Пример #1
0
    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
        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')

        self.provenance = Provenance(
            execution_uuid=uuid.UUID('7e909a23-21e2-44c2-be17-0723fae91dc8'),
            executor_reference=(
                'dummy_action_id. Details on plugin, version, website, etc. '
                'will also be included, see '
                'https://github.com/biocore/qiime2/issues/26'),
            artifact_uuids={
                'input1': uuid.UUID('f16ca3d0-fe83-4b1e-8eea-7e35db3f6b0f'),
                'input2': uuid.UUID('908dece5-db23-4562-ad03-876bb5750145')
            },
            parameter_references={
                'param1': 'abc',
                'param2': '100'
            })
Пример #2
0
    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
        self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
Пример #3
0
    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
        self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
        self.provenance_capture = archive.ImportProvenanceCapture()
Пример #4
0
    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
        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')
Пример #5
0
    def setUp(self):
        self.plugin = get_dummy_plugin()

        self.concatenate_ints_sig = MethodSignature(
            inputs={
                'ints1': (IntSequence1 | IntSequence2, list),
                'ints2': (IntSequence1, list),
                'ints3': (IntSequence2, list)
            },
            parameters={
                'int1': (qiime.plugin.Int, int),
                'int2': (qiime.plugin.Int, int)
            },
            outputs=collections.OrderedDict([
                ('concatenated_ints', (IntSequence1, list))
            ])
        )

        self.split_ints_sig = MethodSignature(
            inputs={
                'ints': (IntSequence1, list)
            },
            parameters={},
            outputs=collections.OrderedDict([
                ('left', (IntSequence1, list)),
                ('right', (IntSequence1, list))
            ])
        )
Пример #6
0
    def setUp(self):
        self.plugin = get_dummy_plugin()

        self.concatenate_ints_sig = Signature(
            inputs={
                'ints1': (IntSequence1 | IntSequence2, list),
                'ints2': (IntSequence1, list),
                'ints3': (IntSequence2, list)
            },
            parameters={
                'int1': (qiime.plugin.Int, int),
                'int2': (qiime.plugin.Int, int)
            },
            outputs=collections.OrderedDict([
                ('concatenated_ints', (IntSequence1, list))
            ])
        )

        self.split_ints_sig = Signature(
            inputs={
                'ints': (IntSequence1, list)
            },
            parameters={},
            outputs=collections.OrderedDict([
                ('left', (IntSequence1, list)),
                ('right', (IntSequence1, list))
            ])
        )
Пример #7
0
    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
        self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')

        self.provenance = Provenance(
            execution_uuid=uuid.UUID('7e909a23-21e2-44c2-be17-0723fae91dc8'),
            executor_reference=(
                'dummy_method_id. Details on plugin, version, website, etc. '
                'will also be included, see '
                'https://github.com/biocore/qiime2/issues/26'
            ),
            artifact_uuids={
                'input1': uuid.UUID('f16ca3d0-fe83-4b1e-8eea-7e35db3f6b0f'),
                'input2': uuid.UUID('908dece5-db23-4562-ad03-876bb5750145')
            },
            parameter_references={
                'param1': 'abc',
                'param2': '100'
            }
        )
Пример #8
0
 def setUp(self):
     # TODO standardize temporary directories created by QIIME
     self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
     self.plugin = get_dummy_plugin()
Пример #9
0
 def setUp(self):
     self.plugin = get_dummy_plugin()
Пример #10
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 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()
Пример #11
0
 def setUp(self):
     self.plugin = get_dummy_plugin()
     # PluginManager is a singleton so there's no issue creating it again.
     self.pm = qiime.sdk.PluginManager()
Пример #12
0
 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()
Пример #13
0
 def setUp(self):
     self.plugin = get_dummy_plugin()
Пример #14
0
 def setUp(self):
     # TODO standardize temporary directories created by QIIME
     self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
     self.plugin = get_dummy_plugin()
Пример #15
0
 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. PluginManager is
     # a singleton so there's no issue creating it again.
     get_dummy_plugin()
     self.pm = qiime.sdk.PluginManager()
Пример #16
0
 def setUp(self):
     self.plugin = get_dummy_plugin()
     # PluginManager is a singleton so there's no issue creating it again.
     self.pm = qiime.sdk.PluginManager()