feat(snomed): conditions and procedures duplications

Refs: #1442

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

@@ -52,40 +52,72 @@ async function computeHashTable(filePath: string, hashTable: Record<string, Hash
 
 async function processFileEntries(filePath: string, hashTable: Record<string, HashTableEntry>) {
  const data = JSON.parse(fs.readFileSync(filePath, "utf8"));
- const encounteredCodes = new Set();
  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 || [];
+ let hasSnomedCode = false;
+
  for (const coding of codings) {
  if (coding.system === "http:https://snomed.info/sct") {
- if (encounteredCodes.has(coding.code)) {
+ hasSnomedCode = true;
+ if (hashTable[coding.code] && hashTable[coding.code].inserted) {
  console.log(`Removing duplicate code ${coding.code} from ${path.basename(filePath)}`);
  entries.splice(i, 1);
+ break;
  } else if (hashTable[coding.code] && !hashTable[coding.code].root) {
  console.log(`Removing non-root code ${coding.code} from ${path.basename(filePath)}`);
  entries.splice(i, 1);
+ break;
  } else {
- encounteredCodes.add(coding.code);
+ hashTable[coding.code].inserted = true;
  const codeDetails = await getCodeDetails(coding.code, "SNOMEDCT_US");
- if (codeDetails && codeDetails.display) {
- if (codeDetails.category == "disorder") {
- // console.log(`Identified disorder for ${coding.code}`);
+ if (codeDetails) {
+ if (codeDetails.category !== "disorder") {
+ console.log(
+ `Removing non-disorder code ${coding.code} from ${path.basename(filePath)}`
+ );
+ entries.splice(i, 1);
+ break;
+ } else {
+ const updatedText = `${codeDetails.display} (${codeDetails.category})`;
+ resource.code.text = updatedText;
+ coding.text = updatedText;
  }
- const updatedText = `${codeDetails.display} (${codeDetails.category})`;
- resource.code.text = updatedText;
- coding.text = updatedText;
  }
  }
  }
  }
+ if (!hasSnomedCode) {
+ console.log(`Removing entry without SNOMED codes from ${path.basename(filePath)}`);
+ entries.splice(i, 1);
+ }
+ } else if (resource && resource.resourceType === "Procedure") {
+ const codings = resource.code?.coding || [];
+ let hasValidCptCode = false;
+
+ for (const coding of codings) {
+ if (coding.system === "http:https://www.ama-assn.org/go/cpt") {
+ const cptCode = parseInt(coding.code, 10);
+ if (cptCode >= 10004 && cptCode <= 69990) {
+ hasValidCptCode = true;
+ break;
+ }
+ }
+ }
+ if (!hasValidCptCode) {
+ console.log(
+ `Removing procedure entry with invalid or missing CPT code from ${path.basename(
+ filePath
+ )}`
+ );
+ entries.splice(i, 1);
+ }
  }
  }
-
- // Write the updated data back to the same file
  fs.writeFileSync(filePath, JSON.stringify(data, null, 2), "utf8");
 }
 
@@ -96,7 +128,7 @@ async function main() {
  process.exit(1);
  }
  const hashTable: Record<string, HashTableEntry> = {};
- // call compute hash table and then after thats done call process file entries
+
  await processDirectoryOrFile(directoryPath, async filePath => {
  await computeHashTable(filePath, hashTable);
  });

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

@@ -3,6 +3,7 @@ export type HashTableEntry = {
  children: Set<string>;
  parents: Set<string>;
  root: boolean;
+ inserted: boolean;
 };
 
 export type CodeDetailsResponse = {
@@ -44,7 +45,13 @@ export async function populateHashTableFromCodeDetails(
  hashTable[queriedCode] = { ...hashTable[queriedCode], found: true, root: false };
  }
  } else {
- hashTable[queriedCode] = { found: true, parents: new Set(), children: new Set(), root: true };
+ hashTable[queriedCode] = {
+ found: true,
+ parents: new Set(),
+ children: new Set(),
+ root: true,
+ inserted: false,
+ };
  codeDetails.parameter.forEach(param => {
  if (param.name === "property") {
  const valuePart = param.part.find(part => part.name === "value");
@@ -61,6 +68,7 @@ export async function populateHashTableFromCodeDetails(
  parents: new Set(),
  children: new Set(),
  root: false,
+ inserted: false,
  };
  hashTable[queriedCode].parents.add(value);
  // having children indicates your a parent node
@@ -75,6 +83,7 @@ export async function populateHashTableFromCodeDetails(
  parents: new Set(),
  children: new Set(),
  root: false,
+ inserted: false,
  };
  hashTable[queriedCode].children.add(value);
  // having parents indicates your a chilld node