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Version: v0.2.0

Tutorial: transform an admission message

In this tutorial we turn one admission message into FHIR R4 and learn to read everything the call hands back. Each step is a complete program you can paste into a file and run with Node.js 22 or later after npm install @cosyte/transform @cosyte/hl7 @cosyte/fhir. The message is synthetic.

Step 1: transform the message​

An ADT^A01 says a patient was admitted. Ours carries the header (MSH), the patient (PID), the visit (PV1), one allergy (AL1), and a site-specific ZPD segment. Parse it with @cosyte/hl7, then pass the parsed message to toFhir.

import { parseHL7 } from "@cosyte/hl7";
import { serializeResource } from "@cosyte/fhir";
import { toFhir } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|SENDAPP|SENDFAC|RCVAPP|RCVFAC|20260721143000-0500||ADT^A01^ADT_A01|MSG00001|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "PV1|1|I||||||||||||||||||||||||||||||||||||||||||20260721140000",
  "AL1|1|DA|70618^Penicillin^RXNORM|SV",
  "ZPD|1|SYNTHETIC",
].join("\r");

const { bundle } = toFhir(parseHL7(raw));

const json = JSON.parse(serializeResource(bundle)) as {
  type: string;
  entry: { resource: { resourceType: string } }[];
};
json.type; // => "message"
json.entry.map((e) => e.resource.resourceType); // => ["MessageHeader", "Patient", "Encounter", "AllergyIntolerance"]

The bundle is a FHIR message: the MessageHeader comes first, then the resources the message is about. The ZPD segment produced nothing, because the guide maps no segment by that name.

Step 2: read the patient​

The Patient carries the name, birth date and sex from PID-5, PID-7 and PID-8, and the medical record number from PID-3. Look at the identifier: it has a value and a type, and no system.

import { parseHL7 } from "@cosyte/hl7";
import { serializeResource } from "@cosyte/fhir";
import { toFhir } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|SENDAPP|SENDFAC|RCVAPP|RCVFAC|20260721143000-0500||ADT^A01^ADT_A01|MSG00001|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "PV1|1|I||||||||||||||||||||||||||||||||||||||||||20260721140000",
  "AL1|1|DA|70618^Penicillin^RXNORM|SV",
  "ZPD|1|SYNTHETIC",
].join("\r");

const json = JSON.parse(serializeResource(toFhir(parseHL7(raw)).bundle)) as {
  entry: { resource: Record<string, unknown> }[];
};
const patient = json.entry[1]?.resource;

patient?.["name"]; // => [{ family: "Public", given: ["Jane", "Q"] }]
patient?.["birthDate"]; // => "1980-01-15"
patient?.["gender"]; // => "female"
patient?.["identifier"]; // => [{ type: { coding: [{ system: "http://terminology.hl7.org/CodeSystem/v2-0203", code: "MR" }] }, value: "MRN12345" }]

The message names the assigning authority only as HOSP, a short code the sender chose. Two hospitals can both call themselves HOSP, so turning that code into a system URI on our own could merge two different patients. The library leaves system out and reports it instead.

Step 3: resolve the identifier system​

You know which system URI HOSP stands for; the library cannot. Say so with a naming system and pass it to toFhir.

import { parseHL7 } from "@cosyte/hl7";
import { serializeResource } from "@cosyte/fhir";
import { createNamingSystem, toFhir } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|SENDAPP|SENDFAC|RCVAPP|RCVFAC|20260721143000-0500||ADT^A01^ADT_A01|MSG00001|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "PV1|1|I||||||||||||||||||||||||||||||||||||||||||20260721140000",
  "AL1|1|DA|70618^Penicillin^RXNORM|SV",
  "ZPD|1|SYNTHETIC",
].join("\r");

const namingSystem = createNamingSystem({
  authorities: { HOSP: "urn:oid:2.16.840.1.113883.19" },
});
const json = JSON.parse(serializeResource(toFhir(parseHL7(raw), { namingSystem }).bundle)) as {
  entry: { resource: { identifier?: { system?: string; value: string }[] } }[];
};

json.entry[1]?.resource.identifier?.[0]?.system; // => "urn:oid:2.16.840.1.113883.19"

Step 4: read the issues​

toFhir also returns issues: everything it could not map faithfully, as a code, a severity, a v2 location and a FHIR path. An issue never carries a value from the message, so it is safe to log.

