feat(snomed): adding special snomed bundle to html

Refs: #1442

packages/fhir-converter/src/templates/cda/Resources/Condition.hbs

@@ -9,7 +9,6 @@
  {{>DataType/Identifier.hbs id=this}},
  {{/each}}
  ],
- "verificationStatus": {{ProvisionalStatus}},
  "clinicalStatus": {
  "coding": 
  [

packages/fhir-converter/src/templates/cda/Sections/Hospital_Discharge_Medications.hbs

@@ -74,7 +74,7 @@
  {{#if medAdm.substanceAdministration.precondition}}
  {{#each (toArray medAdm.substanceAdministration.precondition) as |precondition|}}
  {{#if precondition.criterion.value.code}}
- {{>Resources/Condition.hbs conditionEntry=precondition.criterion ProvisionalStatus="true" ID=(generateUUID (toJsonString precondition.criterion))}},
+ {{>Resources/Condition.hbs conditionEntry=precondition.criterion ID=(generateUUID (toJsonString precondition.criterion))}},
  {{>References/MedicationAdministration/reasonReference.hbs ID=(generateUUID (toJsonString medAdm.substanceAdministration)) REF=(concat 'Condition/' (generateUUID (toJsonString precondition.criterion)))}},
  {{/if}}
  {{/each}}

packages/fhir-converter/src/templates/cda/Sections/Medication.hbs

@@ -48,7 +48,7 @@
  {{#if medEntry.substanceAdministration.precondition}}
  {{#each (toArray medEntry.substanceAdministration.precondition) as |precondition|}}
  {{#if precondition.criterion.value.code}}
- {{>Resources/Condition.hbs conditionEntry=precondition.criterion ProvisionalStatus="true" ID=(generateUUID (toJsonString criterion.value))}},
+ {{>Resources/Condition.hbs conditionEntry=precondition.criterion ID=(generateUUID (toJsonString criterion.value))}},
  {{>References/MedicationStatement/reasonReference.hbs ID=(generateUUID (toJsonString medEntry.substanceAdministration)) REF=(concat 'Condition/' (generateUUID (toJsonString criterion.value)))}},
  {{/if}}
  {{/each}}

packages/utils/src/customer-requests/convert-html-to-csv.ts

@@ -113,24 +113,22 @@ export function convertHtmlTablesToCsv(html: string) {
 }
 
 function main() {
- const filePath = process.argv[2]; // Get the file path from command line arguments
+ const filePath = process.argv[2];
 
  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
+ const htmlContent = readFileSync(filePath, "utf8");
+ const csvContent = convertHtmlTablesToCsv(htmlContent);
 
- // 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
@@ -139,7 +137,6 @@ function main() {
  }
 }
 
-// Call main if this script is run directly
 if (require.main === module) {
  main();
 }

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

@@ -3,7 +3,7 @@
 // The script makes consolidated queries, inserts a patient FHIR resource, and then calls the filtering
 // and MR generation logic.
 
-import { bundleToHtml } from "@metriport/core/external/aws/lambda-logic/bundle-to-html";
+import { bundleToHtml } from "@metriport/core/external/aws/lambda-logic/bundle-to-html-snomed";
 import fs from "fs/promises";
 import { convertHtmlTablesToCsv } from "./convert-html-to-csv";
 import * as path from "path";

packages/utils/src/customer-requests/medical-records-local.ts

@@ -1,7 +1,6 @@
 import { bundleToHtml } from "@metriport/core/external/aws/lambda-logic/bundle-to-html";
 import fs from "fs";
 
-// 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);
@@ -11,10 +10,8 @@ const filePath = process.argv[2];
 const bundle = fs.readFileSync(filePath, "utf8");
 const bundleParsed = JSON.parse(bundle);
 
-// FHIR Bundle
 const html = bundleToHtml(bundleParsed);
 
-// Determine the output file name by replacing .json with .html
 const outputFilePath = filePath.replace(".json", ".html");
 
 fs.writeFileSync(outputFilePath, html);

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

@@ -240,7 +240,7 @@ export async function fullProcessing(directoryPath: string) {
  const cptSet = new Set<string>();
  const conditionsSet = new Set<string>();
  const allRemainingEnries = new Set<string>();
- const medicationConditionDict: Record<string, string> = {}; // a mapping of all medications to conditions
+ const medicationConditionDict: Record<string, string> = {};
  await processDirectoryOrFile(directoryPath, async filePath => {
  await removeConditionsProceduresMedAdmins(
  filePath,

packages/utils/src/terminology-server/snomed-heirarchies.ts

@@ -45,7 +45,6 @@ async function populateChildrenRecursively(
  await Promise.all(childPromises);
  }
  } else {
- // this is either a code
  if (hashTable[childCode].found) {
  console.log(`Downgrading ${childCode} to non-root (child)`);
  hashTable[childCode] = { ...hashTable[childCode], root: false };

packages/utils/src/terminology-server/term-server-api.ts

@@ -1,21 +1,34 @@
 import axios from "axios";
 
-interface ParameterPart {
+type ParameterPart = {
  name: string;
  valueCode?: string;
  valueString?: string;
-}
+};
 
-interface Parameter {
+type Parameter = {
  name: string;
  valueString?: string;
  part?: ParameterPart[];
-}
+};
 
-interface CodeSystemUrl {
+type CodeSystemUrl = {
  name: string;
  url: string;
-}
+};
+
+export type CodeDetailsResponse = {
+ parameter: {
+ name: string;
+ part: [
+ {
+ name: string;
+ value?: string;
+ valueCode?: string;
+ }
+ ];
+ }[];
+};
 
 export const codeSystemUrls: Record<string, CodeSystemUrl> = {
  SNOMEDCT_US: {
@@ -48,19 +61,6 @@ export const codeSystemUrls: Record<string, CodeSystemUrl> = {
  },
 };
 
-export type CodeDetailsResponse = {
- parameter: {
- name: string;
- part: [
- {
- name: string;
- value?: string;
- valueCode?: string;
- }
- ];
- }[];
-};
-
 export async function getCodeDetailsFull(
  code: string,
  codeSystemType: string
@@ -80,7 +80,6 @@ export async function getCodeDetailsFull(
  console.error("Connection refused. The server is not reachable at the moment.");
  return undefined;
  } else {
- // console.error(`Error fetching code details. Code Not Found ${code}`);
  return undefined;
  }
  }
@@ -102,12 +101,11 @@ export async function getCodeDisplay(
 
  const displayParameter = response.data.parameter.find((p: Parameter) => p.name === "display");
  if (displayParameter && displayParameter.valueString) {
- // Extract the display text and category using a regular expression
  const match = displayParameter.valueString.match(/^(.+?)\s*\(([^)]+)\)$/);
  if (match) {
  return {
- display: match[1].trim(), // "Domestic abuse of adult"
- category: match[2].trim(), // "event"
+ display: match[1].trim(),
+ category: match[2].trim(),
  };
  } else {
  console.log("Display field format not recognized.");