feat(snomed): procedures, medications, conditions good

Refs: #1442

packages/core/src/external/aws/lambda-logic/bundle-to-html.ts

@@ -11,6 +11,7 @@ import {
  Location,
  Medication,
  MedicationStatement,
+ MedicationAdministration,
  Observation,
  Organization,
  Patient,
@@ -38,6 +39,7 @@ export const bundleToHtml = (fhirBundle: Bundle): string => {
  patient,
  medications,
  medicationStatements,
+
  conditions,
  allergies,
  procedures,
@@ -219,7 +221,6 @@ export const bundleToHtml = (fhirBundle: Bundle): string => {
  <div class="divider"></div>
  <div id="mr-sections">
  ${createMedicationSection(medications, medicationStatements)}
-
  ${createConditionSection(conditions, encounters)}
  ${createAllergySection(allergies)}
  ${createProcedureSection(procedures)}
@@ -241,6 +242,7 @@ function extractFhirTypesFromBundle(bundle: Bundle): {
  practitioners: Practitioner[];
  medications: Medication[];
  medicationStatements: MedicationStatement[];
+ medicationAdministrations: MedicationAdministration[];
  conditions: Condition[];
  allergies: AllergyIntolerance[];
  locations: Location[];
@@ -277,6 +279,7 @@ function extractFhirTypesFromBundle(bundle: Bundle): {
  const tasks: Task[] = [];
  const coverages: Coverage[] = [];
  const organizations: Organization[] = [];
+ const medicationAdministrations: MedicationAdministration[] = [];
 
  if (bundle.entry) {
  for (const entry of bundle.entry) {
@@ -285,6 +288,8 @@ function extractFhirTypesFromBundle(bundle: Bundle): {
  patient = resource as Patient;
  } else if (resource?.resourceType === "MedicationStatement") {
  medicationStatements.push(resource as MedicationStatement);
+ } else if (resource?.resourceType === "MedicationAdministration") {
+ medicationAdministrations.push(resource as MedicationAdministration);
  } else if (resource?.resourceType === "Medication") {
  medications.push(resource as Medication);
  } else if (resource?.resourceType === "Condition") {
@@ -345,6 +350,7 @@ function extractFhirTypesFromBundle(bundle: Bundle): {
  diagnosticReports,
  medications,
  medicationStatements,
+ medicationAdministrations,
  conditions,
  allergies,
  locations,

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

@@ -2,12 +2,7 @@ import fs from "fs";
 import path from "path";
 import { getCodeDisplay, getCodeDetailsFull } from "./term-server-api";
 import { populateHashTableFromCodeDetails, SnomedHierarchyTableEntry } from "./snomed-heirarchies";
-import {
- prettyPrintHashTable,
- RemovalStats,
- createInitialRemovalStats,
- prettyPrintRemovalStats,
-} from "./stats";
+import { RemovalStats, createInitialRemovalStats, prettyPrintRemovalStats } from "./stats";
 
 async function processDirectoryOrFile(
  directoryOrFile: string,
@@ -34,8 +29,7 @@ async function processDirectoryOrFile(
 
 async function computeHashTable(
  filePath: string,
- hashTable: Record<string, SnomedHierarchyTableEntry>,
- conditionIdsDictionary: Record<string, Set<string>>
+ hashTable: Record<string, SnomedHierarchyTableEntry>
 ) {
  const data = JSON.parse(fs.readFileSync(filePath, "utf8"));
  const entries = data.bundle ? data.bundle.entry : data.entry;
@@ -50,7 +44,6 @@ async function computeHashTable(
  if (codeDetails) {
  await populateHashTableFromCodeDetails(
  hashTable,
- conditionIdsDictionary,
  codeDetails,
  coding.code,
  resource.id
@@ -62,9 +55,46 @@ async function computeHashTable(
  }
 }
 
