mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
c35d8f2a06
Also: - Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected by pytest only because they were `unittest.TestCase` derived, but normally pytest collects only test classes whose name starts with `Test`, see https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
159 lines
6.8 KiB
Python
159 lines
6.8 KiB
Python
"""Integration tests for object stores."""
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import os
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import string
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from galaxy.model import Dataset
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from galaxy.model.unittest_utils.store_fixtures import (
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deferred_hda_model_store_dict,
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one_hda_model_store_dict,
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)
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from ._base import (
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BaseObjectStoreIntegrationTestCase,
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files_count,
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)
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SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
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JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_conf.xml")
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JOB_RESOURCE_PARAMETERS_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "selection_job_resource_parameters_conf.xml")
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DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE = string.Template(
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"""<?xml version="1.0"?>
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<object_store type="distributed" id="primary" order="0">
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<backends>
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<backend id="default" type="disk" weight="1" name="Default Store">
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<description>This is my description of the default store with *markdown*.</description>
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<files_dir path="${temp_directory}/files_default"/>
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<extra_dir type="temp" path="${temp_directory}/tmp_default"/>
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<extra_dir type="job_work" path="${temp_directory}/job_working_directory_default"/>
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</backend>
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<backend id="static" type="disk" weight="0">
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<files_dir path="${temp_directory}/files_static"/>
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<extra_dir type="temp" path="${temp_directory}/tmp_static"/>
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<extra_dir type="job_work" path="${temp_directory}/job_working_directory_static"/>
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</backend>
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<backend id="dynamic_ebs" type="disk" weight="0">
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<files_dir path="${temp_directory}/files_dynamic_ebs"/>
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<extra_dir type="temp" path="${temp_directory}/tmp_dynamic_ebs"/>
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<extra_dir type="job_work" path="${temp_directory}/job_working_directory_dynamic_ebs"/>
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</backend>
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<backend id="dynamic_s3" type="disk" weight="0">
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<files_dir path="${temp_directory}/files_dynamic_s3"/>
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<extra_dir type="temp" path="${temp_directory}/tmp_dynamic_s3"/>
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<extra_dir type="job_work" path="${temp_directory}/job_working_directory_dynamic_s3"/>
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</backend>
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</backends>
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</object_store>
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"""
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)
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class TestObjectStoreSelectionIntegration(BaseObjectStoreIntegrationTestCase):
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# populated by config_object_store
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files_default_path: str
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files_static_path: str
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files_dynamic_path: str
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files_dynamic_ebs_path: str
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files_dynamic_s3_path: str
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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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cls._configure_object_store(DISTRIBUTED_OBJECT_STORE_CONFIG_TEMPLATE, config)
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config["job_config_file"] = JOB_CONFIG_FILE
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config["job_resource_params_file"] = JOB_RESOURCE_PARAMETERS_CONFIG_FILE
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config["object_store_store_by"] = "uuid"
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config["metadata_strategy"] = "celery_extended"
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config["outputs_to_working_directory"] = True
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def _object_store_counts(self):
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files_default_count = files_count(self.files_default_path)
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files_static_count = files_count(self.files_static_path)
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files_dynamic_count = files_count(self.files_dynamic_path)
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return files_default_count, files_static_count, files_dynamic_count
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def _assert_file_counts(self, default, static, dynamic_ebs, dynamic_s3):
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files_default_count = files_count(self.files_default_path)
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files_static_count = files_count(self.files_static_path)
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files_dynamic_ebs_count = files_count(self.files_dynamic_ebs_path)
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files_dynamic_s3_count = files_count(self.files_dynamic_s3_path)
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assert default == files_default_count
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assert static == files_static_count
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assert dynamic_ebs == files_dynamic_ebs_count
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assert dynamic_s3 == files_dynamic_s3_count
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def _assert_no_external_filename(self):
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# Should maybe be its own test case ...
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for external_filename_tuple in self._app.model.session.query(Dataset.external_filename).all():
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assert external_filename_tuple[0] is None
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def test_tool_simple_constructs(self):
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with self.dataset_populator.test_history() as history_id:
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def _run_tool(tool_id, inputs):
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self.dataset_populator.run_tool(
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tool_id,
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inputs,
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history_id,
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)
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self.dataset_populator.wait_for_history(history_id)
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self._assert_file_counts(0, 0, 0, 0)
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hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
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self.dataset_populator.wait_for_history(history_id)
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hda1_input = {"src": "hda", "id": hda1["id"]}
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storage_info = self.dataset_populator.dataset_storage_info(hda1["id"])
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assert "Default Store" == storage_info["name"]
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assert "*markdown*" in storage_info["description"]
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# One file uploaded, added to default object store ID.
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self._assert_file_counts(1, 0, 0, 0)
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# should create two files in static object store.
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_run_tool("multi_data_param", {"f1": hda1_input, "f2": hda1_input})
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self._assert_file_counts(1, 2, 0, 0)
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# should create two files in ebs object store.
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create_10_inputs_1 = {
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"input1": hda1_input,
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"input2": hda1_input,
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}
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_run_tool("create_10", create_10_inputs_1)
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self._assert_file_counts(1, 2, 10, 0)
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# should create 10 files in S3 object store.
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create_10_inputs_2 = {
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"__job_resource|__job_resource__select": "yes",
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"__job_resource|how_store": "slow",
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"input1": hda1_input,
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"input2": hda1_input,
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}
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_run_tool("create_10", create_10_inputs_2)
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self._assert_file_counts(1, 2, 10, 10)
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self._assert_no_external_filename()
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assert self._latest_dataset.object_store_id == "dynamic_s3"
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# assure discarded datsets don't have an object store ID populated
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# and don't create files in the object store.
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self.dataset_populator.create_contents_from_store(
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history_id,
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store_dict=one_hda_model_store_dict(),
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)
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self._assert_file_counts(1, 2, 10, 10)
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assert self._latest_dataset.object_store_id is None
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# assure deferred datsets don't have an object store ID populated
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# and don't create files in the object store.
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self.dataset_populator.create_contents_from_store(
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history_id,
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store_dict=deferred_hda_model_store_dict(),
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)
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self._assert_file_counts(1, 2, 10, 10)
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assert self._latest_dataset.object_store_id is None
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@property
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def _latest_dataset(self):
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latest_dataset = self._app.model.session.query(Dataset).order_by(Dataset.table.c.id.desc()).first()
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return latest_dataset
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