1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
|
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# ----------------------------------------------------------------------------
from unittest import TestCase, main
import pandas as pd
import tempfile
import os
from skbio.util import get_data_path
from skbio.util._decorator import overrides
from skbio.metadata._metadata import SampleMetadata
from skbio.io.format.sample_metadata import (
_sample_metadata_sniffer, _sample_metadata_read)
class SnifferTests(TestCase):
def setUp(self):
self.positive_fps = list(map(get_data_path, [
'sample-metadata-comments-comment-char-id.tsv',
'sample-metadata-comments.tsv',
'sample-metadata-comments-mixed-case.tsv',
'sample-metadata-complete-types-directive.tsv',
'sample-metadata-empty-rows.tsv',
'sample-metadata-leading-trailing-whitespace.tsv',
'sample-metadata-leading-trailing-whitespace-split-id.tsv',
]))
self.negative_fps = list(map(get_data_path, [
'empty',
'whitespace_only',
]))
def test_positives(self):
for fp in self.positive_fps:
self.assertEqual(_sample_metadata_sniffer(fp), (True, {}))
def test_negatives(self):
for fp in self.negative_fps:
self.assertEqual(_sample_metadata_sniffer(fp), (False, {}))
class TestSampleMetadataReader(TestCase):
def test_reader(self):
fp = get_data_path('sample-metadata-complete-types-directive.tsv')
obs_md = SampleMetadata.read(fp)
exp_index = pd.Index(['id1', 'id2', 'id3'], name='id')
exp_df = pd.DataFrame({'col1': ['1', '2', '3'],
'col2': ['a', 'b', 'c'],
'col3': ['foo', 'bar', '42']},
index=exp_index)
exp_md = SampleMetadata(exp_df)
self.assertEqual(obs_md, exp_md)
class TestRoundtrip(TestCase):
def setUp(self):
self.temp_dir_obj = tempfile.TemporaryDirectory(
prefix='sample-metadata-temp')
self.temp_dir = self.temp_dir_obj.name
self.filepath = os.path.join(self.temp_dir, 'metadata.tsv')
def tearDown(self):
self.temp_dir_obj.cleanup()
def test_simple(self):
fp = get_data_path('sample-metadata-comments-mixed-case.tsv')
md1 = SampleMetadata.read(fp)
md1.write(self.filepath)
md2 = SampleMetadata.read(self.filepath)
self.assertEqual(md1, md2)
if __name__ == '__main__':
main()
|
