def test_variadic_inputs(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
output_path = os.path.join(self.tempdir, 'output.qza')
ints1 = Artifact.import_data('IntSequence1', [1, 2, 3]).save(
os.path.join(self.tempdir, 'ints1.qza'))
ints2 = Artifact.import_data('IntSequence2', [4, 5, 6]).save(
os.path.join(self.tempdir, 'ints2.qza'))
set1 = Artifact.import_data('SingleInt', 7).save(
os.path.join(self.tempdir, 'set1.qza'))
set2 = Artifact.import_data('SingleInt', 8).save(
os.path.join(self.tempdir, 'set2.qza'))
result = self.runner.invoke(command, [
'variadic-input-method', '--i-ints', ints1, '--i-ints', ints2,
'--i-int-set', set1, '--i-int-set', set2, '--p-nums', '9',
'--p-nums', '10', '--p-opt-nums', '11', '--p-opt-nums', '12',
'--p-opt-nums', '13', '--o-output', output_path, '--verbose'
])
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(output_path))
output = Artifact.load(output_path)
self.assertEqual(output.view(list), list(range(1, 14)))
def test_repeated_multiple_option(self):
input_path = os.path.join(self.tempdir, 'ints.qza')
artifact = Artifact.import_data(IntSequence1, [0, 42, 43], list)
artifact.save(input_path)
metadata_path1 = os.path.join(self.tempdir, 'metadata1.tsv')
with open(metadata_path1, 'w') as f:
f.write('id\tcol1\nid1\tfoo\nid2\tbar\n')
metadata_path2 = os.path.join(self.tempdir, 'metadata2.tsv')
with open(metadata_path2, 'w') as f:
f.write('id\tcol2\nid1\tbaz\nid2\tbaa\n')
output_path = os.path.join(self.tempdir, 'out.qza')
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
result = self.runner.invoke(command, [
'identity-with-metadata', '--i-ints', input_path, '--o-out',
output_path, '--m-metadata-file', metadata_path1,
'--m-metadata-file', metadata_path2, '--verbose'
])
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(output_path))
self.assertEqual(Artifact.load(output_path).view(list), [0, 42, 43])
def test_list_commands(self):
# top level commands, including a plugin, are present
qiime_cli = RootCommand()
commands = qiime_cli.list_commands(ctx=None)
self.assertTrue('info' in commands)
self.assertTrue('tools' in commands)
self.assertTrue('dummy-plugin' in commands)
def test_split_ints(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output file names
left_path = os.path.join(self.tempdir, 'left.qza')
right_path = os.path.join(self.tempdir, 'right.qza')
# TODO: currently must pass `--verbose` to commands invoked by Click's
# test runner because redirecting stdout/stderr raises an
# "io.UnsupportedOperation: fileno" error. Likely related to Click
# mocking a filesystem in the test runner.
result = self.runner.invoke(command, [
'split-ints', '--i-ints', self.artifact1_path, '--o-left',
left_path, '--o-right', right_path, '--verbose'
])
# command completes successfully and creates the correct
# output files
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(left_path))
self.assertTrue(os.path.exists(right_path))
# results are correct
left = Artifact.load(left_path)
right = Artifact.load(right_path)
self.assertEqual(left.view(list), [0])
self.assertEqual(right.view(list), [42, 43])
def test_variadic_inputs(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
output_path = os.path.join(self.tempdir, 'output.qza')
ints1 = Artifact.import_data('IntSequence1', [1, 2, 3]).save(
os.path.join(self.tempdir, 'ints1.qza'))
ints2 = Artifact.import_data('IntSequence2', [4, 5, 6]).save(
os.path.join(self.tempdir, 'ints2.qza'))
set1 = Artifact.import_data('SingleInt', 7).save(
os.path.join(self.tempdir, 'set1.qza'))
set2 = Artifact.import_data('SingleInt', 8).save(
os.path.join(self.tempdir, 'set2.qza'))
result = self.runner.invoke(
command,
['variadic-input-method', '--i-ints', ints1, '--i-ints', ints2,
'--i-int-set', set1, '--i-int-set', set2, '--p-nums', '9',
'--p-nums', '10', '--p-opt-nums', '11', '--p-opt-nums', '12',
'--p-opt-nums', '13', '--o-output', output_path, '--verbose'])
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(output_path))
output = Artifact.load(output_path)
self.assertEqual(output.view(list), list(range(1, 14)))
def test_list_commands(self):
# top level commands, including a plugin, are present
qiime_cli = RootCommand()
commands = qiime_cli.list_commands(ctx=None)
self.assertTrue('info' in commands)
self.assertTrue('tools' in commands)
self.assertTrue('dummy-plugin' in commands)
def test_split_ints(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output file names
left_path = os.path.join(self.tempdir, 'left.qza')
right_path = os.path.join(self.tempdir, 'right.qza')
