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[BI-2814] Create Sub Entity Dataset: Update OUs to supply levelNameDbIds #506

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c735d10
Support for level order uniqueness use case for sub entity dataset cr…
jloux-brapi Mar 31, 2026
344a966
Merge branch 'develop' into feature/BI-2814
jloux-brapi Apr 2, 2026
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -89,7 +89,7 @@
<guava.version>31.0.1-jre</guava.version>
<okhttp.version>4.9.3</okhttp.version>
<mockito.version>4.3.1</mockito.version>
<brapi-java-client.version>2.1-SNAPSHOT</brapi-java-client.version>
<brapi-java-client.version>2.2-SNAPSHOT</brapi-java-client.version>
<commons-io.version>2.11.0</commons-io.version>
<tika-app.version>2.2.1</tika-app.version>
<!-- Version of apache-poi depends on version of tika. Tika uses these. -->
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123 changes: 105 additions & 18 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationLevelDAO.java
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Expand Up @@ -20,23 +20,38 @@
import com.google.gson.Gson;
import io.micronaut.http.HttpResponse;
import io.micronaut.http.HttpStatus;
import io.micronaut.http.server.exceptions.InternalServerException;
import lombok.extern.slf4j.Slf4j;
import okhttp3.HttpUrl;
import okhttp3.MediaType;
import okhttp3.Request;
import okhttp3.RequestBody;
import org.brapi.client.v2.ApiResponse;
import org.brapi.client.v2.JSON;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.client.v2.modules.phenotype.ObservationLevelNamesApi;
import org.brapi.client.v2.modules.phenotype.ObservationUnitsApi;
import org.brapi.v2.model.pheno.BrAPIObservationUnitHierarchyLevel;
import org.brapi.v2.model.pheno.BrAPIObservationUnitLevelRelationship;
import org.brapi.v2.model.pheno.response.BrAPIObservationLevelListResponse;
import org.brapi.v2.model.pheno.response.BrAPIObservationLevelListResponseResult;
import org.brapi.v2.model.pheno.response.BrAPIObservationLevelSingleResponse;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.model.DatasetLevel;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.utilities.BrAPIDAOUtil;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import org.breedinginsight.utilities.Utilities;

import javax.inject.Inject;
import javax.inject.Singleton;
import java.util.List;
import java.util.Optional;

@Slf4j
@Singleton
Expand All @@ -46,12 +61,19 @@ public class BrAPIObservationLevelDAO {
private final BrAPIDAOUtil brAPIDAOUtil;
private final Gson gson = new JSON().getGson();

private final BrAPIEndpointProvider brAPIEndpointProvider;
private final ProgramDAO programDAO;

@Inject
public BrAPIObservationLevelDAO(BrAPIDAOUtil brAPIDAOUtil) {
public BrAPIObservationLevelDAO(BrAPIDAOUtil brAPIDAOUtil,
BrAPIEndpointProvider brAPIEndpointProvider,
ProgramDAO programDAO) {
this.brAPIDAOUtil = brAPIDAOUtil;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.programDAO = programDAO;
}

public HttpResponse<String> createObservationLevelName(Program program, String levelName, DatasetLevel levelOrder, String programDbId) throws ApiException {
public HttpResponse<String> createObservationLevelName(Program program, String levelName, DatasetLevel levelOrder, String programDbId) {
HttpUrl url = HttpUrl.parse(brAPIDAOUtil.getProgramBrAPIBaseUrl(program.getId()))
.newBuilder()
.addPathSegment("observationlevelnames")
Expand All @@ -75,25 +97,90 @@ public HttpResponse<String> createObservationLevelName(Program program, String l
return brAPIDAOUtil.makeCall(request);
}

public BrAPIObservationUnitHierarchyLevel createLevelName(Program program,
String programDbId,
String levelName,
DatasetLevel levelOrder) throws ApiException {
ObservationLevelNamesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationLevelNamesApi.class);

ApiResponse<BrAPIObservationLevelListResponse> response;


