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Generalize BrAPI Entity GET code, and pagination/sorting/filtering code #527

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0f8a05d
Generalize sorting and filtering code for reusability for future cach…
jloux-brapi Jun 15, 2026
8067d5c
Create generalized brapi get method
jloux-brapi Jun 17, 2026
a470ef9
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jloux-brapi Jun 17, 2026
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23 changes: 23 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v1/model/request/query/BrapiQuery.java
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Expand Up @@ -26,6 +26,7 @@

import javax.validation.constraints.Positive;
import javax.validation.constraints.PositiveOrZero;
import java.util.Map;

@Getter
@Setter
Expand Down Expand Up @@ -58,4 +59,26 @@ protected FilterRequest constructFilterRequest(String field, String value) {
.value(value)
.build();
}

/**
* For BrapiQuery objects that have implemented this method, this map is used by the BrAPIDAOUtil
* to iterate through all valid filter columns and their associated values that are submitted from the fe.
*
* See @ExperimentQuery for example implementation
*/
public Map<String, String> getFilterValuesByBrAPIColumnName() {
throw new UnsupportedOperationException(
String.format("Server side BrAPI filtering not implemented for class [%s]", this.getClass().getSimpleName())
);
}

/**
* For BrapiQuery objects that have implemented this method, this map is used by the BrAPIDAOUtil
* to match submitted sortField column names to the associated brapi column name for sorting.
*
* See @ExperimentQuery for example implementation
*/
public Map<String, String> getBrAPIColumnNamesByBiColumnName() {
throw new UnsupportedOperationException(String.format("Server side BrAPI sorting not implemented for class [%s]", this.getClass().getSimpleName()));
}
}
1 change: 0 additions & 1 deletion src/main/java/org/breedinginsight/brapi/v2/BrAPITrialsController.java
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Expand Up @@ -93,7 +93,6 @@ public HttpResponse<Response<DataResponse<BrAPITrial>>> getExperiments(
Optional<Program> program = programService.getById(programId);
if (program.isEmpty()) { return HttpResponse.notFound(); }

SearchRequest searchRequest = queryParams.constructSearchRequest();
log.debug("fetching trials for program: " + programId);

// If the program user is an experimental collaborator, filter results for only authorized experiments.
Expand Down
76 changes: 15 additions & 61 deletions src/main/java/org/breedinginsight/brapi/v2/dao/impl/BrAPITrialDAOImpl.java
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Expand Up @@ -27,7 +27,6 @@
import org.brapi.client.v2.model.queryParams.core.TrialQueryParams;
import org.brapi.client.v2.modules.core.TrialsApi;
import org.brapi.v2.model.BrAPIFilterBy;
import org.brapi.v2.model.BrAPIResponse;
import org.brapi.v2.model.BrAPISortBy;
import org.brapi.v2.model.core.BrAPIProgram;
import org.brapi.v2.model.core.BrAPITrial;
Expand Down Expand Up @@ -83,7 +82,6 @@ public BrAPITrialDAOImpl(ProgramDAO programDAO,
* This method requires a BI-API program. If the BrAPIProgram inside this data model is not set,
* this method will retrieve it.
*/
// TODO: Generalize Code for General Get By Program for BrAPI Entities [BI-2932]
private List<BrAPITrial> getBrAPITrialsUsingBrAPIProgramId(Program program) throws ApiException {

if (program == null || program.getId() == null) {
Expand All @@ -99,37 +97,16 @@ private List<BrAPITrial> getBrAPITrialsUsingBrAPIProgramId(Program program) thro
brapiProgramDbId = programDAO.getProgramBrAPI(program).getProgramDbId();
}

// TODO: Configurable max amount of trials per program, or paginate [BI-2932]

TrialQueryParams trialQueryParams =
TrialQueryParams.builder()
.programDbId(brapiProgramDbId)
.pageSize(1000)
.page(0)
.build();

return getTrialsFromBrAPI(program, trialQueryParams);
}

private List<BrAPITrial> getTrialsFromBrAPI(Program program, TrialQueryParams trialQueryParams) throws ApiException {
TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), TrialsApi.class);

ApiResponse<BrAPITrialListResponse> response;

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

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

List<BrAPITrial> trialsFromResponse = response.getBody().getResult().getData();
List<BrAPITrial> result = brAPIDAOUtil.get(api::trialsGet, trialQueryParams);

return processExperimentsForDisplay(trialsFromResponse, program.getKey());
return processExperimentsForDisplay(result, program.getKey());
}

@Override
Expand Down Expand Up @@ -193,12 +170,21 @@ public Optional<BrAPITrial> getTrialById(UUID programId, UUID trialId) throws Ap

TrialQueryParams params = TrialQueryParams.builder()
.trialDbId(trialId.toString())
.pageSize(1)
.page(0)
.build();

TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), TrialsApi.class);

