Merge pull request #17 from miracum/16-add-error-handling-for-unmappa…

…ble-tumor-body-side fix: fixes NullPointerException for unmappable body site naming in oB…
bzkf · Jan 4, 2024 · 9d77cd2 · 9d77cd2
2 parents 830a833 + 819482b
commit 9d77cd2
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Showing 3 changed files with 27 additions and 14 deletions.
diff --git a/src/main/java/org/miracum/streams/ume/obdstofhir/lookup/SideEffectTherapyGradingLookup.java b/src/main/java/org/miracum/streams/ume/obdstofhir/lookup/SideEffectTherapyGradingLookup.java
@@ -21,10 +21,10 @@ public SideEffectTherapyGradingLookup() {
   }
 
   public final String lookupSideEffectTherapyGradingCode(String code) {
-    return lookup.get(code).get(0);
+    return lookup.get(code) != null ? lookup.get(code).get(0) : null;
   }
 
   public final String lookupSideEffectTherapyGradingDisplay(String code) {
-    return lookup.get(code).get(1);
+    return lookup.get(code) != null ? lookup.get(code).get(1) : null;
   }
 }
diff --git a/...main/java/org/miracum/streams/ume/obdstofhir/lookup/SnomedCtSeitenlokalisationLookup.java b/...main/java/org/miracum/streams/ume/obdstofhir/lookup/SnomedCtSeitenlokalisationLookup.java
@@ -21,10 +21,10 @@ public SnomedCtSeitenlokalisationLookup() {
   }
 
   public final String lookupSnomedCode(String AdtCode) {
-    return lookup.get(AdtCode).get(0);
+    return lookup.get(AdtCode) != null ? lookup.get(AdtCode).get(0) : null;
   }
 
   public final String lookupSnomedDisplay(String AdtCode) {
-    return lookup.get(AdtCode).get(1);
+    return lookup.get(AdtCode) != null ? lookup.get(AdtCode).get(1) : null;
   }
 }
diff --git a/src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsConditionMapper.java b/src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsConditionMapper.java
@@ -116,16 +116,29 @@ public Bundle mapOnkoResourcesToCondition(
     var adtBodySite = primDia.getSeitenlokalisation();
 
     if (adtBodySite != null) {
-      bodySiteADTCoding
-          .setSystem(fhirProperties.getSystems().getAdtSeitenlokalisation())
-          .setCode(adtBodySite)
-          .setDisplay(
-              displayAdtSeitenlokalisationLookup.lookupAdtSeitenlokalisationDisplay(adtBodySite));
-      bodySiteSNOMEDCoding
-          .setSystem(fhirProperties.getSystems().getSnomed())
-          .setCode(snomedCtSeitenlokalisationLookup.lookupSnomedCode(adtBodySite))
-          .setDisplay(snomedCtSeitenlokalisationLookup.lookupSnomedDisplay(adtBodySite));
-
+      var adtSeitenlokalisationDisplay =
+          displayAdtSeitenlokalisationLookup.lookupAdtSeitenlokalisationDisplay(adtBodySite);
+      var snomedCtSeitenlokalisationCode =
+          snomedCtSeitenlokalisationLookup.lookupSnomedCode(adtBodySite);
+      var snomedCtSeitenlokalisationDisplay =
+          snomedCtSeitenlokalisationLookup.lookupSnomedDisplay(adtBodySite);
+
+      if (adtSeitenlokalisationDisplay != null) {
+        bodySiteADTCoding
+            .setSystem(fhirProperties.getSystems().getAdtSeitenlokalisation())
+            .setCode(adtBodySite)
+            .setDisplay(adtSeitenlokalisationDisplay);
+      } else {
+        LOG.warn("Unmappable body site in oBDS data: " + adtBodySite);
+      }
+      if (adtSeitenlokalisationDisplay != null) {
+        bodySiteSNOMEDCoding
+            .setSystem(fhirProperties.getSystems().getSnomed())
+            .setCode(snomedCtSeitenlokalisationCode)
+            .setDisplay(snomedCtSeitenlokalisationDisplay);
+      } else {
+        LOG.warn("Unmappable body site in oBDS data: " + adtBodySite);
+      }
       var bodySiteConcept = new CodeableConcept();
       bodySiteConcept.addCoding(bodySiteADTCoding).addCoding(bodySiteSNOMEDCoding);
       onkoCondition.addBodySite(bodySiteConcept);