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repair-galaxy-draft-topology

Re-wire a Galaxy draft region when a step's declared output can't be computed from its wired inputs.

Mold health

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  • Source layout

    Directory Mold with only index.md frontmatter.

  • Axis fields

    target-specific fields are coherent.

  • Eval plan

    Abstract oracle: fixture-independent property checks any run must satisfy.

    eval.md has a Case section — concrete cases belong in scenarios.md.

    eval.md ↗
  • Scenarios

    Concrete cases: fixtures bound to expected values, run against the eval properties.

    scenarios.md not written yet.

  • Typed refs

    7 typed references; 0 resolver issues.

  • On-demand triggers

    All on-demand references describe triggers.

  • Evidence checks

    Hypothesis references include verification.

axis
target-specific
target
galaxy
name
repair-galaxy-draft-topology
contract

Reference Loading

Typed Mold references describe what casting consumes and when the generated skill should load each artifact.

Schemagalaxy-workflow-draft

Structured contract copied for validation or lookup.

Purpose
In/out contract: the draft this Mold reads and re-wires conforms to [[galaxy-workflow-draft]]; cast bundles the JSON Schema so the re-wired draft stays inside the superset the per-step loop expects.
Researchgalaxy-workflow-draft-format

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose
Emit re-wired steps in the draft superset (TODO tool_id, _plan_* fields) so existing per-step machinery realizes them; respect the settle-vs-repair boundary.
Verify
Promote after a repair run inserts a producer the per-step loop then realizes without re-running the template Mold over the whole draft.
Researchopen-requirements-ledger

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose
Read open blocking entries to scope the repair; mark each resolved or surrender it, feeding the loop's decreasing-blocker convergence gate.
Verify
Promote after a run closes a blocking entry and the loop terminates on the reduced open count.
Researchgalaxy-data-flow-draft-contract

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose
Re-wire the affected region consistently with the data-flow design that settled the surrounding topology.
Verify
Promote after two repairs preserve the surrounding data-flow design without re-deriving it from the source.
Researchgalaxy-collection-semantics

Background synthesis loaded by explicit progressive-disclosure metadata.

Purpose
Preserve collection typing and map-over/reduction semantics when an inserted producer step joins or reshapes collection inputs.
Trigger
When the repair inserts or rewires steps touching collection inputs, outputs, or mapped/reduced connections.
Patterngalaxy-collection-patterns

Workflow-construction idiom. Usually condensed during casting.

Purpose
Choose a corpus-attested collection recipe when the missing producer is a collection construction, reshape, or bridge.
Trigger
When the repair sub-path needs collection cleanup, reshaping, relabeling, identifier synchronization, or a collection-tabular bridge.
Patterngalaxy-tabular-patterns

Workflow-construction idiom. Usually condensed during casting.

Purpose
Choose a corpus-attested tabular recipe when the missing evidence is a column, key, or aggregate a tabular step can produce.
Trigger
When the repair sub-path needs a computed column, join key, filter criterion, or aggregate the blocked step depends on.

Artifact handoffs

/ pipeline contract

Produces

repair-galaxy-draft-topology

Topology is settled upstream by the *-summary-to-galaxy-template Mold, and the per-step loop is wrapper-tier — it does not edit topology. This Mold is the escalation target the loop reaches when implementation proves the settled topology cannot support a declared step: a step output that needs evidence no wired input carries (the connection graph validates fine, but nothing produces what the output requires). Wrapper-tier gaps — no Tool Shed wrapper picked yet — are not this case; those route through the discover-or-author branch.

You are invoked with the partially-realized draft and the open-requirements-ledger. Read the open blocking entries: each names a step, the uncomputable output, and the missing evidence. Your job is bounded topology repair — not re-settling the workflow. Repair the named region and nothing else; the surrounding topology, already-realized steps, and workflow interface stay put.

Decide the shape of the fix from the missing evidence, the surrounding data-flow design (galaxy-data-flow-draft-contract), IWC structure, and the pattern pages. It may be one producer step, or a small sub-path of a few tools, or — when the declared output is genuinely uncomputable and no producer exists — narrowing the step to what its inputs can support. Insert the new step(s) in the draft superset (galaxy-workflow-draft-format): concrete topology and edges, wrapper-tier TODO for tool_id and ports, _plan_* fields carrying intent. The existing discover-or-author → summarize-galaxy-toolimplement-galaxy-tool-step machinery realizes them on later loop iterations; do not resolve wrappers here.

Then update the ledger. For each blocking entry your repair addresses, mark it resolved with a note on how (producer added, sub-path added, output narrowed). The loop’s convergence gate counts open blocking entries and requires each escalation to strictly reduce that count, under a hard cap on escalations. If you cannot close an entry — no producer is discoverable and the output cannot be honestly narrowed — surrender it: leave it open with a note, so the terminal path writes it into the final draft as a labelled gap rather than spinning or fabricating. Never insert a producer whose own output is uncomputable from what feeds it; that grows the DAG without reducing the open count and the loop will not converge.

Incoming References (4)

  • advance-galaxy-draft-steprelated mold— Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
  • apply-galaxy-workflow-changesetrelated mold— Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps.
  • Galaxy workflow draft formatrelated mold— gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step.
  • Open-requirements ledgerrelated mold— Carried unresolved-requirements artifact the source→Galaxy pipeline discharges or explicitly surrenders, autonomously.