BrAPIObservationUnitHierarchyLevel level = new BrAPIObservationUnitHierarchyLevel();

level.setLevelName(levelName.toLowerCase());
level.setLevelOrder(levelOrder.getValue());
level.setProgramDbId(programDbId);

try {
response = api.observationLevelNamesPost(List.of(level));
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Error making BrAPI call", e);
}

return Optional.of(response)
.map(ApiResponse::getBody)
.map(BrAPIObservationLevelListResponse::getResult)
.map(BrAPIObservationLevelListResponseResult::getData)
.flatMap(data -> data.stream().findFirst())
.orElseThrow(() -> new ApiException(String.format("BrAPI indicated level name [%s] was created but no levelNameDbId was returned upon its creation", levelName)));
}

public List<BrAPIObservationUnitHierarchyLevel> getObservationLevelNamesByProgramId(Program program, String programDbId) {
ObservationLevelNamesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationLevelNamesApi.class);

ApiResponse<BrAPIObservationLevelListResponse> response;

int pageSize = 100;

try {
response = api.observationLevelNamesGet(programDbId,
false,
0,
pageSize);
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Error making BrAPI call", e);
}

if (response.getBody().getMetadata().getPagination().getTotalCount() > 100) {
throw new InternalServerException(String.format("More level names exist than requested [%s]", pageSize));
}

return response.getBody().getResult().getData();
}

public List<BrAPIObservationUnitHierarchyLevel> getGlobalObservationLevelNames(Program program) {
return getObservationLevelNamesByProgramId(program, null);
}

public void deleteObservationLevelName(Program program, String levelDbId) {
HttpUrl url = HttpUrl.parse(brAPIDAOUtil.getProgramBrAPIBaseUrl(program.getId()))
.newBuilder()
.addPathSegment("observationlevelnames")
.addPathSegment(levelDbId)
.build();
var request = new Request.Builder()
.url(url)
.delete()
.addHeader("Content-Type", "application/json")
.build();
ObservationLevelNamesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationLevelNamesApi.class);

try {
HttpResponse<String> response = brAPIDAOUtil.makeCall(request);
if (response.getStatus() != HttpStatus.OK && response.getStatus() != HttpStatus.NO_CONTENT && response.getStatus() != HttpStatus.ACCEPTED) {
log.warn("Observation level delete returned status {} for {}", response.getStatus(), levelDbId);
}
} catch (Exception e) {
log.warn("Failed to delete observation level {}", levelDbId, e);
api.observationLevelNameDbIdDelete(levelDbId);
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Error making BrAPI call", e);
}
}

public BrAPIObservationUnitHierarchyLevel updateObservationLevelName(Program program,
String levelNameDbId,
BrAPIObservationUnitHierarchyLevel level) {
ObservationLevelNamesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationLevelNamesApi.class);

ApiResponse<BrAPIObservationLevelSingleResponse> response;

try {
response = api.observationLevelNameDbIdPut(levelNameDbId, level);
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Error making BrAPI call", e);
}

return response.getBody().getResult();
}

}
60 changes: 60 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPIObservationLevelService.java
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@@ -0,0 +1,60 @@
package org.breedinginsight.brapi.v2.services;

import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.brapi.client.v2.ApiResponse;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.client.v2.modules.phenotype.ObservationUnitsApi;
import org.brapi.v2.model.pheno.BrAPIObservationUnitHierarchyLevel;
import org.brapi.v2.model.pheno.BrAPIObservationUnitLevelRelationship;
import org.brapi.v2.model.pheno.response.BrAPIObservationLevelListResponse;
import org.breedinginsight.brapi.v2.dao.BrAPIObservationLevelDAO;
import org.breedinginsight.model.DatasetLevel;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.ProgramService;
import org.breedinginsight.services.exceptions.DoesNotExistException;

import javax.inject.Inject;
import javax.inject.Singleton;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

@Slf4j
@Singleton
public class BrAPIObservationLevelService {
private final BrAPIObservationLevelDAO brAPIObservationLevelDAO;
private final ProgramService programService;


@Inject
public BrAPIObservationLevelService(BrAPIObservationLevelDAO brAPIObservationLevelDAO,
ProgramService programService) {
this.brAPIObservationLevelDAO = brAPIObservationLevelDAO;
this.programService = programService;
}

