improvements from code review

Author: sagely1

apps/model-ad/api-next/src/main/java/org/sagebionetworks/model/ad/api/next/api/GeneExpressionApiDelegateImpl.java

@@ -22,41 +22,13 @@ public class GeneExpressionApiDelegateImpl implements GeneExpressionApiDelegate
 
   @Override
   public ResponseEntity<GeneExpressionsPageDto> getGeneExpressions(
-    GeneExpressionSearchQueryDto geneExpressionSearchQuery
+    GeneExpressionSearchQueryDto query
   ) {
-    // Extract query parameters with defaults
-    List<String> categories = geneExpressionSearchQuery != null
-      ? geneExpressionSearchQuery.getCategories()
-      : null;
-    List<String> items = geneExpressionSearchQuery != null &&
-      geneExpressionSearchQuery.getItems() != null
-      ? geneExpressionSearchQuery.getItems()
-      : List.of();
-    ItemFilterTypeQueryDto filterType = geneExpressionSearchQuery != null &&
-      geneExpressionSearchQuery.getItemFilterType() != null
-      ? geneExpressionSearchQuery.getItemFilterType()
-      : ItemFilterTypeQueryDto.INCLUDE;
-    Integer pageNumber = geneExpressionSearchQuery != null &&
-      geneExpressionSearchQuery.getPageNumber() != null
-      ? geneExpressionSearchQuery.getPageNumber()
-      : 0;
-    Integer pageSize = geneExpressionSearchQuery != null &&
-      geneExpressionSearchQuery.getPageSize() != null
-      ? geneExpressionSearchQuery.getPageSize()
-      : 10;
-
-    String[] tissueAndSex = extractTissueAndSex(categories);
+    String[] tissueAndSex = extractTissueAndSex(query.getCategories());
     String tissue = tissueAndSex[0];
     String sex = tissueAndSex[1];
 
-    GeneExpressionsPageDto results = geneExpressionService.loadGeneExpressions(
-      tissue,
-      sex,
-      items,
-      filterType,
-      pageNumber,
-      pageSize
-    );
+    GeneExpressionsPageDto results = geneExpressionService.loadGeneExpressions(query, tissue, sex);
 
     return ResponseEntity.ok()
       .headers(ApiHelper.createNoCacheHeaders(MediaType.APPLICATION_JSON))

apps/model-ad/api-next/src/main/java/org/sagebionetworks/model/ad/api/next/configuration/CacheConfiguration.java

@@ -25,7 +25,8 @@ public CacheManager cacheManager() {
     CaffeineCacheManager cacheManager = new CaffeineCacheManager();
 
     // Configure cache
-    cacheManager.setCaffeine(Caffeine.newBuilder().recordStats()); // Enable cache statistics for monitoring
+    // Enable cache statistics for monitoring
+    cacheManager.setCaffeine(Caffeine.newBuilder().recordStats());
 
     // Define the cache names used by query services
     cacheManager.setCacheNames(

apps/model-ad/api-next/src/main/java/org/sagebionetworks/model/ad/api/next/exception/DiseaseCorrelationNotFoundException.java

@@ -19,42 +19,6 @@
 @ControllerAdvice
 public class GlobalExceptionHandler extends ResponseEntityExceptionHandler {
 
-  @ExceptionHandler(ModelOverviewNotFoundException.class)
-  protected ResponseEntity<BasicErrorDto> handleModelOverviewNotFound(
-    ModelOverviewNotFoundException ex,
-    NativeWebRequest request,
-    Locale locale
-  ) {
-    return ResponseEntity.status(HttpStatus.NOT_FOUND)
-      .contentType(MediaType.APPLICATION_PROBLEM_JSON)
-      .body(
-        BasicErrorDto.builder()
-          .title(ErrorConstants.ENTITY_NOT_FOUND.getTitle())
-          .status(HttpStatus.NOT_FOUND.value())
-          .detail(ex.getMessage())
-          .instance(resolveInstance(request))
-          .build()
-      );
-  }
-
-  @ExceptionHandler(DiseaseCorrelationNotFoundException.class)
-  protected ResponseEntity<BasicErrorDto> handleDiseaseCorrelationNotFound(
-    DiseaseCorrelationNotFoundException ex,
-    NativeWebRequest request,
-    Locale locale
-  ) {
-    return ResponseEntity.status(HttpStatus.NOT_FOUND)
-      .contentType(MediaType.APPLICATION_PROBLEM_JSON)
-      .body(
-        BasicErrorDto.builder()
-          .title(ErrorConstants.ENTITY_NOT_FOUND.getTitle())
-          .status(HttpStatus.NOT_FOUND.value())
-          .detail(ex.getMessage())
-          .instance(resolveInstance(request))
-          .build()
-      );
-  }
-
   @ExceptionHandler(InvalidObjectIdException.class)
   protected ResponseEntity<BasicErrorDto> handleInvalidObjectId(
     InvalidObjectIdException ex,

apps/model-ad/api-next/src/main/java/org/sagebionetworks/model/ad/api/next/exception/GeneExpressionNotFoundException.java