# TODO: currently must pass `--verbose` to commands invoked by Click's
# test runner because redirecting stdout/stderr raises an
# "io.UnsupportedOperation: fileno" error. Likely related to Click
# mocking a filesystem in the test runner.
result = self.runner.invoke(
command, ['split-ints', '--i-ints', self.artifact1_path,
'--o-left', left_path, '--o-right', right_path,
'--verbose'])
# command completes successfully and creates the correct
# output files
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(left_path))
self.assertTrue(os.path.exists(right_path))
# results are correct
left = Artifact.load(left_path)
right = Artifact.load(right_path)
self.assertEqual(left.view(list), [0])
self.assertEqual(right.view(list), [42, 43])
def test_repeated_multiple_option(self):
input_path = os.path.join(self.tempdir, 'ints.qza')
artifact = Artifact.import_data(IntSequence1, [0, 42, 43], list)
artifact.save(input_path)
metadata_path1 = os.path.join(self.tempdir, 'metadata1.tsv')
with open(metadata_path1, 'w') as f:
f.write('id\tcol1\nid1\tfoo\nid2\tbar\n')
metadata_path2 = os.path.join(self.tempdir, 'metadata2.tsv')
with open(metadata_path2, 'w') as f:
f.write('id\tcol2\nid1\tbaz\nid2\tbaa\n')
output_path = os.path.join(self.tempdir, 'out.qza')
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
result = self.runner.invoke(
command, ['identity-with-metadata', '--i-ints', input_path,
'--o-out', output_path, '--m-metadata-file',
metadata_path1, '--m-metadata-file', metadata_path2,
'--verbose'])
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(output_path))
self.assertEqual(Artifact.load(output_path).view(list), [0, 42, 43])
def test_deprecated_help_text(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
result = self.runner.invoke(command, ['deprecated-method', '--help'])
self.assertEqual(result.exit_code, 0)
self.assertTrue('WARNING' in result.output)
self.assertTrue('deprecated' in result.output)
def test_repeated_action_option(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
out_path = os.path.join(self.tempdir, 'out.qza')
result = self.runner.invoke(
command,
['no-input-method', '--o-out', out_path, '--o-out', out_path])
self._assertRepeatedOptionError(result, '--o-out')
def test_plugin_list_commands(self):
# plugin commands are present including a method and visualizer
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
commands = command.list_commands(ctx=None)
self.assertTrue('split-ints' in commands)
self.assertTrue('mapping-viz' in commands)
self.assertFalse('split_ints' in commands)
self.assertFalse('mapping_viz' in commands)
def test_repeated_action_option(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
out_path = os.path.join(self.tempdir, 'out.qza')
result = self.runner.invoke(
command, ['no-input-method', '--o-out', out_path,
'--o-out', out_path])
self._assertRepeatedOptionError(result, '--o-out')
def test_plugin_list_commands(self):
# plugin commands are present including a method and visualizer
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
commands = command.list_commands(ctx=None)
self.assertTrue('split-ints' in commands)
self.assertTrue('mapping-viz' in commands)
self.assertFalse('split_ints' in commands)
self.assertFalse('mapping_viz' in commands)
def test_verbose_shows_stacktrace(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
output = os.path.join(self.tempdir, 'never-happens.qza')
