# ---------------------------------------------------------------------------- # 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 sys import subprocess import tempfile import unittest from q2cli.core.usage import CLIUsage from qiime2.core.testing.util import get_dummy_plugin import pytest def _rt_labeler(val): if hasattr(val, 'id'): return val.id return val @pytest.fixture def dummy_plugin(monkeypatch): monkeypatch.setenv('QIIMETEST', '') return get_dummy_plugin() def get_templated_tests(): return [ ('concatenate_ints', """\ # This example demonstrates basic usage. qiime dummy-plugin concatenate-ints \\ --i-ints1 ints-a.qza \\ --i-ints2 ints-b.qza \\ --i-ints3 ints-c.qza \\ --p-int1 4 \\ --p-int2 2 \\ --o-concatenated-ints ints-d.qza # This example demonstrates chained usage (pt 1). qiime dummy-plugin concatenate-ints \\ --i-ints1 ints-a.qza \\ --i-ints2 ints-b.qza \\ --i-ints3 ints-c.qza \\ --p-int1 4 \\ --p-int2 2 \\ --o-concatenated-ints ints-d.qza # This example demonstrates chained usage (pt 2). qiime dummy-plugin concatenate-ints \\ --i-ints1 ints-d.qza \\ --i-ints2 ints-b.qza \\ --i-ints3 ints-c.qza \\ --p-int1 41 \\ --p-int2 0 \\ --o-concatenated-ints concatenated-ints.qza # comment 1 # comment 2 # comment 1 # comment 2"""), ('identity_with_metadata', """\ qiime dummy-plugin identity-with-metadata \\ --i-ints ints.qza \\ --m-metadata-file md.tsv \\ --o-out out.qza qiime dummy-plugin identity-with-metadata \\ --i-ints ints.qza \\ --m-metadata-file md1.tsv md2.tsv \\ --o-out out.qza"""), ('identity_with_metadata_column', """\ qiime dummy-plugin identity-with-metadata-column \\ --i-ints ints.qza \\ --m-metadata-file md.tsv \\ --m-metadata-column a \\ --o-out out.qza"""), ('typical_pipeline', """\ qiime dummy-plugin typical-pipeline \\ --i-int-sequence ints.qza \\ --i-mapping mapper.qza \\ --p-do-extra-thing \\ --o-out-map out-map.qza \\ --o-left left.qza \\ --o-right right.qza \\ --o-left-viz left-viz.qzv \\ --o-right-viz right-viz.qzv qiime dummy-plugin typical-pipeline \\ --i-int-sequence ints1.qza \\ --i-mapping mapper1.qza \\ --p-do-extra-thing \\ --o-out-map out-map1.qza \\ --o-left left1.qza \\ --o-right right1.qza \\ --o-left-viz left-viz1.qzv \\ --o-right-viz right-viz1.qzv qiime dummy-plugin typical-pipeline \\ --i-int-sequence left1.qza \\ --i-mapping out-map1.qza \\ --p-no-do-extra-thing \\ --o-out-map out-map2.qza \\ --o-left left2.qza \\ --o-right right2.qza \\ --o-left-viz left-viz2.qzv \\ --o-right-viz right-viz2.qzv qiime dev assert-result-data right2.qza \\ --zip-data-path ints.txt \\ --expression 1 qiime dev assert-result-type right2.qza \\ --qiime-type IntSequence1 qiime dev assert-result-type out-map1.qza \\ --qiime-type Mapping"""), ('optional_artifacts_method', """\ qiime dummy-plugin optional-artifacts-method \\ --i-ints ints.qza \\ --p-num1 1 \\ --o-output output1.qza qiime dummy-plugin optional-artifacts-method \\ --i-ints ints.qza \\ --p-num1 1 \\ --p-num2 2 \\ --o-output output2.qza qiime dummy-plugin optional-artifacts-method \\ --i-ints ints.qza \\ --p-num1 1 \\ --o-output output3.qza qiime dummy-plugin optional-artifacts-method \\ --i-ints ints.qza \\ --i-optional1 output3.qza \\ --p-num1 3 \\ --p-num2 4 \\ --o-output output4.qza"""), ('variadic_input_method', """\ qiime dummy-plugin variadic-input-method \\ --i-ints ints-a.qza ints-b.qza \\ --i-int-set single-int1.qza single-int2.qza \\ --p-nums 7 8 9 \\ --o-output out.qza"""), ('list_of_ints', """\ qiime dummy-plugin list-of-ints \\ --i-ints ints/ \\ --o-output out/"""), ] _templ_ids = [x[0] for x in get_templated_tests()] @pytest.mark.parametrize('action,exp', get_templated_tests(), ids=_templ_ids) def test_templated(dummy_plugin, action, exp): action = dummy_plugin.actions[action] obs = '' for example_f in action.examples.values(): use = CLIUsage(enable_assertions=True) example_f(use) obs += use.render() obs += '\n' # trim final newline obs = obs[:-1] assert exp == obs def get_rt_tests(): tests = [] try: plugin = get_dummy_plugin() except RuntimeError: return tests for action in plugin.actions.values(): for name in action.examples: tests.append((action, name)) return tests @pytest.mark.parametrize('action,example', get_rt_tests(), ids=_rt_labeler) def test_round_trip(action, example): example_f = action.examples[example] use = CLIUsage(enable_assertions=True) example_f(use) rendered = use.render() if sys.platform.startswith('linux'): # TODO: remove me when arrays are not used in shell extra = dict(executable='/bin/bash') else: extra = dict() with tempfile.TemporaryDirectory() as tmpdir: for ref, data in use.get_example_data(): data.save(os.path.join(tmpdir, ref)) subprocess.run(rendered, shell=True, check=True, cwd=tmpdir, env={**os.environ}, **extra) class ReplayResultCollectionTests(unittest.TestCase): @classmethod def setUpClass(cls): cls.plugin = get_dummy_plugin() def test_construct_and_access_collection(self): action = self.plugin.actions['dict_of_ints'] use = CLIUsage() action.examples['construct_and_access_collection'](use) exp = """\ ## constructing result collection ## rc_name=rc-in/ ext=.qza keys=( a b ) names=( ints-a.qza ints-b.qza ) construct_result_collection ## qiime dummy-plugin dict-of-ints \\ --i-ints rc-in/ \\ --o-output rc-out/ ## accessing result collection member ## ln -s rc-out/b.qza ints-b-from-collection.qza ##""" self.assertEqual(exp, use.render())