feat(snomed): cx specific workflow

Refs: #1442
metriport · jonahkaye · Feb 23, 2024 · Mar 6, 2024 · Mar 26, 2024 · Mar 27, 2024
commit 9dfda6ce3184a9fa596b347a4bcec8fcbb9abd2a
diff --git a/packages/core/src/external/aws/lambda-logic/bundle-to-html.ts b/packages/core/src/external/aws/lambda-logic/bundle-to-html.ts
@@ -36,33 +36,18 @@ const CPT_CODE = "cpt";
 export const bundleToHtml = (fhirBundle: Bundle): string => {
  const {
  patient,
- practitioners,
- diagnosticReports,
  medications,
  medicationStatements,
  conditions,
  allergies,
- locations,
  procedures,
- observationOther,
- observationSocialHistory,
- observationVitals,
- observationLaboratory,
  encounters,
- immunizations,
- familyMemberHistories,
- relatedPersons,
- tasks,
- coverages,
- organizations,
  } = extractFhirTypesFromBundle(fhirBundle);
 
  if (!patient) {
  throw new Error("No patient found in bundle");
  }
 
- const aweVisits = getAnnualWellnessVisits(conditions);
-
  const htmlPage = `
  <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http:https://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
  <html xmlns="http:https://www.w3.org/1999/xhtml" xml:lang="en">
@@ -233,27 +218,11 @@ export const bundleToHtml = (fhirBundle: Bundle): string => {
  ${createMRHeader(patient)}
  <div class="divider"></div>
  <div id="mr-sections">
- ${createAWESection(diagnosticReports, practitioners, aweVisits, organizations)}
  ${createMedicationSection(medications, medicationStatements)}
- ${createDiagnosticReportsSection(
- diagnosticReports,
- practitioners,
- aweVisits,
- organizations
- )}
+
  ${createConditionSection(conditions, encounters)}
  ${createAllergySection(allergies)}
  ${createProcedureSection(procedures)}
- ${createObservationSocialHistorySection(observationSocialHistory)}
- ${createObservationVitalsSection(observationVitals)}
- ${createObservationLaboratorySection(observationLaboratory)}
- ${createOtherObservationsSection(observationOther)}
- ${createImmunizationSection(immunizations)}
- ${createFamilyHistorySection(familyMemberHistories)}
- ${createRelatedPersonSection(relatedPersons)}
- ${createTaskSection(tasks)}
- ${createCoverageSection(coverages, organizations)}
- ${createEncountersSection(encounters, locations)}
  </div>
  </body>
  </html>
@@ -435,12 +404,6 @@ function createMRHeader(patient: Patient) {
  <h4>Table of Contents</h4>
  <ul id="nav">
  <div class='half'>
- <li>
- <a href="#awe">Annual Wellness Exams</a>
- </li>
- <li>
- <a href="#reports">Reports</a>
- </li>
  <li>
  <a href="#medications">Medications</a>
  </li>
@@ -455,39 +418,7 @@ function createMRHeader(patient: Patient) {
  >Procedures</a
  >
  </li>
- <li>
- <a href="#social-history">Social History</a>
- </li>
- <li>
- <a href="#vitals">Vitals</a>
- </li>
- </div>
- <div class='half'>
- <li>
- <a href="#laboratory">Laboratory</a>
- </li>
- <li>
- <a href="#other-observations">Other Observations</a>
- </li>
- <li>
- <a href="#immunizations">Immunizations</a>
- </li>
- <li>
- <a href="#family-member-history">Family Member History</a>
- </li>
- <li>
- <a href="#related-persons">Related Persons</a>
- </li>
- <li>
- <a href="#tasks">Tasks</a>
- </li>
- <li>
- <a href="#coverage">Coverage</a>
- </li>
- <li>
- <a href="#encounters">Encounters</a>
- </li>
- </div>
+
  </ul>
  </div>
  </div>
@@ -521,7 +452,7 @@ type EncounterSection = {
  };
 };
 
-function createAWESection(
+export function createAWESection(
  diagnosticReports: DiagnosticReport[],
  practitioners: Practitioner[],
  aweVisits: Condition[],
@@ -563,7 +494,7 @@ function createAWESection(
  `;
 }
 
-function createDiagnosticReportsSection(
+export function createDiagnosticReportsSection(
  diagnosticReports: DiagnosticReport[],
  practitioners: Practitioner[],
  aweVisits: Condition[],
@@ -969,9 +900,9 @@ function createConditionSection(conditions: Condition[], encounter: Encounter[])
  return aDate === bDate && aText === bText;
  })
  .reduce((acc, condition) => {
- const codeName = getSpecificCode(condition.code?.coding ?? [], [ICD_10_CODE, SNOMED_CODE]);
+ const codeName = getSpecificCode(condition.code?.coding ?? [], [SNOMED_CODE, ICD_10_CODE]);
  const idc10Code = condition.code?.coding?.find(code =>
- code.system?.toLowerCase().includes(ICD_10_CODE)
+ code.system?.toLowerCase().includes(SNOMED_CODE)
  );
 
  const name =
@@ -1286,7 +1217,7 @@ type RenderObservation = {
  lastDate: string;
 };
 
