feat(utils): added and updated the bulk-update-patients script

packages/utils/src/bulk-update-patients.ts

@@ -0,0 +1,192 @@
+import * as dotenv from "dotenv";
+dotenv.config();
+// keep that ^ on top
+import { Address, MetriportMedicalApi, PatientDTO, USState } from "@metriport/api-sdk";
+import { getEnvVarOrFail } from "@metriport/core/util/env-var";
+import { sleep } from "@metriport/shared";
+import dayjs from "dayjs";
+import duration from "dayjs/plugin/duration";
+import { chunk } from "lodash";
+import { QueryTypes, Sequelize } from "sequelize";
+import z from "zod";
+
+/**
+ * This script looks at all of the patients created after a certain date and triggers the UPDATE PATIENT
+ * for those patients, who do not have a link in the cq_patient_data table.
+ *
+ * To run:
+ * 1. Set the env vars:
+ * -CX_ID
+ * -API_KEY
+ * -API_URL
+ * -DB_CREDS - Must use the read replica
+ * 2. Set the patientCreatedDate string in the format YYYY-MM-DD
+ * 3. Run the script with `ts-node src/bulk-update-patients.ts`
+ */
+
+dayjs.extend(duration);
+
+const confirmationTime = dayjs.duration(10, "seconds");
+const delayTime = confirmationTime.asMilliseconds();
+
+const apiKey = getEnvVarOrFail("API_KEY");
+const apiUrl = getEnvVarOrFail("API_URL");
+const sqlDBCreds = getEnvVarOrFail("DB_CREDS"); // Must use the read replica
+const cxId = getEnvVarOrFail("CX_ID");
+const CHUNK_DELAY_MAX_MS = dayjs.duration({ minutes: 1 }).asMilliseconds();
+const PATIENT_CHUNK_SIZE = 5;
+
+const patientCreatedDate = ""; // YYYY-MM-DD format
+
+const metriportAPI = new MetriportMedicalApi(apiKey, {
+ baseAddress: apiUrl,
+});
+
+const cqPatientDataResultSchema = z.array(
+ z.object({
+ id: z.string(),
+ cx_id: z.string(),
+ data: z.object({
+ links: z.array(z.object({ oid: z.string(), url: z.string() })),
+ }),
+ created_at: z.date(),
+ })
+);
+type CqPatientDataResult = z.infer<typeof cqPatientDataResultSchema>;
+
+async function main() {
+ const dbCreds = JSON.parse(sqlDBCreds);
+ if (!patientCreatedDate) {
+ console.log("Please provide a date string in the format YYYY-MM-DD");
+ return;
+ }
+ const targetDate = new Date(patientCreatedDate);
+
+ const sequelize = new Sequelize(dbCreds.dbname, dbCreds.username, dbCreds.password, {
+ host: dbCreds.host,
+ port: dbCreds.port,
+ dialect: dbCreds.engine,
+ });
+
+ try {
+ const facilities = await metriportAPI.listFacilities();
+ await displayInitialWarningAndConfirmation(facilities.length);
+ const patientCQLinks = await getPatientCqLinks(sequelize, cxId);
+
+ let totalFacilities = 0;
+ let totalPatients = 0;
+ let patientsNoLinks = 0;
+
+ for (let i = 0; i < facilities.length; i++) {
+ const facility = facilities[i];
+ totalFacilities++;
+ const patientsList = await metriportAPI.listPatients(facility.id);
+
+ await displayWarningAndConfirmation(facilities.length);
+ const patientsCreatedAfter = patientsList.filter(
+ // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+ patient => new Date(patient.dateCreated!) > targetDate
+ );
+
+ totalPatients += patientsCreatedAfter.length;
+
+ const patientsWithNoLinks = [];
+
+ for (const patient of patientsCreatedAfter) {
+ const hasPatientLinks = patientCQLinks.filter(link => link.id === patient.id);
+ if (hasPatientLinks.length > 0) {
+ continue;
+ }
+
+ patientsWithNoLinks.push(patient);
+ patientsNoLinks++;
+ }
+
+ const patientChunks = chunk(patientsWithNoLinks, PATIENT_CHUNK_SIZE);
+ console.log(`Facility ${facility.id} has ${patientsWithNoLinks.length} patients`);
+
+ for (const [j, patients] of patientChunks.entries()) {
+ console.log(`Chunk ${j + 1} of ${patientChunks.length}`);
+ console.log(`# of patients ${patients.length}`);
+
+ for (const patient of patients) {
+ console.log(`Updating patient ${patient.id}`);
+ const addressObject = Array.isArray(patient.address)
+ ? patient.address[0]
+ : patient.address;
+ const address = addressObject as Address;
+ await updatePatient(patient, address, facility.id);
+ }
+ if (j < patientChunks.length - 1) {
+ await sleep(CHUNK_DELAY_MAX_MS * patients.length);
+ }
+ }
+ if (i < facilities.length - 1) {
+ await sleep(CHUNK_DELAY_MAX_MS);
+ }
+ }
+
+ console.log(`Total facilities: ${totalFacilities}`);
+ console.log(`Total patients: ${totalPatients}`);
+ console.log(`Patients with no links: ${patientsNoLinks}`);
+ } catch (err) {
+ console.error(err);
+ } finally {
+ sequelize.close();
+ }
+}
+
+async function getPatientCqLinks(sequelize: Sequelize, cxId: string): Promise<CqPatientDataResult> {
+ const query = `SELECT * FROM cq_patient_data WHERE cx_id=:cxId`;
+ const patientResults = await sequelize.query(query, {
+ replacements: { cxId },
+ type: QueryTypes.SELECT,
+ });
+
+ const patientCQLinks = cqPatientDataResultSchema.parse(patientResults);
+ return patientCQLinks;
+}
+
+async function updatePatient(patient: PatientDTO, address: Address, facilityId: string) {
+ await metriportAPI.updatePatient(
+ {
+ id: patient.id,
+ firstName: patient.firstName,
+ lastName: patient.lastName,
+ dob: patient.dob,
+ genderAtBirth: patient.genderAtBirth,
+ address: [
+ {
+ state: address.state as USState,
+ city: address.city,
+ country: "USA",
+ addressLine1: address.addressLine1,
+ ...(address.addressLine2 && { addressLine2: address.addressLine2 }),
+ zip: address.zip,
+ },
+ ],
+ },
+ facilityId
+ );
+}
+
+async function displayInitialWarningAndConfirmation(numberFacilities: number) {
+ const org = await metriportAPI.getOrganization();
+ if (!org) {
+ throw new Error("Organization not found");
+ }
+ console.log("\n\x1b[31m%s\x1b[0m\n", "---- ATTENTION - THIS IS NOT A SIMULATED RUN ----"); // https://stackoverflow.com/a/41407246/2099911
+ console.log(
+ `Updating patients created after ${patientCreatedDate} for organization ${org.name} (${org.id}).\nThere's ${numberFacilities} different facilities. Sleeping ${delayTime} ms before starting.`
+ );
+ await sleep(delayTime);
+}
+
+async function displayWarningAndConfirmation(numberPatients: number) {
+ console.log(
+ `There are a total of ${numberPatients} patients created after ${patientCreatedDate}.\nUpdating patients without links. Sleeping ${delayTime} ms before starting..`
+ );
+ await sleep(delayTime);
+}
+
+main();