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): 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): # 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()
def dummy_plugin(monkeypatch): monkeypatch.setenv('QIIMETEST', '') return 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'})