def test_sample_metadata_samples_not_represented_in_context(self):
redbiom.admin.create_context('test', 'a nice test')
redbiom.admin.load_sample_metadata(metadata)
with self.assertRaisesRegexp(ValueError, "None of the samples"):
# sample data have not been loaded into the context
sample_metadata(['10317.000047188', '10317.000046868'],
context='test')
def test_sample_metadata_context(self):
redbiom.admin.create_context('test', 'a nice test')
redbiom.admin.load_sample_metadata(metadata)
redbiom.admin.load_sample_data(table, 'test', tag='foo')
exp = metadata.copy()
exp.set_index('#SampleID', inplace=True)
exp.index = ["%s.foo" % i for i in exp.index]
obs, ambig = sample_metadata(table.ids(), common=False, context='test')
obs.set_index('#SampleID', inplace=True)
self.assertEqual(sorted(exp.index), sorted(obs.index))
self.assertTrue(set(obs.columns).issubset(exp.columns))
for col in set(exp.columns) - set(obs.columns):
self.assertTrue(set(exp[col].values), {
'Unspecified',
})
obs = obs.loc[exp.index]
# we cannot do a full table == table test. Round tripping is not
# assured as we do not store null values in redbiom, and there is a
# litany of possible null values.
pdt.assert_series_equal(obs['BMI'], exp['BMI'])
obs['AGE_YEARS'] = [
v if v is not None else 'Unknown' for v in obs['AGE_YEARS']
]
pdt.assert_series_equal(obs['AGE_YEARS'], exp['AGE_YEARS'])
pdt.assert_series_equal(obs['SAMPLE_TYPE'], exp['SAMPLE_TYPE'])
def test_sample_metadata_with_tagged(self):
tagged_md = [(ix, 'abc', i % 2)
for i, ix in enumerate(metadata['#SampleID'])]
tagged_md = pd.DataFrame(tagged_md,
columns=['#SampleID', 'foo', 'bar'],
dtype=str)
redbiom.admin.create_context('test', 'a nice test')
redbiom.admin.load_sample_metadata(metadata)
redbiom.admin.load_sample_metadata(tagged_md, 'testtag')
redbiom.admin.load_sample_data(table, 'test', tag='testtag')
exp = metadata.copy()
exp['#SampleID'] = [i + '.testtag' for i in exp['#SampleID']]
exp['foo'] = tagged_md['foo']
exp['bar'] = tagged_md['bar']
exp.set_index('#SampleID', inplace=True)
obs, ambig = sample_metadata(table.ids(),
common=False,
context='test',
tagged=True)
obs.set_index('#SampleID', inplace=True)
self.assertEqual(sorted(exp.index), sorted(obs.index))
self.assertTrue(set(obs.columns).issubset(exp.columns))
self.assertIn('foo', obs.columns)
self.assertIn('bar', obs.columns)
def test_sample_metadata_restrict(self):
redbiom.admin.load_sample_metadata(metadata)
exp = metadata.copy()
exp.set_index('#SampleID', inplace=True)
exp = exp[['BMI', 'AGE_YEARS']]
exp = exp.sort_values('BMI')
obs, ambig = sample_metadata(table.ids(),
restrict_to=['BMI', 'AGE_YEARS'])
obs.set_index('#SampleID', inplace=True)
obs = obs.sort_values('BMI')
obs = obs[['BMI', 'AGE_YEARS']]
obs['AGE_YEARS'] = [
v if v is not None else 'Unknown' for v in obs['AGE_YEARS']
]
pdt.assert_frame_equal(obs, exp)
def test_sample_metadata_have_data(self):
redbiom.admin.load_sample_metadata(metadata)
exp = metadata.copy()
exp.set_index('#SampleID', inplace=True)
obs, ambig = sample_metadata(table.ids(), common=True)
self.assertEqual(sorted(exp.index), sorted(obs.index))
self.assertNotEqual(sorted(exp.columns), sorted(obs.columns))
obs = obs.loc[exp.index]
# we cannot do a full table == table test. Round tripping is not
# assured as we do not store null values in redbiom, and there is a
# litany of possible null values.
pdt.assert_series_equal(obs['BMI'], exp['BMI'])
pdt.assert_series_equal(obs['SAMPLE_TYPE'], exp['SAMPLE_TYPE'])
# one sample has "Unknown" as its AGE_YEARS value. This means that
# it is not informative for that column, so that value is not stored
# for that sample. As a result, the AGE_YEARS columns is not considered
# to be represented across all samples
self.assertNotIn('AGE_YEARS', obs.columns)
def test_sample_metadata_restrict_bad_cols(self):
redbiom.admin.load_sample_metadata(metadata)
with self.assertRaises(KeyError):
sample_metadata(table.ids(), restrict_to=['BMI', 'foo'])