] test_data_description = [ TestData(*items) for items in zip(files, datatypes, uploadable) ] return { os.path.basename(data.path): data for data in test_data_description } class UploadTestDatatypeDataTestCase(BaseUploadContentConfigurationInstance): framework_tool_and_types = False datatypes_conf_override = DATATYPES_CONFIG instance = integration_util.integration_module_instance( UploadTestDatatypeDataTestCase) @pytest.fixture def temp_file(): with tempfile.NamedTemporaryFile(delete=True, mode='wb') as fh: yield fh registry = Registry() registry.load_datatypes(root_dir=GALAXY_ROOT, config=DATATYPES_CONFIG) TEST_CASES = collect_test_data(registry) @pytest.mark.parametrize('test_data', TEST_CASES.values(),
"""Integration tests for the Pulsar embedded runner.""" import os from base import integration_util SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__)) EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.xml") class EmbeddedPulsarIntegrationInstance(integration_util.IntegrationInstance): """Describe a Galaxy test instance with embedded pulsar configured.""" framework_tool_and_types = True @classmethod def handle_galaxy_config_kwds(cls, config): config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE instance = integration_util.integration_module_instance( EmbeddedPulsarIntegrationInstance) test_tools = integration_util.integration_tool_runner([ "simple_constructs", "multi_data_param", "output_filter", "vcf_bgzip_test", ])
"""Integration tests for the Pulsar embedded runner with outputs to working directory.""" import os from base import integration_util SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__)) EMBEDDED_PULSAR_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "embedded_pulsar_job_conf.yml") class EmbeddedCopyWorkingPulsarIntegrationInstance( integration_util.IntegrationInstance): """Describe a Galaxy test instance with embedded pulsar configured.""" framework_tool_and_types = True @classmethod def handle_galaxy_config_kwds(cls, config): config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE config["outputs_to_working_directory"] = True instance = integration_util.integration_module_instance( EmbeddedCopyWorkingPulsarIntegrationInstance) test_tools = integration_util.integration_tool_runner(["output_format"])