Merge pull request plantbreeding#11 from plantbreeding/obs-opts

jloux-brapi · web-flow · commit 38a027293a41 · 2025-08-04T16:13:46.000-04:00
Observation and ObservationUnits Optimizations
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/controller/pheno/ObservationsApiController.java b/src/main/java/org/brapi/test/BrAPITestServer/controller/pheno/ObservationsApiController.java
@@ -121,7 +121,7 @@ public ResponseEntity<ObservationSingleResponse> observationsObservationDbIdPut(
 		log.debug("Request: " + request.getRequestURI());
 		validateSecurityContext(request, "ROLE_USER");
 		validateAcceptHeader(request);
-		Observation data = observationService.updateObservation(observationDbId, body);
+		Observation data = observationService.updateObservationAndConvert(observationDbId, body);
 		return responseOK(new ObservationSingleResponse(), data);
 	}
 
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/dto/ObservationUnitGermplasmData.java b/src/main/java/org/brapi/test/BrAPITestServer/model/dto/ObservationUnitGermplasmData.java
@@ -0,0 +1,30 @@
+package org.brapi.test.BrAPITestServer.model.dto;
+
+import java.util.UUID;
+
+public class ObservationUnitGermplasmData {
+    private String germplasmDbId;
+    private String germplasmName;
+
+    public ObservationUnitGermplasmData(String germplasmDbId,
+                                        String germplasmName) {
+        this.germplasmDbId = germplasmDbId;
+        this.germplasmName = germplasmName;
+    }
+
+    public String getGermplasmDbId() {
+        return germplasmDbId;
+    }
+
+    public void setGermplasmDbId(String germplasmDbId) {
+        this.germplasmDbId = germplasmDbId;
+    }
+
+    public String getGermplasmName() {
+        return germplasmName;
+    }
+
+    public void setGermplasmName(String germplasmName) {
+        this.germplasmName = germplasmName;
+    }
+}
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/ExperimentalDesignEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/ExperimentalDesignEntity.java
@@ -3,23 +3,12 @@
 import jakarta.persistence.*;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
 
-@Entity
-@Table(name = "study_experimental_design")
-public class ExperimentalDesignEntity extends BrAPIBaseEntity {
-	@Column
+@Embeddable
+public class ExperimentalDesignEntity {
+	@Column(name = "pui", table = "study_experimental_design")
 	private String PUI;
-	@Column
+    @Column(name = "description", table = "study_experimental_design")
 	private String description;
-	@OneToOne(fetch = FetchType.LAZY)
-	private StudyEntity study;
-
-    public StudyEntity getStudy() {
-        return study;
-    }
-
-    public void setStudy(StudyEntity study) {
-        this.study = study;
-    }
 
     public String getPUI() {
         return PUI;
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/GrowthFacilityEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/GrowthFacilityEntity.java
@@ -3,23 +3,12 @@
 import jakarta.persistence.*;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
 
-@Entity
-@Table(name = "study_growth_facility")
-public class GrowthFacilityEntity extends BrAPIBaseEntity {
-	@Column
+@Embeddable
+public class GrowthFacilityEntity {
+	@Column(name = "pui", table = "study_growth_facility")
 	private String PUI;
-	@Column
+	@Column(name = "description", table = "study_growth_facility")
 	private String description;
-	@OneToOne(fetch = FetchType.LAZY)
-	private StudyEntity study;
-
-    public StudyEntity getStudy() {
-        return study;
-    }
-
-    public void setStudy(StudyEntity study) {
-        this.study = study;
-    }
 
     public String getPUI() {
         return PUI;
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyEntity.java
@@ -12,6 +12,11 @@
 
 @Entity
 @Table(name = "study")
+@SecondaryTables({
+        @SecondaryTable(name = "study_experimental_design", pkJoinColumns = @PrimaryKeyJoinColumn(name = "study_id")),
+        @SecondaryTable(name = "study_growth_facility", pkJoinColumns = @PrimaryKeyJoinColumn(name = "study_id")),
+        @SecondaryTable(name = "study_last_update", pkJoinColumns = @PrimaryKeyJoinColumn(name = "study_id"))
+})
 @Where(clause = "soft_deleted = false")
 public class StudyEntity extends BrAPIPrimaryEntity {
 
@@ -32,11 +37,11 @@ public class StudyEntity extends BrAPIPrimaryEntity {
 	private Date endDate;
 	@OneToMany(mappedBy = "study")
 	private List<EnvironmentParametersEntity> environmentParameters;
-	@OneToOne(mappedBy = "study", cascade = CascadeType.ALL, orphanRemoval = true, fetch = FetchType.LAZY)
+	@Embedded
 	private ExperimentalDesignEntity experimentalDesign;
-	@OneToOne(mappedBy = "study", cascade = CascadeType.ALL, orphanRemoval = true, fetch = FetchType.LAZY)
+	@Embedded
 	private GrowthFacilityEntity growthFacility;
-	@OneToOne(mappedBy = "study", cascade = CascadeType.ALL, orphanRemoval = true, fetch = FetchType.LAZY)
+	@Embedded
 	private StudyLastUpdateEntity lastUpdate;
 	@Column
 	private String license;
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyLastUpdateEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyLastUpdateEntity.java
@@ -5,23 +5,12 @@
 
 import java.util.Date;
 
