]
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"])