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Biofact

Biofact

by biranjan01
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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provenance_report

Print a run's provenance details—steps, tools, hashed files, environment, and timings—for citing in manuscript methods or availability statements.

Instructions

Print the provenance report for a run: steps, tools used, files hashed, environment, timings. Cite this in a manuscript's methods/availability.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "run_file": "<run_file>"
    },
    "name": "provenance_report"
  }
}

Input Schema

NameRequiredDescriptionDefault
run_fileYes

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

B3.4/5.0
Behavior3/5

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

No annotations are supplied, so the description carries the full behavioral burden. 'Print' implies a non-mutating read and the enumerated contents disclose what the report surfaces, which is useful, but nothing is said about permissions, behavior on a missing or invalid run file, or whether the run must already be stored.

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

Conciseness5/5

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

Two compact sentences, front-loaded with the action and artifact, then the content list, then the usage note. No filler or repetition.

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 formatting is properly out of scope, and the description covers purpose, contents, and usage context. The main residual gap is input specification for run_file and error/edge behavior for a single-parameter tool.

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

Parameters2/5

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

The single parameter run_file has 0% schema description coverage, so the description must compensate. 'For a run' gestures at the input but never states the expected form (path, ID, extension) or where such a file comes from, leaving the parameter effectively undocumented.

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

Purpose4/5

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

The description gives a specific verb and resource ('Print the provenance report for a run') and enumerates exactly what the artifact contains (steps, tools, files hashed, environment, timings). It is clearer than check_run or list_stored_runs would be from name alone, though it never explicitly contrasts itself with those siblings.

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

Usage Guidelines3/5

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

'Cite this in a manuscript's methods/availability' supplies a real usage context that implies this is the reporting/summary tool rather than a validation or replay tool. However, there are no when-not conditions and no named alternative among replay_run, check_run, or list_stored_runs, so routing remains inferential.

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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