Add 99717-49 Local Code to 76030-6 LOINC mapping

etor/src/main/java/gov/hhs/cdc/trustedintermediary/etor/ruleengine/transformation/custom/MapLocalObservationCodes.java

@@ -23,52 +23,68 @@
 public class MapLocalObservationCodes implements CustomFhirTransformation {
     protected final Logger logger = ApplicationContext.getImplementation(Logger.class);
 
-    private HashMap<String, IdentifierCode> codingMap;
-
-    public MapLocalObservationCodes() {
-        initMap();
-    }
-
     @Override
     public void transform(HealthData<?> resource, Map<String, Object> args) {
+        var codingMap = getMapFromArgs(args);
+
         var bundle = (Bundle) resource.getUnderlyingData();
+        var msh41Identifier = extractMsh41Identifier(bundle);
+        var messageId = HapiHelper.getMessageControlId(bundle);
         var observations = HapiHelper.resourcesInBundle(bundle, Observation.class);
 
-        for (Observation obv : observations.toList()) {
-            var codingList = obv.getCode().getCoding();
+        observations
+                .filter(this::hasValidCoding)
+                .forEach(
+                        observation ->
+                                processCoding(observation, codingMap, msh41Identifier, messageId));
+    }
 
-            if (codingList.size() != 1) {
-                continue;
-            }
+    private boolean hasValidCoding(Observation observation) {
+        var codingList = observation.getCode().getCoding();
+        return codingList.size() == 1 && isLocalCode(codingList.get(0));
+    }
 
-            var coding = codingList.get(0);
-            if (!HapiHelper.hasDefinedCoding(
-                    coding, HapiHelper.EXTENSION_ALT_CODING, HapiHelper.LOCAL_CODE)) {
-                continue;
-            }
+    private boolean isLocalCode(Coding coding) {
+        return HapiHelper.hasDefinedCoding(
+                coding, HapiHelper.EXTENSION_ALT_CODING, HapiHelper.LOCAL_CODE);
+    }
 
-            var identifier = codingMap.get(coding.getCode());
-            if (identifier == null) {
-                logUnmappedLocalCode(bundle, coding);
-                continue;
-            }
+    private String extractMsh41Identifier(Bundle bundle) {
+        var msh41Identifier = HapiHelper.getMSH4_1Identifier(bundle);
+        return msh41Identifier != null ? msh41Identifier.getValue() : null;
+    }
 
-            var mappedCoding = getMappedCoding(identifier);
+    private void processCoding(
+            Observation observation,
+            Map<String, IdentifierCode> codingMap,
+            String msh41Identifier,
+            String messageId) {
+        var originalCoding = observation.getCode().getCoding().get(0);
+        IdentifierCode identifier = codingMap.get(originalCoding.getCode());
+
+        if (identifier == null) {
+            logUnmappedLocalCode(originalCoding, msh41Identifier, messageId);
+            return;
+        }
 
-            // Add the mapped code as the first in the list, ahead of the existing alternate code
-            codingList.add(0, mappedCoding);
+        var mappedCoding = getMappedCoding(identifier);
+        observation.getCode().getCoding().add(0, mappedCoding);
+    }
+
+    private String validateField(String field, String fieldName) {
+        if (field == null || field.isBlank()) {
+            throw new IllegalArgumentException("missing or empty required field " + fieldName);
         }
+        return field;
     }
 
-    private void logUnmappedLocalCode(Bundle bundle, Coding coding) {
-        var msh41Identifier = HapiHelper.getMSH4_1Identifier(bundle);
-        var msh41Value = msh41Identifier != null ? msh41Identifier.getValue() : null;
+    private void logUnmappedLocalCode(Coding coding, String msh41Identifier, String messageId) {
 
         logger.logWarning(
                 "Unmapped local code detected: '{}', from sender: '{}', message Id: '{}'",
                 coding.getCode(),
-                msh41Value,
-                HapiHelper.getMessageControlId(bundle));
+                msh41Identifier,
+                messageId);
     }
 
     private Coding getMappedCoding(IdentifierCode identifierCode) {
@@ -85,92 +101,30 @@ private Coding getMappedCoding(IdentifierCode identifierCode) {
         return mappedCoding;
     }
 
