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[BI-2903] Support for program_id in germplasm table#23

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[BI-2903] Support for program_id in germplasm table #23

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2bd1d47
Create migration script, add programDbId to entity and model
jloux-brapi Aug 10, 2026
2bad4ff
Support for programId in GermplasmApi
jloux-brapi Aug 11, 2026
bd8e00a
Merge branch 'feature/BI-2996' into feature/BI-2903
jloux-brapi Aug 19, 2026
ad1c04a
Merge branch 'feature/BI-2996' into feature/BI-2903
jloux-brapi Aug 20, 2026
7248c4d
Merge branch 'feature/BI-2996' into feature/BI-2903
jloux-brapi Aug 20, 2026
ef2bade
Merge branch 'feature/BI-2996' into feature/BI-2903
jloux-brapi Aug 24, 2026
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1 change: 1 addition & 0 deletions src/main/java/io/swagger/api/germ/GermplasmApi.java
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Expand Up@@ -143,6 +143,7 @@ ResponseEntity<GermplasmListResponse> germplasmGet(
@ApiParam(value = "progenyDbId") @Valid @RequestParam(value = "progenyDbId", required = false) String progenyDbId,
@ApiParam(value = "commonCropName") @Valid @RequestParam(value = "commonCropName", required = false) String commonCropName,
@ApiParam(value = "programDbId") @Valid @RequestParam(value = "programDbId", required = false) String programDbId,
@ApiParam(value = "programName") @Valid @RequestParam(value = "programName", required = false) String programName,
@ApiParam(value = "externalReferenceID") @Valid @RequestParam(value = "externalReferenceID", required = false) String externalReferenceID,
@ApiParam(value = "externalReferenceId") @Valid @RequestParam(value = "externalReferenceId", required = false) String externalReferenceId,
@ApiParam(value = "externalReferenceSource") @Valid @RequestParam(value = "externalReferenceSource", required = false) String externalReferenceSource,
Expand Down
30 changes: 28 additions & 2 deletions src/main/java/io/swagger/model/germ/GermplasmNewRequest.java
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Expand Up@@ -97,6 +97,12 @@ public class GermplasmNewRequest extends BrAPIDataModel {
@JsonProperty("taxonIds")
private List<TaxonID> taxonIds = null;

@JsonProperty("programDbId")
private String programDbId = null;

@JsonProperty("programName")
private String programName = null;

public String getBreedingMethodName() {
return breedingMethodName;
}
Expand DownExpand Up@@ -510,6 +516,22 @@ public void setTaxonIds(List<TaxonID> taxonIds) {
this.taxonIds = taxonIds;
}

public String getProgramDbId() {
return programDbId;
}

public void setProgramDbId(String programDbId) {
this.programDbId = programDbId;
}

public String getProgramName() {
return programName;
}

public void setProgramName(String programName) {
this.programName = programName;
}

@Override
public boolean equals(java.lang.Object o) {
if (this == o) {
Expand DownExpand Up@@ -550,7 +572,9 @@ public boolean equals(java.lang.Object o) {
&& Objects.equals(this.subtaxa, germplasmNewRequest.subtaxa)
&& Objects.equals(this.subtaxaAuthority, germplasmNewRequest.subtaxaAuthority)
&& Objects.equals(this.synonyms, germplasmNewRequest.synonyms)
&& Objects.equals(this.taxonIds, germplasmNewRequest.taxonIds);
&& Objects.equals(this.taxonIds, germplasmNewRequest.taxonIds)
&& Objects.equals(this.programDbId, germplasmNewRequest.programDbId)
&& Objects.equals(this.programName, germplasmNewRequest.programName);
}

