Merge pull request #47 from icanbwell/HHRE-919-remove-print-patient-b…

…undle HHRE-919 removed logging the Patient PHI data, updated for minor changes
icanbwell · Sep 2, 2022 · 105237a · 105237a
2 parents 815d4f5 + 630e52f
commit 105237a
Show file tree

Hide file tree

Showing 5 changed files with 27 additions and 17 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -36,6 +36,6 @@ COPY ./src/ /bsights-engine-spark/src/
 
 ## skip running tests since it requires a fhir server
 RUN mvn -Dmaven.test.skip package -s ./settings.xml && \
-    cp ./target/bsights-engine-spark-1.0.10.jar /opt/spark/jars/
+    cp ./target/bsights-engine-spark-1.0.11.jar /opt/spark/jars/
 
 # USER 1001
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>com.bwell</groupId>
     <artifactId>bsights-engine-spark</artifactId>
-    <version>1.0.10</version>
+    <version>1.0.11</version>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

diff --git a/src/main/java/com/bwell/infrastructure/FhirJsonExporter.java b/src/main/java/com/bwell/infrastructure/FhirJsonExporter.java
@@ -57,10 +57,12 @@ public static String getMapSetAsJson(String fhirVersion, Set<Map.Entry<String, O
         for (Map.Entry<String, Object> libraryEntry : entrySet) {
             String key = libraryEntry.getKey();
             Object value = libraryEntry.getValue();
+
+            // IF the value is FHIR resource, just get the Id of this resource object
             if (value instanceof IBaseResource) {
-                jsonMap.put(key, getResourceAsJson(fhirVersion, (IBaseResource) value));
+                jsonMap.put(key + "Id", ((IBaseResource) value).getIdElement().getIdPart());
             } else {
-                jsonMap.put(key, value != null ? value.toString(): null);
+                jsonMap.put(key, value != null ? value.toString() : null);
             }
         }
         return getMapAsJson(jsonMap);

diff --git a/src/main/java/com/bwell/services/application/MeasureService.java b/src/main/java/com/bwell/services/application/MeasureService.java
@@ -75,7 +75,8 @@ public Map<String, String> runCqlLibrary(
             libraryParameter.context.contextValue = contextValue;
         }
 
-        myLogger.info("Running with libraryUrl={}, terminologyUrl={}, fhir={}", libraryUrl, terminologyUrl, fhirBundle);
+        myLogger.info("Running with libraryName={}, libraryVersion={}, libraryUrl={}, terminologyUrl={}",
+                libraryName, libraryVersion, libraryUrl, terminologyUrl);
 
         if(authUrl != null){
             List<String> headers = headers(authUrl, authId, authSecret, authScope);
@@ -92,31 +93,32 @@ public Map<String, String> runCqlLibrary(
 
             Set<Map.Entry<String, Object>> entrySet = result.expressionResults.entrySet();
 
-            myLogger.info("Received result from CQL Engine={} for bundle={}",
-                    FhirJsonExporter.getMapSetAsJson(fhirVersion, entrySet),
-                    fhirBundle);
+            myLogger.info("Received result from CQL Engine={}",
+                    FhirJsonExporter.getMapSetAsJson(fhirVersion, entrySet));
 
             for (Map.Entry<String, Object> libraryEntry : entrySet) {
                 String key = libraryEntry.getKey();
                 Object value = libraryEntry.getValue();
 
                 if ("Patient".equals(key)) {
                     Patient patient = (Patient) value;
-                    myLogger.info("Received Patient in CQL result={}",
-                            patient != null ? FhirJsonExporter.getResourceAsJson(fhirVersion, patient) : null);
-                    newMap.put("PatientId", (patient != null) ? patient.getIdElement().getIdPart() : null);
+
+                    String patientId = (patient != null) ? patient.getIdElement().getIdPart() : null;
+                    myLogger.info("Received Patient in CQL result, Patient Id={}", patientId);
+
+                    newMap.put("PatientId", patientId);
                 } else {
                     if (cqlVariables.contains(key)) {
                         newMap.put(key, value != null ? value.toString() : null);
                     }
                 }
             }
         } catch (Exception ex) {
-            myLogger.error("Error={} for bundle={}", ex, fhirBundle);
+            myLogger.error("Error={}", ex);
             throw ex;
         }
 
-        myLogger.info("Calculated CQL variables={} for bundle={}", FhirJsonExporter.getMapAsJson(newMap), fhirBundle);
+        myLogger.info("Calculated CQL variables={}", FhirJsonExporter.getMapAsJson(newMap));
 
         return newMap;
     }

diff --git a/src/main/java/com/bwell/services/domain/ResourceLoader.java b/src/main/java/com/bwell/services/domain/ResourceLoader.java
@@ -96,12 +96,18 @@ public IBaseBundle loadResourceFromString(String fhirVersion, String resourceJso
                 bundle = (Bundle) baseResource;
             }
 
-            myLogger.info("Read resources from {}: {}", resourceJson, FhirJsonExporter.getResourceAsJson(fhirVersion, bundle));
+            String resourceId = null;
+            List<Bundle.BundleEntryComponent> entries = ((Bundle)bundle).getEntry();
+            if (entries.size() > 0) {
+                resourceId = entries.get(0).getResource().getIdElement().getIdPart();
+            }
+
+            myLogger.info("Read resources for resource Id: {}", resourceId);
             bundle = moveContainedResourcesToTopLevel(bundle);
 
             //noinspection ConstantConditions
-            bundle = clean_and_fix_bundle(bundle);
-            myLogger.info("Cleaned resources from {}: {}", resourceJson, FhirJsonExporter.getResourceAsJson(fhirVersion, bundle));
+            bundle = cleanFixBundle(bundle);
+            myLogger.info("Cleaned resources for resource Id: {}", resourceId);
 
             return bundle;
         } catch (FHIRFormatError | FhirException ex) {
@@ -139,7 +145,7 @@ private IBaseBundle moveContainedResourcesToTopLevel(IBaseBundle bundle) {
         return bundle;
     }
 
-    private IBaseBundle clean_and_fix_bundle(IBaseBundle bundle) {
+    private IBaseBundle cleanFixBundle(IBaseBundle bundle) {
         // some data we get is bad FHIR ,so we have to fix it
         return bundle;
     }