add cascade delete constraints for study foreign keys

dmeidlin · dmeidlin · commit e1761f866c59 · 2024-12-13T16:24:49.000-05:00
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/controller/core/TrialsApiController.java b/src/main/java/org/brapi/test/BrAPITestServer/controller/core/TrialsApiController.java
@@ -11,7 +11,6 @@
 import org.brapi.test.BrAPITestServer.service.DateUtility;
 import org.brapi.test.BrAPITestServer.service.SearchService;
 import org.brapi.test.BrAPITestServer.service.core.TrialService;
-import org.hibernate.SessionFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.http.ResponseEntity;
@@ -30,14 +29,12 @@ public class TrialsApiController extends BrAPIController implements TrialsApi {
 	private final HttpServletRequest request;
 	private final TrialService trialService;
 	private final SearchService searchService;
-	private final SessionFactory sessionFactory;
 
 	@org.springframework.beans.factory.annotation.Autowired
-	public TrialsApiController(TrialService trialService, SearchService searchService, HttpServletRequest request, SessionFactory sessionFactory) {
+	public TrialsApiController(TrialService trialService, SearchService searchService, HttpServletRequest request) {
 		this.trialService = trialService;
 		this.searchService = searchService;
 		this.request = request;
-        this.sessionFactory = sessionFactory;
     }
 
 	@CrossOrigin
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/factory/BrAPIComponent.java b/src/main/java/org/brapi/test/BrAPITestServer/factory/BrAPIComponent.java
@@ -11,7 +11,6 @@
 public interface BrAPIComponent<T, R extends SearchRequest> {
     List<T> findEntities(@Valid R request, Metadata metadata);
     BatchTypes getBatchType();
-    SearchRequestEntity.SearchRequestTypes getSearchType();
     List<String> collectDbIds(List<T> entities);
     void deleteBatchData(List<String> dbIds);
     void softDeleteBatchData(List<String> dbIds);
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/factory/core/ListComponent.java b/src/main/java/org/brapi/test/BrAPITestServer/factory/core/ListComponent.java
@@ -33,10 +33,6 @@ public BatchTypes getBatchType() {
         return BatchTypes.LISTS;
     }
 
-    @Override
-    public SearchRequestEntity.SearchRequestTypes getSearchType() {
-        return SearchRequestEntity.SearchRequestTypes.LISTS;
-    }
 
     @Override
     public List<String> collectDbIds(List<ListSummary> entities) {
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/factory/core/TrialComponent.java b/src/main/java/org/brapi/test/BrAPITestServer/factory/core/TrialComponent.java
@@ -32,10 +32,6 @@ public BatchTypes getBatchType() {
         return BatchTypes.TRIALS;
     }
 
-    @Override
-    public SearchRequestEntity.SearchRequestTypes getSearchType() {
-        return SearchRequestEntity.SearchRequestTypes.TRIALS;
-    }
 
     @Override
     public List<String> collectDbIds(List<Trial> entities) {
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/factory/geno/SampleComponent.java b/src/main/java/org/brapi/test/BrAPITestServer/factory/geno/SampleComponent.java
@@ -32,10 +32,6 @@ public BatchTypes getBatchType() {
         return BatchTypes.SAMPLES;
     }
 
-    @Override
-    public SearchRequestEntity.SearchRequestTypes getSearchType() {
-        return SearchRequestEntity.SearchRequestTypes.SAMPLES;
-    }
 
     @Override
     public List<String> collectDbIds(List<Sample> entities) {
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/factory/germ/GermplasmComponent.java b/src/main/java/org/brapi/test/BrAPITestServer/factory/germ/GermplasmComponent.java
@@ -33,10 +33,6 @@ public BatchTypes getBatchType() {
         return BatchTypes.GERMPLASM;
     }
 
-    @Override
-    public SearchRequestEntity.SearchRequestTypes getSearchType() {
-        return SearchRequestEntity.SearchRequestTypes.GERMPLASM;
-    }
 
