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jean — Molecular Biology & Genomics

cancel_research_run

Read-only

Withdraw a research run's pending hypotheses (all of them, or the ones named) so no resume runs them, and return the sealed run file. Nothing is deleted: a cancelled hypothesis stays registered and still counts in e-BH with e 1, because it was registered before any result and dropping it would raise the others' chance of support after the fact. Answered and settled hypotheses cannot be cancelled. To stop a run that is advancing in budgeted slices, stop calling resume_research_run; cancel when the pending hypotheses should never run.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
runYesthe run file to cancel pending hypotheses in.
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
reasonNowhy, recorded on each cancelled attempt.
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
hypothesesNothe pending hypotheses to cancel, by id; unset cancels every pending one.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
runYesthe whole programme as a sealed jane.research-run file: the ledger, every corpus input pinned by SHA-256, the last attempt at each hypothesis. Pass it back to continue
statusYesthe cancelled run's status: counts, pending (now none of the cancelled), settled and cancelled hypotheses
cancelledYesthe hypotheses this call cancelled

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior1/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

The annotations declare readOnlyHint=true, but the description describes a state-changing operation: pending hypotheses are withdrawn 'so no resume runs them' and a reason is 'recorded on each cancelled attempt' in the run file, and the call 'return[s] the sealed run file'. That is a modification of the run's environment, not a read, so the description contradicts the annotation.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The action and its scope are front-loaded in the first clause, and the routing guidance lands in the final sentence. The middle clause about e-BH and registration timing is dense and run-on, but it justifies why the operation is additive rather than destructive, so it mostly earns its place.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need not be explained, yet the description still notes it returns the sealed run file. Combined with explicit when-to-use, the alternative tool, and the non-deletion/e-BH invariant, an agent has everything needed to call this correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3, and the description still adds semantics beyond the schema: unset hypotheses cancels every pending one (corroborated) and, more usefully, the invariant that answered and settled hypotheses cannot be cancelled, which constrains what ids may be passed. The nature of the returned sealed run file is also clarified.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description names a specific verb+resource ('Withdraw a research run's pending hypotheses') and states the scope precisely: all pending hypotheses or only the ones named by id. It also contrasts itself with the sibling resume_research_run, so an agent can distinguish the two without opening either schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicit routing is given: 'To stop a run that is advancing in budgeted slices, stop calling resume_research_run; cancel when the pending hypotheses should never run.' It also states the eligibility boundary (answered and settled hypotheses cannot be cancelled), so the agent knows the conditions under which the call is valid.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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