-@Entity
-@Table(name = "study_last_update")
-public class StudyLastUpdateEntity extends BrAPIBaseEntity {
-	@Column
+@Embeddable
+public class StudyLastUpdateEntity {
+	@Column(name = "timestamp", table = "study_last_update")
 	private Date timestamp;
-	@Column
+	@Column(name = "version", table = "study_last_update")
 	private String version;
-	@OneToOne(fetch = FetchType.LAZY)
-	private StudyEntity study;
-
-    public StudyEntity getStudy() {
-        return study;
-    }
-
-    public void setStudy(StudyEntity study) {
-        this.study = study;
-    }
 
     public Date getTimestamp() {
         return timestamp;
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationUnitEntity.java b/src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationUnitEntity.java
@@ -10,6 +10,7 @@
 import org.brapi.test.BrAPITestServer.model.entity.germ.CrossEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.SeedLotEntity;
+import org.hibernate.annotations.BatchSize;
 import org.hibernate.annotations.Where;
 
 import java.util.List;
@@ -28,6 +29,7 @@ public class ObservationUnitEntity extends BrAPIPrimaryEntity {
 	private String observationUnitPUI;
 	@ManyToOne(fetch = FetchType.LAZY)
 	private SeedLotEntity seedLot;
+	@BatchSize(size = 50)
 	@OneToMany(mappedBy="observationUnit", cascade=CascadeType.ALL)
 	private List<TreatmentEntity> treatments;
 	@OneToOne(mappedBy="observationUnit", cascade=CascadeType.ALL, fetch = FetchType.LAZY)
@@ -40,6 +42,7 @@ public class ObservationUnitEntity extends BrAPIPrimaryEntity {
 	private TrialEntity trial;
 	@ManyToOne(fetch = FetchType.LAZY)
 	private StudyEntity study;
+	@BatchSize(size = 50)
 	@OneToMany(mappedBy="observationUnit", cascade=CascadeType.ALL, fetch = FetchType.LAZY)
 	private List<ObservationEntity> observations;
 	
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/repository/BrAPIRepository.java b/src/main/java/org/brapi/test/BrAPITestServer/repository/BrAPIRepository.java
@@ -3,6 +3,7 @@
 import java.io.Serializable;
 import java.util.List;
 import java.util.Optional;
+import java.util.UUID;
 
 import org.brapi.test.BrAPITestServer.exceptions.InvalidPagingException;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
@@ -30,7 +31,7 @@ public interface BrAPIRepository<T extends BrAPIPrimaryEntity, ID extends Serial
 	
 	public <S extends T> void refresh(S entity);
 
-	public void fetchXrefs(Page<T> page, Class<T> searchClass) throws InvalidPagingException;
+	public void fetchXrefs(List<UUID> page, Page<T> pagedEntities, Class<T> searchClass) throws InvalidPagingException;
 
 	List<T> findByIdIn(List<ID> ids);
 }
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/repository/BrAPIRepositoryImpl.java b/src/main/java/org/brapi/test/BrAPITestServer/repository/BrAPIRepositoryImpl.java
@@ -14,6 +14,7 @@
 import org.brapi.test.BrAPITestServer.exceptions.InvalidPagingException;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
 import org.brapi.test.BrAPITestServer.model.entity.ExternalReferenceEntity;
+import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmEntity;
 import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
 import org.brapi.test.BrAPITestServer.service.SecurityUtils;
 
@@ -141,17 +142,17 @@ public <S extends T> void refresh(S entity) {
 		this.entityManager.refresh(entity);
 	}
 
-	public void fetchXrefs(Page<T> page, Class<T> searchClass) throws InvalidPagingException {
-		SearchQueryBuilder<T> searchQuery = new SearchQueryBuilder<T>(searchClass);
+	public void fetchXrefs(List<UUID> ids, Page<T> pagedEntities, Class<T> searchClass) {
+		SearchQueryBuilder<T> searchQuery = new SearchQueryBuilder<>(searchClass);
 		searchQuery.leftJoinFetch("externalReferences", "externalReferences")
-				   .appendList(page.stream().map(p -> p.getId().toString()).collect(Collectors.toList()), "id");
+				   .appendIds(ids);
 
-		Page<T> xrefs = findAllBySearchAndPaginate(searchQuery, PageRequest.of(0, page.getSize()));
+		List<T> xrefs = findAllBySearch(searchQuery);
 
