Merge pull request #2224 from metriport/1603-add-immunizations-section

1603 add immunizations and vital signs sections

packages/core/src/external/fhir/shared/index.ts

@@ -8,6 +8,7 @@ import {
  DocumentReference,
  Encounter,
  Extension,
+ Immunization,
  Location,
  Medication,
  MedicationStatement,
@@ -165,6 +166,10 @@ export function isEncounter(resource: Resource | undefined): resource is Encount
  return resource?.resourceType === "Encounter";
 }
 
+export function isImmunization(resource: Resource | undefined): resource is Immunization {
+ return resource?.resourceType === "Immunization";
+}
+
 export function isObservation(resource: Resource | undefined): resource is Observation {
  return resource?.resourceType === "Observation";
 }

packages/core/src/fhir-to-cda/cda-templates/clinical-document/structured-body.ts

@@ -1,11 +1,13 @@
 import { Bundle } from "@medplum/fhirtypes";
 import { buildAllergies } from "../components/allergies";
-import { buildMedications } from "../components/medications";
 import { buildEncounters } from "../components/encounters";
+import { buildImmunizations } from "../components/immunizations";
+import { buildMedications } from "../components/medications";
 import { buildMentalStatus } from "../components/mental-status";
 import { buildProblems } from "../components/problems";
 import { buildResult } from "../components/results";
 import { buildSocialHistory } from "../components/social-history";
+import { buildVitalSigns } from "../components/vital-signs";
 
 export function buildStructuredBody(fhirBundle: Bundle): unknown {
  const structuredBodySections = [
@@ -16,6 +18,8 @@ export function buildStructuredBody(fhirBundle: Bundle): unknown {
  buildProblems(fhirBundle),
  buildAllergies(fhirBundle),
  buildEncounters(fhirBundle),
+ buildImmunizations(fhirBundle),
+ buildVitalSigns(fhirBundle),
  ];
 
  return {

packages/core/src/fhir-to-cda/cda-templates/commons.ts

@@ -14,7 +14,7 @@ import localizedFormat from "dayjs/plugin/localizedFormat";
 import utc from "dayjs/plugin/utc";
 import {
  AssignedEntity,
- CDAOriginalText,
+ CdaOriginalText,
  CdaAddress,
  CdaAddressUse,
  CdaCodeCe,
@@ -43,6 +43,7 @@ import {
  placeholderOrgOid,
  providerTaxonomy,
  snomedSystemCode,
+ vaccineAdministeredCodeSet,
 } from "./constants";
 
 dayjs.extend(localizedFormat);
@@ -56,6 +57,8 @@ CODING_MAP.set("http:https://www.ama-assn.org/go/cpt", amaAssnSystemCode);
 CODING_MAP.set("http:https://fdasis.nlm.nih.gov", fdasisSystemCode);
 CODING_MAP.set("http:https://terminology.hl7.org/codesystem/v3-actcode", hl7ActCode);
 CODING_MAP.set("http:https://nucc.org/provider-taxonomy", providerTaxonomy);
+CODING_MAP.set("http:https://hl7.org/fhir/sid/cvx", vaccineAdministeredCodeSet);
+
 CODING_MAP.set("icd-10", icd10SystemCode);
 
 export const TIMESTAMP_CLEANUP_REGEX = /-|T|:|\.\d+Z$/g;
@@ -113,7 +116,7 @@ export function buildCodeCe({
  return codeObject;
 }
 
-export function buildOriginalTextReference(value: string): CDAOriginalText {
+export function buildOriginalTextReference(value: string): CdaOriginalText {
  return {
  reference: {
  _value: value,
@@ -459,10 +462,10 @@ export function getTextFromCode(code: CodeableConcept | undefined): string {
 }
 
 export function getDisplaysFromCodeableConcepts(
- concepts: CodeableConcept[] | undefined
+ concepts: CodeableConcept | CodeableConcept[] | undefined
 ): string | undefined {
  if (!concepts) return undefined;
- return concepts
+ return toArray(concepts)
  .map(concept => {
  const code = buildCodeCeFromCoding(concept.coding);
  if (code?._displayName) return code._displayName.trim();
@@ -495,13 +498,45 @@ export function buildPerformer(practitioners: Practitioner[] | undefined): Assig
  family: p.name?.flatMap(n => n.family).join(", "),
  },
  },
+ representedOrganization: {
+ _classCode: "ORG",
+ name: {
+ "#text": "",
+ },
+ addr: buildAddress(p.address),
+ telecom: buildTelecom(p.telecom),
+ },
  },
  } || []
  );
  }) || []
  );
 }
 
