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113 lines
3.9 KiB
Python
113 lines
3.9 KiB
Python
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import os
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import string
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import subprocess
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from galaxy_test.driver import integration_util
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OBJECT_STORE_HOST = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_HOST', '127.0.0.1')
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OBJECT_STORE_PORT = int(os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_PORT', 9000))
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OBJECT_STORE_ACCESS_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_ACCESS_KEY', 'minioadmin')
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OBJECT_STORE_SECRET_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_SECRET_KEY', 'minioadmin')
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OBJECT_STORE_CONFIG = string.Template("""
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<object_store type="hierarchical" id="primary">
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<backends>
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<object_store id="swifty" type="swift" weight="1" order="0">
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<auth access_key="${access_key}" secret_key="${secret_key}" />
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<bucket name="galaxy" use_reduced_redundancy="False" max_chunk_size="250"/>
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<connection host="${host}" port="${port}" is_secure="False" conn_path="" multipart="True"/>
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<cache path="${temp_directory}/object_store_cache" size="1000" />
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<extra_dir type="job_work" path="${temp_directory}/job_working_directory_swift"/>
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<extra_dir type="temp" path="${temp_directory}/tmp_swift"/>
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</object_store>
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</backends>
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</object_store>
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""")
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TEST_TOOL_IDS = [
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"multi_output",
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"multi_output_configured",
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"multi_output_assign_primary",
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"multi_output_recurse",
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"tool_provided_metadata_1",
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"tool_provided_metadata_2",
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"tool_provided_metadata_3",
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"tool_provided_metadata_4",
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"tool_provided_metadata_5",
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"tool_provided_metadata_6",
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"tool_provided_metadata_7",
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"tool_provided_metadata_8",
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"tool_provided_metadata_9",
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"tool_provided_metadata_10",
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"tool_provided_metadata_11",
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"tool_provided_metadata_12",
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"composite_output",
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"composite_output_tests",
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"metadata",
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"metadata_bam",
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"output_format",
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"output_auto_format",
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]
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def start_minio(container_name):
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minio_start_args = [
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'docker',
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'run',
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'-p',
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'{port}:9000'.format(port=OBJECT_STORE_PORT),
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'-d',
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'--name',
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container_name,
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# '--rm',
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'minio/minio:latest',
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'server',
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'/tmp/data']
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subprocess.check_call(minio_start_args)
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def stop_minio(container_name):
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subprocess.check_call(['docker', 'rm', '-f', container_name])
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@integration_util.skip_unless_docker()
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class SwiftObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
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@classmethod
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def setUpClass(cls):
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cls.container_name = "%s_container" % cls.__name__
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start_minio(cls.container_name)
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super(SwiftObjectStoreIntegrationTestCase, cls).setUpClass()
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@classmethod
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def tearDownClass(cls):
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stop_minio(cls.container_name)
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super(SwiftObjectStoreIntegrationTestCase, cls).tearDownClass()
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@classmethod
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def handle_galaxy_config_kwds(cls, config):
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temp_directory = cls._test_driver.mkdtemp()
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cls.object_stores_parent = temp_directory
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config_path = os.path.join(temp_directory, "object_store_conf.xml")
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config["object_store_store_by"] = "uuid"
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config["metadata_strategy"] = "extended"
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config["outpus_to_working_dir"] = True
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config["retry_metadata_internally"] = False
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with open(config_path, "w") as f:
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f.write(
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OBJECT_STORE_CONFIG.safe_substitute(
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{
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"temp_directory": temp_directory,
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"host": OBJECT_STORE_HOST,
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"port": OBJECT_STORE_PORT,
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"access_key": OBJECT_STORE_ACCESS_KEY,
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"secret_key": OBJECT_STORE_SECRET_KEY,
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}
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)
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)
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config["object_store_config_file"] = config_path
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instance = integration_util.integration_module_instance(SwiftObjectStoreIntegrationTestCase)
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test_tools = integration_util.integration_tool_runner(TEST_TOOL_IDS)
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