Merge pull request #54 from Breeding-Insight/bug/BI-2650

nickpalladino · web-flow · commit daa90d58f1c7 · 2025-05-30T14:25:10.000-04:00
BI-2650 - BrAPI server changes for issues found with bi-api automated tests
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/controller/geno/SamplesApiController.java b/src/main/java/org/brapi/test/BrAPITestServer/controller/geno/SamplesApiController.java
@@ -52,22 +52,22 @@ public SamplesApiController(SampleService sampleService, SearchService searchSer
 	@Override
 	public ResponseEntity<SampleListResponse> samplesGet(
 			@Valid @RequestParam(value = "batchDeleteDbId", required = false) String batchDeleteDbId,
-			@RequestParam(value = "sampleDbId", required = false) String sampleDbId,
-			@RequestParam(value = "sampleName", required = false) String sampleName,
-			@RequestParam(value = "sampleGroupDbId", required = false) String sampleGroupDbId,
-			@RequestParam(value = "observationUnitDbId", required = false) String observationUnitDbId,
-			@RequestParam(value = "plateDbId", required = false) String plateDbId,
-			@RequestParam(value = "plateName", required = false) String plateName,
-			@RequestParam(value = "germplasmDbId", required = false) String germplasmDbId,
-			@RequestParam(value = "studyDbId", required = false) String studyDbId,
-			@RequestParam(value = "trialDbId", required = false) String trialDbId,
-			@RequestParam(value = "commonCropName", required = false) String commonCropName,
-			@RequestParam(value = "programDbId", required = false) String programDbId,
-			@RequestParam(value = "externalReferenceID", required = false) String externalReferenceId,
-			@RequestParam(value = "externalReferenceID", required = false) String externalReferenceID,
-			@RequestParam(value = "externalReferenceSource", required = false) String externalReferenceSource,
-			@RequestParam(value = "page", required = false) Integer page,
-			@RequestParam(value = "pageSize", required = false) Integer pageSize,
+			@Valid @RequestParam(value = "sampleDbId", required = false) String sampleDbId,
+			@Valid @RequestParam(value = "sampleName", required = false) String sampleName,
+			@Valid @RequestParam(value = "sampleGroupDbId", required = false) String sampleGroupDbId,
+			@Valid @RequestParam(value = "observationUnitDbId", required = false) String observationUnitDbId,
+			@Valid @RequestParam(value = "plateDbId", required = false) String plateDbId,
+			@Valid @RequestParam(value = "plateName", required = false) String plateName,
+			@Valid @RequestParam(value = "germplasmDbId", required = false) String germplasmDbId,
+			@Valid @RequestParam(value = "studyDbId", required = false) String studyDbId,
+			@Valid @RequestParam(value = "trialDbId", required = false) String trialDbId,
+			@Valid @RequestParam(value = "commonCropName", required = false) String commonCropName,
+			@Valid @RequestParam(value = "programDbId", required = false) String programDbId,
+			@Valid @RequestParam(value = "externalReferenceID", required = false) String externalReferenceId,
+			@Valid @RequestParam(value = "externalReferenceID", required = false) String externalReferenceID,
+			@Valid @RequestParam(value = "externalReferenceSource", required = false) String externalReferenceSource,
+			@Valid @RequestParam(value = "page", required = false) Integer page,
+			@Valid @RequestParam(value = "pageSize", required = false) Integer pageSize,
 			@RequestHeader(value = "Authorization", required = false) String authorization)
 			throws BrAPIServerException {
 
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/PlateEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/PlateEntity.java
@@ -19,7 +19,7 @@
 @Where(clause = "soft_deleted = false")
 public class PlateEntity extends BrAPIPrimaryEntity {
     @Column
-    private UUID clientPlateDbId;
+    private String clientPlateDbId;
     @Column
     private String clientPlateBarcode;
     @Column
@@ -93,10 +93,10 @@ public VendorPlateSubmissionEntity getSubmission() {
 	public void setSubmission(VendorPlateSubmissionEntity submission) {
 		this.submission = submission;
 	}
-	public UUID getClientPlateDbId() {
+	public String getClientPlateDbId() {
 		return clientPlateDbId;
 	}
-	public void setClientPlateDbId(UUID clientPlateDbId) {
+	public void setClientPlateDbId(String clientPlateDbId) {
 		this.clientPlateDbId = clientPlateDbId;
 	}
 	public String getClientPlateBarcode() {
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/vendor/VendorOrderEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/vendor/VendorOrderEntity.java
@@ -14,7 +14,7 @@
 @Table(name = "vendor_order")
 public class VendorOrderEntity extends BrAPIPrimaryEntity {
     @Column
-    private UUID clientPlateDbId;
+    private String clientPlateDbId;
     @Column
     private String clientPlateBarcode;
     @Column
@@ -73,11 +73,11 @@ public void setPlateSubmission(VendorPlateSubmissionEntity plateSubmission) {
         this.plateSubmission = plateSubmission;
     }
 
