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.
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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).
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Extract structured data from clinical notes with span-level provenance and null-safety. Use when users say "extract [variables] from this note", "abstract this chart", "pull structured data from these notes", "what does this note say about [field]", or when building a chart-abstraction, registry, or cohort dataset from unstructured clinical text.
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Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for [intervention]", or when developing FDA submission documentation for investigational products.
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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).
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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.
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FHIR API development guide for building healthcare endpoints. Use when: (1) Creating FHIR REST endpoints (Patient, Observation, Encounter, Condition, MedicationRequest), (2) Validating FHIR resources and returning proper HTTP status codes and error responses, (3) Implementing SMART on FHIR authorization and OAuth scopes, (4) Working with Bundles, transactions, batch operations, or search pagination. Covers FHIR R4 resource structures, required fields, value sets (status codes, gender, intent), coding systems (LOINC, SNOMED, RxNorm, ICD-10), and OperationOutcome error handling.
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Screen a Medicare/Medicaid claims corpus for fraud, waste, and abuse and produce ranked, fully-cited investigation referrals for an SIU / program-integrity team. Use when asked to run a fraud sweep, screen claims for FWA, find billing anomalies, or generate investigation referrals over a claims dataset.
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