@Override
Expand All@@ -560,7 +584,7 @@ public int hashCode() {
countryOfOriginCode, defaultDisplayName, documentationURL, donors, externalReferences, genus,
germplasmName, germplasmOrigin, germplasmPUI, germplasmPreprocessing, instituteCode, instituteName,
pedigree, seedSource, seedSourceDescription, species, speciesAuthority, storageTypes, subtaxa,
subtaxaAuthority, synonyms, taxonIds);
subtaxaAuthority, synonyms, taxonIds, programDbId, programName);
}

@Override
Expand DownExpand Up@@ -600,6 +624,8 @@ public String toString() {
sb.append(" subtaxaAuthority: ").append(toIndentedString(subtaxaAuthority)).append("\n");
sb.append(" synonyms: ").append(toIndentedString(synonyms)).append("\n");
sb.append(" taxonIds: ").append(toIndentedString(taxonIds)).append("\n");
sb.append(" programDbId: ").append(toIndentedString(programDbId)).append("\n");
sb.append(" programName: ").append(toIndentedString(programName)).append("\n");
sb.append("}");
return sb.toString();
}
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/brapi/test/BrAPITestServer/controller/germ/GermplasmApiController.java
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Expand Up@@ -156,6 +156,7 @@ public ResponseEntity<GermplasmListResponse> germplasmGet(
@RequestParam(value = "progenyDbId", required = false) String progenyDbId,
@RequestParam(value = "commonCropName", required = false) String commonCropName,
@RequestParam(value = "programDbId", required = false) String programDbId,
@RequestParam(value = "programName", required = false) String programName,
@RequestParam(value = "externalReferenceID", required = false) String externalReferenceID,
@RequestParam(value = "externalReferenceId", required = false) String externalReferenceId,
@RequestParam(value = "externalReferenceSource", required = false) String externalReferenceSource,
Expand All@@ -170,7 +171,7 @@ public ResponseEntity<GermplasmListResponse> germplasmGet(
Metadata metadata = generateMetaDataTemplate(page, pageSize);
List<Germplasm> data = germplasmService.findGermplasm(germplasmPUI, germplasmDbId, germplasmName,
accessionNumber, collection, binomialName, genus, species, trialDbId, studyDbId, synonym, parentDbId,
progenyDbId, commonCropName, programDbId, externalReferenceId, externalReferenceID,
progenyDbId, commonCropName, programDbId, programName, externalReferenceId, externalReferenceID,
externalReferenceSource, metadata);
return responseOK(new GermplasmListResponse(), new GermplasmListResponseResult(), data, metadata);
}
Expand Down
11 changes: 11 additions & 0 deletions src/main/java/org/brapi/test/BrAPITestServer/model/entity/germ/GermplasmEntity.java
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Expand Up@@ -9,6 +9,7 @@
import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
import org.brapi.test.BrAPITestServer.model.entity.SearchRequestEntity;
import org.brapi.test.BrAPITestServer.model.entity.core.CropEntity;
import org.brapi.test.BrAPITestServer.model.entity.core.ProgramEntity;
import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmInstituteEntity.InstituteTypeEnum;
import org.brapi.test.BrAPITestServer.model.entity.pheno.ObservationUnitEntity;
import org.brapi.test.BrAPITestServer.model.entity.pheno.TaxonEntity;
Expand DownExpand Up@@ -96,6 +97,8 @@ public class GermplasmEntity extends BrAPIPrimaryEntity {
private List<GermplasmStorageTypesEnum> typeOfGermplasmStorageCode;
@Column(name = "soft_deleted")
private boolean softDeleted;
@ManyToOne(cascade = CascadeType.DETACH, fetch = FetchType.LAZY)
private ProgramEntity program;

public GermplasmInstituteEntity getHostInstitute() {
if (getInstitutes() != null) {
Expand DownExpand Up@@ -368,4 +371,12 @@ public void setTypeOfGermplasmStorageCode(List<GermplasmStorageTypesEnum> typeOf

public void setSoftDeleted(boolean sofDeleted) { this.softDeleted = sofDeleted; }