-    public UUID getClientPlateDbId() {
+    public String getClientPlateDbId() {
         return clientPlateDbId;
     }
 
-    public void setClientPlateDbId(UUID clientPlateDbId) {
+    public void setClientPlateDbId(String clientPlateDbId) {
         this.clientPlateDbId = clientPlateDbId;
     }
 
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/vendor/VendorPlateSubmissionEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/vendor/VendorPlateSubmissionEntity.java
@@ -13,7 +13,7 @@
 public class VendorPlateSubmissionEntity extends BrAPIPrimaryEntity {
 
     @Column
-    private UUID clientId;
+    private String clientId;
     @Column
     private Integer numberOfSamples;
     @Column
@@ -30,10 +30,10 @@ public VendorOrderEntity getOrder() {
 	public void setOrder(VendorOrderEntity order) {
 		this.order = order;
 	}
-	public UUID getClientId() {
+	public String getClientId() {
 		return clientId;
 	}
-	public void setClientId(UUID clientId) {
+	public void setClientId(String clientId) {
 		this.clientId = clientId;
 	}
 	public Integer getNumberOfSamples() {
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/repository/core/ListRepository.java b/src/main/java/org/brapi/test/BrAPITestServer/repository/core/ListRepository.java
@@ -14,10 +14,10 @@ public interface ListRepository extends BrAPIRepository<ListEntity, UUID>{
     @Modifying
     @Transactional
     @Query("UPDATE ListEntity l SET l.softDeleted = :softDeleted WHERE l.id = :listId")
-    int updateSoftDeletedStatus(@Param("listId") String listId, @Param("softDeleted") boolean softDeleted);
+    int updateSoftDeletedStatus(@Param("listId") UUID listId, @Param("softDeleted") boolean softDeleted);
 
     @Modifying
     @Transactional
     @Query("UPDATE ListEntity l SET l.softDeleted = :softDeleted WHERE l.id IN :listIds")
-    int updateSoftDeletedStatusBatch(@Param("listIds") List<String> listIds, @Param("softDeleted") boolean softDeleted);
+    int updateSoftDeletedStatusBatch(@Param("listIds") List<UUID> listIds, @Param("softDeleted") boolean softDeleted);
 }
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/repository/core/TrialRepository.java b/src/main/java/org/brapi/test/BrAPITestServer/repository/core/TrialRepository.java
@@ -29,11 +29,11 @@ Page<TrialEntity> findBySearch(
 	@Modifying
 	@Transactional
 	@Query("UPDATE TrialEntity t SET t.softDeleted = :softDeleted WHERE t.id = :trialId")
-	int updateSoftDeletedStatus(@Param("trialId") String trialId, @Param("softDeleted") boolean softDeleted);
+	int updateSoftDeletedStatus(@Param("trialId") UUID trialId, @Param("softDeleted") boolean softDeleted);
 
 	@Modifying
 	@Transactional
 	@Query("UPDATE TrialEntity t SET t.softDeleted = :softDeleted WHERE t.id IN :trialIds")
-	int updateSoftDeletedStatusBatch(@Param("trialIds") List<String> trialIds, @Param("softDeleted") boolean softDeleted);
+	int updateSoftDeletedStatusBatch(@Param("trialIds") List<UUID> trialIds, @Param("softDeleted") boolean softDeleted);
 
