Address build / compiler warnings (#1167)

cli/src/main/java/bio/terra/tanagra/cli/command/BaseCommand.java

@@ -56,7 +56,7 @@ public Integer call() {
     ERR = UserIO.getErr();
 
     // Execute the command
-    LOGGER.debug("[COMMAND ARGS] " + String.join(" ", BaseMain.getArgList()));
+    LOGGER.debug("[COMMAND ARGS] {}", String.join(" ", BaseMain.getArgList()));
     execute();
 
     // Set the command exit code

indexer/src/main/java/bio/terra/tanagra/indexing/jobexecutor/SequencedJobSet.java

@@ -49,10 +49,6 @@ public int getNumStages() {
     return stages.size();
   }
 
-  public long getNumJobs() {
-    return stages.stream().map(List::size).count();
-  }
-
   public String getDescription() {
     return description;
   }

indexer/src/main/java/bio/terra/tanagra/indexing/jobexecutor/SerialRunner.java

@@ -1,10 +1,8 @@
 package bio.terra.tanagra.indexing.jobexecutor;
 
-import bio.terra.tanagra.exception.SystemException;
 import bio.terra.tanagra.indexing.job.IndexingJob;
 import java.util.Iterator;
 import java.util.List;
-import java.util.concurrent.ExecutionException;
 
 /** Utility class that runs multiple job sets in serial. */
 public final class SerialRunner extends JobRunner {
@@ -21,20 +19,12 @@ public String getName() {
   /** Run all job sets serially. */
   @Override
   public void runJobSetsWithoutTimer() {
-    jobSets.forEach(
-        jobSet -> {
-          try {
-            runSingleJobSet(jobSet);
-          } catch (InterruptedException | ExecutionException ex) {
-            throw new SystemException("Job set execution failed", ex);
-          }
-        });
+    jobSets.forEach(this::runSingleJobSet);
   }
 
   /** Run a single job set. Run the stages serially, and the jobs within each stage serially. */
   @Override
-  protected void runSingleJobSet(SequencedJobSet sequencedJobSet)
-      throws InterruptedException, ExecutionException {
+  protected void runSingleJobSet(SequencedJobSet sequencedJobSet) {
     // Iterate through the job stages, running all jobs in each stage.
     Iterator<List<IndexingJob>> jobStagesIterator = sequencedJobSet.iterator();
     while (jobStagesIterator.hasNext()) {

service/src/main/java/bio/terra/tanagra/service/filter/FilterBuilderService.java

@@ -60,7 +60,6 @@ public FilterBuilderService(UnderlayService underlayService) {
     this.underlayService = underlayService;
   }
 
-  @SuppressWarnings("unchecked")
   public EntityFilter buildCohortFilterForCriteriaGroup(
       String underlayName, CohortRevision.CriteriaGroup criteriaGroup) {
     if (criteriaGroup.isDisabled() || criteriaGroup.getCriteria().isEmpty()) {
@@ -77,12 +76,11 @@ public EntityFilter buildCohortFilterForCriteriaGroup(
             .collect(Collectors.toList());
 
     Underlay underlay = underlayService.getUnderlay(underlayName);
-    FilterBuilder filterBuilder =
+    FilterBuilder<?, ?> filterBuilder =
         underlay.getCriteriaSelector(criteriaSelectorName).getFilterBuilder();
     return filterBuilder.buildForCohort(underlay, selectionData);
   }
 
-  @SuppressWarnings("unchecked")
   private List<EntityOutput> buildDataFeatureOutputForTemporalCriteriaGroup(
       String underlayName, CohortRevision.CriteriaGroup criteriaGroup) {
     if (criteriaGroup.getCriteria().isEmpty()) {
@@ -213,7 +211,6 @@ public EntityFilter buildFilterForCohortRevisions(
     }
   }
 
