# ---------------------------------------------------------------------------- # 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 os import shutil import unittest import tempfile import configparser from click.testing import CliRunner from qiime2 import Artifact from qiime2.core.testing.type import IntSequence1 from qiime2.core.testing.util import get_dummy_plugin import q2cli.util from q2cli.builtin.dev import dev class TestDev(unittest.TestCase): path = os.path.join(q2cli.util.get_app_dir(), 'cli-colors.theme') old_settings = None if os.path.exists(path): old_settings = configparser.ConfigParser() old_settings.read(path) def setUp(self): get_dummy_plugin() self.parser = configparser.ConfigParser() self.runner = CliRunner(mix_stderr=False) self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-') self.generated_config = os.path.join(self.tempdir, 'generated-theme') self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-') self.artifact1_path = os.path.join(self.tempdir, 'a1.qza') self.mapping_path = os.path.join(self.tempdir, 'mapping.qza') artifact1 = Artifact.import_data(IntSequence1, [0, 42, 43]) artifact1.save(self.artifact1_path) self.artifact1_root_dir = str(artifact1.uuid) mapping = Artifact.import_data('Mapping', {'foo': '42'}) mapping.save(self.mapping_path) self.config = os.path.join(self.tempdir, 'good-config.ini') self.parser['type'] = {'underline': 't'} with open(self.config, 'w') as fh: self.parser.write(fh) def tearDown(self): if self.old_settings is not None: with open(self.path, 'w') as fh: self.old_settings.write(fh) shutil.rmtree(self.tempdir) def test_import_theme(self): result = self.runner.invoke( dev, ['import-theme', '--theme', self.config]) self.assertEqual(result.exit_code, 0) def test_export_default_theme(self): result = self.runner.invoke( dev, ['export-default-theme', '--output-path', self.generated_config]) self.assertEqual(result.exit_code, 0) def test_reset_theme(self): result = self.runner.invoke( dev, ['reset-theme', '--yes']) self.assertEqual(result.exit_code, 0) def test_reset_theme_no_yes(self): result = self.runner.invoke( dev, ['reset-theme']) self.assertNotEqual(result.exit_code, 0) # result_type & result_data tests def test_assert_result_type_artifact_success(self): result = self.runner.invoke(dev, ['assert-result-type', self.mapping_path, '--qiime-type', 'Mapping']) # single regex to account for tempdir path expected_regex = r'The input file \(.*mapping.qza\) type and the'\ r' expected type \(Mapping\) match' self.assertEqual(result.exit_code, 0) self.assertRegex(result.stdout, expected_regex) def test_assert_result_type_visualization_success(self): dummy_plugin = get_dummy_plugin() self.viz_path = os.path.join(self.tempdir, 'viz.qzv') most_common_viz = dummy_plugin.actions['most_common_viz'] viz = most_common_viz(Artifact.load(self.artifact1_path)) viz.visualization.save(self.viz_path) result = self.runner.invoke(dev, ['assert-result-type', self.viz_path, '--qiime-type', 'Visualization']) expected_regex = r'The input file \(.*viz\.qzv\) type and the'\ r' expected type \(Visualization\) match' self.assertEqual(result.exit_code, 0) self.assertRegex(result.stdout, expected_regex) def test_assert_result_type_load_failure(self): result = self.runner.invoke(dev, ['assert-result-type', 'turkey_sandwhere.qza', '--qiime-type', 'Mapping']) self.assertEqual(result.exit_code, 1) self.assertRegex(result.stderr, r'File\s*\'turkey_sandwhere\.qza\'\s*does not exist') def test_assert_result_type_invalid_qiime_type(self): result = self.runner.invoke(dev, ['assert-result-type', self.mapping_path, '--qiime-type', 'Squid']) self.assertEqual(result.exit_code, 1) self.assertIn('Expected Squid, observed Mapping', result.stderr) def test_assert_result_data_success(self): result = self.runner.invoke(dev, ['assert-result-data', self.mapping_path, '--zip-data-path', 'mapping.tsv', '--expression', '42']) self.assertEqual(result.exit_code, 0) self.assertIn(r'"42" was found in mapping.tsv', result.stdout) def test_assert_result_data_load_failure(self): result = self.runner.invoke(dev, ['assert-result-data', 'turkey_sandwhen.qza', '--zip-data-path', 'mapping.tsv', '--expression', '42']) self.assertEqual(result.exit_code, 1) self.assertRegex(result.stderr, r'File\s*\'turkey_sandwhen\.qza\'\s*does not exist') def test_assert_result_data_zip_data_path_zero_matches(self): result = self.runner.invoke(dev, ['assert-result-data', self.mapping_path, '--zip-data-path', 'turkey_sandwhy.tsv', '--expression', '42']) self.assertEqual(result.exit_code, 1) self.assertRegex(result.stderr, r'did not produce exactly one match.\n' r'Matches: \[\]\n') def test_assert_result_data_zip_data_path_multiple_matches(self): self.double_path = os.path.join(self.tempdir, 'double.qza') double_artifact = Artifact.import_data('SingleInt', 3) double_artifact.save(self.double_path) result = self.runner.invoke(dev, ['assert-result-data', self.double_path, '--zip-data-path', 'file*.txt', '--expression', '3']) self.assertEqual(result.exit_code, 1) self.assertRegex(result.stderr, r'Value provided for zip_data_path' r' \(file\*\.txt\) did not produce' r' exactly one match\.') def test_assert_result_data_match_expression_not_found(self): result = self.runner.invoke(dev, ['assert-result-data', self.mapping_path, '--zip-data-path', 'mapping.tsv', '--expression', 'foobar']) self.assertEqual(result.exit_code, 1) self.assertRegex(result.stderr, r'Expression \'foobar\'' r' not found in .*\/data\/mapping\.tsv\.')