     @Override
     public List<String> collectDbIds(List<Germplasm> entities) {
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/repository/core/TraitRepository.java b/src/main/java/org/brapi/test/BrAPITestServer/repository/core/TraitRepository.java
@@ -2,12 +2,6 @@
 
 import org.brapi.test.BrAPITestServer.model.entity.pheno.TraitEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
-import org.springframework.data.jpa.repository.Modifying;
-import org.springframework.data.jpa.repository.Query;
-import org.springframework.data.repository.query.Param;
-import org.springframework.transaction.annotation.Transactional;
-
-import java.util.List;
 
 public interface TraitRepository extends BrAPIRepository<TraitEntity, String> {
 }
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/BatchService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/BatchService.java
@@ -110,9 +110,7 @@ private BatchDetails convertToDetails(BatchEntity entity) {
 		BatchDetails details = new BatchDetails();
 		details = (BatchDetails) convertToBaseFields(entity, details);
 		details.setBatchDbId(entity.getId());
-		details.setData(entity.getData().stream().map((e) -> {
-			return e.getItem();
-		}).collect(Collectors.toList()));
+		details.setData(entity.getData().stream().map((e) -> e.getItem()).collect(Collectors.toList()));
 
 		return details;
 	}
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
@@ -77,7 +77,7 @@ public List<Sample> findBatchDeleteSamples(String batchDeleteDbId, Metadata meta
 		if (details.getData().isEmpty()) {
 			return new ArrayList<>();
 		}
-		
+
 		// Get the list summaries referenced in the batch delete
 		SampleSearchRequest request = new SampleSearchRequest();
 		details.getData().forEach(request::addSampleDbIdsItem);
diff --git a/src/main/resources/db/migration/V002.009__cascade_delete_observation_unit_position.sql b/src/main/resources/db/migration/V002.009__cascade_delete_observation_unit_position.sql
@@ -0,0 +1,12 @@
+-- This migration will delete an observation unit position that references a deleted observation unit
+
+-- First, drop the existing foreign key constraint
+ALTER TABLE ONLY public.observation_unit_position
+DROP CONSTRAINT IF EXISTS fk2mpgvaq1ppb8kjp3jk0ecpdyr;
+
+-- Then, recreate the constraint with ON DELETE CASCADE
+ALTER TABLE ONLY public.observation_unit_position
+    ADD CONSTRAINT fk2mpgvaq1ppb8kjp3jk0ecpdyr
+         FOREIGN KEY (observation_unit_id)
+             REFERENCES public.observation_unit(id)
+             ON DELETE CASCADE;
diff --git a/src/main/resources/db/migration/V002.010__cascade_delete_study_season.sql b/src/main/resources/db/migration/V002.010__cascade_delete_study_season.sql
@@ -0,0 +1,12 @@
+-- This migration will delete records associated with a deleted study
+
+-- First, drop the existing foreign key constraint
+ALTER TABLE ONLY public.study_season
+DROP CONSTRAINT IF EXISTS fk1r2518mglhwijy5mk31cfxh3h;
+
+-- Then, recreate the constraint with ON DELETE CASCADE
+ALTER TABLE ONLY public.study_season
+    ADD CONSTRAINT fk1r2518mglhwijy5mk31cfxh3h
+        FOREIGN KEY (study_db_id)
+            REFERENCES public.study(id)
+            ON DELETE CASCADE;
diff --git a/src/main/resources/db/migration/V002.011__cascade_delete_study_experiment_design.sql b/src/main/resources/db/migration/V002.011__cascade_delete_study_experiment_design.sql
@@ -0,0 +1,75 @@
+-- This migration will delete records associated with a deleted study
+
+-- First, drop the existing foreign key constraints
+ALTER TABLE ONLY public.study_experimental_design
+DROP CONSTRAINT IF EXISTS fk6p1eig0ibi880tu9yr3vd8yfn;
+
+ALTER TABLE ONLY public.study_environment_parameter
+DROP CONSTRAINT IF EXISTS fkhkcbdh997uw56v7orukh2hssm;
+
+ALTER TABLE ONLY public.study_data_link
+DROP CONSTRAINT IF EXISTS fknhgb2dwb4ffbsmydrhmephyyd;
+
+ALTER TABLE ONLY public.study_contact
+DROP CONSTRAINT IF EXISTS fkojmdovj11j3s8qxewlfjuw08y;
+
+ALTER TABLE ONLY public.study_growth_facility
+DROP CONSTRAINT IF EXISTS fkhie58olkxqm2t1ht6k5hl4wu5;
+
+ALTER TABLE ONLY public.study_last_update
+DROP CONSTRAINT IF EXISTS fkogmwhwbr1qx6vr1qr1nh6owpp;
+
+ALTER TABLE ONLY public.study_observation_level
+DROP CONSTRAINT IF EXISTS fkq886b0f9213w91opmlha96b0g;
+
+ALTER TABLE ONLY public.study_variable
+DROP CONSTRAINT IF EXISTS fkdg1qfle74hjs7s6a31j6poxs;
+
+-- Then, recreate the constraints with ON DELETE CASCADE
+ALTER TABLE ONLY public.study_experimental_design
+    ADD CONSTRAINT fk6p1eig0ibi880tu9yr3vd8yfn
+    FOREIGN KEY (study_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
+
+ALTER TABLE ONLY public.study_environment_parameter
+    ADD CONSTRAINT fkhkcbdh997uw56v7orukh2hssm
+    FOREIGN KEY (study_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
+
+ALTER TABLE ONLY public.study_data_link
+    ADD CONSTRAINT fknhgb2dwb4ffbsmydrhmephyyd
+    FOREIGN KEY (study_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
+
+ALTER TABLE ONLY public.study_contact
+    ADD CONSTRAINT fkojmdovj11j3s8qxewlfjuw08y
+    FOREIGN KEY (study_db_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
+
+ALTER TABLE ONLY public.study_growth_facility
+    ADD CONSTRAINT fkhie58olkxqm2t1ht6k5hl4wu5
+    FOREIGN KEY (study_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
+
+ALTER TABLE ONLY public.study_last_update
+    ADD CONSTRAINT fkogmwhwbr1qx6vr1qr1nh6owpp
+    FOREIGN KEY (study_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
+
+ALTER TABLE ONLY public.study_observation_level
+    ADD CONSTRAINT fkq886b0f9213w91opmlha96b0g
+    FOREIGN KEY (study_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
+
+ALTER TABLE ONLY public.study_variable
+    ADD CONSTRAINT fkdg1qfle74hjs7s6a31j6poxs
+    FOREIGN KEY (study_db_id)
+    REFERENCES public.study(id)
+    ON DELETE CASCADE;
diff --git a/src/main/resources/db/migration/V002.012__cascade_delete_observation_unit_level.sql b/src/main/resources/db/migration/V002.012__cascade_delete_observation_unit_level.sql
@@ -0,0 +1,13 @@
+-- This migration will cascade delete observation unit levels upon deletion of a referenced unit position
+
+-- First, drop the existing foreign key constraints
+ALTER TABLE ONLY public.observation_unit_level
+DROP CONSTRAINT IF EXISTS fkh70bs6tax01tl04ha9qjqo19;
+
+
+-- Then, recreate the constraints with ON DELETE CASCADE
+ALTER TABLE ONLY public.observation_unit_level
+    ADD CONSTRAINT fkh70bs6tax01tl04ha9qjqo19
+    FOREIGN KEY (position_id)
+    REFERENCES public.observation_unit_position(id)
+    ON DELETE CASCADE;

