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https://github.com/galaxyproject/galaxy.git
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John Chilton
fa637518e8
The community took a vote (https://github.com/galaxyproject/galaxy/pull/8511#issuecomment-525886525) and the overwhelming favorite was this programming style declaration of a vaguely C-ish language embedded in quote fenced blocks.
96 lines
3.0 KiB
Python
96 lines
3.0 KiB
Python
from galaxy import model
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from galaxy.managers.markdown_util import resolve_invocation_markdown, validate_galaxy_markdown
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from .test_workflow_progress import TEST_WORKFLOW_YAML
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from .workflow_support import MockTrans, yaml_to_model
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def test_workflow_section_expansion():
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workflow_markdown = """
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## Workflow
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```galaxy
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workflow_display()
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```
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"""
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galaxy_markdown = resolved_markdown(workflow_markdown)
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assert "## Workflow\n" in galaxy_markdown
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assert "```galaxy\nworkflow_display(workflow_id=342)\n```\n" in galaxy_markdown
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def test_inputs_section_expansion():
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workflow_markdown = """
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## Workflow Inputs
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```galaxy
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invocation_inputs()
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```
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"""
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galaxy_markdown = resolved_markdown(workflow_markdown)
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assert "## Workflow Inputs" in galaxy_markdown
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assert "```galaxy\nhistory_dataset_display(history_dataset_id=567)\n" in galaxy_markdown
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assert len(galaxy_markdown.split("```")) == 3
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def test_outputs_section_expansion():
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workflow_markdown = """
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## Workflow Outputs
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```galaxy
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invocation_outputs()
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```
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"""
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galaxy_markdown = resolved_markdown(workflow_markdown)
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assert "## Workflow Outputs" in galaxy_markdown
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assert "```galaxy\nhistory_dataset_display(history_dataset_id=563)" in galaxy_markdown
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def test_input_reference_mapping():
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workflow_markdown = """
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And outputs...
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```galaxy
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history_dataset_peek(input=input1)
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```
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"""
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galaxy_markdown = resolved_markdown(workflow_markdown)
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assert "```galaxy\nhistory_dataset_peek(history_dataset_id=567)\n```" in galaxy_markdown
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def test_output_reference_mapping():
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workflow_markdown = """
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And outputs...
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```galaxy
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history_dataset_as_image(output=output_label)
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```
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"""
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galaxy_markdown = resolved_markdown(workflow_markdown)
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assert "```galaxy\nhistory_dataset_as_image(history_dataset_id=563)\n```" in galaxy_markdown
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def resolved_markdown(workflow_markdown):
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# Convert workflow markdown to internal Galaxy markdown with object id references
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# and with sections expanded.
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trans = MockTrans()
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validate_galaxy_markdown(workflow_markdown)
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galaxy_markdown = resolve_invocation_markdown(trans, example_invocation(trans), workflow_markdown)
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return galaxy_markdown
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def example_invocation(trans):
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invocation = model.WorkflowInvocation()
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workflow = yaml_to_model(TEST_WORKFLOW_YAML)
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workflow.id = 342
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invocation.workflow = workflow
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# TODO: fix this to use workflow id and eliminate hack.
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stored_workflow = model.StoredWorkflow()
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stored_workflow.id = 342
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invocation.workflow.stored_workflow = stored_workflow
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hda = model.HistoryDatasetAssociation(create_dataset=True, sa_session=trans.sa_session)
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hda.id = 567
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invocation.add_input(hda, step=workflow.steps[0])
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out_hda = model.HistoryDatasetAssociation(create_dataset=True, sa_session=trans.sa_session)
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out_hda.id = 563
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wf_output = model.WorkflowOutput(workflow.steps[2], label="output_label")
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invocation.add_output(wf_output, workflow.steps[2], out_hda)
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return invocation
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