-    /**
-     * Initializes the local-to-LOINC/PLT hash map, customized for CDPH and UCSD. Currently, the
-     * mapping is hardcoded for simplicity. If expanded to support additional entities, the
-     * implementation may be updated to allow dynamic configuration via
-     * transformation_definitions.json or a database-driven mapping.
-     */
-    private void initMap() {
-        this.codingMap = new HashMap<>();
-        // ALD
-        codingMap.put(
-                "99717-32",
-                new IdentifierCode(
-                        "85269-9",
-                        "X-linked Adrenoleukodystrophy (X- ALD) newborn screen interpretation",
-                        HapiHelper.LOINC_CODE));
-        codingMap.put(
-                "99717-33",
-                new IdentifierCode(
-                        "85268-1",
-                        "X-linked Adrenoleukodystrophy (X- ALD) newborn screening comment-discussion",
-                        HapiHelper.LOINC_CODE));
-        codingMap.put(
-                "99717-34",
-                new IdentifierCode(
-                        "PLT325",
-                        "ABCD1 gene mutation found [Identifier] in DBS by Sequencing",
-                        HapiHelper.PLT_CODE));
-        // CAH
-        codingMap.put(
-                "99717-6",
-                new IdentifierCode(
-                        "53340-6",
-                        "17-Hydroxyprogesterone [Moles/volume] in DBS",
-                        HapiHelper.LOINC_CODE));
-        // CF
-        codingMap.put(
-                "99717-35",
-                new IdentifierCode(
-                        "PLT3289",
-                        "CFTR gene mutation found [Interpretation] in DBS by Sequencing",
-                        HapiHelper.PLT_CODE));
-        codingMap.put(
-                "99717-36",
-                new IdentifierCode(
-                        "PLT3290",
-                        "CFTR gene variant found [Identifier] in DBS by Sequencing comments/discussion",
-                        HapiHelper.PLT_CODE));
-        // MPS I
-        codingMap.put(
-                "99717-48",
-                new IdentifierCode(
-                        "PLT3258",
-                        "IDUA gene mutations found [Identifier] in DBS by Sequencing",
-                        HapiHelper.PLT_CODE));
-        codingMap.put(
-                "99717-44",
-                new IdentifierCode(
-                        "PLT3291",
-                        "IDUA gene variant analysis in DBS by Sequencing comments/discussion",
-                        HapiHelper.PLT_CODE));
-        // MPS II
-        codingMap.put(
-                "99717-50",
-                new IdentifierCode(
-                        "PLT3294",
-                        "IDS gene mutations found [Identifier] in Dried Bloodspot by Molecular genetics method",
-                        HapiHelper.PLT_CODE));
-        // Pompe
-        codingMap.put(
-                "99717-47",
-                new IdentifierCode(
-                        "PLT3252",
-                        "GAA gene mutation found [Identifier] in DBS by Sequencing",
-                        HapiHelper.PLT_CODE));
-        codingMap.put(
-                "99717-46",
-                new IdentifierCode(
-                        "PLT3292",
-                        "GAA gene variant analysis in DBS by Sequencing comments/discussion",
-                        HapiHelper.PLT_CODE));
-        // SMA
-        codingMap.put(
-                "99717-60",
-                new IdentifierCode(
-                        "PLT3293",
-                        "SMN1 exon 7 deletion analysis in DBS by Sequencing",
-                        HapiHelper.PLT_CODE));
+    private Map<String, IdentifierCode> getMapFromArgs(Map<String, Object> args) {
+        var codingMap = new HashMap<String, IdentifierCode>();
+
+        // Suppressing the unchecked cast warning. The assignment below will throw a
+        // ClassCastException if it fails.
+        @SuppressWarnings("unchecked")
+        var argsCodingMap = (Map<String, Map<String, String>>) args.get("codingMap");
+
+        for (Map.Entry<String, Map<String, String>> entry : argsCodingMap.entrySet()) {
+            var localCode = entry.getKey();
+            var mappedCode = getIdentifierCode(entry);
+
+            codingMap.put(localCode, mappedCode);
+        }
+
+        return codingMap;
+    }
+
+    private IdentifierCode getIdentifierCode(Map.Entry<String, Map<String, String>> entry) {
+        var value = entry.getValue();
+        var code = validateField(value.get("code"), "code");
+        var display = validateField(value.get("display"), "display");
+        var codingSystem = validateField(value.get("codingSystem"), "codingSystem");
+
+        return new IdentifierCode(code, display, codingSystem);
     }
 }

etor/src/main/resources/transformation_definitions.json

@@ -197,7 +197,75 @@
       "rules": [
         {
           "name": "MapLocalObservationCodes",
-          "args": {}
+          "args": {
+            "codingMap" : {
+              "99717-6": {
+                "code": "53340-6",
+                "display": "17-Hydroxyprogesterone [Moles/volume] in DBS",
+                "codingSystem": "LN"
+              },
+              "99717-32": {
+                "code": "85269-9",
+                "display": "X-linked Adrenoleukodystrophy (X- ALD) newborn screen interpretation",
+                "codingSystem": "LN"
+              },
+              "99717-33": {
+                "code": "85268-1",
+                "display": "X-linked Adrenoleukodystrophy (X- ALD) newborn screening comment-discussion",
+                "codingSystem": "LN"
+              },
+              "99717-34": {
+                "code": "PLT325",
+                "display": "ABCD1 gene mutation found [Identifier] in DBS by Sequencing",
+                "codingSystem": "PLT"
+              },
+              "99717-35": {
+                "code": "PLT3289",
+                "display": "CFTR gene mutation found [Interpretation] in DBS by Sequencing",
+                "codingSystem": "PLT"
+              },
+              "99717-36": {
+                "code": "PLT3290",
+                "display": "CFTR gene variant found [Identifier] in DBS by Sequencing comments/discussion",
+                "codingSystem": "PLT"
+              },
+              "99717-44": {
+                "code": "PLT3291",
+                "display": "IDUA gene variant analysis in DBS by Sequencing comments/discussion",
+                "codingSystem": "PLT"
+              },
+              "99717-46": {
+                "code": "PLT3292",
+                "display": "GAA gene variant analysis in DBS by Sequencing comments/discussion",
+                "codingSystem": "PLT"
+              },
+              "99717-47": {
+                "code": "PLT3252",
+                "display": "GAA gene mutation found [Identifier] in DBS by Sequencing",
+                "codingSystem": "PLT"
+              },
+              "99717-48": {
+                "code": "PLT3258",
+                "display": "IDUA gene mutations found [Identifier] in DBS by Sequencing",
+                "codingSystem": "PLT"
+              },
+              "99717-49": {
+                "code": "76030-6",
+                "display": "IDS gene full mutation analysis in Blood or Tissue by Sequencing",
+                "codingSystem": "LN"
+              },
+              "99717-50": {
+                "code": "PLT3294",
+                "display": "IDS gene mutations found [Identifier] in Dried Bloodspot by Molecular genetics method",
+                "codingSystem": "PLT"
+              },
+              "99717-60": {
+                "code": "PLT3293",
+                "display": "SMN1 exon 7 deletion analysis in DBS by Sequencing",
+                "codingSystem": "PLT"
+              }
+            }
+          }
         }
       ]
     },