result = self.runner.invoke(command, [
'failing-pipeline', '--i-int-sequence', self.artifact1_path,
'--o-mapping', output, '--p-break-from', 'internal', '--verbose'
])
self.assertEqual(result.exit_code, 1)
self.assertIn('Traceback (most recent call last)', result.output)
def test_verbose_shows_stacktrace(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
output = os.path.join(self.tempdir, 'never-happens.qza')
result = self.runner.invoke(
command,
['failing-pipeline', '--i-int-sequence', self.artifact1_path,
'--o-mapping', output, '--p-break-from', 'internal', '--verbose'])
self.assertEqual(result.exit_code, 1)
self.assertIn('Traceback (most recent call last)', result.output)
def test_without_inputs_or_parameters(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
output_path = os.path.join(self.tempdir, 'output.qza')
result = self.runner.invoke(
command, ['no-input-method', '--o-out', output_path, '--verbose'])
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(output_path))
artifact = Artifact.load(output_path)
self.assertEqual(artifact.view(dict), {'foo': '42'})
def test_without_inputs_or_parameters(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
output_path = os.path.join(self.tempdir, 'output.qza')
result = self.runner.invoke(
command, ['no-input-method', '--o-out', output_path, '--verbose'])
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(output_path))
artifact = Artifact.load(output_path)
self.assertEqual(artifact.view(dict), {'foo': '42'})
def test_visualization(self):
# make a viz first:
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output parameter arguments and expected output file names
viz_path = os.path.join(self.tempdir, 'viz.qzv')
result = self.runner.invoke(
command, ['most-common-viz', '--i-ints', self.ints1,
'--o-visualization', viz_path, '--verbose'])
result = self.runner.invoke(tools, ['inspect-metadata', viz_path])
self.assertEqual(result.exit_code, 1)
self.assertIn("Visualizations cannot be viewed as QIIME 2 metadata",
result.output)
def test_visualization(self):
# make a viz first:
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output parameter arguments and expected output file names
viz_path = os.path.join(self.tempdir, 'viz.qzv')
result = self.runner.invoke(
command, ['most-common-viz', '--i-ints', self.ints1,
'--o-visualization', viz_path, '--verbose'])
result = self.runner.invoke(tools, ['inspect-metadata', viz_path])
self.assertEqual(result.exit_code, 1)
self.assertIn("Visualizations cannot be viewed as QIIME 2 metadata",
result.output)
def setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
self.plugin_command = RootCommand().get_command(ctx=None,
name='dummy-plugin')
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
self.input_artifact = os.path.join(self.tempdir, 'in.qza')
Artifact.import_data(IntSequence1, [0, 42, 43],
list).save(self.input_artifact)
self.output_artifact = os.path.join(self.tempdir, 'out.qza')
self.metadata_file1 = os.path.join(self.tempdir, 'metadata1.tsv')
with open(self.metadata_file1, 'w') as f:
f.write('id\tcol1\n0\tfoo\nid1\tbar\n')
self.metadata_file_alt_id_header = os.path.join(
self.tempdir, 'metadata-alt-id-header.tsv')
with open(self.metadata_file_alt_id_header, 'w') as f:
f.write('#SampleID\tcol1\n0\tfoo\nid1\tbar\n')
self.metadata_file2 = os.path.join(self.tempdir, 'metadata2.tsv')
