build: added nullaway (#177)

* build: added nullaway * applied nullaway recommendations * setup coverage analysis for sonarcloud integration
miracum · Nov 5, 2024 · 14949f0 · 14949f0
1 parent d16d60f
commit 14949f0
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Showing 6 changed files with 49 additions and 14 deletions.
diff --git a/build.gradle b/build.gradle
@@ -4,7 +4,8 @@ plugins {
     id 'java'
     id 'jacoco'
     id 'com.diffplug.spotless' version "6.25.0"
-	id "net.ltgt.errorprone" version "4.1.0"
+    id "net.ltgt.errorprone" version "4.1.0"
+    id "org.sonarqube" version "5.1.0.4882"
 }
 
 group = "org.miracum.etl"
@@ -53,6 +54,7 @@ dependencies {
     testRuntimeOnly 'org.junit.platform:junit-platform-launcher'
 
     errorprone("com.google.errorprone:error_prone_core:2.34.0")
+    errorprone("com.uber.nullaway:nullaway:0.12.0")
 }
 
 dependencyManagement {
@@ -84,3 +86,18 @@ spotless {
         googleJavaFormat()
     }
 }
+
+import net.ltgt.gradle.errorprone.CheckSeverity
+
+tasks.withType(JavaCompile).configureEach {
+    options.errorprone {
+        check("NullAway", CheckSeverity.ERROR)
+        option("NullAway:AnnotatedPackages", "org.miracum")
+    }
+    // Include to disable NullAway on test code
+    if (name.toLowerCase().contains("test")) {
+        options.errorprone {
+            disable("NullAway")
+        }
+    }
+}
diff --git a/src/main/java/org/miracum/etl/fhirgateway/FhirSystemsConfig.java b/src/main/java/org/miracum/etl/fhirgateway/FhirSystemsConfig.java
@@ -1,14 +1,16 @@
 package org.miracum.etl.fhirgateway;
 
+import jakarta.annotation.Nullable;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Configuration;
 
 @Configuration
 @ConfigurationProperties(prefix = "fhir.systems")
 public class FhirSystemsConfig {
 
-  private String loinc;
+  @Nullable private String loinc;
 
+  @Nullable
   public String getLoinc() {
     return loinc;
   }

diff --git a/src/main/java/org/miracum/etl/fhirgateway/models/loinc/LoincConversion.java b/src/main/java/org/miracum/etl/fhirgateway/models/loinc/LoincConversion.java
@@ -3,28 +3,35 @@
 import com.fasterxml.jackson.annotation.JsonFormat;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import jakarta.annotation.Nullable;
 import java.math.BigDecimal;
 
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public class LoincConversion {
 
   @JsonProperty("loinc")
+  @Nullable
   private String loinc;
 
   @JsonProperty("unit")
+  @Nullable
   private String unit;
 
   @JsonProperty("value")
   @JsonFormat(shape = JsonFormat.Shape.STRING)
+  @Nullable
   private BigDecimal value;
 
   @JsonProperty("id")
+  @Nullable
   private String id;
 
   @JsonProperty("display")
+  @Nullable
   private String display;
 
   @JsonProperty("loinc")
+  @Nullable
   public String getLoinc() {
     return loinc;
   }
@@ -36,6 +43,7 @@ public LoincConversion setLoinc(String loinc) {
   }
 
   @JsonProperty("unit")
+  @Nullable
   public String getUnit() {
     return unit;
   }
@@ -47,6 +55,7 @@ public LoincConversion setUnit(String unit) {
   }
 
   @JsonProperty("value")
+  @Nullable
   public BigDecimal getValue() {
     return value;
   }
@@ -58,6 +67,7 @@ public LoincConversion setValue(BigDecimal value) {
   }
 
   @JsonProperty("id")
+  @Nullable
   public String getId() {
     return id;
   }
@@ -69,6 +79,7 @@ public LoincConversion setId(String id) {
   }
 
   @JsonProperty("display")
+  @Nullable
   public String getDisplay() {
     return display;
   }

diff --git a/src/main/java/org/miracum/etl/fhirgateway/processors/BaseKafkaProcessor.java b/src/main/java/org/miracum/etl/fhirgateway/processors/BaseKafkaProcessor.java
@@ -2,6 +2,7 @@
 
 import static net.logstash.logback.argument.StructuredArguments.kv;
 