-  @SuppressWarnings("unchecked")
   public List<EntityOutputPreview> buildOutputPreviewsForFeatureSets(
       List<FeatureSet> featureSets, boolean includeAllAttributes) {
     // No feature sets = no entity outputs.
@@ -280,7 +277,7 @@ public List<EntityOutputPreview> buildOutputPreviewsForFeatureSets(
                     }
 
                     // Generate the entity outputs for each feature set criteria.
-                    FilterBuilder filterBuilder =
+                    FilterBuilder<?, ?> filterBuilder =
                         underlay.getCriteriaSelector(criteriaSelectorName).getFilterBuilder();
                     List<EntityOutput> entityOutputs =
                         filterBuilder.buildForDataFeature(underlay, selectionData);

service/src/test/java/bio/terra/tanagra/service/FeatureSetServiceTest.java

@@ -110,7 +110,7 @@ void createUpdateDelete() throws InterruptedException {
     assertEquals(createdFeatureSet.getCreated(), createdFeatureSet.getLastModified());
     assertEquals(1, createdFeatureSet.getCriteria().size());
     assertTrue(createdFeatureSet.getCriteria().contains(GENDER_EQ_WOMAN.getValue()));
-    assertEquals(1, createdFeatureSet.getExcludeOutputAttributesPerEntity().keySet().size());
+    assertEquals(1, createdFeatureSet.getExcludeOutputAttributesPerEntity().size());
     assertEquals(
         PERSON_ATTRIBUTES.stream().sorted().toList(),
         createdFeatureSet
@@ -157,7 +157,7 @@ void createUpdateDelete() throws InterruptedException {
     assertTrue(updatedFeatureSet.getLastModified().isAfter(updatedFeatureSet.getCreated()));
     assertEquals(1, updatedFeatureSet.getCriteria().size());
     assertTrue(updatedFeatureSet.getCriteria().contains(CONDITION_EQ_TYPE_2_DIABETES.getValue()));
-    assertEquals(1, updatedFeatureSet.getExcludeOutputAttributesPerEntity().keySet().size());
+    assertEquals(1, updatedFeatureSet.getExcludeOutputAttributesPerEntity().size());
     assertEquals(
         outputAttributes.stream().sorted().toList(),
         updatedFeatureSet.getExcludeOutputAttributesPerEntity().get(outputEntity).stream()

underlay/src/main/java/bio/terra/tanagra/filterbuilder/impl/core/EntityGroupFilterBuilderBase.java

@@ -47,8 +47,8 @@ public EntityGroupFilterBuilderBase(CriteriaSelector criteriaSelector) {
 
   // A SelectionGroup is the parameters that must be the same to be applied to a list of ids.
   protected static class SelectionGroup implements Comparable<SelectionGroup> {
-    public String entityGroupId;
-    public ValueDataOuterClass.ValueData valueData;
+    public final String entityGroupId;
+    public final ValueDataOuterClass.ValueData valueData;
 
     public SelectionGroup(String entityGroupId, ValueDataOuterClass.ValueData valueData) {
       this.entityGroupId = entityGroupId;
@@ -90,7 +90,6 @@ public boolean equals(Object o) {
         return false;
       }
 
-      @SuppressWarnings("unchecked")
       SelectionGroup sg = (SelectionGroup) o;
       return entityGroupId.equals(sg.entityGroupId) && Objects.equals(valueData, sg.valueData);
     }
@@ -102,8 +101,8 @@ public int hashCode() {
   }
 
   protected static class SelectionItem {
-    public Literal id;
-    public SelectionGroup group;
+    public final Literal id;
+    public final SelectionGroup group;
 
     public SelectionItem(Literal id, SelectionGroup group) {
       this.id = id;

underlay/src/main/java/bio/terra/tanagra/query/bigquery/translator/field/BQAttributeFieldTranslator.java

