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# ----------------------------------------------------------------------------
# Copyright (c) 2017-2023, 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 os
import pandas as pd
import pandas.testing as pdt
import numpy as np
import biom
import qiime2
from qiime2.plugins import sample_classifier
from q2_sample_classifier.tests.test_base_class import \
SampleClassifierTestPluginBase
from q2_sample_classifier.tests.test_estimators import SampleEstimatorTestBase
from q2_sample_classifier.classify import summarize
class NowLetsTestTheActions(SampleClassifierTestPluginBase):
def setUp(self):
super().setUp()
md = pd.Series(['a', 'a', 'b', 'b', 'b'],
index=['a', 'b', 'c', 'd', 'e'], name='bugs')
md.index.name = 'SampleID'
self.md = qiime2.CategoricalMetadataColumn(md)
tab = biom.Table(
np.array([[3, 6, 7, 3, 6], [3, 4, 5, 6, 2], [8, 6, 4, 1, 0],
[8, 6, 4, 1, 0], [8, 6, 4, 1, 0]]),
observation_ids=['v', 'w', 'x', 'y', 'z'],
sample_ids=['a', 'b', 'c', 'd', 'e'])
self.tab = qiime2.Artifact.import_data('FeatureTable[Frequency]', tab)
md2 = pd.DataFrame({'trash': ['a', 'a', 'b', 'b', 'b', 'junk'],
'floats': [0.1, 0.1, 1.3, 1.8, 1000.1, 0.1],
'ints': [0, 1, 2, 2, 2, 0],
'nans': [1, 1, 2, 2, np.nan, np.nan],
'negatives': [-7, -3, -1.2, -4, -9, -1]},
index=['a', 'b', 'c', 'd', 'e', 'peanut'])
md2.index.name = 'SampleID'
self.md2 = qiime2.Metadata(md2)
# let's make sure the function runs w/o errors and that the correct
# transformers are in place (see issue 114)
def test_action_split_table(self):
res = sample_classifier.actions.split_table(
self.tab, self.md, test_size=0.5)
y_train = res.training_targets.view(pd.Series)
y_test = res.test_targets.view(pd.Series)
# test whether extracted target is correct
self.assertEqual(y_train.name, 'bugs')
# test if complete target column is covered
y_all = pd.concat([y_train, y_test]).sort_index()
y_all.index.name = 'SampleID'
pdt.assert_series_equal(y_all, self.md._series)
def test_metatable(self):
exp = biom.Table(
np.array([[0.1, 0.1, 1.3, 1.8, 1000.1, 0.1],
[0, 1, 2, 2, 2, 0]]),
observation_ids=['floats', 'ints'],
sample_ids=['a', 'b', 'c', 'd', 'e', 'peanut'])
res, = sample_classifier.actions.metatable(
self.md2, missing_values='drop_features')
report = res.view(biom.Table).descriptive_equality(exp)
self.assertIn('Tables appear equal', report, report)
def test_metatable_missing_error(self):
with self.assertRaisesRegex(ValueError, "missing values"):
sample_classifier.actions.metatable(
self.md2, missing_values='error')
def test_metatable_drop_samples(self):
exp = biom.Table(
np.array([[3, 6, 7, 3], [3, 4, 5, 6], [8, 6, 4, 1],
[8, 6, 4, 1], [8, 6, 4, 1],
[0.1, 0.1, 1.3, 1.8],
[0, 1, 2, 2], [1, 1, 2, 2]]),
observation_ids=['v', 'w', 'x', 'y', 'z', 'floats', 'ints',
'nans'],
sample_ids=['a', 'b', 'c', 'd'])
res, = sample_classifier.actions.metatable(
self.md2, self.tab, missing_values='drop_samples')
report = res.view(biom.Table).descriptive_equality(exp)
self.assertIn('Tables appear equal', report, report)
def test_metatable_fill_na(self):
exp = biom.Table(
np.array([[3, 6, 7, 3, 6], [3, 4, 5, 6, 2], [8, 6, 4, 1, 0],
[8, 6, 4, 1, 0], [8, 6, 4, 1, 0],
[0.1, 0.1, 1.3, 1.8, 1000.1],
[0, 1, 2, 2, 2], [1., 1., 2., 2., 0.]]),
