feat(snomed): precondition analysis

Refs: #1442

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

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

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

@@ -71,7 +71,14 @@
  {{/with}}
  {{/if}}
  {{/each}}
-
+ {{#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))}},
+ {{>References/MedicationAdministration/reasonReference.hbs ID=(generateUUID (toJsonString medAdm.substanceAdministration)) REF=(concat 'Condition/' (generateUUID (toJsonString precondition.criterion)))}},
+ {{/if}}
+ {{/each}}
+ {{/if}}
  {{/each}} 
  {{/each}}
  {{/with}}

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

@@ -42,7 +42,15 @@
  {{/with}}
  {{/if}}
  {{/if}}
-
+
+ {{/each}}
+ {{/if}}
+ {{#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))}},
+ {{>References/MedicationStatement/reasonReference.hbs ID=(generateUUID (toJsonString medEntry.substanceAdministration)) REF=(concat 'Condition/' (generateUUID (toJsonString criterion.value)))}},
+ {{/if}}
  {{/each}}
  {{/if}}
 

packages/utils/src/customer-requests/consolidated-query.ts

@@ -5,7 +5,7 @@ import { getEnvVarOrFail } from "@metriport/core/util/env-var";
 const apiKey = getEnvVarOrFail("API_KEY");
 const metriportApi: MetriportMedicalApi = new MetriportMedicalApi(apiKey);
 
-const patientIds: string[] = ["patient1", "patient2", "patient3"];
+const patientIds: string[] = [""];
 const resultsDirectory = "./consolidatedPatients";
 
 const ensureDirectory = async (): Promise<void> => {

packages/utils/src/customer-requests/medical-records-and-csvs.ts → packages/utils/src/customer-requests/full-snomed-pipeline.ts

@@ -2,9 +2,12 @@ import { bundleToHtml } from "@metriport/core/external/aws/lambda-logic/bundle-t
 import fs from "fs";
 import { convertHtmlTablesToCsv } from "./convert-html-to-csv";
 import * as path from "path";
+import { fullProcessing } from "../terminology-server/snomed-dedup-and-filter";
 
 // Function to process each JSON file
-function processFile(filePath: string) {
+async function processFile(filePath: string) {
+ await fullProcessing(filePath);
+
  const bundle = fs.readFileSync(filePath, "utf8");
  const bundleParsed = JSON.parse(bundle);
 
@@ -22,7 +25,7 @@ function processFile(filePath: string) {
 }
 
 // Main function to iterate through the directory
-function main() {
+async function main() {
  const targetPath = process.argv[2];
 
  if (!targetPath) {
@@ -31,12 +34,12 @@ function main() {
  }
 
  const files = fs.readdirSync(targetPath);
- files.forEach(file => {
+ for (const file of files) {
  const fullPath = path.join(targetPath, file);
  if (path.extname(fullPath) === ".json") {
- processFile(fullPath);
+ await processFile(fullPath);
  }
- });
+ }
 }
 
 main();

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

@@ -0,0 +1,80 @@
+import fs from "fs";
+import path from "path";
+import { getCodeDisplay } from "./term-server-api";
+
+function processDirectory(
+ directoryPath: string,
+ hashTable: { [key: string]: number },
+ totalConditionCounts: { count: number }
+) {
+ const filesAndDirectories = fs.readdirSync(directoryPath);
+
+ for (const name of filesAndDirectories) {
+ const currentPath = path.join(directoryPath, name);
+ const stat = fs.statSync(currentPath);
+
+ if (stat.isDirectory()) {
+ processDirectory(currentPath, hashTable, totalConditionCounts);
+ } else if (name.endsWith(".json")) {
+ processFile(currentPath, hashTable, totalConditionCounts);
+ }
+ }
+}
+
+function processFile(
+ filePath: string,
+ hashTable: { [key: string]: number },
+ totalConditionCounts: { count: number }
+) {
+ const data = JSON.parse(fs.readFileSync(filePath, "utf8"));
+ if (data.resourceType === "Bundle" && data.type === "batch") {
+ for (const entry of data.entry) {
+ if (
+ entry.resource?.resourceType === "Condition" &&
+ entry.resource.verificationStatus === true
+ ) {
+ const codeInfo = entry.resource.code;
+ const code = codeInfo.coding[0].code;
+ if (hashTable[code]) {
+ hashTable[code] += 1;
+ } else {
+ hashTable[code] = 1;
+ }
+ }
+ totalConditionCounts.count += 1;
+ }
+ }
+}
+
+async function main() {
+ const directoryPath = process.argv[2];
+ if (!directoryPath) {
+ console.error("Please provide a directory path as an argument.");
+ process.exit(1);
+ }
+
+ const hashTable: { [key: string]: number } = {};
+ const totalConditionCount = { count: 0 };
+ processDirectory(directoryPath, hashTable, totalConditionCount);
+
+ let disorderCount = 0;
+ for (const code of Object.keys(hashTable)) {
+ const codeDetails = await getCodeDisplay(code, "SNOMEDCT_US");
+ if (codeDetails && codeDetails.category === "disorder") {
+ console.log(
+ `${code} with count ${hashTable[code]} is a disorder: ${codeDetails.display} (${codeDetails.category})`
+ );
+ disorderCount += hashTable[code];
+ }
+ }
+
+ const totalCount = Object.values(hashTable).reduce((acc, count) => acc + count, 0);
+
+ console.log(`Total #of Conditions in the directory: ${totalConditionCount.count}`);
+ console.log(`Total #of Conditions generated from <Precondition> in the directory: ${totalCount}`);
+ console.log(
+ `Total #of Conditions generated from <Precondition> in the directory of type disorder: ${disorderCount}`
+ );
+}
+
+main();

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

@@ -75,7 +75,6 @@ async function removeNonRootSnomedCodes(
  entries.splice(i, 1);
  break;
  } else {
- console.log("Keeping SNOMED code:", coding.code, "Resource.id:", resource.id);
  hashTable[coding.code].inserted = true;
  allRemainingEnries.add(resource.id);
  break;
@@ -234,13 +233,7 @@ async function filterMedicationsEntries(
  fs.writeFileSync(filePath, JSON.stringify(data, null, 2), "utf8");
 }
 
-async function main() {
- const [directoryPath] = process.argv.slice(2);
- if (!directoryPath) {
- console.error("Please provide a directory path as an argument.");
- process.exit(1);
- }
-
+export async function fullProcessing(directoryPath: string) {
  const removalStats = createInitialRemovalStats();
 
  // Removal of non-disorder SNOMED codes, invalid CPT codes, and duplicate CPT codes
@@ -297,4 +290,13 @@ async function main() {
  prettyPrintRemovalStats(removalStats);
 }
 
+async function main() {
+ const [directoryPath] = process.argv.slice(2);
+ if (!directoryPath) {
+ console.error("Please provide a directory path as an argument.");
+ process.exit(1);
+ }
+ await fullProcessing(directoryPath);
+}
+
 main();

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

@@ -122,7 +122,6 @@ export async function getCodeDisplay(
  console.error("Connection refused. The server is not reachable at the moment.");
  return undefined;
  } else {
- console.error("Error fetching code details. Code Not Found");
  return undefined;
  }
  }