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76 lines
2.2 KiB
Python
76 lines
2.2 KiB
Python
from galaxy_test.api.test_workflows import RunsWorkflowFixtures
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from galaxy_test.base.populators import (
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DatasetPopulator,
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WorkflowPopulator,
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)
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from galaxy_test.driver.integration_util import IntegrationTestCase
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class TestDirectoryStrategyMetadataFileIntegrationTestCase(IntegrationTestCase, RunsWorkflowFixtures):
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dataset_populator: DatasetPopulator
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workflow_populator: WorkflowPopulator
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framework_tool_and_types = True
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@classmethod
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def handle_galaxy_config_kwds(cls, config):
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config["metadata_strategy"] = "directory"
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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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self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
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def test_metadata_copied_to_copied_outputs(self, history_id):
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summary = self.workflow_populator.run_workflow(
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"""
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class: GalaxyWorkflow
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label: Tests metadata copied to copied outputs
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inputs:
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bam_file:
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type: collection
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collection_type: list
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outputs:
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copied_bam:
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outputSource: extract/output
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steps:
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build_list:
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tool_id: __BUILD_LIST__
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in:
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datasets_0|input: bam_file
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sleep:
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tool_id: cat_data_and_sleep
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tool_state:
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sleep_time: 2
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in:
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input1:
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source: build_list/output
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extract:
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tool_id: __EXTRACT_DATASET__
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tool_state:
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which:
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which_dataset: first
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in:
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input:
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source: sleep/out_file1
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test_data:
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bam_file:
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value: 1.bam
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file_type: bam
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type: File
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""",
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history_id=history_id,
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wait=True,
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assert_ok=True,
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)
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invocation = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
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copied_bam = invocation["outputs"]["copied_bam"]
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dataset = self.dataset_populator.get_history_dataset_details(history_id, content_id=copied_bam["id"])
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assert dataset["peek"] == "Binary bam alignments file"
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assert len(dataset["meta_files"]) == 1
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class TestExtendedMetadataStrategyMetadataFileIntegrationTestCase(TestDirectoryStrategyMetadataFileIntegrationTestCase):
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@classmethod
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def handle_galaxy_config_kwds(cls, config):
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config["metadata_strategy"] = "directory"
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