Galaxy Brain

SIMPLIFY_GXFORMAT2_CONTRACT_IN_GALAXY_PLAN

Simplify gxformat2 Contract in Galaxy

Galaxy uses gxformat2 for Format2↔native workflow conversion but also depends on test-infrastructure abstractions (convert_and_import_workflow, ImporterGalaxyInterface) that conflate format conversion with Galaxy API interaction. This PR simplifies that contract.

Context

What Galaxy actually needs from gxformat2

Production (lib/galaxy/managers/workflows.py):

That’s it. Everything else is test scaffolding.

Changes

1. Rewrite upload_yaml_workflow in populators

File: lib/galaxy_test/base/populators.py (~line 2355)

Replace convert_and_import_workflow(yaml_content, galaxy_interface=self, **kwds) with inline logic:

def upload_yaml_workflow(self, yaml_content, **kwds):
    round_trip_conversion = kwds.get("round_trip_format_conversion", False)
    client_convert = kwds.pop("client_convert", not round_trip_conversion)

    if client_convert:
        from gxformat2 import python_to_workflow
        from gxformat2.yaml import ordered_load
        as_python = ordered_load(yaml_content) if not isinstance(yaml_content, dict) else yaml_content
        workflow = python_to_workflow(as_python, galaxy_interface=None, workflow_directory=None)
    else:
        workflow = {"yaml_content": yaml_content} if not isinstance(yaml_content, dict) else yaml_content

    name = kwds.get("name")
    if name is not None:
        workflow["name"] = name
    import_kwds = {"fill_defaults": kwds.get("fill_defaults", True)}
    if kwds.get("publish"):
        import_kwds["publish"] = True
    if kwds.get("exact_tools"):
        import_kwds["exact_tools"] = True

    result = self.import_workflow(workflow, **import_kwds)
    workflow_id = result["id"]

    if round_trip_conversion:
        workflow_yaml_wrapped = self.download_workflow(workflow_id, style="format2_wrapped_yaml")
        round_trip_content = workflow_yaml_wrapped["yaml_content"]
        workflow_id = self.upload_yaml_workflow(round_trip_content, client_convert=False, round_trip_conversion=False)
    return workflow_id

Consider moving to BaseWorkflowPopulator so both API and Selenium populators share one implementation.

2. Same change in Selenium populator

File: lib/galaxy_test/selenium/framework.py (~line 983)

Same replacement, or inherit from BaseWorkflowPopulator if unified in step 1.

3. Remove ImporterGalaxyInterface from class hierarchies

File: lib/galaxy_test/base/populators.py

# Before
class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator, ImporterGalaxyInterface):
# After
class WorkflowPopulator(GalaxyInteractorHttpMixin, BaseWorkflowPopulator):

File: lib/galaxy_test/selenium/framework.py

# Before
class SeleniumSessionWorkflowPopulator(..., ImporterGalaxyInterface):
# After
class SeleniumSessionWorkflowPopulator(...):

import_workflow methods stay — they’re used directly. They just no longer satisfy a gxformat2 abstract interface.

4. Remove import_tool from WorkflowPopulator

File: lib/galaxy_test/base/populators.py (~line 3061)

Remove the import_tool method. It was only there to implement ImporterGalaxyInterface. If tests need create_tool, they use dataset_populator.create_tool() directly.

5. Update imports

File: lib/galaxy_test/base/populators.py

# Remove
from gxformat2 import convert_and_import_workflow, ImporterGalaxyInterface
# Keep/add
from gxformat2 import python_to_workflow

File: lib/galaxy_test/selenium/framework.py

# Remove
from gxformat2 import convert_and_import_workflow, ImporterGalaxyInterface

6. Follow-up: Remove Format2ConverterGalaxyInterface

File: lib/galaxy/managers/workflows.py (~line 2473)

Once gxformat2 makes galaxy_interface optional on python_to_workflow, remove this class and pass None. This is a 1-liner follow-up, not blocking for this PR. For now passing None already works since the parameter is never used during conversion.

Verification

Questions