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oncofiles: Instructions file for Claude Code

CLAUDE.md

oncofiles CLAUDE.md is an instructions file for Claude Code from peter-fusek/oncofiles. It costs 8,908 tokens per session, scanned A, original, MIT.

A project guide for oncofiles, a document-management service for cancer patients and caregivers. It connects Google Drive, Gmail, and Calendar to AI assistants and describes the project's setup, file naming, and development commands.

In plain words
What is it for?
Use it when developing or testing oncofiles, running its MCP server, managing migrations, checking documents, or following its required filename and Python conventions.
Why use it?
It gives coding agents the project's structure and conventions before they change code. This helps preserve document names, compatibility, tests, and formatting rules.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md.

This is peter-fusek/oncofiles's own configuration. It tells Claude Code how to work on oncofiles itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything oncofiles configures →

not rated 5repo 1mo ago A scan 8,908 tokens original MIT
View source ↗ peter-fusek/oncofiles oncofiles.com
Reuse

Borrowing it

Nothing to install: this file belongs to peter-fusek/oncofiles. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/peter-fusek/oncofiles/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/peter-fusek/oncofiles

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for oncofiles CLAUDE.md

README.md
[![agentmods](https://agentmods.dev/badge/instructions/peter-fusek/oncofiles/claude-md.svg)](https://agentmods.dev/instructions/peter-fusek/oncofiles/claude-md)
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<a href="https://agentmods.dev/instructions/peter-fusek/oncofiles/claude-md"><img src="https://agentmods.dev/badge/instructions/peter-fusek/oncofiles/claude-md.svg" alt="Measured on agentmods" height="20"></a>
Per session 8,908 This file is loaded in full into every session.
When invoked 8,908 The same file — it is already loaded in full.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.08908 $0.08908
Opus 5 $0.04454 $0.04454
Sonnet 5 $0.01782 $0.01782
Haiku 4.5 $0.00891 $0.00891

Measured 7d ago against content hash b25980ccf38a, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

oncofiles CLAUDE.md scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

- **Session cookie URL-encoding (#495)**: Python `SimpleCookie` treats `@` (present in every email address) as outside its `_LegalValueChars` and wraps the entire cookie value in double-quotes. Browsers echo those litera
CLAUDE.md · 118 lines

How it starts

The opening of the file, as written. The whole thing — 118 lines — stays where its author put it; the contents beside it link to each section on GitHub.

oncofiles

AI-powered medical document management for cancer patients and caregivers. Connects Google Drive, Gmail, and Calendar to Claude, ChatGPT, and any MCP client.

Quick start

uv sync --extra dev
uv run pytest
uv run ruff check

Project structure

  • src/oncofiles/ — main package
  • tests/ — pytest tests
  • migrations/ — SQL schema migrations
  • data/ — local dev SQLite database (gitignored)

Conventions

  • Python 3.12+, async-first
  • FastMCP 3.0+ for MCP server
  • Pydantic for data models
  • ruff for linting/formatting
  • Filenames follow standard convention: YYYYMMDD_PatientName_Institution_Category_DescriptionEN.ext
    • Separators: underscores only
    • Description: English, CamelCase, max 60 chars
    • Category tokens: Labs, Report, Pathology, CT, USG, Genetics, Surgery, SurgicalReport, Prescription, Referral, Discharge, DischargeSummary, ChemoSheet, Reference, Advocate, Other, Vaccination, Dental, Preventive
    • Legacy formats (space+dash, underscore-separated) still parsed for backward compat

Key commands

  • uv run oncofiles-mcp — run MCP server (stdio)
  • MCP_BEARER_TOKEN=test MCP_TRANSPORT=streamable-http uv run oncofiles-mcp — run HTTP server locally
  • uv run pytest — run tests
  • uv run ruff check --fix — lint and auto-fix
  • uv run ruff format — format code

Deployment

  • Coolify on Forpsi 194.182.90.104 (NOT Railway — migrated 2026-06-08): oncofiles.com, streamable-http at /mcp, Traefik + Let's Encrypt in front. Build pack Railpack (Beta), install uv sync, start uv run oncofiles-mcp.
  • Push to main does NOT deploy (#549). Deploys are a manual Redeploy click in Coolify → project oncofiles → app oncofiles:main-cj7yxy1gac8mdwempibu27kq. There is no webhook. Pushing and walking away means prod stays on the old commit — this went unnoticed for two months.
  • Env-only changes are cheap: with an unchanged commit SHA, Coolify logs No build configuration changed & image found … Build step skipped and just recreates the container. A new SHA triggers a full Railpack build.
  • Never tick "Available at Buildtime" on a new env var unless the build genuinely needs it. Railpack writes every buildtime-flagged var into a build-time .env, and mise/aqua read it — an expired GITHUB_TOKEN there returned 401 installing uv and broke every deploy for two months (#550).
  • DB is a local libsql file on the Coolify bind mount (TURSO_DATABASE_URL=file:/data/oncofiles.db); Turso Cloud is decommissioned. Data survives rebuilds. A failed deploy is safe — Coolify keeps the old container running.
  • 1360 tests, CI green (CI is lint+test only; it does not deploy)

Read the full file on GitHub · 118 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 7d ago First seen · 118 lines · 8,908 tokens per session scan A b25980ccf38a

Subscribe to this mod's changes

oncofiles CLAUDE.md is an instructions file published in the GitHub repository peter-fusek/oncofiles (5 stars, last pushed 1mo ago), licensed MIT. It adds 8,908 tokens to every session, about $0.0445 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

Documentsanthropicdocument-managementfastmcpfiles-apimcpmedical
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