feat(snomed): full pipeline done

Refs: #1442

packages/utils/src/customer-requests/full-snomed-pipeline.ts

@@ -1,42 +1,101 @@
 import { bundleToHtml } from "@metriport/core/external/aws/lambda-logic/bundle-to-html";
-import fs from "fs";
+import fs from "fs/promises";
 import { convertHtmlTablesToCsv } from "./convert-html-to-csv";
 import * as path from "path";
 import { fullProcessing } from "../terminology-server/snomed-dedup-and-filter";
+import { MetriportMedicalApi } from "@metriport/api-sdk";
+import { getEnvVarOrFail } from "@metriport/core/util/env-var";
+import * as dotenv from "dotenv";
+import axios from "axios";
+dotenv.config();
+
+const apiKey = getEnvVarOrFail("API_KEY");
+const apiLoadBalancerURL = getEnvVarOrFail("API_URL");
+const fhirUrl = getEnvVarOrFail("FHIR_URL");
+const cxId = getEnvVarOrFail("CX_ID");
+const metriportApi: MetriportMedicalApi = new MetriportMedicalApi(apiKey);
+
+const resultsDirectory = "./runs/consolidatedPatients";
+
+async function fetchPatientIds(cxId: string): Promise<string[]> {
+ const url = `${apiLoadBalancerURL}/internal/patient/ids?cxId=${cxId}`;
+ try {
+ const response = await axios.get(url);
+ return response.data.patientIds;
+ } catch (error) {
+ console.error(`Error fetching patient IDs:`, error);
+ return [];
+ }
+}
+
+//eslint-disable-next-line
+async function getFhirPatientData(patientId: string): Promise<any> {
+ const url = `${fhirUrl}/fhir/${cxId}/Patient/${patientId}/`;
+ try {
+ const response = await axios.get(url);
+ return response.data;
+ } catch (error) {
+ console.error(`Error fetching FHIR data for patient ${patientId}:`, error);
+ }
+}
+
+export async function ensureDirectory(): Promise<void> {
+ await fs.mkdir(resultsDirectory, { recursive: true });
+}
+
+async function fetchAndSavePatientData(patientId: string): Promise<void> {
+ try {
+ const data = await metriportApi.getPatientConsolidated(patientId);
+ const fhirPatient = await getFhirPatientData(patientId);
+ const resourceWrappedFhirPatient = { resource: fhirPatient };
+ if (!data.entry) {
+ data.entry = [];
+ }
+ data.entry.push(resourceWrappedFhirPatient);
+ const filePath = `${resultsDirectory}/${patientId}.json`;
+ await fs.writeFile(filePath, JSON.stringify(data, null, 2));
+ console.log(`Data saved for patient ${patientId}`);
+ } catch (error) {
+ console.error(`Error fetching and saving data for patient ${patientId}:`, error);
+ }
+}
+
+async function processPatients(): Promise<void> {
+ console.log("Checking if directory exists...");
+ await ensureDirectory();
+ console.log("Fetching patient IDs...");
+ const patientIds = await fetchPatientIds(cxId);
+ for (const patientId of patientIds) {
+ await fetchAndSavePatientData(patientId);
+ }
+ console.log("All patient data processed.");
+}
 
-// Function to process each JSON file
 async function processFile(filePath: string) {
  await fullProcessing(filePath);
 
- const bundle = fs.readFileSync(filePath, "utf8");
+ const bundle = await fs.readFile(filePath, "utf8");
  const bundleParsed = JSON.parse(bundle);
 
- // Convert JSON to HTML
  const html = bundleToHtml(bundleParsed);
  const htmlOutputFilePath = filePath.replace(".json", ".html");
- fs.writeFileSync(htmlOutputFilePath, html);
+ await fs.writeFile(htmlOutputFilePath, html);
  console.log(`HTML file created at ${htmlOutputFilePath}`);
 
- // Convert HTML to CSV
  const csvContent = convertHtmlTablesToCsv(html);
  const csvOutputFilePath = filePath.replace(".json", ".csv");
- fs.writeFileSync(csvOutputFilePath, csvContent);
+ await fs.writeFile(csvOutputFilePath, csvContent);
  console.log(`CSV file created at ${csvOutputFilePath}`);
 }
 
-// Main function to iterate through the directory
 async function main() {
- const targetPath = process.argv[2];
-
- if (!targetPath) {
- console.log("Usage: node medical-records-local.js <path-to-directory>");
- process.exit(1);
- }
+ await processPatients();
 
- const files = fs.readdirSync(targetPath);
+ const files = await fs.readdir(resultsDirectory);
  for (const file of files) {
- const fullPath = path.join(targetPath, file);
+ const fullPath = path.join(resultsDirectory, file);
  if (path.extname(fullPath) === ".json") {
+ console.log(`Processing file ${fullPath}`);
  await processFile(fullPath);
  }
  }

packages/utils/src/terminology-server/precondition-analysis.ts

@@ -77,4 +77,6 @@ async function main() {
  );
 }
 
-main();
+if (require.main === module) {
+ main();
+}

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

@@ -299,4 +299,6 @@ async function main() {
  await fullProcessing(directoryPath);
 }
 
-main();
+if (require.main === module) {
+ main();
+}