@@ -170,17 +170,17 @@ public ValueDisplay parseValueDisplayFromCountResult(
         Literal displayField = sqlRowResult.get(getDisplayFieldAlias(), DataType.STRING);
         if (displayField.isNull()) {
           LOGGER.warn(
-              "Entity-level hint not found for attribute: "
-                  + attributeField.getAttribute().getName());
+              "Entity-level hint not found for attribute: {}",
+              attributeField.getAttribute().getName());
           return new ValueDisplay(valueField);
         }
         return new ValueDisplay(valueField, displayField.getStringVal());
       }
       Optional<String> displayField = entityLevelHint.get().getEnumDisplay(valueField);
       if (displayField.isEmpty()) {
         LOGGER.warn(
-            "Entity-level hint enum display not found for attribute: "
-                + attributeField.getAttribute().getName());
+            "Entity-level hint enum display not found for attribute: {}",
+            attributeField.getAttribute().getName());
         return new ValueDisplay(valueField);
       }
       return new ValueDisplay(valueField, displayField.get());

underlay/src/main/java/bio/terra/tanagra/underlay/uiplugin/CriteriaSelector.java

@@ -53,9 +53,9 @@ public boolean isSupportsTemporalQueries() {
     return supportsTemporalQueries;
   }
 
-  public FilterBuilder getFilterBuilder() {
+  public FilterBuilder<?, ?> getFilterBuilder() {
     try {
-      return (FilterBuilder)
+      return (FilterBuilder<?, ?>)
           Class.forName(FILTER_BUILDER_PACKAGE + '.' + filterBuilder)
               .getDeclaredConstructor(CriteriaSelector.class)
               .newInstance(this);

underlay/src/main/java/bio/terra/tanagra/utils/RetryUtils.java

@@ -198,6 +198,6 @@ public interface SupplierWithCheckedException<T, E extends Exception> {
    */
   @FunctionalInterface
   public interface RunnableWithCheckedException<E extends Exception> {
-    void run() throws E, InterruptedException;
+    void run() throws E;
   }
 }

underlay/src/test/java/bio/terra/tanagra/filterbuilder/BioVUFilterBuilderTest.java

@@ -3,6 +3,7 @@
 import static bio.terra.tanagra.UnderlayTestConfigs.SD20230831;
 import static bio.terra.tanagra.utils.ProtobufUtils.serializeToJson;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertInstanceOf;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
@@ -220,7 +221,7 @@ void allFlagsCohortFilter() {
     assertNotNull(cohortFilter);
 
     // Order of sub-filters doesn't matter, but check that they're all there.
-    assertTrue(cohortFilter instanceof BooleanAndOrFilter);
+    assertInstanceOf(BooleanAndOrFilter.class, cohortFilter);
     BooleanAndOrFilter combinedFilter = (BooleanAndOrFilter) cohortFilter;
     assertEquals(BooleanAndOrFilter.LogicalOperator.AND, combinedFilter.getOperator());
     assertEquals(4, combinedFilter.getSubFilters().size());

underlay/src/test/java/bio/terra/tanagra/underlay/CriteriaSelectorTest.java

@@ -36,7 +36,7 @@ void gender() {
     assertEquals(SZCorePlugin.ATTRIBUTE.getIdInConfig(), gender.getPlugin());
     assertTrue(gender.getModifiers().isEmpty());
 
-    FilterBuilder filterBuilder = gender.getFilterBuilder();
+    FilterBuilder<?, ?> filterBuilder = gender.getFilterBuilder();
     assertNotNull(filterBuilder);
     assertEquals(PrimaryEntityFilterBuilder.class, filterBuilder.getClass());
   }
@@ -54,7 +54,7 @@ void condition() {
     assertNotNull(ageAtOccurrenceModifier);
     assertEquals(SZCorePlugin.ATTRIBUTE.getIdInConfig(), ageAtOccurrenceModifier.getPlugin());
 
-    FilterBuilder filterBuilder = condition.getFilterBuilder();
+    FilterBuilder<?, ?> filterBuilder = condition.getFilterBuilder();
     assertNotNull(filterBuilder);
     assertEquals(EntityGroupFilterBuilder.class, filterBuilder.getClass());
   }