 		Map<UUID, List<ExternalReferenceEntity>> xrefByEntity = new HashMap<>();
 		xrefs.forEach(entity -> xrefByEntity.put(entity.getId(), entity.getExternalReferences()));
 
-		page.forEach(entity -> entity.setExternalReferences(xrefByEntity.get(entity.getId())));
+		pagedEntities.forEach(entity -> entity.setExternalReferences(xrefByEntity.get(entity.getId())));
 	}
 
 	private void applyUserId(SearchQueryBuilder<T> searchQuery) {
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/repository/pheno/ObservationUnitRepository.java b/src/main/java/org/brapi/test/BrAPITestServer/repository/pheno/ObservationUnitRepository.java
@@ -2,9 +2,24 @@
 
 import org.brapi.test.BrAPITestServer.model.entity.pheno.ObservationUnitEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
+import org.springframework.data.jpa.repository.NativeQuery;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 
+import java.util.List;
 import java.util.UUID;
 
 public interface ObservationUnitRepository extends BrAPIRepository<ObservationUnitEntity, UUID> {
+    @Query("SELECT ou from ObservationUnitEntity ou " +
+            "LEFT JOIN FETCH ou.position " +
+            "WHERE ou.id IN :ids")
+    List<ObservationUnitEntity> findByIds(@Param("ids") List<String> ids);
 
+    @NativeQuery(
+            "SELECT ou.id, g.id, g.germplasm_name " +
+            "FROM  observation_unit ou " +
+            "JOIN germplasm g ON g.id = ou.germplasm_id " +
+            "WHERE ou.id IN :ouIds"
+    )
+    List<Object[]> fetchGermplasmDataForOUs(@Param("ouIds") List<UUID> ouIds);
 }
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/ProgramService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/ProgramService.java
@@ -76,6 +76,16 @@ public List<Program> findPrograms(ProgramSearchRequest request, Metadata metadat
 		return programs;
 	}
 
+	public List<ProgramEntity> findByIds(List<String> programDbIds) {
+		var result = new ArrayList<ProgramEntity>();
+
+		if (programDbIds.isEmpty()) {
+			return result;
+		}
+
+		return programRepository.findByIdIn(programDbIds.stream().map(UUID::fromString).toList());
+	}
+
 	public Program getProgram(String programDbId) throws BrAPIServerException {
 		return convertFromEntity(getProgramEntity(programDbId, HttpStatus.NOT_FOUND));
 	}
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/SeasonService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/SeasonService.java
@@ -109,6 +109,16 @@ public Season convertFromEntity(SeasonEntity entity) {
 		return season;
 	}
 
+	public List<SeasonEntity> findByIds(List<String> seasonIds) {
+		var result = new ArrayList<SeasonEntity>();
+
+		if (!seasonIds.isEmpty()) {
+			return seasonRepository.findByIdIn(seasonIds.stream().map(UUID::fromString).toList());
+		}
+
+		return result;
+	}
+
 	private void updateEntity(SeasonEntity entity, Season request) {
 		if (request.getSeasonName() != null)
 			entity.setSeason(request.getSeasonName());
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/core/StudyService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/core/StudyService.java
@@ -113,6 +113,16 @@ public List<Study> findStudies(String commonCropName, String studyType, String p
 		return findStudies(request, metadata);
 	}
 
+	public List<StudyEntity> findByIds(List<String> studyDbIds) {
+		var result = new ArrayList<StudyEntity>();
+
+		if (studyDbIds.isEmpty()) {
+			return result;
+		}
+
+		return studyRepository.findByIdIn(studyDbIds.stream().map(UUID::fromString).toList());
+	}
+
 	public List<Study> findStudies(StudySearchRequest request, Metadata metaData)
 		throws BrAPIServerException {
 
@@ -245,11 +255,11 @@ private void updateEntity(StudyEntity entity, StudyNewRequest body) throws BrAPI
 					body.getEnvironmentParameters().stream().map(this::convertToEntity).collect(Collectors.toList()));
 		}
 		if (body.getExperimentalDesign() != null)
-			entity.setExperimentalDesign(convertToEntity(body.getExperimentalDesign(), entity));
+			entity.setExperimentalDesign(convertToEntity(body.getExperimentalDesign()));
 		if (body.getGrowthFacility() != null)
-			entity.setGrowthFacility(convertToEntity(body.getGrowthFacility(), entity));
+			entity.setGrowthFacility(convertToEntity(body.getGrowthFacility()));
 		if (body.getLastUpdate() != null)
-			entity.setLastUpdate(convertToEntity(body.getLastUpdate(), entity));
+			entity.setLastUpdate(convertToEntity(body.getLastUpdate()));
 		if (body.getLicense() != null)
 			entity.setLicense(body.getLicense());
 		if (body.getLocationDbId() != null) {
@@ -412,13 +422,12 @@ private StudyLastUpdate convertFromEntity(StudyLastUpdateEntity entity) {
 		return update;
 	}
 