-async function processFileEntries(
+async function removeNonRootSnomedCodes(
  filePath: string,
  hashTable: Record<string, SnomedHierarchyTableEntry>,
+ conditionIdsDictionary: Set<string>,
+ allRemainingEnries: Set<string>,
+ removalStats: RemovalStats
+) {
+ const data = JSON.parse(fs.readFileSync(filePath, "utf8"));
+ 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") {
+ conditionIdsDictionary.add(resource.id);
+ const codings = resource.code?.coding || [];
+ for (const coding of codings) {
+ if (coding.system === "http:https://snomed.info/sct") {
+ if (hashTable[coding.code] && !hashTable[coding.code].root) {
+ removalStats.nonSnomedRootCodes.count += 1;
+ removalStats.nonSnomedRootCodes.codes.add(coding.code);
+ console.log("Removing non-root SNOMED code:", coding.code, "Resource.id:", resource.id);
+ 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;
+ }
+ }
+ }
+ }
+ }
+ fs.writeFileSync(filePath, JSON.stringify(data, null, 2), "utf8");
+}
+
+async function removeConditionsProceduresMedAdmins(
+ filePath: string,
+ conditionSet: Set<string>,
  cptSet: Set<string>,
  medicationConditionDict: Record<string, string>,
  allRemainingEnries: Set<string>,
@@ -82,29 +112,22 @@ async function processFileEntries(
 
  for (const coding of codings) {
  if (coding.system === "http:https://snomed.info/sct") {
- hasSnomedCode = true;
- if (hashTable[coding.code] && hashTable[coding.code].inserted) {
+ if (conditionSet.has(coding.code)) {
  removalStats.duplicateCodes.count += 1;
  removalStats.duplicateCodes.codes.add(coding.code);
- entries.splice(i, 1);
- break;
- } else if (hashTable[coding.code] && !hashTable[coding.code].root) {
- removalStats.nonSnomedRootCodes.count += 1;
- removalStats.nonSnomedRootCodes.codes.add(coding.code);
- entries.splice(i, 1);
  break;
  } else {
+ conditionSet.add(coding.code);
  const codeDetails = await getCodeDisplay(coding.code, "SNOMEDCT_US");
  if (codeDetails && codeDetails.category === "disorder") {
- hashTable[coding.code].inserted = true;
+ hasSnomedCode = true;
  const updatedText = `${codeDetails.display} (${codeDetails.category})`;
  resource.code.text = updatedText;
  coding.text = updatedText;
- allRemainingEnries.add(resource.id);
+ break;
  } else {
  removalStats.nonDisorderCodes.count += 1;
  removalStats.nonDisorderCodes.codes.add(coding.code);
- entries.splice(i, 1);
  break;
  }
  }
@@ -122,20 +145,27 @@ async function processFileEntries(
  if (coding.system === "http:https://www.ama-assn.org/go/cpt") {
  const cptCode = parseInt(coding.code, 10);
  if (cptCode >= 10004 && cptCode <= 69990) {
- hasValidCptCode = true;
  if (cptSet.has(coding.code)) {
  removalStats.duplicateCptCodes.count += 1;
  removalStats.duplicateCptCodes.codes.add(coding.code);
- entries.splice(i, 1);
+ break;
  } else {
+ hasValidCptCode = true;
+ console.log(
+ "Keeping CPT code:",
+ coding.code,
+ "Resource.id:",
+ resource.id,
+ "hasValidCptCode:",
+ hasValidCptCode
+ );
  cptSet.add(coding.code);
  allRemainingEnries.add(resource.id);
+ break;
  }
- break;
  } else {
  removalStats.invalidCptCodes.count += 1;
  removalStats.invalidCptCodes.codes.add(coding.code);
- entries.splice(i, 1);
  break;
  }
  }
@@ -144,17 +174,15 @@ async function processFileEntries(
  removalStats.entriesWithoutCptCodes.count += 1;
  entries.splice(i, 1);
  }
- } else if (
- resource &&
- resource.resourceType === "MedicationAdministration" &&
- resource.reasonReference
- ) {
- const medicationRef = resource.medicationReference?.reference.split("/")[1];
- const conditionRef = resource.reasonReference[0]?.reference.split("/")[1];
+ } else if (resource && resource.resourceType === "MedicationAdministration") {
+ if (resource.reasonReference) {
+ const medicationRef = resource.medicationReference?.reference.split("/")[1];
+ const conditionRef = resource.reasonReference[0]?.reference.split("/")[1];
 