 }
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/ListService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/ListService.java
@@ -169,7 +169,7 @@ public void deleteListBatch(List<String> listDbIds) {
 	}
 
 	public void softDeleteListBatch(List<String> listDbIds) {
-		listRepository.updateSoftDeletedStatusBatch(listDbIds, true);
+		listRepository.updateSoftDeletedStatusBatch(listDbIds.stream().map(UUID::fromString).toList(), true);
 	}
 
 	public void deleteList(String listDbId) throws BrAPIServerException {
@@ -181,7 +181,7 @@ public void deleteList(String listDbId) throws BrAPIServerException {
 	}
 
 	public void softDeleteList(String listDbId) throws BrAPIServerDbIdNotFoundException {
-		int updatedCount = listRepository.updateSoftDeletedStatus(listDbId, true);
+		int updatedCount = listRepository.updateSoftDeletedStatus(UUID.fromString(listDbId), true);
 		if (updatedCount == 0) {
 			throw new BrAPIServerDbIdNotFoundException("list", listDbId, "list database ID", HttpStatus.NOT_FOUND);
 		}
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/TrialService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/TrialService.java
@@ -175,11 +175,11 @@ public void deleteTrialBatch(List<String> trialDbIds) {
 	}
 
 	public void softDeleteTrialBatch(List<String> trialDbIds) {
-		trialRepository.updateSoftDeletedStatusBatch(trialDbIds, true);
+		trialRepository.updateSoftDeletedStatusBatch(trialDbIds.stream().map(UUID::fromString).toList(), true);
 	}
 
 	public void softDeleteTrial(String trialDbId) throws BrAPIServerDbIdNotFoundException {
-		int updatedCount = trialRepository.updateSoftDeletedStatus(trialDbId, true);
+		int updatedCount = trialRepository.updateSoftDeletedStatus(UUID.fromString(trialDbId), true);
 		if (updatedCount == 0) {
 			throw new BrAPIServerDbIdNotFoundException("trial", trialDbId, "trial database ID", HttpStatus.NOT_FOUND);
 		}
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/geno/SampleService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/geno/SampleService.java
@@ -258,7 +258,7 @@ private Sample convertFromEntity(SampleEntity entity) {
 		sample.setSampleBarcode(entity.getSampleBarcode());
 		sample.setSampleDbId(entity.getId().toString());
 		sample.setSampleDescription(entity.getSampleDescription());
-		sample.setSampleGroupDbId(entity.getSampleGroupDbId().toString());
+		sample.setSampleGroupDbId(entity.getSampleGroupDbId() != null ? entity.getSampleGroupDbId().toString(): null);
 		sample.setSampleName(entity.getSampleName());
 		sample.setSamplePUI(entity.getSamplePUI());
 		sample.setSampleTimestamp(DateUtility.toOffsetDateTime(entity.getSampleTimestamp()));
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/geno/VendorSampleService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/geno/VendorSampleService.java
@@ -161,7 +161,7 @@ private VendorPlateSubmissionPlates convertFromEntityToSummary(PlateEntity entit
 	private VendorOrderEntity convertToEntity(VendorOrderSubmissionRequest request) {
 		VendorOrderEntity entity = new VendorOrderEntity();
 		entity.setClientPlateBarcode(request.getClientId());
-		entity.setClientPlateDbId(UUID.fromString(request.getClientId()));
+		entity.setClientPlateDbId(request.getClientId());
 		entity.setRequiredServiceInfo(request.getRequiredServiceInfo());
 		entity.setSampleType(request.getSampleType());
 		entity.setServiceIds(request.getServiceIds());
@@ -190,7 +190,7 @@ private VendorPlateSubmissionEntity convertToEntity(VendorOrderSubmissionRequest
 
 	private PlateEntity convertToEntity(VendorPlateSubmissionRequestPlates newPlate) {
 		PlateEntity plateEntity = new PlateEntity();
-		plateEntity.setClientPlateDbId(UUID.fromString(newPlate.getClientPlateId()));
+		plateEntity.setClientPlateDbId(newPlate.getClientPlateId());
 		plateEntity.setStatusTimeStamp(new Date());
 
 		return plateEntity;
@@ -199,7 +199,7 @@ private PlateEntity convertToEntity(VendorPlateSubmissionRequestPlates newPlate)
 	private VendorOrderEntity convertToEntity(VendorPlateSubmissionRequest request) {
 		VendorOrderEntity entity = new VendorOrderEntity();
 		entity.setClientPlateBarcode(request.getClientId());
-		entity.setClientPlateDbId(UUID.fromString(request.getClientId()));
+		entity.setClientPlateDbId(request.getClientId());
 		entity.setSampleType(request.getSampleType());
 		entity.setStatus(StatusEnum.RECEIVED);
 		entity.setStatusTimeStamp(new Date());
diff --git a/src/main/resources/db/migration/V003__client_and_plate_id_to_string.sql b/src/main/resources/db/migration/V003__client_and_plate_id_to_string.sql
@@ -0,0 +1,32 @@
+-- See the NOTICE file distributed with this work for additional information
+-- regarding copyright ownership.
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--     http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+-- change client_plate_db_id back to text instead of forcing uuid
+ALTER TABLE vendor_order
+ALTER COLUMN client_plate_db_id
+    TYPE text
+    USING client_plate_db_id::text;
+
+-- change client_id back to text instead of forcing uuid
+ALTER TABLE plate_submission
+ALTER COLUMN client_id
+    TYPE text
+    USING client_id::text;
+
+-- change client_plate_db_id back to text instead of forcing uuid
+ALTER TABLE plate
+ALTER COLUMN client_plate_db_id
+    TYPE text
+    USING client_plate_db_id::text;

Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@`
`14`	`14`	`@Table(name = "vendor_order")`
`15`	`15`	`public class VendorOrderEntity extends BrAPIPrimaryEntity {`
`16`	`16`	`@Column`
`17`		`- private UUID clientPlateDbId;`
	`17`	`+ private String clientPlateDbId;`
`18`	`18`	`@Column`
`19`	`19`	`private String clientPlateBarcode;`
`20`	`20`	`@Column`
`@@ -73,11 +73,11 @@ public void setPlateSubmission(VendorPlateSubmissionEntity plateSubmission) {`
`73`	`73`	`this.plateSubmission = plateSubmission;`
`74`	`74`	`}`
`75`	`75`
`76`		`- public UUID getClientPlateDbId() {`
	`76`	`+ public String getClientPlateDbId() {`
`77`	`77`	`return clientPlateDbId;`
`78`	`78`	`}`
`79`	`79`
`80`		`- public void setClientPlateDbId(UUID clientPlateDbId) {`
	`80`	`+ public void setClientPlateDbId(String clientPlateDbId) {`
`81`	`81`	`this.clientPlateDbId = clientPlateDbId;`
`82`	`82`	`}`
`83`	`83`
Original file line number	Diff line number	Diff line change
`@@ -169,7 +169,7 @@ public void deleteListBatch(List<String> listDbIds) {`
`169`	`169`	`}`
`170`	`170`
`171`	`171`	`public void softDeleteListBatch(List<String> listDbIds) {`
`172`		`- listRepository.updateSoftDeletedStatusBatch(listDbIds, true);`
	`172`	`+ listRepository.updateSoftDeletedStatusBatch(listDbIds.stream().map(UUID::fromString).toList(), true);`
`173`	`173`	`}`
`174`	`174`
`175`	`175`	`public void deleteList(String listDbId) throws BrAPIServerException {`
`@@ -181,7 +181,7 @@ public void deleteList(String listDbId) throws BrAPIServerException {`
`181`	`181`	`}`
`182`	`182`
`183`	`183`	`public void softDeleteList(String listDbId) throws BrAPIServerDbIdNotFoundException {`
`184`		`- int updatedCount = listRepository.updateSoftDeletedStatus(listDbId, true);`
	`184`	`+ int updatedCount = listRepository.updateSoftDeletedStatus(UUID.fromString(listDbId), true);`
`185`	`185`	`if (updatedCount == 0) {`
`186`	`186`	`throw new BrAPIServerDbIdNotFoundException("list", listDbId, "list database ID", HttpStatus.NOT_FOUND);`
`187`	`187`	`}`
Original file line number	Diff line number	Diff line change
`@@ -175,11 +175,11 @@ public void deleteTrialBatch(List<String> trialDbIds) {`
`175`	`175`	`}`
`176`	`176`
`177`	`177`	`public void softDeleteTrialBatch(List<String> trialDbIds) {`
`178`		`- trialRepository.updateSoftDeletedStatusBatch(trialDbIds, true);`
	`178`	`+ trialRepository.updateSoftDeletedStatusBatch(trialDbIds.stream().map(UUID::fromString).toList(), true);`
`179`	`179`	`}`
`180`	`180`
`181`	`181`	`public void softDeleteTrial(String trialDbId) throws BrAPIServerDbIdNotFoundException {`
`182`		`- int updatedCount = trialRepository.updateSoftDeletedStatus(trialDbId, true);`
	`182`	`+ int updatedCount = trialRepository.updateSoftDeletedStatus(UUID.fromString(trialDbId), true);`
`183`	`183`	`if (updatedCount == 0) {`
`184`	`184`	`throw new BrAPIServerDbIdNotFoundException("trial", trialDbId, "trial database ID", HttpStatus.NOT_FOUND);`
`185`	`185`	`}`