+export function buildPerformerFromLocation(
+ location: Location | undefined
+): AssignedEntity | undefined {
+ if (!location) return undefined;
+ return {
+ assignedEntity: {
+ id: buildInstanceIdentifier({
+ root: placeholderOrgOid,
+ extension: location.id,
+ }),
+ addr: buildAddress(location.address),
+ telecom: buildTelecom(location.telecom),
+ representedOrganization: {
+ _classCode: "ORG",
+ name: {
+ "#text": "",
+ },
+ addr: buildAddress(location.address),
+ telecom: buildTelecom(location.telecom),
+ },
+ },
+ };
+}
+
 export function buildParticipant(locations: Location[] | undefined): Participant[] | undefined {
  if (!locations) return undefined;
 
@@ -535,3 +570,8 @@ export function buildParticipant(locations: Location[] | undefined): Participant
  return participant;
  });
 }
+
+export function buildAddressText(address: Address | undefined): string | undefined {
+ if (!address) return undefined;
+ return `${address.line?.join(", ")}, ${address.city}, ${address.state} ${address.postalCode}`;
+}

packages/core/src/fhir-to-cda/cda-templates/components/__tests__/immunization.test.ts

@@ -0,0 +1,45 @@
+import { faker } from "@faker-js/faker";
+import { Bundle, Immunization, Location } from "@medplum/fhirtypes";
+import _ from "lodash";
+import path from "path";
+import { removeEmptyFields } from "../../clinical-document/clinical-document";
+import { xmlBuilder } from "../../clinical-document/shared";
+import { buildImmunizations } from "../immunizations";
+import { immunizationFlu } from "./immunizations-examples";
+import { location1 } from "./encounter-examples";
+import { makeImmunization } from "./make-immunization";
+import { createEmptyBundle, getXmlContentFromFile } from "./shared";
+import { makeLocation } from "./make-encounter";
+
+let immunizationId: string;
+let locationId: string;
+let bundle: Bundle;
+let immunization: Immunization;
+let location: Location;
+
+beforeEach(() => {
+ immunizationId = faker.string.uuid();
+ locationId = faker.string.uuid();
+ immunization = makeImmunization({ ...immunizationFlu }, { imm: immunizationId, loc: locationId });
+ location = makeLocation({ ...location1, id: locationId });
+ bundle = createEmptyBundle();
+});
+
+describe("buildImmunizations", () => {
+ it("correctly maps a single Immunization", () => {
+ bundle.entry?.push({ resource: immunization });
+ bundle.entry?.push({ resource: location });
+
+ const filePath = path.join(__dirname, "./xmls/immunization-section-single-entry.xml");
+ const xmlTemplate = _.template(getXmlContentFromFile(filePath));
+ const params = {
+ immunizationId,
+ locationId,
+ };
+ const xmlContent = xmlTemplate(params);
+ const res = buildImmunizations(bundle);
+ const cleanedJsonObj = removeEmptyFields(res);
+ const xmlRes = xmlBuilder.build(cleanedJsonObj);
+ expect(xmlRes).toEqual(xmlContent);
+ });
+});

packages/core/src/fhir-to-cda/cda-templates/components/__tests__/immunizations-examples.ts

@@ -0,0 +1,22 @@
+import { Immunization } from "@medplum/fhirtypes";
+
+export const immunizationFlu: Partial<Immunization> = {
+ status: "completed",
+ vaccineCode: {
+ coding: [
+ {
+ system: "http:https://hl7.org/fhir/sid/cvx",
+ code: "140",
+ display: "Influenza, seasonal, injectable, preservative free",
+ },
+ ],
+ text: "Influenza, seasonal, injectable, preservative free",
+ },
+ patient: {
+ reference: "Patient/018ef2b1-a952-7a43-9124-7a86f10b9d78",
+ },
+ encounter: {
+ reference: "Encounter/90170bdf-3029-49d9-ba31-48c942bf3799",
+ },
+ occurrenceDateTime: "2013-09-19T18:14:30-07:00",
+};

packages/core/src/fhir-to-cda/cda-templates/components/__tests__/make-composition.ts

@@ -18,7 +18,6 @@ export function makeComposition(ids: { enc: string; pract: string }): Compositio
  },
  date: "2024-03-06T21:22:21.000Z",
  title: "Encounter Summary",
- event: [{ period: { start: "2012-07-23T16:45:00.000Z" } }],
  section: [
  {
  title: "Results",

packages/core/src/fhir-to-cda/cda-templates/components/__tests__/make-immunization.ts

