def test_ids_from(self):
redbiom.admin.create_context('test', 'foo')
redbiom.admin.load_sample_metadata(metadata)
redbiom.admin.ScriptManager.load_scripts(read_only=False)
redbiom.admin.load_sample_data(table, 'test', tag=None)
sample_ids = table.ids()[:]
sample_ids = np.array(["UNTAGGED_%s" % i for i in sample_ids])
ids = table.ids(axis='observation').copy()
random.shuffle(ids)
for i in range(1, 5):
fetch = ids[:i]
assoc_ids = []
for id_ in fetch:
assoc_data = table.data(id_, axis='observation')
assoc_ids.append(sample_ids[assoc_data > 0])
exp_exact = reduce(set.intersection, map(set, assoc_ids))
exp_union = reduce(set.union, map(set, assoc_ids))
obs_exact = ids_from(iter(fetch), True, 'feature', ['test'])
obs_union = ids_from(iter(fetch), False, 'feature', ['test'])
self.assertEqual(obs_exact, exp_exact)
self.assertEqual(obs_union, exp_union)
def test_ids_from_multicontext(self):
redbiom.admin.create_context('test', 'foo')
redbiom.admin.create_context('test2', 'foo')
redbiom.admin.ScriptManager.load_scripts(read_only=False)
redbiom.admin.load_sample_metadata(metadata)
redbiom.admin.load_sample_data(table, 'test', tag=None)
redbiom.admin.load_sample_data(table, 'test2', tag=None)
d = table.data(table.ids()[0], dense=True)
ids = table.ids(axis='observation')[d.nonzero()]
exp = set([
'UNTAGGED_' + table.ids()[0],
])
obs = ids_from(iter(ids), True, 'feature', ['test', 'test2'])
self.assertEqual(obs, exp)
redbiom.admin.create_context('testalt', 'foo')
redbiom.admin.load_sample_metadata(metadata_with_alt)
redbiom.admin.load_sample_data(table_with_alt, 'testalt', tag=None)
exp = {'UNTAGGED_10317.000051129alt', 'UNTAGGED_10317.000051129'}
d = table.data('10317.000051129', dense=True)
ids = table.ids(axis='observation')[d.nonzero()]
obs = ids_from(iter(ids), True, 'feature',
['test', 'test2', 'testalt'])
self.assertEqual(obs, exp)
def test_ids_from_filter(self):
redbiom.admin.create_context('test', 'foo')
redbiom.admin.load_sample_metadata(metadata)
redbiom.admin.ScriptManager.load_scripts(read_only=False)
redbiom.admin.load_sample_data(table, 'test', tag=None)
id_ = [
table.ids(axis='observation')[0],
]
obs = ids_from(id_, False, 'feature', [
'test',
], min_count=3)
self.assertEqual(len(obs), 3)
obs = ids_from(id_, False, 'feature', [
'test',
])
self.assertEqual(len(obs), 4)
def test_ids_from_samples(self):
redbiom.admin.create_context('test', 'foo')
redbiom.admin.load_sample_metadata(metadata)
redbiom.admin.ScriptManager.load_scripts(read_only=False)
redbiom.admin.load_sample_data(table, 'test', tag=None)
obs_ids = table.ids(axis='observation')
exp = set(obs_ids[table.data(table.ids()[0]) > 0])
exp.update(set(obs_ids[table.data(table.ids()[1]) > 0]))
to_fetch = ['UNTAGGED_%s' % i for i in table.ids()[:2]]
obs = ids_from(to_fetch, False, 'sample', ['test'])
self.assertEqual(obs, exp)