# ---------------------------------------------------------------------------- # Copyright (c) 2016-2023, 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 pandas as pd from qiime2.plugin.testing import TestPluginBase from qiime2 import Metadata, Artifact from q2_composition._ancombc import ancombc class TestBase(TestPluginBase): package = 'q2_composition.tests' def setUp(self): super().setUp() self.md = Metadata.load(self.get_data_path('sample-md-ancombc.tsv')) self.missing_md = Metadata.load(self.get_data_path( 'sample-md-ancombc-missing.tsv')) table = Artifact.load(self.get_data_path('table-ancombc.qza')) self.table = table.view(pd.DataFrame) class TestANCOMBC(TestBase): def test_examples(self): self.execute_examples() # error handling for column validation def test_missing_formula_col(self): with self.assertRaisesRegex(ValueError, "'foo' is not a column in" " the metadata"): ancombc(table=self.table, metadata=self.md, formula='foo') def test_missing_ref_levels_col(self): with self.assertRaisesRegex(ValueError, "'foo' is not a column in" " the metadata"): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['foo::tongue']) # error handling for missing IDs in metadata def test_ids_in_table_not_in_md(self): with self.assertRaisesRegex(KeyError, 'Not all samples present within' ' the table were found in the associated' ' metadata file.*L6S68'): ancombc(table=self.table, metadata=self.missing_md, formula='bodysite') # confirm output columns based on formula inputs and ref levels def test_output_cols_single_formula_no_ref_level(self): exp_cols = set(['id', '(Intercept)', 'bodysiteleft palm', 'bodysiteright palm', 'bodysitetongue']) obs_cols = set() dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite') slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: obs_cols.add(col) self.assertNotIn('bodysitegut', col) self.assertEqual(exp_cols, obs_cols) def test_output_cols_single_formula_single_ref_level(self): exp_cols = set(['id', '(Intercept)', 'bodysiteleft palm', 'bodysiteright palm', 'bodysitegut']) obs_cols = set() dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['bodysite::tongue']) slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: obs_cols.add(col) self.assertNotIn('bodysitetongue', col) self.assertEqual(exp_cols, obs_cols) def test_output_cols_multi_formula_no_ref_level(self): exp_cols = set(['id', '(Intercept)', 'bodysiteleft palm', 'bodysiteright palm', 'bodysitetongue', 'animalcat', 'animalcow', 'animaldog']) obs_cols = set() dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite + animal') slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: obs_cols.add(col) self.assertNotIn('bodysitegut', col) self.assertNotIn('animalbird', col) self.assertEqual(exp_cols, obs_cols) def test_output_cols_multi_formula_single_ref_level(self): exp_cols = set(['id', '(Intercept)', 'bodysiteleft palm', 'bodysiteright palm', 'bodysitegut', 'animalcat', 'animalcow', 'animaldog']) obs_cols = set() dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite + animal', reference_levels=['bodysite::tongue']) slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: obs_cols.add(col) self.assertNotIn('bodysitetongue', col) self.assertNotIn('animalbird', col) self.assertEqual(exp_cols, obs_cols) def test_output_cols_multi_formula_multi_ref_levels(self): exp_cols = set(['id', '(Intercept)', 'bodysiteleft palm', 'bodysiteright palm', 'bodysitegut', 'animalcat', 'animalcow', 'animalbird']) obs_cols = set() dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite + animal', reference_levels=['bodysite::tongue', 'animal::dog']) slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: obs_cols.add(col) self.assertNotIn('bodysitetongue', col) self.assertNotIn('animaldog', col) self.assertEqual(exp_cols, obs_cols) # testing type directive in md for categorical columns w/numeric values def test_output_cols_categorical_col_w_numeric_vals_in_formula(self): exp_cols = set(['id', '(Intercept)', 'month1', 'month2', 'month4', 'month10']) obs_cols = set() dataloaf = ancombc(table=self.table, metadata=self.md, formula='month', reference_levels=['month::3']) slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: obs_cols.add(col) self.assertNotIn('month3', col) self.assertEqual(exp_cols, obs_cols) # confirm ref level behavior def test_ref_levels_behavior_A(self): dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite + AZcolumn', reference_levels=['AZcolumn::A']) slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: self.assertNotIn('AZcolumnA', col) def test_ref_levels_behavior_Z(self): dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite + AZcolumn', reference_levels=['AZcolumn::Z']) slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: for col in slice.columns: self.assertNotIn('AZcolumnZ', col) def test_multi_ref_levels(self): dataloaf = ancombc(table=self.table, metadata=self.md, formula='bodysite + month', reference_levels=['bodysite::tongue', 'month::10']) exp_cols = set(['id', '(Intercept)', 'bodysitegut', 'bodysiteleft palm', 'bodysiteright palm', 'month1', 'month2', 'month3', 'month4']) slices = dataloaf.data_slices.iter_views(pd.DataFrame) for _, slice in slices: col_list = [] for col in slice.columns: col_list.append(col) self.assertIn(col, exp_cols) self.assertNotIn('bodysitetongue', col_list) self.assertNotIn('month10', col_list) def test_numerical_md_col_ref_level_failure(self): with self.assertRaisesRegex(TypeError, 'Non-categorical column' ' selected:.*day'): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['day::28']) def test_ref_level_col_not_in_formula_failure(self): with self.assertRaisesRegex(ValueError, 'column "animal" was not' ' found within the `formula` terms.'): ancombc(table=self.table, metadata=self.md, formula='bodysite + month', reference_levels=['bodysite::tongue', 'animal::dog']) def test_ref_level_value_in_md_not_table(self): with self.assertRaisesRegex(ValueError, '.*Value not associated with' ' any IDs in the table: "toe"'): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['bodysite::toe']) def test_multi_ref_levels_with_same_col_failure(self): with self.assertRaisesRegex(ValueError, '.*`reference_level` column' ' with multiple groups that was included:' ' "bodysite"'): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['bodysite::tongue', 'bodysite::toe']) def test_extra_col_value_separator_in_ref_level_failure(self): with self.assertRaisesRegex(ValueError, '.*tongue::.*\n\nNOTE: Your' ' level value appears to contain a `:`.*'): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['bodysite::tongue::']) def test_no_col_value_separator_in_ref_level_failure(self): with self.assertRaisesRegex(ValueError, 'Too few column-value pair' ' separators found.*"bodysite:tongue"'): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['bodysite:tongue']) def test_colon_in_not_found_column(self): with self.assertRaisesRegex(ValueError, '.*:bodysite.*\n\nNOTE: Your' ' column name appears to contain a `:`.*'): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=[':bodysite::tongue']) def test_colon_in_not_found_level(self): with self.assertRaisesRegex(ValueError, '.*tongue:.*\n\nNOTE: Your' ' level value appears to contain a `:`.*'): ancombc(table=self.table, metadata=self.md, formula='bodysite', reference_levels=['bodysite::tongue:'])