Exemplos de integration_tool_runner em Python

Exemplo n.º 1

"""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_metadata_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"])

Exemplo n.º 2

Arquivo: test_pulsar_embedded.py Projeto: davebx/toolshed

"""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",
])

Exemplo n.º 3

Arquivo: test_pulsar_embedded_copy_working.py Projeto: davebx/toolshed

"""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"])