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NoteNest — Clinical Note Prep Toolkit

Website: https://princey9.github.io/NoteNest/

Demo: https://princey9.github.io/NoteNest/demo/

Pricing: https://princey9.github.io/NoteNest/pricing/

Repo: https://github.com/Princey9/NoteNest

Releases: https://github.com/Princey9/NoteNest/releases/latest

NoteNest is a clinical note prep toolkit that works offline to protect sensitive details with placeholders and produce usable summaries. It converts messy notes into a patient-friendly view and clinician-ready structured outputs (SOAP or 5C’s), and it includes Cloak Mode for scan/protect/report workflows.

Why it matters (value)

  • Protects sensitive details (names, emails, phones, IDs, DOB, addresses) using placeholders.
  • Clinician-ready outputs: SOAP or 5C’s, selectable.
  • Patient-ready output: complaint-first, clear, and actionable.
  • Offline-first: no network calls, no paid APIs.
  • Exam-ready: reproducible checks, static GitHub Pages demo, and release workflow.

Quickstart

CLI (from repo root)

cargo run --quiet -- convert - --clinician soap --style protected --format text <<'NOTE'
ER note (messy): JOHN O?? 43M chest tightness x2d, worse stairs + SOB. wife Mary 0176-12345678 called.
email john.osmith@gmail.com MRN 883920 DOB 12/03/1982 addr 12 Hauptstrasse 80331 Muenchen.
pmh HTN/DM2; meds metformin 500 bid + ramipril 5mg od; nkda.
vitals BP168/96 HR108 T37.2. ecg ?st-depr. trop 0.08 ng/mL.
plan: send ED; repeat trop 3h; ASA; consider heparin; f/u cardio.
NOTE

Demo site (local)

python3 -m http.server 8001 --directory docs

Open http://localhost:8001/

Diagrams / Mermaid

  • GitHub renders Mermaid diagrams automatically in Markdown.
  • For local previews in VS Code, install a Mermaid extension (e.g., "Markdown Preview Mermaid Support").
  • Alternatively, use GitHub.dev (press . in the repo) or paste the diagram code into https://mermaid.live.

Verification checklist:

  • Open README on GitHub and confirm diagrams render.
  • Open VS Code preview and confirm diagrams render (with extension installed).
  • If not, paste Mermaid code into mermaid.live.

How it works (offline pipeline)

flowchart LR
  A[Raw clinical note] --> B[Normalize & clean]
  B --> C[Protect sensitive fields]
  C --> D[Extract clinical fields]
  D --> E[Fill typed templates]
  E --> F[Text outputs]
  E --> G[JSON outputs]
  E --> H[Coverage report]
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  • Normalize: whitespace cleanup, bullet normalization, junk trimming.
  • Protect: deterministic placeholder replacement.
  • Extract: heuristic detection (symptoms, duration, meds, vitals, tests, plan, etc.).
  • Render: outputs are generated from typed structures only.

Architecture overview

flowchart TB
  CLI[CLI: notenest] --> Pipeline[Core pipeline]
  Pipeline --> Protect[Protect module]
  Pipeline --> Extract[Extract/Summary module]
  Pipeline --> Render[Render module]
  Render --> TextOut[Text output]
  Render --> JsonOut[JSON output]
  Web[docs/ demo JS] --> Mirror[Client-side mirror of pipeline]
  Mirror --> DemoOut[Demo outputs]
Loading

Features

  • Patient View (complaint-first, plain language, actionable).
  • Clinician View (SOAP or 5C’s toggle).
  • Protected placeholders (Protected/Masked/Hidden/Removed/ styles).
  • Coverage report (fields found/missing + protected counts).
  • Cloak Mode: scan/protect/report for safer sharing.

Privacy (Protected language only)

  • NoteNest replaces sensitive fields with placeholders like [EMAIL_PROTECTED].
  • Runs locally only. No network calls.
  • Designed for safe sharing and auditability.

Clinician formats

  • SOAP: S (Subjective), O (Objective), A (Assessment), P (Plan).
  • 5C’s: Chief complaint, Course, Context, Concerns, Coping.
  • Toggle with --clinician soap or --clinician 5cs.

Cloak Mode (ClinCloak integration)

Commands are available under notenest cloak:

  • scan — PHI scan summary by type (counts only).
  • protect — generate protected outputs + JSON/CSV/MD reports.
  • config init / config validate — YAML config scaffold and checks.
  • report — export run summary.
  • git-hook install — optional hook that runs scan before commit.

