test_maf2tile.py 文件源码

def setUpClass(self):
        self.TESTDB_URI = "postgresql+psycopg2://@:5432/mafend2end"
        if not database_exists(self.TESTDB_URI):
            create_database(self.TESTDB_URI)

        engine = create_engine(self.TESTDB_URI)
        models.bind_engine(engine)
        self.config_path = os.path.join(os.path.realpath(
            sys.argv[-1]), "utils/example_configs/icgc_config.json")
        with open(self.config_path, 'r') as readFP:
            config_json = json.load(readFP)
            config_json["TileDBConfig"] = os.path.join(os.path.realpath(
                sys.argv[-1]), "utils/example_configs/tiledb_config.json")
            config_json["TileDBAssembly"] = os.path.join(
                os.path.realpath(sys.argv[-1]), "utils/example_configs/hg19.json")
            config_json["VariantSetMap"]["VariantConfig"] = os.path.join(
                os.path.realpath(sys.argv[-1]), "utils/example_configs/icgc_variants.json")
        with open(self.config_path, 'w') as writeFP:
            writeFP.write(json.dumps(config_json))

        config = ConfigReader(self.config_path)
        config.DB_URI = self.TESTDB_URI
        imp.helper.registerWithMetadb(config)