some sonar fixes

DataBiosphere · Oct 4, 2024 · 434b42e · 434b42e
1 parent dcbc4bf
commit 434b42e
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Showing 5 changed files with 8 additions and 19 deletions.
diff --git a/...ce/src/main/java/bio/terra/pipelines/stairway/imputation/RunImputationAzureJobFlight.java b/...ce/src/main/java/bio/terra/pipelines/stairway/imputation/RunImputationAzureJobFlight.java
@@ -53,9 +53,7 @@ public RunImputationAzureJobFlight(FlightMap inputParameters, Object beanBag) {
 
     addStep(
         new PrepareImputationInputsStep(
-            flightBeanBag.getPipelinesService(),
-            flightBeanBag.getPipelineRunsService(),
-            flightBeanBag.getImputationConfiguration()),
+            flightBeanBag.getPipelinesService(), flightBeanBag.getImputationConfiguration()),
         dbRetryRule);
 
     addStep(new CheckLeonardoHealthStep(flightBeanBag.getLeonardoService()), dataPlaneAppRetryRule);

diff --git a/service/src/main/java/bio/terra/pipelines/stairway/imputation/RunImputationGcpJobFlight.java b/service/src/main/java/bio/terra/pipelines/stairway/imputation/RunImputationGcpJobFlight.java
@@ -69,9 +69,7 @@ public RunImputationGcpJobFlight(FlightMap inputParameters, Object beanBag) {
 
     addStep(
         new PrepareImputationInputsStep(
-            flightBeanBag.getPipelinesService(),
-            flightBeanBag.getPipelineRunsService(),
-            flightBeanBag.getImputationConfiguration()),
+            flightBeanBag.getPipelinesService(), flightBeanBag.getImputationConfiguration()),
         dbRetryRule);
 
     addStep(

diff --git a/.../main/java/bio/terra/pipelines/stairway/imputation/steps/PrepareImputationInputsStep.java b/.../main/java/bio/terra/pipelines/stairway/imputation/steps/PrepareImputationInputsStep.java
@@ -8,7 +8,6 @@
 import bio.terra.pipelines.common.utils.PipelinesEnum;
 import bio.terra.pipelines.db.entities.PipelineInputDefinition;
 import bio.terra.pipelines.dependencies.stairway.JobMapKeys;
-import bio.terra.pipelines.service.PipelineRunsService;
 import bio.terra.pipelines.service.PipelinesService;
 import bio.terra.pipelines.stairway.imputation.RunImputationJobFlightMapKeys;
 import bio.terra.stairway.FlightContext;
@@ -35,16 +34,12 @@
  */
 public class PrepareImputationInputsStep implements Step {
   private final PipelinesService pipelinesService;
-  private final PipelineRunsService pipelineRunsService;
   private final ImputationConfiguration imputationConfiguration;
   private final Logger logger = LoggerFactory.getLogger(PrepareImputationInputsStep.class);
 
   public PrepareImputationInputsStep(
-      PipelinesService pipelinesService,
-      PipelineRunsService pipelineRunsService,
-      ImputationConfiguration imputationConfiguration) {
+      PipelinesService pipelinesService, ImputationConfiguration imputationConfiguration) {
     this.pipelinesService = pipelinesService;
-    this.pipelineRunsService = pipelineRunsService;
     this.imputationConfiguration = imputationConfiguration;
   }
 

diff --git a/...t/java/bio/terra/pipelines/stairway/imputation/steps/PrepareImputationInputsStepTest.java b/...t/java/bio/terra/pipelines/stairway/imputation/steps/PrepareImputationInputsStepTest.java
@@ -13,7 +13,6 @@
 import bio.terra.pipelines.db.entities.PipelineInputDefinition;
 import bio.terra.pipelines.db.repositories.PipelineRunsRepository;
 import bio.terra.pipelines.db.repositories.PipelinesRepository;
-import bio.terra.pipelines.service.PipelineRunsService;
 import bio.terra.pipelines.service.PipelinesService;
 import bio.terra.pipelines.stairway.imputation.RunImputationJobFlightMapKeys;
 import bio.terra.pipelines.testutils.BaseEmbeddedDbTest;
@@ -39,7 +38,6 @@
 class PrepareImputationInputsStepTest extends BaseEmbeddedDbTest {
 
   @Autowired private PipelinesService pipelinesService;
-  @Autowired private PipelineRunsService pipelineRunsService;
   @Autowired PipelinesRepository pipelinesRepository;
   @Autowired ImputationConfiguration imputationConfiguration;
   @Autowired PipelineRunsRepository pipelineRunsRepository;
@@ -101,8 +99,7 @@ void doStepSuccess() {
 
     // do the step
     var prepareImputationInputsStep =
-        new PrepareImputationInputsStep(
-            pipelinesService, pipelineRunsService, imputationConfiguration);
+        new PrepareImputationInputsStep(pipelinesService, imputationConfiguration);
     var result = prepareImputationInputsStep.doStep(flightContext);
 
     assertEquals(StepStatus.STEP_RESULT_SUCCESS, result.getStepStatus());
@@ -172,8 +169,7 @@ void doStepSuccess() {
   @Test
   void undoStepSuccess() {
     var prepareImputationInputsStep =
-        new PrepareImputationInputsStep(
-            pipelinesService, pipelineRunsService, imputationConfiguration);
+        new PrepareImputationInputsStep(pipelinesService, imputationConfiguration);
     var result = prepareImputationInputsStep.undoStep(flightContext);
 
     assertEquals(StepStatus.STEP_RESULT_SUCCESS, result.getStepStatus());

diff --git a/service/src/test/java/bio/terra/pipelines/testutils/TestFlightContext.java b/service/src/test/java/bio/terra/pipelines/testutils/TestFlightContext.java
@@ -142,5 +142,7 @@ public ProgressMeter getProgressMeter(String name) {
   }
 
   @Override
-  public void setProgressMeter(String name, long v1, long v2) throws InterruptedException {}
+  public void setProgressMeter(String name, long v1, long v2) throws InterruptedException {
+    // no-op
+  }
 }