Aperivue 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), notDocument(). - Convert .doc → .docx via LibreOffice headless before any editing.
pandoc -f docis not supported;textutilcorrupts table structure. - Match cells by left-label text, not row/column coordinates. Templates evolve and coordinate matching breaks silently.
- Apply
cantSplitto every filled row so a row never breaks across pages. - For CJK languages, set the
eastAsiafont attribute, not justrun.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
Bundled setup script
The skill ships a setup.sh that detects what is missing and installs only
those parts, with a confirmation prompt before each step:
bash setup.sh check # report what's installed (read-only)
bash setup.sh install # install missing pieces (asks before each)
Auto-install behavior (for Claude as the caller)
When invoking this skill on behalf of a user:
- Before calling
doc_to_docx.py, runbash setup.sh check. If LibreOffice is missing, ask the user before installing — the cask is ~700 MB and proceeding silently is unfriendly. - Skip LibreOffice entirely if the template is already
.docx. Only surface the install prompt when a.docis encountered. - Never pass
--yestosetup.sh installunless the user has explicitly authorized unattended installation in this session. - If the user declines installation, fall back to asking them to convert
the
.docmanually (open in Word/LibreOffice/Pages → Save As → .docx) and then re-run with the converted file.
Workflow
Step 1 — Convert legacy .doc to .docx (if needed)
python scripts/doc_to_docx.py path/to/template.doc path/to/template.docx
Step 2 — Inspect the template structure
python scripts/inspect_template.py path/to/template.docx
This lists every table, every cell (with row/column coordinates and content preview), and every top-level paragraph. Use this output to identify the labels you will match against in your YAML content file.
Step 3 — Author a content YAML
The YAML supports three fill modes. All keys are optional.
protections:
korean_font: "맑은 고딕" # CJK font (set to "Noto Sans CJK KR", "SimSun",
# "MS Mincho", etc. for other locales)
cant_split: true # Apply <w:cantSplit/> to every filled row
# Readability options (see "Readability" section below for full semantics)
blank_between_paragraphs: true # default true — Enter between \n\n chunks
blank_around_section_header: true # default true — Enter above/below filled sections
blank_around_all_section_headers: false # default false — opt-in; also touches untouched sections
# Mode 1 — table key/value (left-label cell → right value cell)
table_kv:
"Study Title": "Multi-center prospective validation of ..."
"Principal Investigator": "Last, First (Department)"
"연구 목적": "본 연구는 ..."
# Mode 2 — section replacement (find numbered header, replace until next header)
section_replace:
"1. Background":
"Hepatocellular carcinoma is the third leading cause of ..."
"4. 연구 배경 및 이론적 근거":
"..."
# Mode 3 — single paragraph in-place text replacement
paragraph_replace:
"Title:":
"Title: Multi-center prospective validation of ..."
Readability — three blank-line knobs
All blank paragraphs inserted by these options use a forced single-line height
(<w:spacing w:line="240" w:before="0" w:after="0"/>) so the gap is exactly
one body-text line — never inflates the document's apparent line spacing.
| Option | Default | What it does | When to flip |
|---|---|---|---|
blank_between_paragraphs |
true |
Inserts a blank line between every \n\n-split chunk inside section_replace |
Disable only for forms where every line must be packed tight |
blank_around_section_header |
true |
Wraps each header that you section_replace with a blank above and a blank below |
Disable when the template style already adds visual gaps via space_before/after |
blank_around_all_section_headers |
false |
After all fills, scans every numbered header (\d+\.\s+) — including ones you didn't replace — and adds blank lines around them |
Enable when uniform readability matters more than form fidelity. Default off because IRB / public-document submissions favor template fidelity over visual consistency (page count stability, boilerplate untouched, reviewer-expected layout) |
normalize_page_breaks |
true |
On save, converts dangling empty paragraphs whose sole content is <w:br w:type="page"/> into a <w:pageBreakBefore/> attribute on the next content paragraph. Prevents visible blank pages when the preceding content (e.g. an abstract table) grows or shrinks and pushes the empty paragraph onto a page of its own, causing the break to land one page later. |
Disable only if your template intentionally relies on the empty-paragraph-as-separator pattern for spacing |
The third option exists because section_replace only touches sections you
list in the YAML. If a template has 18 numbered sections and you only fill 12,
the other 6 stay tight against their content — visually inconsistent. Turn the
opt-in on for documents where you'd rather the consistency than the fidelity.