+import jakarta.annotation.Nullable;
 import java.util.UUID;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleType;
@@ -24,6 +25,7 @@ protected BaseKafkaProcessor(ResourcePipeline pipeline) {
     this.pipeline = pipeline;
   }
 
+  @Nullable
   public Bundle process(Message<Resource> message) {
 
     if (message == null) {

diff --git a/src/main/java/org/miracum/etl/fhirgateway/processors/KafkaProcessor.java b/src/main/java/org/miracum/etl/fhirgateway/processors/KafkaProcessor.java
@@ -2,6 +2,7 @@
 
 import static net.logstash.logback.argument.StructuredArguments.kv;
 
+import jakarta.annotation.Nullable;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.function.Function;
@@ -24,7 +25,7 @@ public class KafkaProcessor extends BaseKafkaProcessor {
   private final String generateTopicMatchExpression;
   private final String generateTopicReplacement;
   private final KafkaProcessorConfig config;
-  private HmacUtils hmac;
+  @Nullable private HmacUtils hmac;
 
   public KafkaProcessor(ResourcePipeline pipeline, KafkaProcessorConfig config) {
     super(pipeline);
@@ -46,7 +47,7 @@ Function<Message<Resource>, Message<Bundle>> process() {
 
       var messageKey = message.getHeaders().getOrDefault(KafkaHeaders.RECEIVED_KEY, "").toString();
 
-      if (config.cryptoHashMessageKeys().enabled()) {
+      if (config.cryptoHashMessageKeys().enabled() && hmac != null) {
         messageKey = hmac.hmacHex(messageKey);
       }
 

diff --git a/src/main/java/org/miracum/etl/fhirgateway/processors/LoincHarmonizer.java b/src/main/java/org/miracum/etl/fhirgateway/processors/LoincHarmonizer.java
@@ -9,6 +9,7 @@
 import java.time.Duration;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Optional;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Quantity;
@@ -81,9 +82,9 @@ private Observation harmonizeObservation(final Observation originalObservation)
       // harmonize the observation's main code/value
       var result = getHarmonizedQuantity(originalObservation.getValueQuantity(), originalCode);
 
-      if (result != null) {
-        harmonized.setValue(result.getFirst());
-        Pair<Quantity, LoincConversion> finalResult = result;
+      if (result.isPresent()) {
+        harmonized.setValue(result.get().getFirst());
+        Pair<Quantity, LoincConversion> finalResult = result.get();
         harmonized.getCode().getCoding().stream()
             .filter(obs -> obs.getSystem().equals(fhirSystems.getLoinc()))
             .findFirst()
@@ -105,8 +106,8 @@ private Observation harmonizeObservation(final Observation originalObservation)
 
           result = getHarmonizedQuantity(rangeLow, originalCode);
 
-          if (result != null) {
-            rangeComponent.setLow(result.getFirst());
+          if (result.isPresent()) {
+            rangeComponent.setLow(result.get().getFirst());
           }
         }
 
@@ -115,8 +116,8 @@ private Observation harmonizeObservation(final Observation originalObservation)
 
           result = getHarmonizedQuantity(rangeHigh, originalCode);
 
-          if (result != null) {
-            rangeComponent.setHigh(result.getFirst());
+          if (result.isPresent()) {
+            rangeComponent.setHigh(result.get().getFirst());
           }
         }
       }
@@ -144,7 +145,8 @@ private Observation harmonizeObservation(final Observation originalObservation)
     return harmonized;
   }
 
-  private Pair<Quantity, LoincConversion> getHarmonizedQuantity(Quantity input, String loincCode) {
+  private Optional<Pair<Quantity, LoincConversion>> getHarmonizedQuantity(
+      Quantity input, String loincCode) {
 
     var requestUrl =
         UriComponentsBuilder.fromUri(loincConverterBaseUri)
@@ -176,9 +178,9 @@ private Pair<Quantity, LoincConversion> getHarmonizedQuantity(Quantity input, St
       quantity.setUnit(response.getUnit());
       quantity.setCode(response.getUnit());
       quantity.setSystem(input.getSystem());
-      return Pair.of(quantity, response);
+      return Optional.of(Pair.of(quantity, response));
     }
 
-    return null;
+    return Optional.empty();
   }
 }