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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
import warnings
import biom
import qiime2
import pandas as pd
import numpy as np
import numpy.testing as npt
from q2_feature_table import _rename
class TestRename(unittest.TestCase):
def setUp(self):
self.old_ids = ['S1', 'S2', 'S3']
self.name_map = pd.Series({'S1': 'S1_new',
'S2': 'S2_new',
'S4': 'S4_name'})
self.known = {'S1': 'S1_new', 'S2': 'S2_new', 'S3': 'S3'}
def test_generate_new_names_non_unique(self):
name_map = pd.Series({'S1': 'S2_new', 'S2': 'S2_new'})
with self.assertRaises(ValueError) as cm:
_rename._generate_new_names(self.old_ids,
name_map,
strict=True,
verbose=False)
self.assertEqual(
str(cm.exception),
('All new ids must be unique.\n'
'Try the group method in this plugin if you want '
'to combine multiple samples in the same table.')
)
def test_generate_new_names_old_disjoint_strict(self):
with self.assertRaises(ValueError) as cm:
_rename._generate_new_names(self.old_ids,
self.name_map,
strict=True,
verbose=False)
self.assertEqual(
str(cm.exception),
("There are ids in the table which do not have new names.\n"
"Either turn off strict mode or provide a remapping for "
"all ids.\nThe following ids are not mapped:\n S3")
)
def test_generate_new_names_verbose_warnings(self):
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
new_names = \
_rename._generate_new_names(self.old_ids,
self.name_map,
strict=False,
verbose=True)
self.assertEqual(len(w), 2)
self.assertTrue(isinstance(w[0].message, UserWarning))
self.assertEqual(str(w[0].message),
'There are ids in the original table which do not '
'have new names.\nThe following ids will not be '
'included:\n S3')
self.assertTrue(isinstance(w[1].message, UserWarning))
self.assertEqual(str(w[1].message),
'There are ids supplied for renaming that are not in'
' the table.\nThe following ids will not be mapped:'
'\n S4'
)
self.assertEqual(new_names.keys(), self.known.keys())
for k, v in new_names.items():
self.assertEqual(v, self.known[k])
def test_generate_new_names_no_verbse(self):
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
new_names = \
_rename._generate_new_names(self.old_ids,
self.name_map,
strict=False,
verbose=False)
self.assertEqual(len(w), 0)
self.assertEqual(new_names.keys(), self.known.keys())
for k, v in new_names.items():
self.assertEqual(v, self.known[k])
def test_rename_samples(self):
table = biom.Table(np.array([[0, 1, 2], [3, 4, 5]]),
observation_ids=['01', '02'],
sample_ids=['S1', 'S2', 'S3'])
meta1 = qiime2.Metadata(pd.DataFrame(
data=np.array([['cat'], ['rat'], ['dog']]),
index=pd.Index(['S1', 'S2', 'S3'], name='sample-id'),
columns=['animal']
))
meta2 = qiime2.Metadata(pd.DataFrame(
data=[['CATCATCAT'], ['WANTCAT']],
index=pd.Index(['01', '02'], name='feature-id'),
columns=['sequence']
))
updated = _rename.rename_ids(table,
meta1.get_column('animal'))
updated = _rename.rename_ids(updated,
meta2.get_column('sequence'),
axis='feature')
npt.assert_array_equal(np.array(updated.ids(axis='sample')),
np.array(['cat', 'rat', 'dog']))
npt.assert_array_equal(np.array(updated.ids(axis='observation')),
np.array(['CATCATCAT', 'WANTCAT']))
if __name__ == "__main__":
unittest.main()
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