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118 lines
4.0 KiB
Python
118 lines
4.0 KiB
Python
import os
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import string
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import subprocess
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from galaxy_test.base.populators import DatasetPopulator
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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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"""
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<object_store type="hierarchical" id="primary">
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<backends>
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<object_store id="swifty" type="generic_s3" 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="${temp_directory}/object_store_cache" size="1000" cache_updated_data="${cache_updated_data}" />
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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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)
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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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f"{OBJECT_STORE_PORT}:9000",
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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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"/data",
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]
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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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class BaseObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase, integration_util.ConfiguresObjectStores):
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dataset_populator: DatasetPopulator
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framework_tool_and_types = True
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def setUp(self):
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super().setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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def get_files(directory):
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for rel_directory, _, files in os.walk(directory):
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for file_ in files:
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yield os.path.join(rel_directory, file_)
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def files_count(directory):
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return sum(1 for _ in get_files(directory))
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@integration_util.skip_unless_docker()
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class BaseSwiftObjectStoreIntegrationTestCase(BaseObjectStoreIntegrationTestCase):
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object_store_cache_path: str
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@classmethod
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def setUpClass(cls):
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cls.container_name = f"{cls.__name__}_container"
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start_minio(cls.container_name)
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super().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().tearDownClass()
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@classmethod
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def handle_galaxy_config_kwds(cls, config):
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super().handle_galaxy_config_kwds(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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cls.object_store_cache_path = f"{temp_directory}/object_store_cache"
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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["outputs_to_working_directory"] = 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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"cache_updated_data": cls.updateCacheData(),
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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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def setUp(self):
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super().setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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@classmethod
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def updateCacheData(cls):
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return True
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