-	private StudyLastUpdateEntity convertToEntity(StudyLastUpdate update, StudyEntity study) {
+	private StudyLastUpdateEntity convertToEntity(StudyLastUpdate update) {
 		StudyLastUpdateEntity entity = null;
 		if (update != null) {
 			entity = new StudyLastUpdateEntity();
 			entity.setTimestamp(DateUtility.toDate(update.getTimestamp()));
 			entity.setVersion(update.getVersion());
-			entity.setStudy(study);
 		}
 		return entity;
 	}
@@ -433,13 +442,12 @@ private StudyGrowthFacility convertFromEntity(GrowthFacilityEntity entity) {
 		return gf;
 	}
 
-	private GrowthFacilityEntity convertToEntity(StudyGrowthFacility facility, StudyEntity study) {
+	private GrowthFacilityEntity convertToEntity(StudyGrowthFacility facility) {
 		GrowthFacilityEntity entity = null;
 		if (facility != null) {
 			entity = new GrowthFacilityEntity();
 			entity.setDescription(facility.getDescription());
 			entity.setPUI(facility.getPUI());
-			entity.setStudy(study);
 		}
 		return entity;
 	}
@@ -454,13 +462,12 @@ private StudyExperimentalDesign convertFromEntity(ExperimentalDesignEntity entit
 		return ed;
 	}
 
-	private ExperimentalDesignEntity convertToEntity(StudyExperimentalDesign design, StudyEntity study) {
+	private ExperimentalDesignEntity convertToEntity(StudyExperimentalDesign design) {
 		ExperimentalDesignEntity entity = null;
 		if (design != null) {
 			entity = new ExperimentalDesignEntity();
 			entity.setDescription(design.getDescription());
 			entity.setPUI(design.getPUI());
-			entity.setStudy(study);
 		}
 		return entity;
 	}
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
@@ -135,6 +135,16 @@ public List<Trial> findTrials(@Valid TrialSearchRequest request, Metadata metada
 		return trials;
 	}
 
+	public List<TrialEntity> findByIds(List<String> trialDbIds) {
+		var result = new ArrayList<TrialEntity>();
+
+		if (trialDbIds.isEmpty()) {
+			return result;
+		}
+
+		return trialRepository.findByIdIn(trialDbIds.stream().map(UUID::fromString).toList());
+	}
+
 	public Trial getTrial(String trialDbId) throws BrAPIServerException {
 		return convertFromEntity(getTrialEntity(trialDbId, HttpStatus.NOT_FOUND));
 	}
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/germ/CrossService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/germ/CrossService.java
@@ -63,6 +63,16 @@ public List<PlannedCross> findPlannedCrosses(String crossingProjectDbId, String
 		return crosses;
 	}
 
+	public List<CrossEntity> findByIds(List<String> crossDbIds) {
+		var result = new ArrayList<CrossEntity>();
+
+		if (crossDbIds.isEmpty()) {
+			return result;
+		}
+
+		return crossRepository.findByIdIn(crossDbIds.stream().map(UUID::fromString).toList());
+	}
+
 	public Page<CrossEntity> findCrossEntities(String crossingProjectDbId, String crossingProjectName, String crossDbId,
 			String crossName, String status, String commonCropName, String programDbId, String externalReferenceId,
 			String externalReferenceID, String externalReferenceSource, Boolean plannedCross, Metadata metadata)
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/germ/SeedLotService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/germ/SeedLotService.java
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationService.java
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationUnitService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationUnitService.java
diff --git a/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationVariableService.java b/src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationVariableService.java
diff --git a/src/main/resources/db/migration/U001.002__add_ids_to_study_join_tables.sql b/src/main/resources/db/migration/U001.002__add_ids_to_study_join_tables.sql
diff --git a/src/main/resources/db/migration/V001.002__drop_study_join_ids.sql b/src/main/resources/db/migration/V001.002__drop_study_join_ids.sql

Original file line number	Diff line number	Diff line change
`@@ -121,7 +121,7 @@ public ResponseEntity<ObservationSingleResponse> observationsObservationDbIdPut(`
`121`	`121`	`log.debug("Request: " + request.getRequestURI());`
`122`	`122`	`validateSecurityContext(request, "ROLE_USER");`
`123`	`123`	`validateAcceptHeader(request);`
`124`		`- Observation data = observationService.updateObservation(observationDbId, body);`
	`124`	`+ Observation data = observationService.updateObservationAndConvert(observationDbId, body);`
`125`	`125`	`return responseOK(new ObservationSingleResponse(), data);`
`126`	`126`	`}`
`127`	`127`