Python ProvDocument.update方法代码示例

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import update [as 别名]
    def test_document_update_simple(self):
        d1 = ProvDocument()
        d1.set_default_namespace(EX_URI)
        d1.entity('e')

        b1 = d1.bundle('b1')
        b1.entity('e')

        d2 = ProvDocument()
        d2.set_default_namespace(EX_URI)
        d2.entity('e')

        b1 = d2.bundle('b1')
        b1.entity('e')
        b2 = d2.bundle('b2')
        b2.entity('e')

        self.assertRaises(ProvException, lambda: d1.update(1))

        d1.update(d2)
        self.assertEqual(len(d1.get_records()), 2)
        self.assertEqual(len(d1.bundles), 2)

# 需要导入模块: from prov.model import ProvDocument [as 别名]
# 或者: from prov.model.ProvDocument import update [as 别名]
class NIDMObjectsUnitTesting(unittest.TestCase):
    """
    Unit testing of NIDM objects (compared to examples provided in 
    nidm-results.owl)
    """

    def setUp(self):
        self.export_dir = os.path.join(TEST_FOLDER, 'nidm')
        if not os.path.isdir(self.export_dir):
            os.mkdir(self.export_dir)

        # Retreive owl file for NIDM-Results
        owl_file = os.path.join(TERM_RESULTS_DIR, 'nidm-results.owl')
        assert owl_file
        self.owl = OwlReader(owl_file)

        self.doc = ProvDocument()
        # self.bundle = ProvBundle(identifier=NIIRI[software_lc+'_results_id'])

        self.provn_file = os.path.join(self.export_dir, 'unit_test.provn')

        namespaces_file = os.path.join(TERM_RESULTS_DIR, "templates", \
            "Namespaces.txt")
        namespaces_fid = open(namespaces_file)
        self.prefixes = namespaces_fid.read()
        namespaces_fid.close()

        self.to_delete_files = [self.provn_file]
        self.gt_ttl_files = list()

    def test_design_matrix(self):
        mat = np.matrix('1 2; 3 4')

        mat_image = os.path.join(os.path.dirname(TEST_FOLDER), "data", \
            "fmri.feat", "design.png")

        design_matrix = DesignMatrix(mat, mat_image, self.export_dir)
        self.doc.update(design_matrix.export())

        # In the FSL export the design matrix contains both the Design Matrix
        # entity and the Image entity representing the design matrix 
        # visualisation.
        self.to_delete_files.append(os.path.join(self.export_dir, \
            "DesignMatrix.csv"))
        self.to_delete_files.append(os.path.join(self.export_dir, \
            "DesignMatrix.png")) 

        gt_file = self.owl.get_example(NIDM['DesignMatrix'])
        self.gt_ttl_files = [os.path.join(TERM_RESULTS_DIR, \
            gt_file.replace("file://./", "")), 
            os.path.join(TERM_RESULTS_DIR, "examples", "Image-DesignMatrix.txt")]

        self._create_gt_and_compare("Design Matrix")

    def test_data(self):
        data = Data(grand_mean_scaling=True, target=100.0)
        self.doc.update(data.export())

        gt_file = self.owl.get_example(NIDM['Data'])
        self.gt_ttl_files.append(os.path.join(TERM_RESULTS_DIR, \
            gt_file.replace("file://./", "")))

        self._create_gt_and_compare("Data")

# INDEPEDENT_CORR = NIDM['IndependentError']
# SERIALLY_CORR = NIDM['SeriallyCorrelatedError']
# COMPOUND_SYMMETRY_CORR = NIDM['CompoundSymmetricError']
# ARBITRARILY_CORR = NIDM['ArbitriralyCorrelatedError']


    # def test_error_model_indepdt_global(self):
    #     error_distribution = GAUSSIAN_DISTRIBUTION
    #     variance_homo = True
    #     variance_spatial = SPATIALLY_GLOBAL
    #     dependance = INDEPEDENT_CORR
    #     dependance_spatial = SPATIALLY_GLOBAL

    #     error_model = ErrorModel(error_distribution, variance_homo, 
    #         variance_spatial, dependance, dependance_spatial)
    #     self.doc.update(error_model.export())

    #     nidm_classes = {
    #         "ErrorModel": dict(
    #             error_model_id="niiri:error_model_id",
    #             noise_distribution="nidm:GaussianDistribution",
    #             variance_homo="true",
    #             variance_spatial="nidm:SpatiallyGlobal",
    #             dependence="nidm:IndependentError",
    #             dependence_spatial="nidm:SpatiallyLocal"
    #         )
    #         }
    #     self._create_gt_and_compare(nidm_classes, "Data")

    def _create_gt_and_compare(self, class_name):
        # Write-out current example in a provn file and convert to turtle
        provn_fid = open(self.provn_file, 'w')
        provn_fid.write(self.doc.get_provn())
        provn_fid.close()

        ttl_file = self.provn_file.replace(".provn", ".ttl")
#.........这里部分代码省略.........