PR #20936 Research: Wire up and test resource requirement via TPV

• URL: https://github.com/galaxyproject/galaxy/pull/20936
• Author: mvdbeek (Marius van den Beek)
• State: MERGED (2025-10-01)
• Base: dev <- resource_requirements_tpv
• Merge commit: 34fac8921b15cd4b57c0e99c0186fd50f4cfa567
• Stats: +119 / -6 across 9 files

Purpose and Motivation

This PR wires up Galaxy’s tool resource requirements (e.g. cores_min, ram_min) to be consumed by Total Perspective Vortex (TPV) for job destination routing. Previously, resource requirements declared on tools were parsed but not actually forwarded to TPV for scheduling decisions.

The PR depends on upstream TPV changes:

• https://github.com/galaxyproject/total-perspective-vortex/pull/166 (“Implement basic version of resource requirements”)
• TPV 3.1.0 introduces the ability to read resource requirements from Galaxy tools and use them for destination mapping (e.g. setting {cores} in env vars based on cores_min).

Key Changes

1. Bug fix: Skip null resource requirement values

File: lib/galaxy/tool_util/deps/requirements.py (lines ~303-308)

The core logic change. When iterating resource requirement fields from a tool definition, None values are now skipped instead of being passed to ResourceRequirement(). All CWL ResourceRequirement fields are optional, so a tool might declare only coresMin without ramMin, etc. Before this fix, None values would be passed through, likely causing errors or incorrect behavior in TPV.

# Before:
rr.append(ResourceRequirement(value_or_expression=value, resource_type=key))

# After:
if value is not None:
    # all resoure requirement fields are optional
    rr.append(ResourceRequirement(value_or_expression=value, resource_type=key))

2. TPV version bump to 3.x

File: lib/galaxy/dependencies/conditional-requirements.txt

• total-perspective-vortex>=2.3.2,<3 -> total-perspective-vortex>=3.1.0,<4

File: pyproject.toml

• Added total-perspective-vortex>=3.1.0,<4 to [project.optional-dependencies] test section
• Fixed nodejs-wheel==22 -> nodejs-wheel>=22,<23 (incidental fix)

3. New TPV job configuration for integration tests

File: test/integration/embedded_pulsar_tpv_job_conf.yml (new file, 44 lines)

A complete TPV-based job configuration that:

• Defines local and pulsar_embed runners
• Uses dynamic_tpv as the default execution environment
• Configures inline TPV configs with two destinations:
  • local: runs locally, sets GALAXY_SLOTS to {cores}
  • user_defined: runs on pulsar_embed with docker, sets GALAXY_SLOTS to {cores}, accepts support_user_defined scheduling tag
• Defines a default tool template with cores: 1 (abstract)
• Routes user_defined-* tools to require support_user_defined scheduling tag
• The {cores} template in GALAXY_SLOTS env var is the key mechanism: TPV resolves this from the tool’s resource requirements

4. Integration test for resource requirements via TPV

File: test/integration/test_user_defined_tool_job_conf.py

Refactored existing test class and added new TPV-specific test:

• Extracted job_config_file as a class attribute (was hardcoded in handle_galaxy_config_kwds)
• Added TOOL_WITH_RESOURCE_SPECIFICATION - a user-defined tool YAML with:
  • cores_min: 2 resource requirement
  • Shell command echo $GALAXY_SLOTS > galaxy_cores.txt
  • Output that captures the cores value
• New test class TestUserDefinedToolRecommendedJobSetupTPV inherits from the existing test class but uses the TPV job config
• test_user_defined_applies_resource_requirements():
  1. Creates a user-defined tool with cores_min: 2
  2. Runs the tool
  3. Asserts output file contains 2.0\n (TPV set GALAXY_SLOTS to 2.0 based on cores_min)

5. Dependency updates (incidental)

• nodejs-wheel pinned version updated 22.13.0 -> 22.20.0
• nodejs-wheel-binaries==22.20.0 added
• Various type stubs added: types-cachetools, types-requests, types-urllib3
• mypy, cachetools, pathspec added to test dependencies

6. ToolSourceSchema.json regenerated

Single-line JSON schema file regenerated (likely reflects the resource requirement model changes or other schema updates at the time).

Architecture / Design Decisions

1. TPV inline config: The test uses inline TPV configuration (tpv_configs with literal YAML) rather than external TPV config files. This keeps the test self-contained.

2. {cores} template variable: TPV’s {cores} template in the GALAXY_SLOTS env var is resolved at job dispatch time from the tool’s resource requirements. This is the core wiring mechanism.

3. Inheritance-based test design: The TPV test class inherits from the existing Pulsar test class, overriding only job_config_file. This means the TPV class also runs test_user_defined_runs_in_correct_destination from the parent.

4. Null filtering in resource_requirements_from_list: Rather than changing the ResourceRequirement constructor to accept None, the fix filters at the list-building level. This is cleaner because ResourceRequirement should always have a meaningful value.

Data Flow

Tool YAML (cores_min: 2)
  -> parse_requirements() in yaml.py
  -> resource_requirements_from_list() in requirements.py
  -> [ResourceRequirement(value_or_expression=2, resource_type="cores_min")]
  -> Tool.resource_requirements attribute
  -> TPV reads resource_requirements at dispatch time
  -> TPV resolves {cores} template to 2.0
  -> GALAXY_SLOTS env var set to "2.0"
  -> Shell command: echo $GALAXY_SLOTS > galaxy_cores.txt
  -> Output: "2.0\n"

Cross-Reference with Current Codebase

All files from the PR exist at the same paths in the current codebase (cwl_tool_state branch).

Files with the PR changes present (merged and current):

Summary of Divergences

The only divergences are version bumps in TPV dependencies, which were subsequently updated by later PRs (e.g. #21014 “Bump up total-perspective-vortex dependency”). The core logic change in requirements.py and the test infrastructure are unchanged from what this PR introduced.

Review Notes

• Reviewer: nsoranzo (approved)
• Minor review comment about commented-out test assertions, which mvdbeek addressed by uncommenting them (was a local docker issue during development).