Step 4 — Run the fill
python scripts/fill_form.py \
--template path/to/template.docx \
--content content.yaml \
--output path/to/filled.docx
The CLI prints [OK] / [MISS] for every fill operation and a summary at the
end. Investigate any [MISS] before submitting.
Step 5 — Visual verification
soffice --headless --convert-to pdf path/to/filled.docx
Open the PDF and visually confirm: page count is sensible, no table row was split across pages, no font fell back to Times New Roman, all required fields are populated.
Python API
from fill_form import FormFiller
filler = FormFiller("template.docx", korean_font="맑은 고딕")
# Fill table cells
filler.fill_table_kv("Study Title", "...")
filler.fill_table_kv("연구 목적", "...")
# Replace section content (header to next header)
filler.replace_paragraphs_after("4. Background", new_content)
# Replace a single paragraph
filler.replace_paragraph_matching("Title:", "Title: ...")
# Validate and save
warnings = filler.validate()
for w in warnings:
print(w)
filler.save("filled.docx")
Anti-Patterns (Do Not Do)
| Anti-pattern | Consequence |
|---|---|
Document() then rebuild table |
Loss of header logo, custom margins, footer placeholders, and page numbering |
pandoc -f doc -t docx |
"Unknown input format doc" — pandoc does not parse .doc |
textutil -convert docx |
Table cell merging is dropped or corrupted |
cell.text = "value" (single assignment) |
Run-level styles (bold, color, eastAsia font) are erased |
Coordinate-based matching table.cell(2, 1) |
Silent breakage when the template adds or reorders rows |
run.font.name alone for Hangul |
Hangul characters render in the default Western font |
Companion Skills
write-protocol— drafts the scientific content (Background, Study Design, Sample Size, Statistical Plan) thatfill-protocolthen renders into the formhwp-pipeline— converts Korean Hangul .hwp / .hwpx files; chain it beforefill-protocolwhen the institutional form is distributed in HWP formatcheck-reporting— validates that the filled protocol satisfies CONSORT / STARD / TRIPOD / CLAIM checklists before submissioncalc-sample-size— produces the sample size text thatfill-protocolslots into the corresponding section
Files
scripts/doc_to_docx.py— LibreOffice headless wrapper for .doc → .docxscripts/inspect_template.py— reports tables, cells, and paragraphsscripts/fill_form.py— theFormFillerlibrary and CLI entry pointexamples/— worked examples for IRB, ethics waiver, and grant templatesreferences/best_practices.md— formatting notes (cantSplit, eastAsia, multi-line cell text)
Known Limitations
- HWP / HWPX input is not handled directly — chain with
hwp-pipelineto convert HWP → HWPX → DOCX first. - Merged cells: filling a label cell that participates in a vertical merge may overwrite the merged region's content. Test on a copy first.
- Embedded form fields (Word's content controls): not yet supported. Plain paragraph and table cell content only.
- Right-to-left scripts (Arabic, Hebrew): untested.
Anti-Hallucination
- Never fabricate references. All citations must be verified via
/search-litwith confirmed DOI or PMID. Mark unverified references as[UNVERIFIED - NEEDS MANUAL CHECK]. - Never invent clinical definitions, diagnostic criteria, or guideline recommendations. If uncertain, flag with
[VERIFY]and ask the user. - Never fabricate numerical results — compliance percentages, scores, effect sizes, or sample sizes must come from actual data or analysis output.
- If a reporting guideline item, journal policy, or clinical standard is uncertain, state the uncertainty rather than guessing.