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 setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
self.parser = configparser.ConfigParser()
self.path = os.path.join(q2cli.util.get_app_dir(), 'cli-colors.theme')
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME 2
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.provenance_capture = archive.ImportProvenanceCapture()
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME 2
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.provenance_capture = archive.ImportProvenanceCapture()
def setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
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)
def setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
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)
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME 2
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.data_dir = os.path.join(self.test_dir.name, 'viz-output')
os.mkdir(self.data_dir)
mapping_viz(self.data_dir,
{'abc': 'foo', 'def': 'bar'},
{'ghi': 'baz', 'jkl': 'bazz'},
key_label='Key', value_label='Value')
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 setUp(self):
dummy_plugin = get_dummy_plugin()
self.runner = CliRunner()
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
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\n0\t42\tabc\n1\t-1.5\tdef\n')
self.bad_metadata_file = os.path.join(
self.tempdir, 'bad-metadata.tsv')
with open(self.bad_metadata_file, 'w') as f:
f.write('wrong\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)
self.ints1 = os.path.join(self.tempdir, 'ints1.qza')
ints1 = Artifact.import_data(
'IntSequence1', [0, 42, 43], list)
ints1.save(self.ints1)
self.ints2 = os.path.join(self.tempdir, 'ints')
ints1.export_data(self.ints2)
self.viz = os.path.join(self.tempdir, 'viz.qzv')
most_common_viz = dummy_plugin.actions['most_common_viz']
self.viz = most_common_viz(ints1).visualization.save(self.viz)
def setUp(self):
dummy_plugin = get_dummy_plugin()
self.runner = CliRunner()
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
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\n0\t42\tabc\n1\t-1.5\tdef\n')
self.bad_metadata_file = os.path.join(self.tempdir, 'bad-metadata.tsv')
with open(self.bad_metadata_file, 'w') as f:
f.write('wrong\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)
self.ints1 = os.path.join(self.tempdir, 'ints1.qza')
ints1 = Artifact.import_data('IntSequence1', [0, 42, 43], list)
ints1.save(self.ints1)
self.ints2 = os.path.join(self.tempdir, 'ints')
ints1.export_data(self.ints2)
self.viz = os.path.join(self.tempdir, 'viz.qzv')
most_common_viz = dummy_plugin.actions['most_common_viz']
self.viz = most_common_viz(ints1).visualization.save(self.viz)
def setUp(self):
self.plugin = get_dummy_plugin()
self.concatenate_ints_sig = MethodSignature(
concatenate_ints,
inputs={
'ints1': IntSequence1 | IntSequence2,
'ints2': IntSequence1,
'ints3': IntSequence2
},
parameters={
'int1': qiime2.plugin.Int,
'int2': qiime2.plugin.Int
},
outputs=[
('concatenated_ints', IntSequence1)
]
)
self.split_ints_sig = MethodSignature(
split_ints,
inputs={
'ints': IntSequence1
},
parameters={},
outputs=[
('left', IntSequence1),
('right', IntSequence1)
]
)
def setUp(self):
self.plugin = get_dummy_plugin()
# TODO standardize temporary directories created by QIIME 2
# create a temporary data_dir for sample Visualizations
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.data_dir = os.path.join(self.test_dir.name, 'viz-output')
os.mkdir(self.data_dir)
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)
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-column]\n'
'm-metadata-file=%s\n'
'm-metadata-column=col1\n' % self.metadata_file1)
f.write('[dummy-plugin.identity-with-optional-metadata-column]\n'
'm-metadata-file=%s\n'
'm-metadata-column=col1\n' % self.metadata_file1)
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 setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME 2
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.data_dir = os.path.join(self.test_dir.name, 'viz-output')
os.mkdir(self.data_dir)
mapping_viz(self.data_dir, {
'abc': 'foo',
'def': 'bar'
}, {
'ghi': 'baz',
'jkl': 'bazz'
},
key_label='Key',
value_label='Value')
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
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 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)
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)
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 setUp(self):
self.plugin = get_dummy_plugin()
self.concatenate_ints_sig = MethodSignature(
concatenate_ints,
inputs={
'ints1': IntSequence1 | IntSequence2,
'ints2': IntSequence1,
'ints3': IntSequence2
},
parameters={
'int1': qiime2.plugin.Int,
'int2': qiime2.plugin.Int
},
outputs=[('concatenated_ints', IntSequence1)])
self.split_ints_sig = MethodSignature(split_ints,
inputs={'ints': IntSequence1},
parameters={},
outputs=[('left', IntSequence1),
('right', IntSequence1)
])
def setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
def setUp(self):
self.plugin = get_dummy_plugin()
self.single_int = qiime2.Artifact.import_data(SingleInt, -1)
self.int_sequence = qiime2.Artifact.import_data(IntSequence1,
[1, 2, 3])
self.mapping = qiime2.Artifact.import_data(Mapping, {'foo': '42'})
def setUp(self):
plugin = get_dummy_plugin()
self.action = plugin.actions[self.ACTION]
def setUp(self):
self.plugin = get_dummy_plugin()
self.method = self.plugin.methods['deprecated_method']
def setUp(self):
self.plugin = get_dummy_plugin()
# PluginManager is a singleton so there's no issue creating it again.
self.pm = qiime2.sdk.PluginManager()
def setUp(self):
self.plugin = get_dummy_plugin()
# TODO standardize temporary directories created by QIIME 2
# create a temporary data_dir for sample Visualizations
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
def setUp(self):
self.plugin = get_dummy_plugin()
def setUp(self):
self.plugin = get_dummy_plugin()
# PluginManager is a singleton so there's no issue creating it again.
self.pm = qiime2.sdk.PluginManager()
def setUp(self):
# TODO standardize temporary directories created by QIIME 2
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.plugin = get_dummy_plugin()
def setUp(self):
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.plugin = get_dummy_plugin()
def setUp(self):
self._sys_modules = sys.modules.copy()
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
def setUp(self):
get_dummy_plugin()
self.runner = CliRunner()
self.tempdir = tempfile.mkdtemp(prefix='qiime2-q2cli-test-temp-')
def setUp(self):
get_dummy_plugin()
def dummy_plugin(monkeypatch):
monkeypatch.setenv('QIIMETEST', '')
return get_dummy_plugin()
def setUp(self):
self.plugin = get_dummy_plugin()
def setUp(self):
get_dummy_plugin()
def setUp(self):
# TODO standardize temporary directories created by QIIME 2
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.plugin = get_dummy_plugin()
def setUp(self):
self._sys_modules = sys.modules.copy()
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
def setUp(self):
self.plugin = get_dummy_plugin()
self.single_int = qiime2.Artifact.import_data(SingleInt, -1)
self.int_sequence = qiime2.Artifact.import_data(
IntSequence1, [1, 2, 3])
self.mapping = qiime2.Artifact.import_data(Mapping, {'foo': '42'})
