def test_resolve_ambiguities(self):
import redbiom._requests
import redbiom
config = redbiom.get_config()
get = redbiom._requests.make_get(config)
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)
# all samples as ambiguous
samples = {'10317.000047188', '10317.000046868', '10317.000051129',
'10317.000012975', '10317.000033804', '10317.000001405',
'10317.000022252', '10317.000001378', '10317.000005080',
'10317.000003302'}
exp_stable = {"%s.UNTAGGED" % k: k for k in samples}
exp_unobserved = []
exp_ambiguous = {k: ["UNTAGGED_%s" % k] for k in samples}
exp_ri = {'UNTAGGED_%s' % k: '%s.UNTAGGED' % k for k in samples}
obs_stable, obs_unobserved, obs_ambiguous, obs_ri = \
resolve_ambiguities('test', samples, get)
self.assertEqual(obs_stable, exp_stable)
self.assertEqual(obs_unobserved, exp_unobserved)
self.assertEqual(obs_ambiguous, exp_ambiguous)
self.assertEqual(obs_ri, exp_ri)
def test_resolve_ambiguities_ambigbug(self):
import redbiom._requests
import redbiom
config = redbiom.get_config()
get = redbiom._requests.make_get(config)
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='fromtest')
redbiom.admin.load_sample_metadata(metadata_with_alt)
redbiom.admin.load_sample_data(table_with_alt, 'test',
tag='fromalt')
samples = {'fromtest_10317.000005080', 'fromalt_10317.000005080'}
exp_stable = {'10317.000005080.fromtest': 'fromtest_10317.000005080',
'10317.000005080.fromalt': 'fromalt_10317.000005080'}
exp_unobserved = []
exp_ambiguous = {'10317.000005080': ['fromtest_10317.000005080',
'fromalt_10317.000005080']}
exp_ri = {'fromtest_10317.000005080': '10317.000005080.fromtest',
'fromalt_10317.000005080': '10317.000005080.fromalt'}
obs_stable, obs_unobserved, obs_ambiguous, obs_ri = \
resolve_ambiguities('test', samples, get)
self.assertEqual(obs_stable, exp_stable)
self.assertEqual(obs_unobserved, exp_unobserved)
self.assertEqual({k: set(v) for k, v in obs_ambiguous.items()},
{k: set(v) for k, v in exp_ambiguous.items()})
self.assertEqual(obs_ri, exp_ri)
def test_resolve_ambiguities_mixed(self):
import redbiom._requests
import redbiom
config = redbiom.get_config()
get = redbiom._requests.make_get(config)
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)
samples = {
'10317.000047188', '10317.000046868', '10317.000051129',
'10317.000012975', '10317.000033804', '10317.000001405',
'10317.000022252', '10317.000001378', 'foo', 'UNTAGGED_bar',
'UNTAGGED_10317.000003302'
}
exp_stable = {
"%s.UNTAGGED" % k: k
for k in samples if 'foo' not in k and 'bar' not in k
}
exp_stable.pop('UNTAGGED_10317.000003302.UNTAGGED')
exp_stable['10317.000003302.UNTAGGED'] = 'UNTAGGED_10317.000003302'
exp_unobserved = ['foo', 'UNTAGGED_bar']
exp_ambiguous = {
'10317.000047188': ['UNTAGGED_10317.000047188'],
'10317.000046868': ['UNTAGGED_10317.000046868'],
'10317.000051129': ['UNTAGGED_10317.000051129'],
'10317.000012975': ['UNTAGGED_10317.000012975'],
'10317.000033804': ['UNTAGGED_10317.000033804'],
'10317.000001405': ['UNTAGGED_10317.000001405'],
'10317.000022252': ['UNTAGGED_10317.000022252'],
'10317.000001378': ['UNTAGGED_10317.000001378'],
'10317.000003302': ['UNTAGGED_10317.000003302']
}
exp_ri = {
'UNTAGGED_10317.000047188': '10317.000047188.UNTAGGED',
'UNTAGGED_10317.000046868': '10317.000046868.UNTAGGED',
'UNTAGGED_10317.000051129': '10317.000051129.UNTAGGED',
'UNTAGGED_10317.000012975': '10317.000012975.UNTAGGED',
'UNTAGGED_10317.000033804': '10317.000033804.UNTAGGED',
'UNTAGGED_10317.000001405': '10317.000001405.UNTAGGED',
'UNTAGGED_10317.000022252': '10317.000022252.UNTAGGED',
'UNTAGGED_10317.000001378': '10317.000001378.UNTAGGED',
'UNTAGGED_10317.000003302': '10317.000003302.UNTAGGED'
}
obs_stable, obs_unobserved, obs_ambiguous, obs_ri = \
resolve_ambiguities('test', samples, get)
self.assertEqual(obs_stable, exp_stable)
self.assertEqual(obs_unobserved, exp_unobserved)
self.assertEqual(obs_ambiguous, exp_ambiguous)
self.assertEqual(obs_ri, exp_ri)