Original file line number	Diff line number	Diff line change
`@@ -33,10 +33,6 @@ public BatchTypes getBatchType() {`
`33`	`33`	`return BatchTypes.LISTS;`
`34`	`34`	`}`
`35`	`35`
`36`		`- @Override`
`37`		`- public SearchRequestEntity.SearchRequestTypes getSearchType() {`
`38`		`- return SearchRequestEntity.SearchRequestTypes.LISTS;`
`39`		`- }`
`40`	`36`
`41`	`37`	`@Override`
`42`	`38`	`public List<String> collectDbIds(List<ListSummary> entities) {`
Original file line number	Diff line number	Diff line change
`@@ -32,10 +32,6 @@ public BatchTypes getBatchType() {`
`32`	`32`	`return BatchTypes.TRIALS;`
`33`	`33`	`}`
`34`	`34`
`35`		`- @Override`
`36`		`- public SearchRequestEntity.SearchRequestTypes getSearchType() {`
`37`		`- return SearchRequestEntity.SearchRequestTypes.TRIALS;`
`38`		`- }`
`39`	`35`
`40`	`36`	`@Override`
`41`	`37`	`public List<String> collectDbIds(List<Trial> entities) {`
Original file line number	Diff line number	Diff line change
`@@ -77,7 +77,7 @@ public List<Sample> findBatchDeleteSamples(String batchDeleteDbId, Metadata meta`
`77`	`77`	`if (details.getData().isEmpty()) {`
`78`	`78`	`return new ArrayList<>();`
`79`	`79`	`}`
`80`		`-`
	`80`	`+`
`81`	`81`	`// Get the list summaries referenced in the batch delete`
`82`	`82`	`SampleSearchRequest request = new SampleSearchRequest();`
`83`	`83`	`details.getData().forEach(request::addSampleDbIdsItem);`