with open(self.metadata_file2, 'w') as f:
f.write('id\tcol2\n0\tbaz\nid1\tbaa\n')
self.metadata_file_mixed_types = os.path.join(
self.tempdir, 'metadata-mixed-types.tsv')
with open(self.metadata_file_mixed_types, 'w') as f:
f.write('id\tnumbers\tstrings\nid1\t42\tabc\nid2\t-1.5\tdef\n')
self.metadata_artifact = os.path.join(self.tempdir, 'metadata.qza')
Artifact.import_data('Mapping', {
'a': 'dog',
'b': 'cat'
}).save(self.metadata_artifact)
def test_syntax_error_in_env(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
viz_path = os.path.join(self.tempdir, 'viz')
with unittest.mock.patch('qiime2.sdk.Result.load',
side_effect=SyntaxError):
result = self.runner.invoke(command, [
'most-common-viz', '--i-ints', self.artifact1_path,
'--o-visualization', viz_path, '--verbose'
])
self.assertEqual(result.exit_code, 1)
self.assertTrue('problem loading' in result.output)
self.assertTrue(self.artifact1_path in result.output)
def test_run_deprecated_gets_warning_msg(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
output_path = os.path.join(self.tempdir, 'output.qza')
result = self.runner.invoke(
command,
['deprecated-method', '--o-out', output_path, '--verbose'])
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(output_path))
artifact = Artifact.load(output_path)
# Just make sure that the command ran as expected
self.assertEqual(artifact.view(dict), {'foo': '43'})
self.assertTrue('deprecated' in result.output)
def test_qzv_extension(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output parameter arguments and expected output file names
viz_path = os.path.join(self.tempdir, 'viz')
expected_viz_path = os.path.join(self.tempdir, 'viz.qzv')
result = self.runner.invoke(
command, ['most-common-viz', '--i-ints', self.artifact1_path,
'--o-visualization', viz_path, '--verbose'])
# command completes successfully and creates the correct
# output file
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(expected_viz_path))
# Visualization contains expected contents
viz = Visualization.load(expected_viz_path)
self.assertEqual(viz.get_index_paths(), {'html': 'data/index.html',
'tsv': 'data/index.tsv'})
def test_action_parameter_types(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
results = self.runner.invoke(command, ['typical-pipeline', '--help'])
help_text = results.output
# Check the help text to make sure the types are displayed correctly
# boolean primitive
self.assertIn('--p-do-extra-thing / --p-no-do-extra-thing', help_text)
# int primitive
self.assertIn('--p-add INTEGER', help_text)
# Run it to make sure the types are converted correctly, the framework
# will error if it recieves the wrong type from the interface.
output_dir = os.path.join(self.tempdir, 'output-test')
result = self.runner.invoke(command, [
'typical-pipeline', '--i-int-sequence', self.artifact1_path,
'--i-mapping', self.mapping_path, '--p-do-extra-thing', '--p-add',
'10', '--output-dir', output_dir, '--verbose'])
self.assertEqual(result.exit_code, 0)
def test_action_parameter_types(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
results = self.runner.invoke(command, ['typical-pipeline', '--help'])
help_text = results.output
# Check the help text to make sure the types are displayed correctly
# boolean primitive
self.assertIn('--p-do-extra-thing / --p-no-do-extra-thing', help_text)
# int primitive
self.assertIn('--p-add INTEGER', help_text)
