos) as mcat:
prov.retrieve(staged_image, cdstar, [], mcat)
self.assertTrue(cdstar.create.called)
self.assertEqual(len(MediaCatalog(media.name, repos=repos)), 1)
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_wikimedia():
prov, img, data = _provider_img_data(Wikimedia)
with patch('pytsammalex.util.requests',
MockRequests(content=data['metadata'])):
assert (prov.metadata(img)['source_url'] ==
'https://upload.wikimedia.org/wikipedia/'
'commons/1/1d/Alcelaphus_caama.jpg')
def test_Eol(self):
from pytsammalex.image_providers.eol import Eol
prov, img, data = self._provider_img_data(Eol)
with patch('pytsammalex.util.requests', MockRequests(json=data['metadata'])):
self.assertEqual(
prov.metadata(img)['source_url'],
'http://media.eol.org/content/2012/08/24/08/75619_orig.jpg')
def test_Senckenberg(self):
from pytsammalex.image_providers.senckenberg import Senckenberg
prov, img, data = self._provider_img_data(Senckenberg)
with patch('pytsammalex.util.requests', MockRequests(text=data['metadata'])):
self.assertEqual(
prov.metadata(img)['source_url'],
'http://www.westafricanplants.senckenberg.de/images/pictures/ficus_polita_img_04024_ralfbiechele_722_fc6e25.jpg')
def test_Wikimedia(self):
from pytsammalex.image_providers.wikimedia import Wikimedia
prov, img, data = self._provider_img_data(Wikimedia)
with patch('pytsammalex.util.requests', MockRequests(content=data['metadata'])):
self.assertEqual(
prov.metadata(img)['source_url'],
'https://upload.wikimedia.org/wikipedia/commons/1/1d/Alcelaphus_caama.jpg')
def test_Zimbabweflora(self):
from pytsammalex.image_providers.zimbabweflora import Zimbabweflora
prov, img, data = self._provider_img_data(Zimbabweflora)
with patch('pytsammalex.util.requests', MockRequests(text=data['metadata'])):
self.assertEqual(
prov.metadata(img)['source_url'],
'http://www.zimbabweflora.co.zw/speciesdata/images/10/100760-2.jpg')
def test_DataProvider(self):
from pytsammalex.data_providers.base import DataProvider
prov = DataProvider(self.tmp_path())
self.assertEqual(prov.name, 'dataprovider')
with patch('pytsammalex.util.requests', MockRequests()):
prov = DataProvider(self.tmp_path())
self.assertEqual(prov.get(None, type_='json')['a'], 'b')
self.assertEqual(prov.get(None, type_='xml').tag, 'a')
self.assertIsInstance(prov.get(None), MockResponse)
self.assertRaises(NotImplementedError, prov.identify, None)
self.assertRaises(NotImplementedError, prov.metadata, None)
self.assertRaises(NotImplementedError, prov.update, None, None)
self.assertIsNone(prov.cached_metadata(None, None))
prov.items[1] = 1
self.assertEqual(prov.cached_metadata(1, None), 1)
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_data_provider(tmpdir):
prov = DataProvider(Path(tmpdir))
assert (prov.name == 'dataprovider')
with patch('pytsammalex.util.requests', MockRequests()):
prov = DataProvider(Path(tmpdir))
assert (prov.get(None, type_='json')['a'] == 'b')
assert (prov.get(None, type_='xml').tag == 'a')
assert (isinstance(prov.get(None), MockResponse))
with pytest.raises(NotImplementedError):
prov.identify(None)
with pytest.raises(NotImplementedError):
prov.metadata(None)
with pytest.raises(NotImplementedError):
prov.update(None, None)
assert (prov.cached_metadata(None, None) is None)
prov.items[1] = 1
assert (prov.cached_metadata(1, None) == 1)
def test_image_provider_retrieve(tmpdir):
repos = create_repos(tmpdir)
fname = tmpdir.join('test')
with fname.open('w', encoding='utf8') as fp:
fp.write('test')
class TestProvider(ImageProvider):
def identify(self, name):
pass
def __init__(self, md):
self._md = md
ImageProvider.__init__(self, repos)
def metadata(self, item):
return self._md
assert (TestProvider({}).retrieve(None, None, None, None) is None)
staged_image = Staged_images.fromdict({'id': 'abc', 'taxa__id': 'abc'})
prov = TestProvider({'source_url': fname})
with pytest.raises(ValueError):
prov.retrieve(staged_image, None, [md5(fname)], None)
cdstar = MagicMock(create=MagicMock(return_value=[(None, None,
MOCK_CDSTAR_OBJECT)]))
prov = TestProvider({'source_url': 'x'})
with patch('pytsammalex.util.requests', MockRequests()):
with MediaCatalog('media.json', repos=Path(repos)) as mcat:
prov.retrieve(staged_image, cdstar, [], mcat)
assert (cdstar.create.called is True)
assert (len(MediaCatalog('media.json', repos=Path(repos))) == 1)
def test_eol():
prov, img, data = _provider_img_data(Eol)
with patch('pytsammalex.util.requests',
MockRequests(json=data['metadata'])):
assert (prov.metadata(img)['source_url'] ==
'http://media.eol.org/content/2012/08/24/08/75619_orig.jpg')
