def test_alpha_group_significance_numeric_only(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame({'value': ['1.0', '2.0', '3.0']},
index=['sample1', 'sample2', 'sample3']))
with tempfile.TemporaryDirectory() as output_dir:
with self.assertRaisesRegex(ValueError, 'Only numeric'):
alpha_group_significance(output_dir, alpha_div, md)
def test_alpha_group_significance_single_quote(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame({'a or b': ['a', "b'", 'b']},
index=['sample1', 'sample2', 'sample3']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue("\'" in open(index_fp).read())
def test_alpha_group_significance_numeric_only(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame(
{'col1': [1, 2, 1],
'col2': [4.2, 4.2, 4.3]},
index=pd.Index(['sample1', 'sample2', 'sample3'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
err_msg = ("does not contain any columns that satisfy this "
"visualizer's requirements")
with self.assertRaisesRegex(ValueError, err_msg):
alpha_group_significance(output_dir, alpha_div, md)
def test_alpha_group_significance_forward_slash_in_metadata_col(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame(
{'a/b': ['a', 'b', 'b']},
index=pd.Index(['sample1', 'sample2', 'sample3'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
with open(index_fp) as index_fh:
self.assertTrue("/" in index_fh.read())
jsonp_fp = os.path.join(output_dir, 'column-a%2Fb.jsonp')
self.assertTrue(os.path.exists(jsonp_fp))
csv_fp = os.path.join(output_dir,
'kruskal-wallis-pairwise-a%2Fb.csv')
self.assertTrue(os.path.exists(csv_fp))
def test_alpha_group_significance_KW_value_error(self):
alpha_div = pd.Series([2.0, 2.0, 3.0, 2.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3',
'sample4'])
md = qiime2.Metadata(
pd.DataFrame({'x': ['a', 'b', 'b', 'c']},
index=['sample1', 'sample2', 'sample3', 'sample4']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue(os.path.exists(
os.path.join(output_dir,
'category-x.jsonp')))
self.assertTrue('pairwise group comparisons have been omitted'
in open(index_fp).read())
self.assertTrue('x:c (n=1) vs x:a (n=1)' in open(index_fp).read())
def test_alpha_group_significance(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame({'a or b': ['a', 'b', 'b']},
index=['sample1', 'sample2', 'sample3']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue(os.path.exists(
os.path.join(output_dir,
'category-a%20or%20b.jsonp')))
self.assertTrue('Kruskal-Wallis (all groups)'
in open(index_fp).read())
self.assertTrue('Kruskal-Wallis (pairwise)'
in open(index_fp).read())
def test_alpha_group_significance_forward_slash_in_metadata_col(self):
alpha_div = pd.Series([2.0, 4.0, 6.0],
name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame({'a/b': ['a', 'b', 'b']},
index=pd.Index(['sample1', 'sample2', 'sample3'],
name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
with open(index_fp) as index_fh:
self.assertTrue("/" in index_fh.read())
jsonp_fp = os.path.join(output_dir, 'column-a%2Fb.jsonp')
self.assertTrue(os.path.exists(jsonp_fp))
csv_fp = os.path.join(output_dir,
'kruskal-wallis-pairwise-a%2Fb.csv')
self.assertTrue(os.path.exists(csv_fp))
def test_alpha_group_significance_one_group_single_value(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame({'a or b': ['a', 'b', 'b'],
'bad': ['x', 'x', 'x']},
index=['sample1', 'sample2', 'sample3']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue(os.path.exists(
os.path.join(output_dir,
'category-a%20or%20b.jsonp')))
self.assertFalse(os.path.exists(
os.path.join(output_dir,
'category-bad.jsonp')))
self.assertTrue('only a single' in open(index_fp).read())
self.assertTrue('<strong>bad' in open(index_fp).read())
def test_alpha_group_significance(self):
alpha_div = pd.Series([2.0, 4.0, 6.0],
name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame({'a or b': ['a', 'b', 'b']},
index=pd.Index(['sample1', 'sample2', 'sample3'],
name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue(
os.path.exists(
os.path.join(output_dir, 'column-a%20or%20b.jsonp')))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('Kruskal-Wallis (all groups)' in index_content)
self.assertTrue('Kruskal-Wallis (pairwise)' in index_content)
def test_alpha_group_significance_one_group_single_value(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame({'a or b': ['a', 'b', 'b'],
'bad': ['x', 'x', 'x']},
index=['sample1', 'sample2', 'sample3']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue(os.path.exists(
os.path.join(output_dir,
'category-a%20or%20b.jsonp')))
self.assertFalse(os.path.exists(
os.path.join(output_dir,
'category-bad.jsonp')))
self.assertTrue('only a single' in open(index_fp).read())
self.assertTrue('<strong>bad' in open(index_fp).read())
def test_alpha_group_significance_KW_value_error(self):
alpha_div = pd.Series([2.0, 2.0, 3.0, 2.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3',
'sample4'])
md = qiime2.Metadata(
pd.DataFrame({'x': ['a', 'b', 'b', 'c']},
index=pd.Index(['sample1', 'sample2', 'sample3',
'sample4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue(os.path.exists(
os.path.join(output_dir,
'column-x.jsonp')))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('pairwise group comparisons have been omitted'
in index_content)
self.assertTrue('x:c (n=1) vs x:a (n=1)' in index_content)
def test_alpha_group_significance_one_group_all_unique_values(self):
alpha_div = pd.Series([2.0, 4.0, 6.0], name='alpha-div',
index=['sample1', 'sample2', 'sample3'])
md = qiime2.Metadata(
pd.DataFrame(
{'a or b': ['a', 'b', 'b'],
'bad': ['x', 'y', 'z']},
index=pd.Index(['sample1', 'sample2', 'sample3'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_group_significance(output_dir, alpha_div, md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue(os.path.exists(
os.path.join(output_dir,
'column-a%20or%20b.jsonp')))
self.assertFalse(os.path.exists(
os.path.join(output_dir,
'column-bad.jsonp')))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('number of samples' in index_content)
self.assertTrue('<strong>bad' in index_content)
