Make --test_data resolve tool test inputs

[jmchilton]

Fixes #1536 — --test_data was inert for test input resolution.

What was wrong

Two independent gaps, either one alone enough to break the option.

1. The Galaxy config key does not exist. planemo/galaxy/config.py wrote

test_data_dir=test_data_dir,  # TODO: make gx respect this

Galaxy has no test_data_dir option — grep -rn 'test_data_dir\b' lib/galaxy/config/ finds nothing. The real key is tool_test_data_directories, read at lib/galaxy/config/__init__.py:1020 and wired to TestDataResolver at lib/galaxy/app/__init__.py:988. The TODO was accurate; Galaxy was never going to respect a key it doesn't have.

2. The client-side fallback was never given the directory. Test inputs resolve in two stages (galaxy/tool_util/verify/interactor.py:528-579): first GET /api/tools/{id}/test_data_download, then a local fallback over self.test_data_directories, populated from a test_data kwarg at :256. galaxy-tool-util's own runner passes it (verify/script.py:426); planemo's galaxy_interactor_kwds did not.

Both are planemo-side. Galaxy and galaxy-tool-util already provide the hooks.

Reproduction

Before, against a tool whose input lives outside its directory:

AssertionError: Test input file (planemo_external_test_data.txt) cannot be found.
  .../galaxy/tool_util/verify/interactor.py:579, via remote_to_input -> _get_path_or_location

which is simonbray's report verbatim.

Test

tests/test_cmd_test.py::CmdTestTestCase::test_test_data_option — an integration test, not a unit test: it stands up Galaxy, uploads, and runs the tool.

The fixture matters. The input is named planemo_external_test_data.txt and kept in tests/data/external_test_data/, deliberately not a test-data/ directory. A stock filename would be served by TestDataResolver's default galaxy-test-data.git resolver and the test would pass without the fix.

Verified red-to-green, and each fix isolated:

	result
neither fix	fails, at interactor.py:579
config key only	passes
interactor kwarg only	passes
both (this PR)	passes

Also re-ran test_tool_in_directory and test_test_index, which exercise the no---test_data path — both still pass, since an unset option leaves the key None and Galaxy falls back to its defaults.

Open question for review

Each fix is independently sufficient, so this is belt-and-braces. Worth deciding whether both belong.

The one behavioural tradeoff is in the config key. TestDataResolver splits its value on commas and defaults to test-data,https://github.com/galaxyproject/galaxy-test-data.git, so setting tool_test_data_directories replaces those defaults — including the remote resolver. I read an explicit --test_data as "use this", so overriding seems right, and the tool's own directory is still searched first server-side. But it would change behaviour for someone passing --test_data while relying on stock Galaxy test data. Alternatives:

• keep as-is (override)
• append instead: f"{test_data_dir},test-data", though that hardcodes part of an upstream default
• drop the config change and ship only the interactor kwarg, which is purely additive

Happy to go whichever way. Draft until that's settled.

🤖 Generated with Claude Code