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jean — Molecular Biology & Genomics

research_run_status

Read-only

Read a research run file without running anything: whether its seal holds (an edited or truncated file is refused), every hypothesis's verdict and the rule its evidence was merged by, which hypotheses a resume would run (no evidence, and the last attempt failed or was deferred by a call's budget) and which are settled or cancelled, and what resuming would do. Given the corpus, also reports every pinned input whose content changed under the same name, which a resume refuses.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
runYesthe run file run_discovery_programme or resume_research_run returned.
_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.
_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.
sequencesNooptionally, the corpus as it is now, to check against the run's pinned inputs.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
driftYespinned inputs whose content changed, when a corpus was given; null when none was
statusYesid, hypothesis counts by verdict, pending and settled hypotheses, and the next action
pendingYeshypotheses a resume would run
decisionsYesevery hypothesis's verdict, merged e-value, tests and merge rule

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.3/5.0
Behavior5/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered, yet the description adds substantial behavior beyond them: seal enforcement (edited or truncated files are refused), the exact resume-eligibility rule (no evidence and last attempt failed or deferred by a call's budget), and the pinned-input content-drift check that blocks resumption. This is genuinely useful operational context a caller could not derive from the schema.

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 read-only, non-executing framing is front-loaded, and every clause carries distinct information (seal, verdicts, resume set, settled/cancelled, drift). It is a long single sentence with heavy parenthetical nesting, which slightly hurts scanability, but there is little outright filler.

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

Completeness4/5

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 spelled out, and the description still enumerates the categories of information returned. For a 4-parameter nested-object tool with a rich schema, the description covers purpose, safety, and refusal conditions adequately; only explicit sibling routing is missing.

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

Parameters3/5

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

Schema description coverage is 100%, so the schema already documents all four parameters including the run file's origin and the sequences corpus. The description echoes the sequences/pinned-input relationship but adds no syntax, format, or edge-case detail beyond the schema. Baseline 3 is appropriate when the schema does the heavy lifting.

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?

States a specific verb and resource ('Read a research run file') plus a sharp scope qualifier ('without running anything') that immediately separates it from run_discovery_programme and resume_research_run. The enumerations of what it reports (seal status, verdicts, merge rules, resume eligibility, pinned-input drift) make the purpose unmistakable.

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

Usage Guidelines4/5

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

'Without running anything' plus repeated framing around what 'a resume would run' and 'what resuming would do' makes the inspection-vs-execution context clear. However, it never names resume_research_run or run_discovery_programme explicitly as the alternatives an agent should pick when it does want to execute, so routing is inferred rather than stated.

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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