feat(snomed): medadmin to medstatement

Refs: #1442

packages/core/src/external/aws/lambda-logic/bundle-to-html-snomed.ts

@@ -38,7 +38,6 @@ export const bundleToHtml = (fhirBundle: Bundle): string => {
  const {
  patient,
  medications,
- medicationAdministrations,
  medicationStatements,
  conditions,
  allergies,
@@ -220,7 +219,6 @@ export const bundleToHtml = (fhirBundle: Bundle): string => {
  ${createMRHeader(patient)}
  <div class="divider"></div>
  <div id="mr-sections">
- ${createDischargeMedicationsSection(medications, medicationAdministrations)}
  ${createMedicationSection(medications, medicationStatements)}
  ${createConditionSection(conditions, encounters, patient)}
  ${createAllergySection(allergies)}
@@ -746,7 +744,7 @@ function createOrganiztionField(
  return organization?.name ? `<p>Facility: ${organization.name}</p>` : "";
 }
 
-function createDischargeMedicationsSection(
+export function createDischargeMedicationsSection(
  medications: Medication[],
  medicationAdministrations: MedicationAdministration[]
 ) {
@@ -827,14 +825,14 @@ export function createMedicationSection(
  return dayjs(a.effectivePeriod?.start).isBefore(dayjs(b.effectivePeriod?.start)) ? 1 : -1;
  });
 
- const removeDuplicate = uniqWith(medicationsSortedByDate, (a, b) => {
- const aDate = dayjs(a.effectivePeriod?.start).format(ISO_DATE);
- const bDate = dayjs(b.effectivePeriod?.start).format(ISO_DATE);
+ // const removeDuplicate = uniqWith(medicationsSortedByDate, (a, b) => {
+ //  const aDate = dayjs(a.effectivePeriod?.start).format(ISO_DATE);
+ //  const bDate = dayjs(b.effectivePeriod?.start).format(ISO_DATE);
 
- return aDate === bDate && a.dosage?.[0]?.text === b.dosage?.[0]?.text;
- });
+ //  return aDate === bDate && a.dosage?.[0]?.text === b.dosage?.[0]?.text;
+ // });
 
- const activeMedications = removeDuplicate.filter(
+ const activeMedications = medicationsSortedByDate.filter(
  medicationStatement => medicationStatement.status === "active"
  );
 
@@ -876,11 +874,11 @@ function getPeriodDateFromMedicationStatement(
  const end = v.effectivePeriod?.end ? dayjs(v.effectivePeriod.end) : undefined;
  const yearDiff = start && end ? end.diff(start, "year") : undefined;
 
- if (type === "start" && yearDiff !== undefined && yearDiff < 5) {
+ if (type === "start" && (yearDiff == undefined || yearDiff < 5)) {
  return v.effectivePeriod?.start;
- } else if (type === "end" && yearDiff !== undefined && yearDiff < 5) {
+ } else if (type === "end" && (yearDiff == undefined || yearDiff < 5)) {
  return v.effectivePeriod?.end;
- } else if (type === "lastSeen" && yearDiff !== undefined && yearDiff > 5) {
+ } else if (type === "lastSeen" && yearDiff && yearDiff > 5) {
  return v.effectivePeriod?.end;
  }
  return undefined;

packages/utils/src/terminology-server/fhir.ts

@@ -0,0 +1,74 @@
+import {
+ MedicationAdministration,
+ MedicationAdministrationDosage,
+ MedicationStatement,
+ Dosage,
+} from "@medplum/fhirtypes";
+
+export function convertMedicationAdministrationToStatement(
+ medAdmin: MedicationAdministration
+): MedicationStatement {
+ const medStatement: MedicationStatement = {
+ resourceType: "MedicationStatement",
+ id: medAdmin.id,
+ meta: medAdmin.meta,
+ implicitRules: medAdmin.implicitRules,
+ language: medAdmin.language,
+ text: medAdmin.text,
+ contained: medAdmin.contained,
+ extension: medAdmin.extension,
+ modifierExtension: medAdmin.modifierExtension,
+ identifier: medAdmin.identifier,
+ partOf: medAdmin.partOf,
+ status: convertStatus(medAdmin.status),
+ statusReason: medAdmin.statusReason,
+ category: medAdmin.category,
+ medicationCodeableConcept: medAdmin.medicationCodeableConcept,
+ medicationReference: medAdmin.medicationReference,
+ subject: medAdmin.subject,
+ context: medAdmin.context,
+ effectiveDateTime: medAdmin.effectiveDateTime,
+ effectivePeriod: medAdmin.effectivePeriod,
+ derivedFrom: [],
+ reasonCode: medAdmin.reasonCode,
+ reasonReference: medAdmin.reasonReference,
+ note: medAdmin.note,
+ dosage: convertDosage(medAdmin.dosage),
+ };
+
+ return medStatement;
+}
+
+function convertStatus(status: MedicationAdministration["status"]): MedicationStatement["status"] {
+ const statusMapping: { [key: string]: MedicationStatement["status"] } = {
+ completed: "completed",
+ "entered-in-error": "entered-in-error",
+ "in-progress": "active",
+ stopped: "stopped",
+ // Add more mappings as required
+ };
+
+ const mappedStatus = status ? statusMapping[status] : "unknown";
+ return mappedStatus;
+}
+
+function convertDosage(dosage: MedicationAdministrationDosage | undefined): Dosage[] {
+ if (!dosage) return [];
+
+ const convertedDosage: Dosage = {
+ text: dosage.text,
+ site: dosage.site,
+ route: dosage.route,
+ method: dosage.method,
+ doseAndRate: [
+ {
+ doseQuantity: dosage.dose,
+ rateRatio: dosage.rateRatio,
+ rateQuantity: dosage.rateQuantity,
+ },
+ ],
+ timing: {},
+ };
+
+ return [convertedDosage];
+}

packages/utils/src/terminology-server/snomed-dedup-and-filter.ts

@@ -4,6 +4,7 @@ import daysjs from "dayjs";
 import { getCodeDisplay, getCodeDetailsFull } from "./term-server-api";
 import { populateHashTableFromCodeDetails, SnomedHierarchyTableEntry } from "./snomed-heirarchies";
 import { RemovalStats, createInitialRemovalStats, prettyPrintRemovalStats } from "./stats";
+import { convertMedicationAdministrationToStatement } from "./fhir";
 
 async function processDirectoryOrFile(
  directoryOrFile: string,
@@ -269,6 +270,22 @@ async function filterMedicationStatements({
  fs.writeFileSync(filePath, JSON.stringify(data, null, 2), "utf8");
 }
 
+function convertMedicationAdministrationsToMedicationStatements({
+ filePath,
+}: {
+ filePath: string;
+}) {
+ const data = JSON.parse(fs.readFileSync(filePath, "utf8"));
+ const entries = data.bundle ? data.bundle.entry : data.entry;
+ for (const entry of entries) {
+ const resource = entry.resource;
+ if (resource && resource.resourceType === "MedicationAdministration") {
+ entry.resource = convertMedicationAdministrationToStatement(resource);
+ }
+ }
+ fs.writeFileSync(filePath, JSON.stringify(data, null, 2), "utf8");
+}
+
 export async function fullProcessing(directoryPath: string) {
  const removalStats = createInitialRemovalStats();
 
@@ -323,6 +340,12 @@ export async function fullProcessing(directoryPath: string) {
  });
  });
 
+ await processDirectoryOrFile(directoryPath, async filePath => {
+ await convertMedicationAdministrationsToMedicationStatements({
+ filePath,
+ });
+ });
+
  prettyPrintRemovalStats(removalStats);
 }