List<BrAPITrial> result = brAPIDAOUtil.get(api::trialsGet, params);

if (result.isEmpty()) {
throw new DoesNotExistException(String.format("Trial with ID [%s] does not exist", trialId));
} else if (result.size() > 1) {
throw new InternalServerException(String.format("Trial with ID [%s] found multiple times in database. This should not be possible.", trialId));
}

processExperimentsForDisplay(result, program.getKey());

return getTrialsFromBrAPI(program, params).stream().findFirst();
return result.stream().findFirst();
}

@Override
Expand Down Expand Up @@ -284,40 +270,8 @@ private BrAPITrialSearchRequest buildSearchRequest(Program program, List<UUID> b
searchRequest.setTrialDbIds(brapiTrialIds.stream().map(UUID::toString).collect(Collectors.toList()));
}

// Set FilterBy
List<BrAPIFilterBy> brAPIFilterBy = new ArrayList<>();

if (StringUtils.isNotBlank(experimentQuery.getName())) {
brAPIFilterBy.add(brAPIDAOUtil.constructFilterBy(brAPITrialsMapper.getBrAPIName(BI_FILTER_COLUMN_NAME), experimentQuery.getName()));
}
if (StringUtils.isNotBlank(experimentQuery.getActive())) {
brAPIFilterBy.add(brAPIDAOUtil.constructFilterBy(brAPITrialsMapper.getBrAPIName(BI_FILTER_COLUMN_ACTIVE), experimentQuery.getActive()));
}
if (StringUtils.isNotBlank(experimentQuery.getCreatedBy())) {
brAPIFilterBy.add(brAPIDAOUtil.constructFilterBy(brAPITrialsMapper.getBrAPIName(BI_FILTER_COLUMN_CREATED_BY), experimentQuery.getCreatedBy()));
}
if (StringUtils.isNotBlank(experimentQuery.getCreatedDate())) {
brAPIFilterBy.add(brAPIDAOUtil.constructFilterBy(brAPITrialsMapper.getBrAPIName(BI_FILTER_COLUMN_CREATED_DATE), experimentQuery.getCreatedDate()));
}

if (!brAPIFilterBy.isEmpty()) {
searchRequest.setFilterBy(brAPIFilterBy);
}

// Set SortBy
List<BrAPISortBy> brAPISortBy = new ArrayList<>();

if (StringUtils.isNotBlank(experimentQuery.getSortField()) && brAPITrialsMapper.exists(experimentQuery.getSortField())) {
brAPISortBy.add(brAPIDAOUtil.constructSortBy(brAPITrialsMapper.getBrAPIName(experimentQuery.getSortField()), experimentQuery.getSortOrder().toString()));
}

if (!brAPISortBy.isEmpty()) {
searchRequest.setSortBy(brAPISortBy);
}

brAPIDAOUtil.setPagination(searchRequest, experimentQuery);
brAPIDAOUtil.setGenericSearchParameters(searchRequest, experimentQuery);

return searchRequest;

}
}
44 changes: 24 additions & 20 deletions src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentQuery.java
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Expand Up @@ -2,13 +2,10 @@

import io.micronaut.core.annotation.Introspected;
import lombok.Getter;
import org.breedinginsight.api.model.v1.request.query.FilterRequest;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
import org.jooq.tools.StringUtils;

import java.util.ArrayList;
import java.util.List;
import java.util.HashMap;
import java.util.Map;

@Getter
@Introspected
Expand All @@ -18,20 +15,27 @@ public class ExperimentQuery extends BrapiQuery {
private String createdBy;
private String createdDate;

public SearchRequest constructSearchRequest() {
List<FilterRequest> filters = new ArrayList<>();
if (!StringUtils.isBlank(getName())) {
filters.add(constructFilterRequest("name", getName()));
}
if (!StringUtils.isBlank(getActive())) {
filters.add(constructFilterRequest("active", getActive()));
}
if (!StringUtils.isBlank(getCreatedBy())) {
filters.add(constructFilterRequest("createdBy", getCreatedBy()));
}
if (!StringUtils.isBlank(getCreatedDate())) {
filters.add(constructFilterRequest("createdDate", getCreatedDate()));
}
return new SearchRequest(filters);
@Override
public Map<String, String> getFilterValuesByBrAPIColumnName() {
Map<String, String> filterValuesByBrAPIColumnName = new HashMap<>();

filterValuesByBrAPIColumnName.put("trialName", getName());
filterValuesByBrAPIColumnName.put("active", getActive());
filterValuesByBrAPIColumnName.put("createdBy", getCreatedBy());
filterValuesByBrAPIColumnName.put("createdDate", getCreatedDate());

return filterValuesByBrAPIColumnName;
}

@Override
public Map<String, String> getBrAPIColumnNamesByBiColumnName() {
Map<String, String> brAPIColumnNamesByBiColumnName = new HashMap<>();