-function createObservationSocialHistorySection(observations: Observation[]) {
+export function createObservationSocialHistorySection(observations: Observation[]) {
  if (!observations) {
  return "";
  }
@@ -1417,7 +1348,7 @@ function renderSocialHistoryValue(observation: Observation) {
  }
 }
 
-function createObservationVitalsSection(observations: Observation[]) {
+export function createObservationVitalsSection(observations: Observation[]) {
  if (!observations) {
  return "";
  }
@@ -1501,7 +1432,7 @@ function renderVitalsValue(observation: Observation) {
  }
 }
 
-function createObservationLaboratorySection(observations: Observation[]) {
+export function createObservationLaboratorySection(observations: Observation[]) {
  if (!observations) {
  return "";
  }
@@ -1607,7 +1538,7 @@ function createObservationsByDate(observations: Observation[]): string {
  .join("");
 }
 
-function createOtherObservationsSection(observations: Observation[]) {
+export function createOtherObservationsSection(observations: Observation[]) {
  if (!observations) {
  return "";
  }
@@ -1728,7 +1659,7 @@ function renderClassDisplay(encounter: Encounter) {
  }
 }
 
-function createImmunizationSection(immunizations: Immunization[]) {
+export function createImmunizationSection(immunizations: Immunization[]) {
  if (!immunizations) {
  return "";
  }
@@ -1787,7 +1718,7 @@ function createImmunizationSection(immunizations: Immunization[]) {
  return createSection("Immunizations", immunizationTableContents);
 }
 
-function createFamilyHistorySection(familyMemberHistories: FamilyMemberHistory[]) {
+export function createFamilyHistorySection(familyMemberHistories: FamilyMemberHistory[]) {
  if (!familyMemberHistories) {
  return "";
  }
@@ -1867,7 +1798,7 @@ function renderAdministrativeGender(familyMemberHistory: FamilyMemberHistory): s
  return null;
 }
 
-function createRelatedPersonSection(relatedPersons: RelatedPerson[]) {
+export function createRelatedPersonSection(relatedPersons: RelatedPerson[]) {
  if (!relatedPersons) {
  return "";
  }
@@ -1937,7 +1868,7 @@ function renderRelatedPersonAddresses(relatedPerson: RelatedPerson) {
  });
 }
 
-function createTaskSection(tasks: Task[]) {
+export function createTaskSection(tasks: Task[]) {
  if (!tasks) {
  return "";
  }
@@ -1999,7 +1930,7 @@ function createTaskSection(tasks: Task[]) {
  return createSection("Tasks", taskTableContents);
 }
 
-function createEncountersSection(encounters: Encounter[], locations: Location[]) {
+export function createEncountersSection(encounters: Encounter[], locations: Location[]) {
  const mappedLocations = mapResourceToId<Location>(locations);
 
  if (!encounters) {
@@ -2061,7 +1992,7 @@ function createEncountersSection(encounters: Encounter[], locations: Location[])
  return createSection("Encounters", encounterTableContents);
 }
 
-function createCoverageSection(coverages: Coverage[], organizations: Organization[]) {
+export function createCoverageSection(coverages: Coverage[], organizations: Organization[]) {
  if (!coverages) {
  return "";
  }
@@ -2195,7 +2126,7 @@ function mapResourceToId<ResourceType>(resources: Resource[]): Record<string, Re
 }
 
 // find condition with code Z00 in the past year
-function getAnnualWellnessVisits(conditions: Condition[]) {
+export function getAnnualWellnessVisits(conditions: Condition[]) {
  const annualWellnessVisit = conditions.filter(condition => {
  const code = getSpecificCode(condition.code?.coding ?? [], [ICD_10_CODE]);
 

@@ -1,5 +1,6 @@
 import { DOMParser } from "xmldom";
-
+import { readFileSync, writeFileSync } from "fs";
+import * as path from "path";
 // This is temporary function that will eventually be introduced
 // as another way to render patient data. (Will need refactoring)
 export function convertHtmlTablesToCsv(html: string) {
@@ -110,3 +111,35 @@ export function convertHtmlTablesToCsv(html: string) {
 
  return convertedCsv;
 }
+
+function main() {
+ const filePath = process.argv[2]; // Get the file path from command line arguments
+
+ if (!filePath) {
+ console.error("Please provide an HTML file path.");
+ process.exit(1);
+ }
+
+ try {
+ const htmlContent = readFileSync(filePath, "utf8"); // Read the HTML file content
+ const csvContent = convertHtmlTablesToCsv(htmlContent); // Convert HTML to CSV
+
+ // Construct the CSV file path by changing the extension
+ const csvFilePath = path.join(
+ path.dirname(filePath),
+ path.basename(filePath, path.extname(filePath)) + ".csv"
+ );
+
+ // Write the CSV content to the new file
+ writeFileSync(csvFilePath, csvContent);
+ console.log(`CSV file has been created at: ${csvFilePath}`);
+ // eslint-disable-next-line
+ } catch (error: any) {
+ console.error("Error processing the HTML file:", error.message);
+ }
+}
+
+// Call main if this script is run directly
+if (require.main === module) {
+ main();
+}
@@ -1,15 +1,21 @@
 import { bundleToHtml } from "@metriport/core/external/aws/lambda-logic/bundle-to-html";
 import fs from "fs";
 
