cwl-to-test-data

SKILL.md

# cwl-to-test-data

Follow the procedure below and use the artifact/reference sections as the runtime contract.

## When To Use

- Resolve a CWL workflow's own declared test cases into Galaxy workflow test-data refs.

## Inputs

- Read artifact `summary-cwl`. Schema: summary-cwl. Produced by `summarize-cwl`. Structured CWL summary from summarize-cwl; carries the source's test cases (`tests[]`) — each a `job_path` (a CWL job file naming the test inputs) plus `expected_outputs`.
- Read artifact `cwl-galaxy-interface`. Produced by `cwl-summary-to-galaxy-interface`. Galaxy interface brief from cwl-summary-to-galaxy-interface pinning the workflow input labels, collection shapes, and datatypes each resolved fixture must map onto.

## Outputs

- Write artifact `test-data-refs` as `test-data-refs.json`. Format: `json`. Test data resolved from the CWL source's declared test cases, expressed as URLs/paths plus expected shapes for downstream test authoring. Shared id with find-test-data — the branch's search fallback fills only the inputs this Mold leaves unresolved.

## Required Tools

- None declared. Procedure should not assume external CLIs are present.

## Load Upfront

- `references/schemas/summary-cwl.schema.json`: Schema file copied verbatim into the bundle. Input contract: read `tests[]` — each case's `job_path` inputs and `expected_outputs` — as the declared source of test data.

## Load On Demand

- `references/notes/component-cwl-workflow-anatomy.md`: Research note copied verbatim into the bundle. Interpret a CWL job file's input objects (File/Directory, secondaryFiles, arrays, inline literals) before mapping them onto Galaxy inputs. Use when: reading a `job_path`'s declared inputs to decide their Galaxy shape.
- `references/notes/galaxy-workflow-testability-design.md`: Research note copied verbatim into the bundle. Map each declared job input to an addressable Galaxy input label and the collection shape it must populate. Use when: mapping a CWL File-array or secondaryFiles input onto a Galaxy collection shape.
- `references/notes/iwc-test-data-conventions.md`: Research note copied verbatim into the bundle. Express each ref remote-URL-first with SHA-1 integrity and per-input collection layout when recording resolved fixtures. Use when: writing each `test-data-refs` entry.

## Validation

- None declared.

## Procedure

Resolve the CWL workflow's own declared test cases into Galaxy `test-data-refs`. The CWL summary carries the source's test cases (`tests[]`) — each a `job_path` (a CWL job file naming the test inputs) plus `expected_outputs`. Read the declared inputs and map them onto the Galaxy workflow's inputs, emitting one ref per input, ready for implement-galaxy-workflow-test to stage.

This skill is the source-specific first leg of the harness's `test-data-resolution` branch. It resolves what the CWL source itself declares; any input it cannot resolve from a declared test case stays a reported gap and the harness falls through to find-test-data (search), then to `user-supplied`. Deciding to fall through is a harness concern, not this skill's — its job is an honest map of the source's own test cases.

### Sequence

1. **Enumerate Galaxy inputs and their required shape.** From the interface brief, list each workflow input: label, Galaxy collection shape (File / list / paired / list:paired / record), and datatype. This is the *target shape* every ref must satisfy.
2. **Read the declared test cases.** From the summary's `tests[]`, read each case's `job_path` inputs — File/Directory objects with their `location`/`path`, `secondaryFiles`, arrays, and inline literals — plus `expected_outputs`. Prefer the case whose inputs best cover the workflow's inputs.
3. **Map each declared input onto a Galaxy input.** Match by id and shape onto the interface's input labels. A CWL File array maps to a Galaxy list; a File carrying `secondaryFiles` may map to a record or composite datatype — record element identifiers and any prep needed to reach the Galaxy collection shape (galaxy-workflow-testability-design).
4. **Emit refs.** Write one `test-data-refs.json` entry per resolved input: prefer a remote `location` URL when the job references one (remote-URL-first, iwc-test-data-conventions); fall back to the in-tree `path` plus provenance only when no URL is published. Carry datatype, collection element identifiers, and any subset/split prep. Each entry maps to an addressable workflow input label.
5. **Report genuine gaps.** An input with no declared test-case input of the right shape stays `resolved: false` with a reason — this is what the harness hands to find-test-data. Do not search public sources here; searching is find-test-data's job, not this skill's.

### No fabrication

Never invent a URL, accession, or path, and never emit a placeholder for an input you could not resolve from a declared test case. A declared input with no published URL is recorded by its in-tree `path` plus provenance, not papered over with a guessed URL. Every emitted ref points at data the source actually declares; everything else is an honest gap for the next leg of the branch.

## Feedback Mode

- Feedback mode is off unless the caller explicitly enables `--feedback` or supplies a feedback-ledger path.
- When enabled, read `_feedback.md` before doing the work and use its registered `foundry-feedback.ledger.yml` protocol.
- Preserve harness-owned run and phase state. Append only concrete observations about a canonical Foundry source asset or a related project that this run showed to be at fault; do not put ordinary workflow requirements in this ledger.
- Before reporting completion, make one explicit pass over the work you just did. Do not ask yourself whether anything was unclear — recall what happened: where you guessed at something the instructions should have settled, needed information this bundle does not carry, hit an instruction that contradicted another or contradicted the artifacts in front of you, used a packaged reference that did not cover your case, or did something the procedure never describes.
- Append an entry for each such event that clears the protocol's bar. If none do, append nothing and report `no feedback` explicitly. Silence and a clean pass are not the same thing, and nothing downstream can tell them apart unless you say which one it was.
- Pass the same ledger path to any subagent used for this work, and merge updates serially so one writer cannot overwrite another.

## Runtime Notes

- Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
- Preserve declared artifact filenames unless the user or harness supplies explicit paths.
- Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.