plugins/healthcare/skills/doc-extract/SKILL.md
Extract plain text from a document file - PDF, DOCX, XLSX, PPTX, RTF, or plain text/markdown/HTML. Use when a binary document needs to be turned into text, for example a contract PDF or an EHR DocumentReference attachment. Other skills (fhir) invoke scripts/extract.ts directly; the contracts MCP server bundles its own copy (servers/documents/src/extract.mjs) so its bundle stays self-contained — port fixes to both.
npx skillsauth add anthropics/healthcare doc-extractInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Shared document-to-text extraction. One script, no state: reads an input file, prints JSON to stdout, writes nothing to disk (PHI-safe — no caches, no temp files; callers own any caching).
cd <this skill dir> && bun install
This pulls liteparse (the lit bin, used for PDF/DOCX/XLSX/PPTX, OCR included) and rtf-to-text (RTF). Without it, PDFs still work via a pdftotext -layout fallback if poppler is installed; other binary formats require liteparse.
bun <this skill dir>/scripts/extract.ts <input-file> [--content-type <mime>]
Output on stdout:
{ "text": "...", "method": "liteparse | pdftotext | rtf-to-text | passthrough", "pages": 12 }
text is page-anchored for paged formats: === [page N] === markers between pages.pages is present when page markers exist.method is the extractor that actually produced the text.--content-type (e.g. application/pdf) when the file has no useful extension, as with downloaded EHR attachments. Note liteparse refuses extension-less files, so those PDFs go through the pdftotext fallback.{"error": "..."} to stderr and exit 1.Tables with multiple value columns (option A vs option B, in-tier vs out-of-tier) can interleave columns line-by-line in the extracted text: fragments of adjacent cells alternate, and a cell's text can even land mid-sentence inside a neighboring column. Values usually survive, but which column a value belongs to can become ambiguous. When an answer comes from one column of a multi-column table and the document has no redundant restatement of the value elsewhere, verify it by reading the original page directly before treating it as ground truth. The extracted text's === [page N] === anchor tells you which page: pass it to the Read tool's pages parameter (e.g. pages: "37") to render just that page to vision instead of the whole document.
Import the functions instead of shelling out when you're already in bun TS:
import { extract, resolveLit } from "../doc-extract/scripts/extract";
const lit = resolveLit([myRoot]); // also checks myRoot/node_modules/.bin/lit
const text = extract(lit, "/path/to/file.pdf"); // string | null
The contracts skill consumes it this way (its ingest caching stays on the contracts side).
testing
Answer a question across a corpus of contract documents with verified citations. Use when the user asks what a contract says, which contracts have a clause, what changed between amendments, or any question that needs reading and citing across a set of contract files. The corpus must be on the local filesystem (see README).
tools
Connect to a hospital's FHIR R4 server (Epic, Oracle Health/Cerner, MEDITECH, athenahealth, or any SMART-on-FHIR endpoint), pull a patient's clinical data and notes, and extract structured findings. Use when users say "connect to the EHR", "connect to Epic/Cerner", "pull notes for patient X", "what do the last 6 months of notes say about Y", or any task that starts from a live EHR rather than pasted text.
tools
Assign CPT and HCPCS Level II procedure codes from clinical documentation the way a professional coder builds the claim. Use when users say "code this encounter for procedures", "what CPT codes apply", "assign HCPCS codes", "code this op note", or when turning visit notes or operative reports into claim-ready procedure codes.
tools
Fan out over the scoped document set via the saved sweep workflow. Workers full-read their shard and write findings + citations directly via cli.ts. Recall over precision — never skip a scoped doc.