import { parseHL7 } from "@cosyte/hl7";
import { createNamingSystem, toFhir } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|SENDAPP|SENDFAC|RCVAPP|RCVFAC|20260721143000-0500||ADT^A01^ADT_A01|MSG00001|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "PV1|1|I||||||||||||||||||||||||||||||||||||||||||20260721140000",
  "AL1|1|DA|70618^Penicillin^RXNORM|SV",
  "ZPD|1|SYNTHETIC",
].join("\r");

const { issues } = toFhir(parseHL7(raw), {
  namingSystem: createNamingSystem({ authorities: { HOSP: "urn:oid:2.16.840.1.113883.19" } }),
});

issues.map((i) => `${i.severity} ${i.code} ${i.v2Location}`); // => ["warning TRANSFORM_TIMESTAMP_NO_TIMEZONE TS.1", "information TRANSFORM_REQUIRED_ELEMENT_UNKNOWN MSH.3", "information TRANSFORM_SEGMENT_NO_IG_MAP ZPD[1]"]

Read them in order:

  • TRANSFORM_TIMESTAMP_NO_TIMEZONE: the admit time in PV1-44 has a time of day but no offset, and FHIR does not allow a time without a zone. Rather than assume UTC and move the admission by hours, the library kept the date only: Encounter.period.start is 2026-07-21. The location TS.1 is the timestamp component of the field, not a value.
  • TRANSFORM_REQUIRED_ELEMENT_UNKNOWN: FHIR requires MessageHeader.source.endpoint, and MSH-3 is an application name, not an address, so the element carries a data-absent-reason of unknown instead of an invented URL.
  • TRANSFORM_SEGMENT_NO_IG_MAP: the ZPD segment reached no resource, and the guide publishes no map for it. ZPD[1] is its first occurrence.

The fix for the first one is in your hands: if you know the sender's offset, pass assumeTimezoneOffsetMinutes. Keep the time on a timestamp with no offset shows how.

Step 5: make the ids repeatable and return the issues as FHIR​

Each run mints fresh urn:uuid: ids for the bundle entries. Pass generateId to make them repeatable, for golden files or tests; it must return a new, unique value each call. Then turn the issues into a FHIR OperationOutcome you can store or return beside the bundle.

import { parseHL7 } from "@cosyte/hl7";
import { serializeResource } from "@cosyte/fhir";
import { createNamingSystem, toFhir, toOperationOutcome } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|SENDAPP|SENDFAC|RCVAPP|RCVFAC|20260721143000-0500||ADT^A01^ADT_A01|MSG00001|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "PV1|1|I||||||||||||||||||||||||||||||||||||||||||20260721140000",
  "AL1|1|DA|70618^Penicillin^RXNORM|SV",
  "ZPD|1|SYNTHETIC",
].join("\r");

let next = 0;
const { bundle, issues } = toFhir(parseHL7(raw), {
  assumeTimezoneOffsetMinutes: -300,
  namingSystem: createNamingSystem({ authorities: { HOSP: "urn:oid:2.16.840.1.113883.19" } }),
  generateId: () => `00000000-0000-4000-8000-${String((next += 1)).padStart(12, "0")}`,
});

const json = JSON.parse(serializeResource(bundle)) as {
  entry: { fullUrl: string; resource: { resourceType: string; period?: { start: string } } }[];
};
json.entry[1]?.fullUrl; // => "urn:uuid:00000000-0000-4000-8000-000000000001"
json.entry[2]?.resource.period?.start; // => "2026-07-21T14:00:00-05:00"

const outcome = JSON.parse(serializeResource(toOperationOutcome(issues))) as {
  resourceType: string;
  issue: { severity: string; details: { coding: { code: string }[] } }[];
};
outcome.resourceType; // => "OperationOutcome"
outcome.issue.map((i) => i.details.coding[0]?.code); // => ["TRANSFORM_TIMESTAMP_NO_TIMEZONE", "TRANSFORM_REQUIRED_ELEMENT_UNKNOWN", "TRANSFORM_SEGMENT_NO_IG_MAP"]

With the offset asserted, the admit time keeps its time of day. The timezone issue is still raised, because the offset came from you and not from the message; it marks the value as sender-asserted.

What we built, and where to go next​

We transformed an admission into a FHIR message Bundle, resolved the record number's system, read each issue, and returned the issues as an OperationOutcome.