@@ -14,6 +14,7 @@
 @Getter
 public class DiseaseCorrelationIdentifier {
 
+  // MG-586 - Consider using existing CompositeIdentifier utility if applicable
   String name;
   String age;
   String sex;

apps/model-ad/api-next/src/main/java/org/sagebionetworks/model/ad/api/next/exception/GlobalExceptionHandler.java

@@ -14,6 +14,7 @@
 @Getter
 public class GeneExpressionIdentifier {
 
+  // MG-586 - Consider using existing CompositeIdentifier utility if applicable
   String ensemblGeneId;
   String name;
 

apps/model-ad/api-next/src/main/java/org/sagebionetworks/model/ad/api/next/exception/ModelOverviewNotFoundException.java

@@ -2,12 +2,12 @@
 
 import java.math.BigDecimal;
 import java.util.List;
-import org.sagebionetworks.model.ad.api.next.exception.DataIntegrityException;
 import org.sagebionetworks.model.ad.api.next.model.document.DiseaseCorrelationDocument;
 import org.sagebionetworks.model.ad.api.next.model.document.DiseaseCorrelationDocument.CorrelationResult;
 import org.sagebionetworks.model.ad.api.next.model.dto.CorrelationResultDto;
 import org.sagebionetworks.model.ad.api.next.model.dto.DiseaseCorrelationDto;
 import org.sagebionetworks.model.ad.api.next.model.dto.SexDto;
+import org.sagebionetworks.model.ad.api.next.util.EnumConverter;
 import org.springframework.lang.Nullable;
 import org.springframework.stereotype.Component;
 
@@ -31,7 +31,7 @@ public DiseaseCorrelationDto toDto(@Nullable DiseaseCorrelationDocument document
       modifiedGenes,
       document.getCluster(),
       document.getAge(),
-      toSexDto(document.getSex())
+      EnumConverter.toSexDto(document.getSex(), "disease correlation record")
     );
 
     dto.setCBE(toCorrelationDto(document.getCbe()));
@@ -44,20 +44,6 @@ public DiseaseCorrelationDto toDto(@Nullable DiseaseCorrelationDocument document
     return dto;
   }
 
-  private SexDto toSexDto(@Nullable String value) {
-    if (value == null) {
-      throw new DataIntegrityException("Missing sex value in disease correlation record");
-    }
-    try {
-      return SexDto.fromValue(value);
-    } catch (IllegalArgumentException ex) {
-      throw new DataIntegrityException(
-        "Unexpected sex value '" + value + "' in disease correlation record",
-        ex
-      );
-    }
-  }
-
   private String getCompositeId(DiseaseCorrelationDocument document) {
     String name = document.getName();
     String age = document.getAge();

apps/model-ad/api-next/src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/DiseaseCorrelationIdentifier.java

@@ -2,12 +2,12 @@
 
 import java.math.BigDecimal;
 import java.util.List;
-import org.sagebionetworks.model.ad.api.next.exception.DataIntegrityException;
 import org.sagebionetworks.model.ad.api.next.model.document.GeneExpressionDocument;
 import org.sagebionetworks.model.ad.api.next.model.document.GeneExpressionDocument.FoldChangeResult;
 import org.sagebionetworks.model.ad.api.next.model.dto.FoldChangeResultDto;
 import org.sagebionetworks.model.ad.api.next.model.dto.GeneExpressionDto;
 import org.sagebionetworks.model.ad.api.next.model.dto.SexCohortDto;
+import org.sagebionetworks.model.ad.api.next.util.EnumConverter;
 import org.springframework.lang.Nullable;
 import org.springframework.stereotype.Component;
 
@@ -33,7 +33,7 @@ public GeneExpressionDto toDto(@Nullable GeneExpressionDocument document) {
       document.getModelGroup(),
       document.getModelType(),
       document.getTissue(),
-      toSexCohortDto(document.getSex())
+      EnumConverter.toSexCohortDto(document.getSexCohort(), "gene expression record")
     );
 
     dto.set4months(toFoldChangeDto(document.getFourMonths()));
@@ -43,20 +43,6 @@ public GeneExpressionDto toDto(@Nullable GeneExpressionDocument document) {
     return dto;
   }
 
-  private SexCohortDto toSexCohortDto(@Nullable String value) {
-    if (value == null) {
-      throw new DataIntegrityException("Missing sex value in gene expression record");
-    }
-    try {
-      return SexCohortDto.fromValue(value);
-    } catch (IllegalArgumentException ex) {
-      throw new DataIntegrityException(
-        "Unexpected sex value '" + value + "' in gene expression record",
-        ex
-      );
-    }
-  }
-
   private String getCompositeId(GeneExpressionDocument document) {
     String ensemblGeneId = document.getEnsemblGeneId();
     String name = document.getName();