- if (medicationRef && conditionRef) {
- medicationConditionDict[medicationRef] = conditionRef;
- allRemainingEnries.add(resource.id);
+ if (medicationRef && conditionRef) {
+ medicationConditionDict[medicationRef] = conditionRef;
+ allRemainingEnries.add(resource.id);
+ }
  } else {
  console.log("Removing MedicationAdministration entry without condition reference");
  entries.splice(i, 1);
@@ -166,7 +194,7 @@ async function processFileEntries(
 
 async function filterMedicationsEntries(
  filePath: string,
- allRemainingEnries: Set<string>,
+ conditionIdsDictionary: Set<string>,
  medicationConditionDict: Record<string, string>,
  rxNormSet: Set<string>,
  removalStats: RemovalStats
@@ -179,7 +207,9 @@ async function filterMedicationsEntries(
  const resource = entry.resource;
  if (resource && resource.resourceType === "Medication") {
  const conditionRef = medicationConditionDict[resource.id];
- if (allRemainingEnries.has(conditionRef)) {
+
+ // if the medication is linked to a conditon that is a non-duplicate disorder
+ if (conditionIdsDictionary.has(conditionRef)) {
  const codings = resource.code?.coding || [];
  for (const coding of codings) {
  if (coding.system === "http:https://www.nlm.nih.gov/research/umls/rxnorm") {
@@ -189,7 +219,14 @@ async function filterMedicationsEntries(
  entries.splice(i, 1);
  } else {
  rxNormSet.add(coding.code);
- allRemainingEnries.add(resource.id);
+ console.log(
+ "Keeping Medication. RXNORM code:",
+ coding.code,
+ "linked to condition:",
+ conditionRef,
+ "Resource.id:",
+ resource.id
+ );
  }
  }
  }
@@ -208,42 +245,54 @@ async function main() {
  console.error("Please provide a directory path as an argument.");
  process.exit(1);
  }
- const hashTable: Record<string, SnomedHierarchyTableEntry> = {};
- const conditionIdsDictionary: Record<string, Set<string>> = {};
 
- await processDirectoryOrFile(directoryPath, async filePath => {
- await computeHashTable(filePath, hashTable, conditionIdsDictionary);
- });
-
- const filteredConditionIdsDictionary = Object.fromEntries(
- Object.entries(conditionIdsDictionary).filter(([, value]) => value.size > 0)
- );
- console.log("conditionIdsDictionary", filteredConditionIdsDictionary);
-
- prettyPrintHashTable(hashTable);
  const removalStats = createInitialRemovalStats();
 
+ // Removal of non-disorder SNOMED codes, invalid CPT codes, and duplicate CPT codes
  const cptSet = new Set<string>();
- const medicationConditionDict: Record<string, string> = {};
-
+ const conditionsSet = new Set<string>();
  const allRemainingEnries = new Set<string>();
+ const medicationConditionDict: Record<string, string> = {}; // a mapping of all medications to conditions
  await processDirectoryOrFile(directoryPath, async filePath => {
- await processFileEntries(
+ await removeConditionsProceduresMedAdmins(
  filePath,
- hashTable,
+ conditionsSet,
  cptSet,
  medicationConditionDict,
  allRemainingEnries,
  removalStats
  );
  });
 
- const rxNormSet = new Set<string>();
+ prettyPrintRemovalStats(removalStats);
 
+ // Create hierarchy of SNOMED codes
+ const hashTable: Record<string, SnomedHierarchyTableEntry> = {};
  await processDirectoryOrFile(directoryPath, async filePath => {
- await filterMedicationsEntries(
+ await computeHashTable(filePath, hashTable);
+ });
+
+ // Remove non-root SNOMED codes
+ const conditionIdsDictionary = new Set<string>();
+ await processDirectoryOrFile(directoryPath, async filePath => {
+ await removeNonRootSnomedCodes(
  filePath,
+ hashTable,
  allRemainingEnries,
+ conditionIdsDictionary,
+ removalStats
+ );
+ });
+
+ console.log("conditionIdsDictionary", conditionIdsDictionary);
+ console.log("medicationConditionDict", medicationConditionDict);
+
+ // Removal of duplicate RXNORM codes and medications without condition reference
+ const rxNormSet = new Set<string>();
+ await processDirectoryOrFile(directoryPath, async filePath => {
+ await filterMedicationsEntries(
+ filePath,
+ conditionIdsDictionary,
  medicationConditionDict,
  rxNormSet,
  removalStats