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BI-2805 - Fix autocomplete to work with new BrAPI levelNames #505

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Merged
davedrp merged 6 commits into from
Apr 16, 2026
Merged

BI-2805 - Fix autocomplete to work with new BrAPI levelNames #505

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6501476
Initial codex pass
nickpalladino Mar 24, 2026
34bf6a0
Switch to makeCallWithResponse
nickpalladino Mar 30, 2026
243b21a
Merge branch 'develop' into feature/BI-2805
nickpalladino Apr 8, 2026
ce31e05
Cleanup comments
nickpalladino Apr 10, 2026
8df73c0
Update tests
nickpalladino Apr 16, 2026
c9355ac
Merge branch 'develop' into feature/BI-2805
nickpalladino Apr 16, 2026
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23 changes: 23 additions & 0 deletions src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,29 @@ public HttpResponse<Response<List<DatasetMetadata>>> getDatasets(

}

@Get("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/recommended-sub-entity-dataset-names")
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
@Produces(MediaType.APPLICATION_JSON)
public HttpResponse<Response<List<String>>> getRecommendedSubEntityDatasetNames(
@PathVariable("programId") UUID programId,
@PathVariable("experimentId") UUID experimentId) {
try {
Optional<Program> programOptional = programService.getById(programId);
if (programOptional.isEmpty()) {
return HttpResponse.status(HttpStatus.NOT_FOUND, "Program does not exist");
}

Response<List<String>> response = new Response<>(experimentService.getRecommendedSubEntityDatasetNames(programOptional.get(), experimentId));
return HttpResponse.ok(response);
} catch (DoesNotExistException e) {
log.info(e.getMessage());
return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
} catch (Exception e) {
log.error("Error finding recommended sub-entity dataset names", e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error finding recommended sub-entity dataset names");
}
}

/**
* Adds a record to the experiment_program_user_role table
* @param programId The UUID of the program
Expand Down
51 changes: 2 additions & 49 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationLevelDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,86 +17,39 @@

package org.breedinginsight.brapi.v2.dao;

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 org.breedinginsight.utilities.Utilities;
import java.util.Optional;

@Slf4j
@Singleton
public class BrAPIObservationLevelDAO {

private static final MediaType JSON_MEDIA_TYPE = MediaType.get("application/json");
private final BrAPIDAOUtil brAPIDAOUtil;
private final Gson gson = new JSON().getGson();

private final BrAPIEndpointProvider brAPIEndpointProvider;
private final ProgramDAO programDAO;

@Inject
public BrAPIObservationLevelDAO(BrAPIDAOUtil brAPIDAOUtil,
BrAPIEndpointProvider brAPIEndpointProvider,
public BrAPIObservationLevelDAO(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) {
HttpUrl url = HttpUrl.parse(brAPIDAOUtil.getProgramBrAPIBaseUrl(program.getId()))
.newBuilder()
.addPathSegment("observationlevelnames")
.build();
JsonObject levelJson = new JsonObject();
levelJson.addProperty("levelName", levelName);
if (levelOrder != null) {
levelJson.addProperty("levelOrder", levelOrder.getValue());
}
if (programDbId != null) {
levelJson.addProperty("programDbId", programDbId);
}
JsonArray bodyArray = new JsonArray();
bodyArray.add(levelJson);
RequestBody body = RequestBody.create(gson.toJson(bodyArray), JSON_MEDIA_TYPE);
var request = new Request.Builder()
.url(url)
.post(body)
.addHeader("Content-Type", "application/json")
.build();
return brAPIDAOUtil.makeCall(request);
}

public BrAPIObservationUnitHierarchyLevel createLevelName(Program program,
String programDbId,
String levelName,
Expand Down
40 changes: 40 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,8 @@
import org.breedinginsight.model.DownloadFile;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.*;
import org.breedinginsight.model.delta.DeltaEntityFactory;
import org.breedinginsight.model.delta.Experiment;
import org.breedinginsight.services.TraitService;
import org.breedinginsight.services.exceptions.AlreadyExistsException;
import org.breedinginsight.services.exceptions.DoesNotExistException;
Expand Down Expand Up @@ -79,6 +81,7 @@ public class BrAPITrialService {
private final DistributedLockService lockService;
private static final String SHEET_NAME = "Data";
private final DatasetService datasetService;
private final DeltaEntityFactory deltaEntityFactory;
private final BrAPIObservationLevelService observationLevelService;

@Inject
Expand All @@ -96,6 +99,7 @@ public BrAPITrialService(@Property(name = "brapi.server.reference-source") Strin
FileMappingUtil fileMappingUtil,
DistributedLockService lockService,
DatasetService datasetService,
DeltaEntityFactory deltaEntityFactory,
BrAPIObservationLevelService observationLevelService) {

this.referenceSource = referenceSource;
Expand All @@ -112,6 +116,7 @@ public BrAPITrialService(@Property(name = "brapi.server.reference-source") Strin
this.fileMappingUtil = fileMappingUtil;
this.lockService = lockService;
this.datasetService = datasetService;
this.deltaEntityFactory = deltaEntityFactory;
this.observationLevelService = observationLevelService;
}

Expand Down Expand Up @@ -430,6 +435,35 @@ public List<DatasetMetadata> getDatasetsMetadata(Program program, UUID experimen
return datasets;
}

/**
* Returns list of recommended sub entity names based on observation levels for the program that exclude
* level names already used in the experiment and is deduplicated for same name at multiple levels
* @param program Program
* @param experimentId Experiment Id
* @return list of dataset name recommendations
* @throws DoesNotExistException If trial does not exist
* @throws ApiException If BrAPI trial retrieval fails
*/
public List<String> getRecommendedSubEntityDatasetNames(Program program, UUID experimentId) throws DoesNotExistException, ApiException {
BrAPITrial experiment = trialDAO.getTrialById(program.getId(), experimentId).orElseThrow(() -> new DoesNotExistException("Trial does not exist"));
Experiment deltaExperiment = deltaEntityFactory.makeExperimentBean(experiment);
// set to eliminate possible duplicates like plant for exp unit and sub unit
Set<String> currentExperimentDatasetNames = deltaExperiment.getDatasetsMetadata()
.stream()
.map(DatasetMetadata::getName)
.filter(Objects::nonNull)
.map(String::toLowerCase)
.collect(Collectors.toSet());

return getProgramObservationLevelNames(program).stream()
.filter(Objects::nonNull)
.map(String::toLowerCase)
.filter(name -> !currentExperimentDatasetNames.contains(name))
.distinct()
.sorted()
.collect(Collectors.toList());
}

/**
* Creates sub-entity dataset
* TODO: Handle compensating transactions in event of failure. Currently brapi server does not support
Expand Down Expand Up @@ -796,6 +830,12 @@ public int deleteExperiment(Program program, UUID experimentId, boolean hard) th
return existingObservations.size();
}

private List<String> getProgramObservationLevelNames(Program program) {
String programDbId = program.getBrapiProgram() != null ? program.getBrapiProgram().getProgramDbId() : null;
List<BrAPIObservationUnitHierarchyLevel> levelNames = observationLevelService.getProgrammaticLevelNames(program, programDbId);
return levelNames.stream().map(BrAPIObservationUnitHierarchyLevel::getLevelName).collect(Collectors.toList());
}

private Map<String, Object> createExportRow(
BrAPITrial experiment,
Program program,
Expand Down
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