-// get xml file from this folder and bundle to html
+// Check if a file path is provided
+if (process.argv.length < 3) {
+ console.log("Usage: node medical-records-local.js <path-to-json-file>");
+ process.exit(1);
+}
 
-const bundle = fs.readFileSync("test-bundle.json", "utf8");
+const filePath = process.argv[2];
+const bundle = fs.readFileSync(filePath, "utf8");
 const bundleParsed = JSON.parse(bundle);
 
 // FHIR Bundle
 const html = bundleToHtml(bundleParsed);
 
-// Response from FHIR Converter
-// const html = bundleToHtml(bundleParsed.fhirResource);
+// Determine the output file name by replacing .json with .html
+const outputFilePath = filePath.replace(".json", ".html");
 
-fs.writeFileSync("test.html", html);
+fs.writeFileSync(outputFilePath, html);
+console.log(`HTML file created at ${outputFilePath}`);
diff --git a/packages/utils/src/document/document-query-progress/test-conversion-load.ts b/packages/utils/src/document/document-query-progress/test-conversion-load.ts
@@ -80,7 +80,6 @@ async function main() {
  }
 
  await Promise.all(promises);
-
  } catch (error) {
  console.error("Error", error);
  }

diff --git a/packages/utils/src/document/document-query-progress/validate-doc-query-progress.ts b/packages/utils/src/document/document-query-progress/validate-doc-query-progress.ts
@@ -31,7 +31,6 @@ dayjs.extend(duration);
  * the ones seen in ./patients.
  */
 
-
 const apiKey = getEnvVarOrFail("API_KEY");
 const apiUrl = getEnvVarOrFail("API_URL");
 const cxId = getEnvVarOrFail("CX_ID");
@@ -127,7 +126,9 @@ const validateDocQueryProgress = async (
  console.log(
  `The doc query was completed for all patients${
  resetAndRunAgain ? " (resetAndRunAgain)" : ""
- } - status were all queries successful: ${overallSuccess}. Errors: ${failedPatientQueries.length}`,
+ } - status were all queries successful: ${overallSuccess}. Errors: ${
+ failedPatientQueries.length
+ }`
  );
 };
 

@@ -3,6 +3,16 @@ import path from "path";
 import { getCodeDetails } from "./term-server-api";
 
 const processDirectory = async (directory: string) => {
+ // Check if the path is a directory or a file
+ const stat = fs.statSync(directory);
+ if (stat.isFile()) {
+ // If it's a file, process it directly
+ if (directory.endsWith(".json")) {
+ await processFile(directory);
+ }
+ return; // Exit the function as there's nothing more to do for a file
+ }
+
  const items = fs.readdirSync(directory, { withFileTypes: true });
 
  for (const item of items) {
@@ -11,7 +21,7 @@ const processDirectory = async (directory: string) => {
  if (item.isDirectory()) {
  // Recursively process the subdirectory
  await processDirectory(sourcePath);
- } else if (item.isFile() && item.name.endsWith(".xml.json")) {
+ } else if (item.isFile() && item.name.endsWith(".json")) {
  await processFile(sourcePath);
  }
  }
@@ -22,8 +32,10 @@ const processFile = async (filePath: string) => {
  const data = JSON.parse(fs.readFileSync(filePath, "utf8"));
  const encounteredCodes = new Set();
 
- for (let i = data.entry.length - 1; i >= 0; i--) {
- const entry = data.entry[i];
+ const entries = data.bundle ? data.bundle.entry : data.entry;
+
+ for (let i = entries.length - 1; i >= 0; i--) {
+ const entry = entries[i];
  const resource = entry.resource;
  if (resource && resource.resourceType === "Condition") {
  const codings = resource.code?.coding || [];
@@ -32,7 +44,7 @@ const processFile = async (filePath: string) => {
  if (coding.system === snomedSystemUrl) {
  if (encounteredCodes.has(coding.code)) {
  console.log(`Removing duplicate code ${coding.code} from ${path.basename(filePath)}`);
- data.entry.splice(i, 1);
+ entries.splice(i, 1);
  } else {
  encounteredCodes.add(coding.code);
  const codeDetails = await getCodeDetails(coding.code, "SNOMEDCT_US");