observation_ids=['v', 'w', 'x', 'y', 'z', 'floats', 'ints',
'nans'],
sample_ids=['a', 'b', 'c', 'd', 'e'])
res, = sample_classifier.actions.metatable(
self.md2, self.tab, missing_values='fill')
report = res.view(biom.Table).descriptive_equality(exp)
self.assertIn('Tables appear equal', report, report)
def test_metatable_with_merge(self):
exp = biom.Table(
np.array([[3, 6, 7, 3, 6], [3, 4, 5, 6, 2], [8, 6, 4, 1, 0],
[8, 6, 4, 1, 0], [8, 6, 4, 1, 0],
[0.1, 0.1, 1.3, 1.8, 1000.1],
[0, 1, 2, 2, 2]]),
observation_ids=['v', 'w', 'x', 'y', 'z', 'floats', 'ints'],
sample_ids=['a', 'b', 'c', 'd', 'e'])
res, = sample_classifier.actions.metatable(
self.md2, self.tab, missing_values='drop_features')
report = res.view(biom.Table).descriptive_equality(exp)
self.assertIn('Tables appear equal', report, report)
def test_metatable_with_merge_successful_inner_join(self):
exp = biom.Table(
np.array([[3, 6, 7, 3], [3, 4, 5, 6], [8, 6, 4, 1],
[8, 6, 4, 1], [8, 6, 4, 1], [0.1, 0.1, 1.3, 1.8],
[0, 1, 2, 2], [1., 1., 2., 2.]]),
observation_ids=['v', 'w', 'x', 'y', 'z', 'floats', 'ints',
'nans'],
sample_ids=['a', 'b', 'c', 'd'])
res, = sample_classifier.actions.metatable(
self.md2.filter_ids(['a', 'b', 'c', 'd']), self.tab,
missing_values='error')
report = res.view(biom.Table).descriptive_equality(exp)
self.assertIn('Tables appear equal', report, report)
def test_metatable_with_merge_error_inner_join(self):
with self.assertRaisesRegex(ValueError, "Missing samples"):
sample_classifier.actions.metatable(
self.md2.filter_ids(['a', 'b', 'c', 'd']),
self.tab, missing_samples='error',
missing_values='drop_samples')
def test_metatable_empty_metadata_after_drop_all_unique(self):
with self.assertRaisesRegex(
ValueError, "All metadata"): # are belong to us
sample_classifier.actions.metatable(
self.md2.filter_ids(['b', 'c']), self.tab,
missing_values='drop_samples', drop_all_unique=True)
def test_metatable_no_samples_after_filtering(self):
junk_md = pd.DataFrame(
{'trash': ['a', 'a', 'b', 'b', 'b', 'junk'],
'floats': [np.nan, np.nan, np.nan, 1.8, 1000.1, 0.1],
'ints': [0, 1, 2, np.nan, 2, 0],
'nans': [1, 1, 2, 2, np.nan, np.nan],
'negatives': [-7, -4, -1.2, -4, -9, -1]},
index=['a', 'b', 'c', 'd', 'e', 'peanut'])
junk_md.index.name = 'SampleID'
junk_md = qiime2.Metadata(junk_md)
with self.assertRaisesRegex(ValueError, "All metadata samples"):
sample_classifier.actions.metatable(
junk_md, missing_values='drop_samples')
# make sure summarize visualizer works and that rfe_scores are stored properly
class TestSummarize(SampleEstimatorTestBase):
def test_summary_with_rfecv(self):
summarize(self.temp_dir.name, self.pipeline)
self.assertTrue('rfe_plot.pdf' in os.listdir(self.temp_dir.name))
self.assertTrue('rfe_plot.png' in os.listdir(self.temp_dir.name))
self.assertTrue('rfe_scores.tsv' in os.listdir(self.temp_dir.name))
def test_summary_without_rfecv(self):
# nuke the rfe_scores to test the other branch of _summarize_estimator
del self.pipeline.rfe_scores
summarize(self.temp_dir.name, self.pipeline)
self.assertFalse('rfe_plot.pdf' in os.listdir(self.temp_dir.name))
self.assertFalse('rfe_plot.png' in os.listdir(self.temp_dir.name))
self.assertFalse('rfe_scores.tsv' in os.listdir(self.temp_dir.name))
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