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Feature/bi 2805 #505

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6501476
Initial codex pass
nickpalladino Mar 24, 2026
34bf6a0
Switch to makeCallWithResponse
nickpalladino Mar 30, 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
62 changes: 58 additions & 4 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationLevelDAO.java
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Expand Up @@ -18,25 +18,28 @@
package org.breedinginsight.brapi.v2.dao;

import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import io.micronaut.http.HttpResponse;
import io.micronaut.http.HttpStatus;
import lombok.extern.slf4j.Slf4j;
import okhttp3.HttpUrl;
import okhttp3.MediaType;
import okhttp3.Request;
import okhttp3.RequestBody;
import org.apache.commons.lang3.StringUtils;
import org.brapi.client.v2.JSON;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.breedinginsight.model.DatasetLevel;
import org.breedinginsight.model.Program;
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 javax.inject.Inject;
import javax.inject.Singleton;
import java.util.ArrayList;
import java.util.List;

@Slf4j
@Singleton
Expand Down Expand Up @@ -96,4 +99,55 @@ public void deleteObservationLevelName(Program program, String levelDbId) {
}
}

public List<String> getObservationLevelNames(Program program, String programDbId) throws ApiException {
List<String> levelNames = new ArrayList<>();
int currentPage = 0;
int totalPages = 1;

do {
HttpUrl.Builder urlBuilder = HttpUrl.parse(brAPIDAOUtil.getProgramBrAPIBaseUrl(program.getId()))
.newBuilder()
.addPathSegment("observationlevelnames")
.addQueryParameter("page", Integer.toString(currentPage))
.addQueryParameter("pageSize", "1000");
if (StringUtils.isNotBlank(programDbId)) {
urlBuilder.addQueryParameter("programDbId", programDbId);
}

Request request = new Request.Builder()
.url(urlBuilder.build())
.get()
.addHeader("Content-Type", "application/json")
.build();

String responseBody = brAPIDAOUtil.makeCallWithResponse(request);
if (StringUtils.isBlank(responseBody)) {
return levelNames;
}

JsonObject responseJson = JsonParser.parseString(responseBody).getAsJsonObject();
JsonObject resultJson = responseJson.getAsJsonObject("result");
if (resultJson != null) {
JsonArray data = resultJson.getAsJsonArray("data");
if (data != null) {
for (JsonElement level : data) {
if (level.isJsonObject()) {
JsonElement levelName = level.getAsJsonObject().get("levelName");
if (levelName != null && !levelName.isJsonNull()) {
levelNames.add(levelName.getAsString());
}
}
}
}
}

JsonObject metadata = responseJson.getAsJsonObject("metadata");
JsonObject pagination = metadata != null ? metadata.getAsJsonObject("pagination") : null;
totalPages = pagination != null && pagination.has("totalPages") ? pagination.get("totalPages").getAsInt() : currentPage + 1;
currentPage++;
} while (currentPage < totalPages);

return levelNames;
}

}
40 changes: 39 additions & 1 deletion src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
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Expand Up @@ -36,6 +36,8 @@
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 @@ -81,6 +83,7 @@ public class BrAPITrialService {
private final DistributedLockService lockService;
private static final String SHEET_NAME = "Data";
private final DatasetService datasetService;
private final DeltaEntityFactory deltaEntityFactory;

@Inject
public BrAPITrialService(@Property(name = "brapi.server.reference-source") String referenceSource,
Expand All @@ -96,7 +99,8 @@ public BrAPITrialService(@Property(name = "brapi.server.reference-source") Strin
BrAPIGermplasmDAO germplasmDAO,
FileMappingUtil fileMappingUtil,
DistributedLockService lockService,
DatasetService datasetService) {
DatasetService datasetService,
DeltaEntityFactory deltaEntityFactory) {

this.referenceSource = referenceSource;
this.trialDAO = trialDAO;
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;
}

public List<BrAPITrial> getExperiments(UUID programId) throws ApiException, DoesNotExistException {
Expand Down Expand Up @@ -429,6 +434,34 @@ public List<DatasetMetadata> getDatasetsMetadata(Program program, UUID experimen
return datasets;
}

/**
* Assumptions:
* @param program
* @param experimentId
* @return
* @throws DoesNotExistException
* @throws ApiException
*/
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(StringUtils::isNotBlank)
.collect(Collectors.toSet());

return getProgramObservationLevelNames(program).stream()
//.filter(StringUtils::isNotBlank)
//.filter(name -> !BrAPIConstants.REPLICATE.getValue().equalsIgnoreCase(name))
//.filter(name -> !BrAPIConstants.BLOCK.getValue().equalsIgnoreCase(name))
.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 @@ -801,6 +834,11 @@ public int deleteExperiment(Program program, UUID experimentId, boolean hard) th
return existingObservations.size();
}

private List<String> getProgramObservationLevelNames(Program program) throws ApiException {
String programDbId = program.getBrapiProgram() != null ? program.getBrapiProgram().getProgramDbId() : null;
return observationLevelDAO.getObservationLevelNames(program, programDbId);
}

private Map<String, Object> createExportRow(
BrAPITrial experiment,
Program program,
Expand Down
104 changes: 101 additions & 3 deletions src/test/java/org/breedinginsight/api/v1/controller/ExperimentControllerIntegrationTest.java
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Expand Up @@ -213,12 +213,17 @@ void setup() throws Exception {

// Create an experiment with no observations.
private String uploadExperimentWithoutObs() throws Exception {
return uploadExperimentWithoutObs("Without Obs", "Plot");
}

private String uploadExperimentWithoutObs(String title, String expUnit) throws Exception {
ImportTestUtils importTestUtils = new ImportTestUtils();
List<Map<String, Object>> expRows = new ArrayList<>();