@@ -0,0 +1,16 @@
+import { Immunization } from "@medplum/fhirtypes";
+import { makeBaseDomain, makeSubjectReference } from "./shared";
+
+export function makeImmunization(
+ params: Partial<Immunization> = {},
+ ids: { imm: string; loc: string }
+): Immunization {
+ return {
+ ...makeBaseDomain(),
+ ...makeSubjectReference(),
+ resourceType: "Immunization",
+ ...params,
+ id: ids.imm,
+ location: { reference: `Location/${ids.loc}` },
+ };
+}

packages/core/src/fhir-to-cda/cda-templates/components/__tests__/social-history-examples.ts

@@ -34,7 +34,6 @@ export const observationMentalStatus: Partial<Observation> = {
  text: "Low risk",
  },
  effectiveDateTime: "2012-07-23T17:16:00.324-07:00",
- issued: "2012-07-23T17:16:00.324-07:00",
  interpretation: [
  {
  coding: [

packages/core/src/fhir-to-cda/cda-templates/components/__tests__/vital-signs-examples.ts

@@ -0,0 +1,108 @@
+import { Observation } from "@medplum/fhirtypes";
+
+export const vitalSignObservationTemplate: Partial<Observation> = {
+ resourceType: "Observation",
+ status: "final",
+ category: [
+ {
+ coding: [
+ {
+ system: "http:https://terminology.hl7.org/CodeSystem/observation-category",
+ code: "vital-signs",
+ display: "Vital signs",
+ },
+ ],
+ },
+ ],
+ code: {
+ coding: [
+ {
+ system: "http:https://loinc.org",
+ code: "72514-3",
+ display: "Pain severity - 0-10 verbal numeric rating [Score] - Reported",
+ },
+ ],
+ text: "Pain severity - 0-10 verbal numeric rating [Score] - Reported",
+ },
+ effectiveDateTime: "2013-09-19T18:14:30-07:00",
+ valueQuantity: {
+ value: 0,
+ unit: "{score}",
+ system: "http:https://unitsofmeasure.org",
+ code: "{score}",
+ },
+};
+
+export const obsHeartRate: Partial<Observation> = {
+ code: {
+ text: "Heart rate",
+ coding: [{ code: "8867-4", system: "http:https://loinc.org" }],
+ },
+ effectiveDateTime: "2013-09-19T18:14:30-07:00",
+ valueQuantity: { value: 92, unit: "/min", system: "http:https://unitsofmeasure.org" },
+};
+
+export const obsTemperature: Partial<Observation> = {
+ code: {
+ text: "Body temperature",
+ coding: [{ code: "8310-5", system: "http:https://loinc.org" }],
+ },
+ effectiveDateTime: "2013-09-19T18:14:30-07:00",
+ valueQuantity: { value: 36.72, unit: "Cel", system: "http:https://unitsofmeasure.org" },
+};
+
+export const obsRespiratoryRate: Partial<Observation> = {
+ code: {
+ text: "Respiratory rate",
+ coding: [{ code: "9279-1", system: "http:https://loinc.org" }],
+ },
+ effectiveDateTime: "2013-09-19T18:14:30-07:00",
+ valueQuantity: { value: 16, unit: "/min", system: "http:https://unitsofmeasure.org" },
+};
+
+export const obsWeight: Partial<Observation> = {
+ code: {
+ text: "Body weight",
+ coding: [{ code: "29463-7", system: "http:https://loinc.org" }],
+ },
+ effectiveDateTime: "2013-09-02T18:14:30-07:00",
+ valueQuantity: { value: 63.504, unit: "kg", system: "http:https://unitsofmeasure.org" },
+};
+
+export const obsSystolic: Partial<Observation> = {
+ code: {
+ text: "Systolic blood pressure",
+ coding: [{ code: "8480-6", system: "http:https://loinc.org" }],
+ },
+ effectiveDateTime: "2013-09-02T18:14:30-07:00",
+ valueQuantity: { value: 104, unit: "mm[Hg]", system: "http:https://unitsofmeasure.org" },
+};
+
+export const obsDiastolic: Partial<Observation> = {
+ code: {
+ text: "Diastolic blood pressure",
+ coding: [{ code: "8462-4", system: "http:https://loinc.org" }],
+ },
+ effectiveDateTime: "2013-09-02T18:14:30-07:00",
+ valueQuantity: { value: 78, unit: "mm[Hg]", system: "http:https://unitsofmeasure.org" },
+};
+
+export const obsHeight: Partial<Observation> = {
+ code: {
+ coding: [
+ {
+ system: "http:https://loinc.org",
+ code: "8302-2",
+ display: "Body Height",
+ },
+ ],
+ text: "Body Height",
+ },
+ effectiveDateTime: "2013-09-02T18:14:30-07:00",
+ valueQuantity: {
+ value: 172.3,
+ unit: "cm",
+ system: "http:https://unitsofmeasure.org",
+ code: "cm",
+ },
+};