Python Visualization.load方法代碼示例

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_load_with_archive_filepath_modified(self):
        # Save a visualization for use in the following test case.
        fp = os.path.join(self.test_dir.name, 'visualization.qza')
        Visualization._from_data_dir(self.data_dir, None).save(fp)

        # Load the visualization from a filepath then save a different
        # visualization to the same filepath. Assert that both visualizations
        # access the correct data.
        #
        # `load` used to be lazy, only extracting data when it needed to (e.g.
        # when `save` or `get_index_paths` was called). This was buggy as the
        # filepath could have been deleted, or worse, modified to contain a
        # different .qzv file. Thus, the wrong archive could be extracted on
        # demand, or the archive could be missing altogether. There isn't an
        # easy cross-platform compatible way to solve this problem, so
        # Visualization.load is no longer lazy and always extracts its data
        # immediately. The real motivation for lazy loading was for quick
        # inspection of archives without extracting/copying data, so that API
        # is now provided through Visualization.peek.
        visualization1 = Visualization.load(fp)

        new_data_dir = os.path.join(self.test_dir.name, 'viz-output2')
        os.mkdir(new_data_dir)
        most_common_viz(new_data_dir, collections.Counter(range(42)))

        Visualization._from_data_dir(new_data_dir, None).save(fp)
        visualization2 = Visualization.load(fp)

        self.assertEqual(visualization1.get_index_paths(),
                         {'html': 'data/index.html'})
        self.assertEqual(visualization2.get_index_paths(),
                         {'html': 'data/index.html', 'tsv': 'data/index.tsv'})

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_roundtrip(self):
        fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
        fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
        visualization = Visualization._from_data_dir(
            self.data_dir, self.make_provenance_capture())
        visualization.save(fp1)

        visualization1 = Visualization.load(fp1)
        visualization1.save(fp2)
        visualization2 = Visualization.load(fp2)

        self.assertEqual(visualization1.type, visualization2.type)
        self.assertEqual(visualization1.uuid, visualization2.uuid)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_load_and_save(self):
        fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
        fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
        visualization = Visualization._from_data_dir(self.data_dir,
                                                     self.provenance)
        visualization.save(fp1)

        visualization = Visualization.load(fp1)
        # Overwriting its source file works.
        visualization.save(fp1)
        # Saving to a new file works.
        visualization.save(fp2)

        with zipfile.ZipFile(fp1, mode='r') as zf:
            fps = set(zf.namelist())
            expected = {
                'visualization1/VERSION',
                'visualization1/metadata.yaml',
                'visualization1/README.md',
                'visualization1/data/index.html',
                'visualization1/data/css/style.css'
            }
            self.assertEqual(fps, expected)

        with zipfile.ZipFile(fp2, mode='r') as zf:
            fps = set(zf.namelist())
            expected = {
                'visualization2/VERSION',
                'visualization2/metadata.yaml',
                'visualization2/README.md',
                'visualization2/data/index.html',
                'visualization2/data/css/style.css'
            }
            self.assertEqual(fps, expected)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_eq_same_uuid(self):
        fp = os.path.join(self.test_dir.name, 'visualization.qzv')
        visualization1 = Visualization._from_data_dir(
            self.data_dir, self.make_provenance_capture())
        visualization1.save(fp)

        visualization2 = Visualization.load(fp)

        self.assertEqual(visualization1, visualization2)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_get_index_paths_single_load(self):
        fp = os.path.join(self.test_dir.name, 'visualization.qzv')
        visualization = Visualization._from_data_dir(self.data_dir,
                                                     self.provenance)
        visualization.save(fp)
        visualization = Visualization.load(fp)

        actual = visualization.get_index_paths()
        expected = {'html': 'data/index.html'}
        self.assertEqual(actual, expected)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_load(self):
        saved_visualization = Visualization._from_data_dir(self.data_dir, None)
        fp = os.path.join(self.test_dir.name, 'visualization.qzv')
        saved_visualization.save(fp)

        visualization = Visualization.load(fp)

        self.assertEqual(visualization.type, qiime.core.type.Visualization)
        self.assertIsNone(visualization.provenance)
        self.assertEqual(visualization.uuid, saved_visualization.uuid)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_get_index_paths_multiple_html_load(self):
        data_dir = os.path.join(self.test_dir.name, 'multi-html-viz1')
        os.mkdir(data_dir)
        multi_html_viz(data_dir, [1, 42])

        fp = os.path.join(self.test_dir.name, 'visualization.qzv')
        visualization = Visualization._from_data_dir(data_dir,
                                                     self.provenance)
        visualization.save(fp)
        visualization = Visualization.load(fp)

        with self.assertRaises(ValueError):
            visualization.get_index_paths()