public ProgramEntity getProgram() {
return program;
}

public void setProgram(ProgramEntity program) {
this.program = program;
}

}
31 changes: 24 additions & 7 deletions src/main/java/org/brapi/test/BrAPITestServer/service/core/ProgramService.java
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@@ -1,9 +1,7 @@
package org.brapi.test.BrAPITestServer.service.core;

import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import java.util.UUID;
import java.util.*;
import java.util.stream.Collectors;

import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
Expand DownExpand Up@@ -76,14 +74,33 @@ public List<Program> findPrograms(ProgramSearchRequest request, Metadata metadat
return programs;
}

public List<ProgramEntity> findByIds(List<String> programDbIds) {
var result = new ArrayList<ProgramEntity>();
public List<ProgramEntity> findByIds(List<String> programDbIds) throws BrAPIServerException {
List<ProgramEntity> result = new ArrayList<>();

if (programDbIds.isEmpty()) {
return result;
}

return programRepository.findByIdIn(programDbIds.stream().map(UUID::fromString).toList());
// Dedup programIds by loading into set
Set<String> programDbIdSet = new HashSet<>(programDbIds);

result = programRepository.findByIdIn(programDbIds.stream().map(UUID::fromString).toList());

if (programDbIdSet.size() != result.size()) {
List<String> dbIdsNotFound = new ArrayList<>();

Set<String> foundDbIds = result.stream().map(pe -> pe.getId().toString()).collect(Collectors.toSet());

programDbIdSet.forEach(dbId -> {
if (!foundDbIds.contains(dbId)) {
dbIdsNotFound.add(dbId);
}
});

throw new BrAPIServerException(HttpStatus.NOT_FOUND, String.format("The following submitted programDbIds were not found in the db: [%s]", dbIdsNotFound));
}

return result;
}

public Program getProgram(String programDbId) throws BrAPIServerException {
Expand Down
42 changes: 36 additions & 6 deletions src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java
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Expand Up@@ -4,6 +4,7 @@
import java.util.*;
import java.util.stream.Collectors;

import io.swagger.model.core.ProgramSearchRequest;
import io.swagger.model.germ.*;
import jakarta.validation.Valid;

Expand All@@ -12,6 +13,7 @@
import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
import org.brapi.test.BrAPITestServer.model.entity.ExternalReferenceEntity;
import org.brapi.test.BrAPITestServer.model.entity.core.CropEntity;
import org.brapi.test.BrAPITestServer.model.entity.core.ProgramEntity;
import org.brapi.test.BrAPITestServer.model.entity.germ.*;
import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmInstituteEntity.InstituteTypeEnum;
import org.brapi.test.BrAPITestServer.model.entity.pheno.TaxonEntity;
Expand All@@ -23,6 +25,7 @@
import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
import org.brapi.test.BrAPITestServer.service.UpdateUtility;
import org.brapi.test.BrAPITestServer.service.core.CropService;
import org.brapi.test.BrAPITestServer.service.core.ProgramService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
Expand All@@ -44,21 +47,23 @@ public class GermplasmService {
private final GermplasmDonorRepository donorRepository;
private final BreedingMethodService breedingMethodService;
private final CropService cropService;
private final ProgramService programService;

@Autowired
public GermplasmService(GermplasmRepository germplasmRepository, GermplasmDonorRepository donorRepository,
BreedingMethodService breedingMethodService, CropService cropService) {
BreedingMethodService breedingMethodService, CropService cropService, ProgramService programService) {
this.germplasmRepository = germplasmRepository;
this.donorRepository = donorRepository;

this.breedingMethodService = breedingMethodService;
this.cropService = cropService;
this.programService = programService;
}

public List<Germplasm> findGermplasm(String germplasmPUI, String germplasmDbId, String germplasmName,
String accessionNumber, String collection, String binomialName, String genus, String species,
String trialDbId, String studyDbId, String synonym, String parentDbId, String progenyDbId,
String commonCropName, String programDbId, String externalReferenceId, String externalReferenceID,
String commonCropName, String programDbId, String programName, String externalReferenceId, String externalReferenceID,
String externalReferenceSource, Metadata metadata)
throws BrAPIServerException {

