benchline

Install from GitHub

Install directly from GitHub:

hermes plugins install ShalyX/hermes-benchline --enable

After the catalog entry is accepted, users can also install by catalog name:

hermes plugins install benchline --enable

Catalog-name installation depends on acceptance of the upstream catalog entry.

Benchline is a native Hermes plugin for one focused workflow: locally preflight a numeric-result CSV export before a lab operator hands it off to another system. The operator chooses a single file, supplies the lab-owned analyte/unit map and its source/version, and gets a deterministic, row-based QC report.

What it checks

required columns and duplicate column headers
missing patient/specimen identifiers (the identifiers themselves are never returned)
duplicate (specimen_id, analyte) rows
missing, malformed, or non-finite numeric results
analytes absent from the supplied profile
exact unit-label mismatches (no conversion or inference)

The report is a deterministic QC summary; it may include aggregate row/issue counts, affected row numbers, issue codes, missing schema-field names and a scope note. It does not return patient/specimen identifiers, analyte or unit labels, profile-source label, or measured values. The model can use row numbers to guide review in the source file. It checks file structure and transfer consistency only; it does not evaluate whether a numeric result is high, low, normal, critical or clinically significant.

Scope and prior art

The current upstream Hermes catalog includes health-insights (v0.3.2, pinned at d6d09c1f17ada6ca60368a1e0c7a7b5bd4efefc6), which analyzes Apple Health/HealthRelay data and includes lab-result workflows. It operates through a separate CLI and portable skills against a local health database; it can retain imported lab data and send printed values to the configured model/provider. Benchline is narrower: a one-file numeric CSV preflight that checks structure and exact unit labels, without trends, interpretation, persistence or database access. No Benchline entry existed at upstream main commit 1400400907b0259b0f9865358950d9bf6ea28184; this submission proposes one. This is a meaningful workflow distinction, but the overlap is real and the catalog maintainer still decides whether it is sufficiently distinct.

Safety and privacy

Reads one explicitly selected .csv file, at most 1 MiB / 5,000 rows; symlinks and non-regular files are rejected.
No network calls, subprocesses, writes, durable storage or background work.
The input CSV contents are read locally and are not echoed in the tool result. The profile-source label is also not returned. However, the selected path, unit map, and profile-source label are tool-call arguments visible to the session's configured model/provider; do not use this workflow if those details are sensitive.
The bounded QC report is also returned to the session and therefore visible to its configured model/provider.
The operator supplies the analyte/unit map and a short source/version label for each run. Benchline ships no clinical reference intervals.
Findings are not release authorization. A qualified operator must review source rows and correct issues in the lab's approved system.
Supports numeric-result exports only; qualitative panels and nonstandard schemas are out of scope for this MVP.

CSV contract

Headers are case-insensitive and surrounding whitespace is ignored:

patient_id,specimen_id,analyte,result,unit
PSEUDO-001,SYN-001,marker_alpha,8.0,unit_a
PSEUDO-002,SYN-002,marker_beta,4.0,unit_b

The tool call also supplies a run-specific map and provenance label:

{
  "analyte_units": {"marker_alpha": "unit_a", "marker_beta": "unit_b"},
  "profile_source": "Synthetic demo unit profile v1"
}

demo/ contains synthetic identifiers and generic units only. It is not a clinical fixture.

Development

Python 3.10+; runtime uses only the standard library. Linux is the only verified platform.

python -m unittest discover -s tests -v

Hermes source at 1400400907b0259b0f9865358950d9bf6ea28184 was used directly to run the current admission validator and Plugin Doctor against the public Benchline repository. Admission validation passed 15 checks with zero warnings; Plugin Doctor passed runtime registration in a temporary isolated HERMES_HOME. The installed Hermes 0.19.0 CLI does not expose those newer subcommands; the current source implementations were called directly.

License

MIT. See LICENSE.

README from the reviewed commit 2e28dc3; it updates when the author re-pins.

benchline

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Benchline