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_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_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_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_TaxaData(self):
from pytsammalex.taxa import TaxaData
repos = create_repos(self.tmp_path())
with TaxaData(repos) as taxa:
taxa.add(0, Taxa.fromdict({'id': 'abc'}))
self.assertIn('abc', TaxaData(repos))
def test_taxa_data(tmpdir):
repos = Path(create_repos(tmpdir))
with TaxaData(repos) as taxa:
taxa.add(0, Taxa.fromdict({'id': 'abc'}))
assert 'abc' in TaxaData(repos)
def test_ImageProvider(self):
from pytsammalex.image_providers.base import ImageProvider
repos = create_repos(self.tmp_path())
prov = ImageProvider(repos)
with self.assertRaises(NotImplementedError):
'x' in prov
self.assertEqual(len(prov.url_parts({'id': '/path'})), 3)
def test_image_provider(tmpdir):
repos = create_repos(tmpdir)
prov = ImageProvider(repos)
with pytest.raises(NotImplementedError):
'x' in prov
assert (len(prov.url_parts({'id': '/path'})) == 3)
def test_image_provider(tmpdir):
repos = create_repos(tmpdir)
prov = ImageProvider(repos)
with pytest.raises(NotImplementedError):
'x' in prov
assert (len(prov.url_parts({'id': '/path'})) == 3)
def test_JsonData(self):
from pytsammalex.util import JsonData, data_file
tmpdir = create_repos(self.tmp_path())
with JsonData('test.json', repos=tmpdir) as jdat:
jdat['a'] = 1
self.assertTrue(data_file('test.json', repos=tmpdir).exists())
with JsonData('test.json', repos=tmpdir) as jdat:
self.assertEqual(len(jdat), 1)
self.assertEqual(jdat['a'], 1)
def test_json_data(tmpdir):
tmp_ = create_repos(tmpdir)
with JsonData('test.json', repos=Path(tmp_)) as jdat:
jdat['a'] = 1
assert (data_file('test.json', repos=Path(tmp_)).exists() is True)
with JsonData('test.json', repos=Path(tmp_)) as jdat:
assert (len(jdat) == 1)
assert (jdat['a'] == 1)
def test_update(tmpdir):
repos = create_repos(tmpdir)
with patch.multiple('pytsammalex.distribution',
shape=Mock(return_value=Mock(return_value=True)),
Point=Mock()):
update(Path(repos), log=Mock())
data = CsvData('distribution', repos=Path(repos))
assert (len(data) == 1)
assert (data.items[0].ecoregions__ids == [
'AT0110', 'AT0111', 'AT0112', 'AT0113', 'AT0114', 'AT0115', 'AT0116',
'AT0117', 'AT0118', 'AT0119'
])
def test_update(self):
from pytsammalex.distribution import update
repos = create_repos(self.tmp_path())
with patch.multiple('pytsammalex.distribution',
shape=Mock(return_value=Mock(return_value=True)),
Point=Mock()):
update(repos, verbose=False)
data = CsvData('distribution', repos=repos)
self.assertEqual(len(data), 1)
self.assertEqual(data.items[0].ecoregions__ids, [
'AT0110', 'AT0111', 'AT0112', 'AT0113', 'AT0114', 'AT0115',
'AT0116', 'AT0117', 'AT0118', 'AT0119'
])
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_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_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(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'})