Expand DownExpand Up@@ -93,6 +98,8 @@ public List<Germplasm> findGermplasm(String germplasmPUI, String germplasmDbId,
request.addCommonCropNamesItem(commonCropName);
if (programDbId != null)
request.addProgramDbIdsItem(programDbId);
if (programName != null)
request.addProgramNamesItem(programName);

request.addExternalReferenceItem(externalReferenceId, externalReferenceID, externalReferenceSource);

Expand DownExpand Up@@ -172,12 +179,10 @@ private SearchQueryBuilder<GermplasmEntity> buildGermplasmSearchQuery(GermplasmS
.leftJoinFetch("pedigree", "pedigree")
.leftJoinFetch("*pedigree.crossingProject", "crossingProject");

if (request.getProgramDbIds() != null || request.getProgramNames() != null || request.getTrialDbIds() != null
if (request.getTrialDbIds() != null
|| request.getTrialNames() != null || request.getStudyDbIds() != null
|| request.getStudyNames() != null) {
searchQuery = searchQuery.join("observationUnits", "obsunit")
.appendList(request.getProgramDbIds(), "*obsunit.program.id")
.appendList(request.getProgramNames(), "*obsunit.program.name")
.appendList(request.getTrialDbIds(), "*obsunit.trial.id")
.appendList(request.getTrialNames(), "*obsunit.trial.name")
.appendList(request.getStudyDbIds(), "*obsunit.study.id")
Expand All@@ -198,6 +203,7 @@ private SearchQueryBuilder<GermplasmEntity> buildGermplasmSearchQuery(GermplasmS
.appendList(request.getGermplasmNames(), "germplasmName")
.appendList(request.getGermplasmPUIs(), "germplasmPUI")
.appendList(request.getParentDbIds(), "pedigree.parent1.germplasm.id")
.appendList(request.getProgramDbIds(), "program.id").appendList(request.getProgramNames(), "program.name")
// .appendList(request.getProgenyDbIds(), "*progeny.germplasmDbId")
.appendList(request.getGenus(), "genus").appendList(request.getSpecies(), "species")
.appendNamesList(request.getBinomialNames(), "genus", "genus", "species")
Expand DownExpand Up@@ -529,6 +535,12 @@ private Germplasm convertFromEntity(GermplasmEntity entity) {
germ.setCollection(entity.getCollection());
if (entity.getCrop() != null)
germ.setCommonCropName(entity.getCrop().getCropName());

if (entity.getProgram() != null) {
germ.setProgramDbId(entity.getProgram().getId().toString());
germ.setProgramName(entity.getProgram().getName());
}

germ.setCountryOfOriginCode(entity.getCountryOfOriginCode());
germ.setDefaultDisplayName(entity.getDefaultDisplayName());
germ.setDocumentationURL(entity.getDocumentationURL());
Expand DownExpand Up@@ -582,6 +594,11 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
.filter(Objects::nonNull)
.collect(Collectors.toSet());

Set<String> programDbIds = body.stream()
.map(GermplasmNewRequest::getProgramDbId)
.filter(Objects::nonNull)
.collect(Collectors.toSet());

Map<UUID, BreedingMethodEntity> foundBreedingMethodsById
= breedingMethodService.findBreedingMethodsByIds(breedingMethodIds)
.stream()
Expand All@@ -591,6 +608,11 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
.stream()
.collect(Collectors.toMap(CropEntity::getCropName, e -> e));

Map<UUID, ProgramEntity> foundProgramsByDbId
= programService.findByIds(new ArrayList<>(programDbIds))
.stream()
.collect(Collectors.toMap(ProgramEntity::getId, e -> e));

for (GermplasmNewRequest request : body) {
GermplasmEntity entity = new GermplasmEntity();