/**
* @return Pair[GlobalLevelNames, ProgrammaticLevelNames]
*/
public Pair<List<BrAPIObservationUnitHierarchyLevel>, List<BrAPIObservationUnitHierarchyLevel>> getGlobalAndProgrammaticLevelNames(Program program, String brapiProgramDbId) {
List<BrAPIObservationUnitHierarchyLevel> globalLevels = brAPIObservationLevelDAO.getGlobalObservationLevelNames(program);
List<BrAPIObservationUnitHierarchyLevel> programmaticLevels = brAPIObservationLevelDAO.getObservationLevelNamesByProgramId(program, brapiProgramDbId);


return new ImmutablePair<>(globalLevels, programmaticLevels);
}

public List<BrAPIObservationUnitHierarchyLevel> getProgrammaticLevelNames(Program program, String brapiProgramDbId) {
return brAPIObservationLevelDAO.getObservationLevelNamesByProgramId(program, brapiProgramDbId);
}

public BrAPIObservationUnitHierarchyLevel createObservationLevel(Program program,
String brapiProgramDbId,
String levelName,
DatasetLevel levelOrder) throws ApiException {
return brAPIObservationLevelDAO.createLevelName(program, brapiProgramDbId, levelName, levelOrder);
}

}
61 changes: 29 additions & 32 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
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Expand Up @@ -6,8 +6,6 @@
import com.github.filosganga.geogson.model.positions.SinglePosition;
import com.google.gson.JsonObject;
import io.micronaut.context.annotation.Property;
import io.micronaut.http.HttpResponse;
import io.micronaut.http.HttpStatus;
import io.micronaut.http.MediaType;
import io.micronaut.http.server.exceptions.InternalServerException;
import io.micronaut.http.server.types.files.StreamedFile;
Expand Down Expand Up @@ -81,6 +79,7 @@ public class BrAPITrialService {
private final DistributedLockService lockService;
private static final String SHEET_NAME = "Data";
private final DatasetService datasetService;
private final BrAPIObservationLevelService observationLevelService;

@Inject
public BrAPITrialService(@Property(name = "brapi.server.reference-source") String referenceSource,
Expand All @@ -96,7 +95,8 @@ public BrAPITrialService(@Property(name = "brapi.server.reference-source") Strin
BrAPIGermplasmDAO germplasmDAO,
FileMappingUtil fileMappingUtil,
DistributedLockService lockService,
DatasetService datasetService) {
DatasetService datasetService,
BrAPIObservationLevelService observationLevelService) {

this.referenceSource = referenceSource;
this.trialDAO = trialDAO;
Expand All @@ -112,6 +112,7 @@ public BrAPITrialService(@Property(name = "brapi.server.reference-source") Strin
this.fileMappingUtil = fileMappingUtil;
this.lockService = lockService;
this.datasetService = datasetService;
this.observationLevelService = observationLevelService;
}

public List<BrAPITrial> getExperiments(UUID programId) throws ApiException, DoesNotExistException {
Expand Down Expand Up @@ -466,14 +467,13 @@ public Dataset createSubEntityDataset(Program program, UUID experimentId, SubEnt
}

String programBrapiDbId = program.getBrapiProgram() != null ? program.getBrapiProgram().getProgramDbId() : null;
HttpResponse<String> levelResponse = observationLevelDAO.createObservationLevelName(program, datasetName, DatasetLevel.SUB_OBS_UNIT, programBrapiDbId);

// 409 and 200 are expected response codes, anything else error out
// 409 means level already exists so we just use the name in OUs
// 200 means level was created successfully and can use the name in OUs
if (levelResponse.getStatus() != HttpStatus.CONFLICT && levelResponse.getStatus() != HttpStatus.OK) {
throw new ApiException(levelResponse.getStatus().getCode(), "Unable to create observation level: " + levelResponse.getStatus().getReason());
}
String subEntityLevelNameDbId = datasetService.getOrCreateLevelNameForDataset(program,
programBrapiDbId,
datasetName,
DatasetLevel.SUB_OBS_UNIT
);


List<BrAPIObservationUnit> expOUs = ouDAO.getObservationUnitsForDataset(topLevelDataset.getId().toString(), program);
for (BrAPIObservationUnit expUnit : expOUs) {
Expand All @@ -484,14 +484,14 @@ public Dataset createSubEntityDataset(Program program, UUID experimentId, SubEnt
for (int i=1; i<=request.getRepeatedMeasures(); i++) {
subObsUnits.add(
createSubObservationUnit(
datasetName,
Integer.toString(i),
program,
envSeqValue,
expUnit,
this.referenceSource,
subEntityDatasetId,
UUID.randomUUID()
UUID.randomUUID(),
subEntityLevelNameDbId
)
);
}
Expand Down Expand Up @@ -529,14 +529,14 @@ public Dataset createSubEntityDataset(Program program, UUID experimentId, SubEnt
}

public BrAPIObservationUnit createSubObservationUnit(
String subEntityDatasetName,
String subUnitId,
Program program,
String seqVal,
BrAPIObservationUnit expUnit,
String referenceSource,
UUID datasetId,
UUID id
UUID id,
String subEntityLevelNameDbId
) {