// Make test experiment import.
Map<String, Object> row1 = makeExpImportRow("Without Obs", "NewEnv1");
Map<String, Object> row2 = makeExpImportRow("Without Obs", "NewEnv2");
String envBase = title.replaceAll("\\s+", "");
Map<String, Object> row1 = makeExpImportRow(title, envBase + "1", expUnit);
Map<String, Object> row2 = makeExpImportRow(title, envBase + "2", expUnit);

expRows.add(row1);
expRows.add(row2);
Expand Down Expand Up @@ -396,6 +401,75 @@ void downloadSubEntityDataset(String extension) {
parseAndCheck(plantBodyStream, extension, false, plantRows, false, 23);
}

@Test
@Order(1)
public void createSubEntityDatasetRejectsExpUnitNameAlreadyUsedInSameExperiment() throws Exception {
String plantExperimentId = uploadExperimentWithoutObs("Plant Same Experiment", "Plant");

Flowable<HttpResponse<String>> call = client.exchange(
POST(String.format("/programs/%s/experiments/%s/dataset", program.getId(), plantExperimentId),
"{\"name\":\"Plant\",\"repeatedMeasures\":2}")
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")),
String.class
);

HttpClientResponseException e = assertThrows(HttpClientResponseException.class, call::blockingFirst);
assertEquals(HttpStatus.CONFLICT, e.getStatus());
}

@Test
@Order(2)
public void createSubEntityDatasetAllowsExpUnitNameUsedInOtherExperiment() throws Exception {
uploadExperimentWithoutObs("Plant Source Experiment", "Plant");
String recipientExperimentId = uploadExperimentWithoutObs("Plot Recipient Experiment", "Plot");

Flowable<HttpResponse<String>> call = client.exchange(
POST(String.format("/programs/%s/experiments/%s/dataset", program.getId(), recipientExperimentId),
"{\"name\":\"Plant\",\"repeatedMeasures\":2}")
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")),
String.class
);

HttpResponse<String> response = call.blockingFirst();
assertEquals(HttpStatus.OK, response.getStatus());
}

@Test
@Order(3)
public void recommendedSubEntityDatasetNamesIncludeExpUnitNamesFromOtherExperiments() throws Exception {
uploadExperimentWithoutObs("Plant Autocomplete Source", "Plant");
String recipientExperimentId = uploadExperimentWithoutObs("Autocomplete Recipient", "Plot");

List<String> recommendedNames = getRecommendedSubEntityDatasetNames(recipientExperimentId);

assertTrue(recommendedNames.stream().anyMatch(name -> name.equalsIgnoreCase("plant")));
assertFalse(recommendedNames.stream().anyMatch(name -> name.equalsIgnoreCase("plot")));
}

@Test
@Order(4)
public void recommendedSubEntityDatasetNamesDeDuplicateExpUnitAndSubUnitNamesAcrossExperiments() throws Exception {
uploadExperimentWithoutObs("Plant Exp Unit Source", "Plant");
String subEntitySourceExperimentId = uploadExperimentWithoutObs("Plant Sub Unit Source", "Plot");
String recipientExperimentId = uploadExperimentWithoutObs("Plant Unique Recipient", "Plot");

Flowable<HttpResponse<String>> postCall = client.exchange(
POST(String.format("/programs/%s/experiments/%s/dataset", program.getId(), subEntitySourceExperimentId),
"{\"name\":\"Plant\",\"repeatedMeasures\":2}")
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")),
String.class
);
HttpResponse<String> postResponse = postCall.blockingFirst();
assertEquals(HttpStatus.OK, postResponse.getStatus());

List<String> recommendedNames = getRecommendedSubEntityDatasetNames(recipientExperimentId);

assertEquals(1L, recommendedNames.stream().filter(name -> name.equalsIgnoreCase("plant")).count());
}

/**
* Tests for Experimental Collaborator endpoints
*/
Expand Down Expand Up @@ -845,12 +919,36 @@ private File writeDataToFile(List<Map<String, Object>> data, List<Trait> traits)
return file;
}

private List<String> getRecommendedSubEntityDatasetNames(String targetExperimentId) {
Flowable<HttpResponse<String>> call = client.exchange(
GET(String.format("/programs/%s/experiments/%s/recommended-sub-entity-dataset-names",
program.getId(), targetExperimentId))
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")),
String.class
);
HttpResponse<String> response = call.blockingFirst();
assertEquals(HttpStatus.OK, response.getStatus());

JsonArray result = JsonParser.parseString(Objects.requireNonNull(response.body()))
.getAsJsonObject()
.getAsJsonArray("result");

List<String> recommendedNames = new ArrayList<>();
result.forEach(name -> recommendedNames.add(name.getAsString()));
return recommendedNames;
}

private Map<String, Object> makeExpImportRow(String title, String environment) {
return makeExpImportRow(title, environment, "Plot");
}

private Map<String, Object> makeExpImportRow(String title, String environment, String expUnit) {
Map<String, Object> row = new HashMap<>();
row.put(ExperimentObservation.Columns.GERMPLASM_GID, "1");
row.put(ExperimentObservation.Columns.TEST_CHECK, "T");
row.put(ExperimentObservation.Columns.EXP_TITLE, title);
row.put(ExperimentObservation.Columns.EXP_UNIT, "Plot");
row.put(ExperimentObservation.Columns.EXP_UNIT, expUnit);
//row.put(ExperimentObservation.Columns.SUB_OBS_UNIT, "");
row.put(ExperimentObservation.Columns.EXP_TYPE, "Phenotyping");
row.put(ExperimentObservation.Columns.ENV, environment);
Expand Down
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