Expand All@@ -605,7 +627,7 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
if (request.getBiologicalStatusOfAccessionCode() != null)
entity.setBiologicalStatusOfAccessionCode(request.getBiologicalStatusOfAccessionCode());
if (request.getBreedingMethodDbId() != null) {
entity.setBreedingMethod(foundBreedingMethodsById.get(request.getBreedingMethodDbId()));
entity.setBreedingMethod(foundBreedingMethodsById.get(UUID.fromString(request.getBreedingMethodDbId())));
}
if (request.getCollection() != null)
entity.setCollection(request.getCollection());
Expand DownExpand Up@@ -662,6 +684,10 @@ private List<GermplasmEntity> createEntitiesInBatch(List<GermplasmNewRequest> bo
updateSynonymEntities(request.getSynonyms(), entity);
if (request.getTaxonIds() != null)
updateTaxonEntities(request.getTaxonIds(), entity);
if (!foundProgramsByDbId.isEmpty()) {

@nickpalladinonickpalladinoAug 25, 2026

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Not applicable for deltabreed use case but may want to fix for general usage. Since foundProgramsByDbId is shared across germplasm in the batch if some germplasm have a program id and some don't then this could result in a NullPointerException on the UUID.fromString call because request.getProgramDbId() could be null.

Something like this should resolve it:

 if (request.getProgramDbId() != null) {
ProgramEntity program =
foundProgramsByDbId.get(UUID.fromString(request.getProgramDbId()));
entity.setProgram(program);
}

@jloux-brapijloux-brapiAug 25, 2026

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Oop, yea, that's just a big old brain fart. I implemented that for other entities exactly as you described, just did this one wrong.

ProgramEntity program = foundProgramsByDbId.get(UUID.fromString(request.getProgramDbId()));
entity.setProgram(program);
}

toSave.add(entity);
}
Expand DownExpand Up@@ -739,6 +765,10 @@ private void updateEntity(GermplasmEntity entity, GermplasmNewRequest request) t
updateSynonymEntities(request.getSynonyms(), entity);
if (request.getTaxonIds() != null)
updateTaxonEntities(request.getTaxonIds(), entity);
if (request.getProgramDbId() != null) {
ProgramEntity program = programService.getProgramEntity(request.getProgramDbId());
entity.setProgram(program);
}
}

private void updateTaxonEntities(List<TaxonID> taxonIds, GermplasmEntity entity) {
Expand Down
22 changes: 22 additions & 0 deletions src/main/resources/db/migration/V006_003__add_program_id_to_germplasm_and_migrate.sql
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@@ -0,0 +1,22 @@
ALTER TABLE germplasm
ADD COLUMN program_id UUID;

ALTER TABLE germplasm
ADD CONSTRAINT germplasm_program_fk
FOREIGN KEY (program_id)
REFERENCES public.program(id)
ON DELETE CASCADE;

@nickpalladinonickpalladinoAug 25, 2026

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Wonder if we should not cascade, seems the convention for other entities related to program like trials and studies, etc. is no action.


CREATE INDEX germplasm_program_idx ON germplasm (program_id, id);

UPDATE germplasm set program_id = pquery.program_id
FROM (
SELECT g.id AS germplasm_id, p.id AS program_id
from germplasm g
JOIN germplasm_external_references gex ON g.id = gex.germplasm_entity_id
JOIN external_reference ex ON ex.id = gex.external_references_id

@nickpalladinonickpalladinoAug 25, 2026

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Maybe we should also constrain on the germplasm exref source being breedinginsight.org/programs

JOIN external_reference ex2 ON ex2.external_reference_id = ex.external_reference_id
JOIN program_external_references pex ON pex.external_references_id = ex2.id
JOIN program p ON p.id = pex.program_entity_id
) pquery
where id = pquery.germplasm_id;