What is fill-protocol?

A tool for filling existing Word forms used for research protocols, ethics applications, and grant proposals. It places content into the original document while preserving its tables, fonts, spacing, and page layout.

Populating .doc or .docx templates with protocol or application content, including converting older .doc files and keeping table rows from splitting across pages.

Rebuilding an institutional form can break its formatting and structure. Filling the supplied template keeps the document aligned with the institution's required design.

fill-protocol — Skill for Claude Code by Aperivue

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add Aperivue/medsci-skills --skill fill-protocol

Clone the repo

git clone --depth 1 https://github.com/Aperivue/medsci-skills

Made for: Claude Code.

Or install medsci-submission, the plugin that ships this one along with the rest of its 6 skills.

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/aperivue/medsci-skills/fill-protocol/github.svg)](https://agentmods.dev/skills/aperivue/medsci-skills/fill-protocol)

Your own site

<a href="https://agentmods.dev/skills/aperivue/medsci-skills/fill-protocol"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/fill-protocol/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/aperivue/medsci-skills/fill-protocol"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/fill-protocol.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 92 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 2,728 The whole file, excluding the scripts and references it only reads on demand.

Security scan B 1 finding. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector warn 7 Sept 2026

SkillSpector: 3 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

medium Privilege Escalation · line 56
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.

Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
medium Privilege Escalation · line 57
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.

Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
medium Privilege Escalation · line 58
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.

Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.

How audits are shown

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.

Model	Per session	Once invoked
Fable 5.1	$0.00092	$0.02728
Opus 5	$0.00046	$0.01364
Sonnet 5	$0.00018	$0.00546
Haiku 4.5	$0.00009	$0.00273

Measured 9d ago against content hash 848b3711a0d1, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade B, and why

fill-protocol scanned grade B 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 9d ago.

The scan reads SKILL.md. This mod also ships 6 executable files (scripts/doc_to_docx.py, scripts/fill_form.py, scripts/inspect_template.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Asks for rootmediumPrivilege escalation

A mod that escalates privileges can change anything on the machine, not only the project.

sudo apt-get install -y libreoffice # Debian/Ubuntu

skills/fill-protocol/SKILL.md · 249 lines

How it starts

The opening of the file, as written. The whole thing — 249 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Fill-Protocol Skill

You are helping a researcher populate an institutional Word form (IRB protocol, ethics application, grant proposal, etc.) without breaking the original document formatting. This skill is the formatting counterpart to write-protocol: where write-protocol drafts content, fill-protocol lays that content into the institutional template.

Why This Skill Exists

Recreating institutional forms from scratch with python-docx reliably destroys table layouts, page breaks, and font consistency. The only safe approach is to open the existing template and replace cell/paragraph text in place. This skill enforces that pattern.

Core Principles (Do Not Violate)

Open the existing template — never create from scratch. Use Document(template_path), not Document().
Convert .doc → .docx via LibreOffice headless before any editing. pandoc -f doc is not supported; textutil corrupts table structure.
Match cells by left-label text, not row/column coordinates. Templates evolve and coordinate matching breaks silently.
Apply cantSplit to every filled row so a row never breaks across pages.
For CJK languages, set the eastAsia font attribute, not just run.font.name. Hangul/Kanji/Hanzi will render in fallback fonts otherwise.
Validate every fill operation: report unmatched labels, count empty cells, and surface mismatches before saving.

Dependencies

If the template is already .docx, LibreOffice is not required — only the three Python packages below. LibreOffice is needed only when the template is a legacy .doc and must be converted first.

# Python libraries (always required)
pip install --user docxtpl python-docx pyyaml

# LibreOffice (only for legacy .doc input; ~700 MB on macOS)
brew install --cask libreoffice              # macOS
sudo apt-get install -y libreoffice           # Debian/Ubuntu
sudo dnf install -y libreoffice               # Fedora
sudo pacman -S --needed libreoffice-fresh     # Arch

Read the full file on GitHub · 249 lines

Files

What ships with it

9 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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.

9d ago First seen · 249 lines · 92 tokens per session scan B 848b3711a0d1

Subscribe to this mod's changes

fill-protocol is a skill published in the GitHub repository Aperivue/medsci-skills (290 stars, last pushed 2d ago), licensed MIT. It adds 92 tokens to every session and 2,728 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it B with 1 finding (asks for root). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Claude Code Documents biostatistics claude-skills clinical-research diagnostic-accuracy literature-review

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fill-protocol