Examples:

cargo run --quiet -- cloak scan ./sample_notes
cargo run --quiet -- cloak protect ./sample_notes -o ./out_cloak
cargo run --quiet -- cloak config init -o notenest-cloak.yml
cargo run --quiet -- cloak report ./out_cloak --format csv
cargo run --quiet -- cloak git-hook install --mode pre-commit --paths "*.txt"

CLI usage (current commands)

Convert

notenest convert <input|-> \
  [--clinician soap|5cs] \
  [--format text|json|both] \
  [--out <dir>] \
  [--placeholder-style protected|masked|hidden|removed|angle] \
  [--patient] [--redact] [--all] [--offline]

Batch

notenest batch <input_dir> [--glob "*.txt"] [--out <dir>] [--all] [--offline]

Self-check

notenest self-check

Cloak

notenest cloak scan <path> [--config <yaml>] [--csv <file> --col <name>...]
notenest cloak protect <path> -o <out_dir> [--config <yaml>] [--mapping <file>] [--mapping-pass <env:...>] [--format text|json|both] [--emit-structured]
notenest cloak config init [-o <path>]
notenest cloak config validate [--path <yaml>]
notenest cloak report <run_dir_or_run_id> [--out <dir>] [--format csv|json|md]
notenest cloak git-hook install [--mode pre-commit] [--config <yaml>] [--paths <glob>...]

Output structure (headings)

Patient View headings (always in order):

  • What you came in with
  • What it could mean
  • What we found in your note
  • What to do next (checklist)
  • Questions to ask your clinician
  • When to seek urgent care
  • Disclaimer

Clinician View:

  • SOAP (S/O/A/P) or 5C’s (Chief complaint / Course / Context / Concerns / Coping)

Coverage summary:

  • fields_found, missing, protected_counts

Data example (messy input)

ER note (messy): JOHN O?? 43M chest tightness x2d, worse stairs + SOB. wife Mary 0176-12345678 called.
email john.osmith@gmail.com MRN 883920 DOB 12/03/1982 addr 12 Hauptstrasse 80331 Muenchen.
pmh HTN/DM2; meds metformin 500 bid + ramipril 5mg od; nkda.
vitals BP168/96 HR108 T37.2. ecg ?st-depr. trop 0.08 ng/mL.
plan: send ED; repeat trop 3h; ASA; consider heparin; f/u cardio.

Expected output structure (headings only):

  • Placeholder style
  • Protected note
  • Patient View
  • Clinician View
  • Coverage summary

Installation / downloads

From Releases (latest): https://github.com/Princey9/NoteNest/releases/latest

Linux aarch64 (required):

curl -L -o notenest-aarch64.tar.gz \
  https://github.com/Princey9/NoteNest/releases/latest/download/aarch64-unknown-linux-musl.tar.gz
tar -xzf notenest-aarch64.tar.gz
./notenest --help

Linux x86_64 (bonus):

curl -L -o notenest-x86_64.tar.gz \
  https://github.com/Princey9/NoteNest/releases/latest/download/x86_64-unknown-linux-musl.tar.gz
tar -xzf notenest-x86_64.tar.gz
./notenest --help

Demo website usage

  • Visit the live demo: https://princey9.github.io/NoteNest/demo/
  • Choose a mode: Summarize or Cloak.
  • Select placeholder style and clinician format.
  • Paste a messy note or choose a sample.
  • Use Copy/Download buttons for outputs.

Project structure

Rust core:

  • src/lib.rs — public API exports
  • src/main.rs — thin CLI entry
  • src/cli.rs — clap definitions
  • src/notenest/ — pipeline (protect, extract, render, types)
  • src/cloak/ — ClinCloak scan/protect/report engine
  • src/util/ — FS helpers

Static site:

  • docs/index.html
  • docs/pricing/index.html
  • docs/demo/index.html
  • docs/assets/app.js
  • docs/assets/styles.css

Fixtures:

  • fixtures/templates/*.schema.json
  • fixtures/examples/*.example.json

Tests and acceptance checks

Acceptance tests (run from repo root):

cargo fmt --check
cargo clippy -- -D warnings
cargo test
scripts/check_pages.sh

CLI sanity example:

echo "Pt here w chest pain x2d tel +49..." | cargo run --quiet -- convert - --clinician soap --style protected --format text

GitHub Pages setup

Settings → Pages → Source: main branch, /docs folder.

Release workflow

Tagging a version triggers the GitHub Actions workflow at .github/workflows/main.yml to build and publish binaries. Download links on the site point to Releases/latest.

Tag example:

git tag v0.2.0
git push origin v0.2.0

Exam submission checklist

Troubleshooting

  • Cargo.toml not found: run commands from repo root.
  • Port already in use: pick another port, e.g. python3 -m http.server 8002 --directory docs.
  • zsh comments: remove trailing # ... if pasting into shell.
  • GitHub Pages caching: hard refresh or wait a few minutes after pushing.

About section suggestion (GitHub)

NoteNest — offline clinical note prep toolkit with protected placeholders, patient view, clinician SOAP/5C’s, and Cloak Mode scans. Live demo: https://princey9.github.io/NoteNest/

Business

  • Lean Canvas: business/LEAN_CANVAS.md
  • Pitch one-pager: business/PITCH_ONE_PAGER.md

About

NoteNest is a Rust CLI that privacy-reduces clinical notes and patient documents, then converts them into structured, shareable summaries—built for fast workflows, automation, and demos.

princey9.github.io/NoteNest/

Topics

nlp rust cli automation privacy text-processing health-informatics de-identification patient-safety medical-notes data-sanitization clinical-documentation

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Readme

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MIT license
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v0.2.0 Latest
Feb 2, 2026
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