BrAPIObservationUnit observationUnit = new BrAPIObservationUnit();
Expand Down Expand Up @@ -612,42 +612,39 @@ public BrAPIObservationUnit createSubObservationUnit(

// ObservationLevel entry for Sub-Obs Unit.
BrAPIObservationUnitLevelRelationship level = new BrAPIObservationUnitLevelRelationship();
level.setLevelName(subEntityDatasetName);
level.setLevelNameDbId(subEntityLevelNameDbId);
level.setLevelCode(Utilities.appendProgramKey(subUnitId, program.getKey(), seqVal));
level.setLevelOrder(DatasetLevel.SUB_OBS_UNIT.getValue());
position.setObservationLevel(level);

// ObservationLevelRelationships.
List<BrAPIObservationUnitLevelRelationship> levelRelationships = new ArrayList<>();
// TODO: Figure out if we actually need to add the sub entity level to the level relationships BI-2823
levelRelationships.add(level);
// ObservationLevelRelationships for block.
BrAPIObservationUnitLevelRelationship expBlockLevel = expUnit.getObservationUnitPosition()
.getObservationLevelRelationships().stream()
.filter(x -> x.getLevelName().equals(BrAPIConstants.REPLICATE.getValue())).findFirst().orElse(null);
if (expBlockLevel != null) {
BrAPIObservationUnitLevelRelationship blockLevel = new BrAPIObservationUnitLevelRelationship();
blockLevel.setLevelName(expBlockLevel.getLevelName());
blockLevel.setLevelCode(expBlockLevel.getLevelCode());
blockLevel.setLevelOrder(expBlockLevel.getLevelOrder());
levelRelationships.add(blockLevel);
}
// ObservationLevelRelationships for rep.
BrAPIObservationUnitLevelRelationship expRepLevel = expUnit.getObservationUnitPosition()
.getObservationLevelRelationships().stream()
.filter(x -> x.getLevelName().equals(BrAPIConstants.BLOCK.getValue())).findFirst().orElse(null);
.filter(x -> x.getLevelName().equals(BrAPIConstants.REPLICATE.getValue())).findFirst().orElse(null);
if (expRepLevel != null) {
BrAPIObservationUnitLevelRelationship repLevel = new BrAPIObservationUnitLevelRelationship();
repLevel.setLevelName(expRepLevel.getLevelName());
repLevel.setLevelNameDbId(expRepLevel.getLevelNameDbId());
repLevel.setLevelCode(expRepLevel.getLevelCode());
repLevel.setLevelOrder(expRepLevel.getLevelOrder());
levelRelationships.add(repLevel);
}
// ObservationLevelRelationships for block.
BrAPIObservationUnitLevelRelationship expBlockLevel = expUnit.getObservationUnitPosition()
.getObservationLevelRelationships().stream()
.filter(x -> x.getLevelName().equals(BrAPIConstants.BLOCK.getValue())).findFirst().orElse(null);
if (expBlockLevel != null) {
BrAPIObservationUnitLevelRelationship blockLevel = new BrAPIObservationUnitLevelRelationship();
blockLevel.setLevelNameDbId(expBlockLevel.getLevelNameDbId());
blockLevel.setLevelCode(expBlockLevel.getLevelCode());
levelRelationships.add(blockLevel);
}
// ObservationLevelRelationships for top-level Exp Unit linking.
BrAPIObservationUnitLevelRelationship expUnitLevel = new BrAPIObservationUnitLevelRelationship();
expUnitLevel.setLevelName(expUnit.getObservationUnitPosition().getObservationLevel().getLevelName().toLowerCase());
expUnitLevel.setLevelNameDbId(expUnit.getObservationUnitPosition().getObservationLevel().getLevelNameDbId());
String expUnitUUID = Utilities.getExternalReference(expUnit.getExternalReferences(), referenceSource, ExternalReferenceSource.OBSERVATION_UNITS).orElseThrow().getReferenceId();
expUnitLevel.setLevelCode(Utilities.appendProgramKey(expUnitUUID, program.getKey(), seqVal));
expUnitLevel.setLevelOrder(DatasetLevel.EXP_UNIT.getValue());
levelRelationships.add(expUnitLevel);
position.setObservationLevelRelationships(levelRelationships);

Expand Down
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