# Run it to make sure the types are converted correctly, the framework
# will error if it recieves the wrong type from the interface.
output_dir = os.path.join(self.tempdir, 'output-test')
result = self.runner.invoke(command, [
'typical-pipeline', '--i-int-sequence', self.artifact1_path,
'--i-mapping', self.mapping_path, '--p-do-extra-thing', '--p-add',
'10', '--output-dir', output_dir, '--verbose'
])
self.assertEqual(result.exit_code, 0)
def test_qzv_extension(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output parameter arguments and expected output file names
viz_path = os.path.join(self.tempdir, 'viz')
expected_viz_path = os.path.join(self.tempdir, 'viz.qzv')
result = self.runner.invoke(command, [
'most-common-viz', '--i-ints', self.artifact1_path,
'--o-visualization', viz_path, '--verbose'
])
# command completes successfully and creates the correct
# output file
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(expected_viz_path))
# Visualization contains expected contents
viz = Visualization.load(expected_viz_path)
self.assertEqual(viz.get_index_paths(), {
'html': 'data/index.html',
'tsv': 'data/index.tsv'
})
def test_qza_extension(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output parameter arguments and expected output file names
left_path = os.path.join(self.tempdir, 'left')
expected_left_path = os.path.join(self.tempdir, 'left.qza')
right_path = os.path.join(self.tempdir, 'right')
expected_right_path = os.path.join(self.tempdir, 'right.qza')
result = self.runner.invoke(
command, ['split-ints', '--i-ints', self.artifact1_path,
'--o-left', left_path, '--o-right', right_path,
'--verbose'])
# command completes successfully and creates the correct
# output files
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(expected_left_path))
self.assertTrue(os.path.exists(expected_right_path))
# results are correct
left = Artifact.load(expected_left_path)
right = Artifact.load(expected_right_path)
self.assertEqual(left.view(list), [0])
self.assertEqual(right.view(list), [42, 43])
def setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
self.plugin_command = RootCommand().get_command(ctx=None,
name='dummy-plugin')
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
self.ints1 = os.path.join(self.tempdir, 'ints1.qza')
Artifact.import_data(IntSequence1, [0, 42, 43], list).save(self.ints1)
self.ints2 = os.path.join(self.tempdir, 'ints2.qza')
Artifact.import_data(IntSequence1, [99, -22], list).save(self.ints2)
self.ints3 = os.path.join(self.tempdir, 'ints3.qza')
Artifact.import_data(IntSequence2, [43, 43], list).save(self.ints3)
self.output = os.path.join(self.tempdir, 'output.qza')
def test_qza_extension(self):
qiime_cli = RootCommand()
command = qiime_cli.get_command(ctx=None, name='dummy-plugin')
# build output parameter arguments and expected output file names
left_path = os.path.join(self.tempdir, 'left')
expected_left_path = os.path.join(self.tempdir, 'left.qza')
right_path = os.path.join(self.tempdir, 'right')
expected_right_path = os.path.join(self.tempdir, 'right.qza')
result = self.runner.invoke(command, [
'split-ints', '--i-ints', self.artifact1_path, '--o-left',
left_path, '--o-right', right_path, '--verbose'
])
# command completes successfully and creates the correct
# output files
self.assertEqual(result.exit_code, 0)
self.assertTrue(os.path.exists(expected_left_path))
self.assertTrue(os.path.exists(expected_right_path))
# results are correct
left = Artifact.load(expected_left_path)
right = Artifact.load(expected_right_path)
self.assertEqual(left.view(list), [0])
self.assertEqual(right.view(list), [42, 43])
def setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
self.plugin_command = RootCommand().get_command(ctx=None,
name='dummy-plugin')
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
self.input_artifact = os.path.join(self.tempdir, 'in.qza')
Artifact.import_data(IntSequence1, [0, 42, 43],
list).save(self.input_artifact)
self.output_artifact = os.path.join(self.tempdir, 'out.qza')
self.metadata_file1 = os.path.join(self.tempdir, 'metadata1.tsv')
with open(self.metadata_file1, 'w') as f:
f.write('id\tcol1\n0\tfoo\nid1\tbar\n')
self.metadata_file2 = os.path.join(self.tempdir, 'metadata2.tsv')
with open(self.metadata_file2, 'w') as f:
f.write('id\tcol2\n0\tbaz\nid1\tbaa\n')
self.metadata_artifact = os.path.join(self.tempdir, 'metadata.qza')
Artifact.import_data('Mapping', {
'a': 'dog',
'b': 'cat'
}).save(self.metadata_artifact)
self.cmd_config = os.path.join(self.tempdir, 'conf.ini')
with open(self.cmd_config, 'w') as f:
f.write('[dummy-plugin.identity-with-metadata]\n'
'm-metadata-file=%s\n' % self.metadata_file1)
f.write('[dummy-plugin.identity-with-optional-metadata]\n'
'm-metadata-file=%s\n' % self.metadata_file1)
f.write('[dummy-plugin.identity-with-metadata-category]\n'
'm-metadata-file=%s\n'
'm-metadata-category=col1\n' % self.metadata_file1)
f.write('[dummy-plugin.identity-with-optional-metadata-category]\n'
'm-metadata-file=%s\n'
'm-metadata-category=col1\n' % self.metadata_file1)