benchos-akta-chromatogram

name	benchos-akta-chromatogram
description	Generate AKTA or UNICORN chromatograms from uploaded .res or .zip files with PyCORN, export csv or xlsx traces, and attach the results to BenchOS entries or registry items. Use when the user provides a chromatogram export file and wants plots, extracted data, or BenchOS-linked results.
license	Proprietary
compatibility	Requires BenchOS agent runtime with `labbook_cli`, `benchos-cli`, and the curated `akta-chromatogram` capability pack.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS AKTA Chromatogram

Use this skill when the user gives you an AKTA or UNICORN export file and asks you to:

• generate a chromatogram plot
• extract csv or xlsx trace data
• save the outputs in the BenchOS workspace
• attach the results to a BenchOS entry or registry item

Browser Tool

BenchOS also exposes this workflow in the website Tools page as an interactive popup application. Use the browser tool when the user wants a quick upload-and-preview flow; use this skill when they want agent-driven execution, saved workspace artifacts, or BenchOS attachment persistence.

Required Tool

Use labbook_cli with benchos-cli subcommands.

Quick Rules

• Accept only .res or .zip chromatogram source files.
• For .zip uploads, unpack the archive and run PyCORN against the embedded .res file rather than the outer ZIP whenever possible.
• Some .zip exports plot correctly but may fail PyCORN trace extraction; if that happens, keep the plot output and report that extraction was skipped due to an upstream PyCORN compatibility issue.
• Do not pip install inside the persistent sandbox.
• Install the curated capability pack first. If akta-chromatogram is unavailable, stop and explain that the BenchOS runtime image still needs chromatogram support deployed.
• Keep PyCORN subprocess-only. Call its CLI through the shared wrapper and do not import PyCORN modules into BenchOS code.
• Run plotting and extraction through the shared wrapper script: /opt/benchos/shared-skills/benchos-akta-chromatogram/scripts/render_akta_chromatogram.py
• Prefer writing outputs under artifacts/chromatograms/<run-name>/.

Default Workflow

1. Confirm the source file path in /workspace or .chat-context.
2. Ask only the missing execution options:
   • plot format: usually png or pdf
   • extraction: csv, xlsx, both, or none
   • optional plot window: xmin, xmax
   • optional retention alignment: injection index
   • BenchOS destination: workspace only, entry attachment, registry attachment, or both
3. Install the capability pack:

{ "args": ["capabilities", "install", "--name", "akta-chromatogram"] }

4. Generate outputs with the wrapper:

{
  "args": [
    "exec",
    "--capability",
    "akta-chromatogram",
    "--cwd",
    ".",
    "--",
    "/opt/benchos/shared-skills/benchos-akta-chromatogram/scripts/render_akta_chromatogram.py",
    "--input",
    ".chat-context/run.res",
    "--output-dir",
    "artifacts/chromatograms/run-001",
    "--plot-format",
    "png",
    "--extract",
    "csv"
  ]
}

5. Read manifest.json from the output directory and report the generated files.
6. If the user wants BenchOS persistence, use the entry or registry attachment APIs.
7. If the user wants the chromatogram noted inside an entry, append a short HTML summary after uploading the attachment.

BenchOS Persistence Options

• Entry attachments: POST /api/entries/:id/attachments
• Registry attachments: POST /api/registry/:id/attachments
• Entry note append: POST /api/entries/:id/append
• Structured entry metadata update: GET /api/entries/:id then PUT /api/entries/:id with preserved title, project, tags, contentHtml, widgets, and merged metadata

Use metadata updates when the user wants the run recorded as structured BenchOS data. Use append when the user wants a human-readable summary in the note.

Important Parameters

• Injection zeroing: --inject <n> and remember PyCORN counts from 0
• Plot window: --xmin, --xmax
• Secondary axis: --par1 defaults to Cond
• Third axis: --par2 is optional
• Fractions: use --no-fractions only when the user explicitly wants the full run window without fraction markers

Exact Command Patterns

For exact BenchOS attachment and entry-update commands, read references/COMMANDS.md.