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_ne_subclass_same_uuid(self):
        class VisualizationSubclass(Visualization):
            pass

        fp = os.path.join(self.test_dir.name, 'visualization.qzv')
        visualization1 = VisualizationSubclass._from_data_dir(
            self.data_dir, self.make_provenance_capture())
        visualization1.save(fp)

        visualization2 = Visualization.load(fp)

        self.assertNotEqual(visualization1, visualization2)
        self.assertNotEqual(visualization2, visualization1)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_get_index_paths_multiple_load(self):
        data_dir = os.path.join(self.test_dir.name, 'mc-viz-output1')
        os.mkdir(data_dir)
        most_common_viz(data_dir,
                        collections.Counter(range(42)))
        fp = os.path.join(self.test_dir.name, 'visualization.qzv')
        visualization = Visualization._from_data_dir(data_dir,
                                                     self.provenance)
        visualization.save(fp)
        visualization = Visualization.load(fp)

        actual = visualization.get_index_paths()
        expected = {'html': 'data/index.html',
                    'tsv': 'data/index.tsv'}
        self.assertEqual(actual, expected)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_load_and_save(self):
        fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
        fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
        visualization = Visualization._from_data_dir(
            self.data_dir, self.make_provenance_capture())
        visualization.save(fp1)

        visualization = Visualization.load(fp1)
        # Overwriting its source file works.
        visualization.save(fp1)
        # Saving to a new file works.
        visualization.save(fp2)

        root_dir = str(visualization.uuid)
        expected = {
            'VERSION',
            'metadata.yaml',
            'data/index.html',
            'data/css/style.css',
            'provenance/metadata.yaml',
            'provenance/VERSION',
            'provenance/action/action.yaml'
        }

        self.assertArchiveMembers(fp1, root_dir, expected)

        root_dir = str(visualization.uuid)
        expected = {
            'VERSION',
            'metadata.yaml',
            'data/index.html',
            'data/css/style.css',
            'provenance/metadata.yaml',
            'provenance/VERSION',
            'provenance/action/action.yaml'
        }

        self.assertArchiveMembers(fp2, root_dir, expected)

# 需要導入模塊: from qiime.sdk import Visualization [as 別名]
# 或者: from qiime.sdk.Visualization import load [as 別名]
    def test_load_from_externally_created_zipfile(self):
        # If a user unzips a .qzv to inspect contents and rezips using a
        # different ZIP library/implementation than the one provided by Python,
        # loading, saving, etc. should still work as expected. The Python ZIP
        # implementation doesn't store directories as entries when writing, but
        # the `zip` Unix and OS X command line utilities include both
        # directories and filepaths as entries. When reading these files with
        # Python's ZIP implementation, the directory entries are visible, so
        # their presence needs to be accounted for when extracting.
        #
        # The following visualization was created with:
        #
        #     visualization = Visualization._from_data_dir(self.data_dir,
        #                                                  self.provenance)
        #     visualization.save('externally_created_zipfile.qzv')
        #
        # Unzip and rezip using command line utility:
        #
        #     unzip externally_created_zipfile.qzv
        #     rm externally_created_zipfile.qzv
        #     zip -r externally_created_zipfile.qzv externally_created_zipfile
        #
        fp = pkg_resources.resource_filename(
            'qiime.sdk.tests', 'data/externally_created_zipfile.qzv')

        with zipfile.ZipFile(fp, mode='r') as zf:
            fps = set(zf.namelist())
            expected = {
                # These are extra directory entries included by `zip` command
                # line utility.
                'externally_created_zipfile/',
                'externally_created_zipfile/data/',
                'externally_created_zipfile/data/css/',

                'externally_created_zipfile/VERSION',
                'externally_created_zipfile/metadata.yaml',
                'externally_created_zipfile/README.md',
                'externally_created_zipfile/data/index.html',
                'externally_created_zipfile/data/css/style.css'
            }
            self.assertEqual(fps, expected)

        visualization = Visualization.load(fp)

        self.assertEqual(visualization.type, qiime.core.type.Visualization)
        self.assertEqual(visualization.provenance, self.provenance)
        self.assertIsInstance(visualization.uuid, uuid.UUID)

        fp = os.path.join(self.test_dir.name, 'visualization.qzv')
        visualization.save(fp)

        with zipfile.ZipFile(fp, mode='r') as zf:
            fps = set(zf.namelist())
            expected = {
                # Directory entries should not be present.
                'visualization/VERSION',
                'visualization/metadata.yaml',
                'visualization/README.md',
                'visualization/data/index.html',
                'visualization/data/css/style.css'
            }
            self.assertEqual(fps, expected)