brAPIColumnNamesByBiColumnName.put("name", "trialName");
brAPIColumnNamesByBiColumnName.put("active", "active");
brAPIColumnNamesByBiColumnName.put("createdBy", "createdBy");
brAPIColumnNamesByBiColumnName.put("createdDate", "createdDate");

return brAPIColumnNamesByBiColumnName;
}
}
100 changes: 88 additions & 12 deletions src/main/java/org/breedinginsight/utilities/BrAPIDAOUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@
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.model.queryParams.core.BrAPIQueryParams;
import org.brapi.v2.model.*;
import org.breedinginsight.api.model.v1.response.DataResponse;
import org.breedinginsight.brapi.v1.controller.BrapiVersion;
import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
import org.breedinginsight.brapps.importer.model.ImportUpload;
Expand Down Expand Up @@ -76,6 +76,55 @@ public BrAPIDAOUtil(@Property(name = "brapi.search.wait-time") int searchWaitTim
this.programService = programService;
}

public <T extends BrAPIResponse, U extends BrAPIQueryParams, V> List<V> get(Function<U, ApiResponse<T>> getMethod,
U queryParams) throws ApiException {
T brapiResponseResult;

boolean paginationSet = queryParams.page() != null && queryParams.pageSize() != null;

if (!paginationSet) {
queryParams.setPage(0);
queryParams.setPageSize(pageSize);
}

try {
brapiResponseResult = Optional.ofNullable(getMethod.apply(queryParams))
.map(ApiResponse::getBody)
.orElseThrow();
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw e;
} catch (NoSuchElementException e) {
log.debug("Unable to retrieve BrAPIResponse from POST search request", e);
throw new InternalServerException(e.toString(), e);
} catch (Exception e) {
log.debug("error", e);
throw new InternalServerException(e.toString(), e);
}

BrAPIPagination responsePagination = Optional.of(brapiResponseResult)
.map(BrAPIResponse::getMetadata)
.map(BrAPIMetadata::getPagination)
.orElse(null);

if (responsePagination == null) {
throw new InternalServerException("Expected pagination metadata in BrAPI get response not present");
}

if (!paginationSet && responsePagination.getTotalPages() > 1) {
// Size of BrAPI entity GET data can not exceed configured pageSize.
// If it does, it is recommended the GET method not be used for this purpose.
// If you are trying to utilize this method to get a large amount of data for an entity, you can use
// searchInternal for now. In the future, we need a more robust way of transmitting this data using
// compression client techniques to reduce strain on the server and avoid keeping all the database data
// in java memory.
throw new InternalServerException(String.format("More than one page found, meaning there is more data to be returned " +
"with pageSize = [%s]", queryParams.pageSize()));
}

return getListResult(brapiResponseResult);
}

// Performs a POST brapi search on an entity without looping paging logic, utilizing filters and pagination provided in the searchBody.
// Also verifies response paging matches requested paging
public <T extends BrAPIResponse, U extends BrAPISearchRequestParametersPaging, V> T simpleSearch(Function<U, ApiResponse<Pair<Optional<T>, Optional<BrAPIAcceptedSearchResponse>>>> searchMethod,
Expand Down Expand Up @@ -352,14 +401,6 @@ public <T extends BrAPIResponse, V> List<V> getListResult(T response) {
.orElseThrow();
}

// TODO: write generic put code
public <T> List<T> put(List<T> brapiObjects,
ImportUpload upload,
Function<List<T>, ApiResponse> putMethod,
Consumer<ImportUpload> progressUpdateMethod) throws ApiException {
throw new UnsupportedOperationException();
}

public <T, R> List<R> post(List<T> brapiObjects,
ImportUpload upload,
Function<List<T>, ApiResponse> postMethod,
Expand Down Expand Up @@ -506,15 +547,15 @@ public String getProgramBrAPIBaseUrl(UUID programId) {
return programBrAPIBaseUrl.endsWith(BrapiVersion.BRAPI_V2) ? programBrAPIBaseUrl : programBrAPIBaseUrl + BrapiVersion.BRAPI_V2;
}

public BrAPIFilterBy constructFilterBy(String filterOn, String value) {
private BrAPIFilterBy constructFilterBy(String filterOn, String value) {
var filterBy = new BrAPIFilterBy();

filterBy.setFilterOn(filterOn);
filterBy.setValue(value);
return filterBy;
}

public BrAPISortBy constructSortBy(String sortOn, String sortOrder) {
private BrAPISortBy constructSortBy(String sortOn, String sortOrder) {
var sortBy = new BrAPISortBy();
sortBy.setSortedOn(sortOn);

Expand All @@ -529,7 +570,42 @@ public BrAPISortBy constructSortBy(String sortOn, String sortOrder) {
return sortBy;
}

public <T extends BrAPISearchRequestParametersPaging, U extends BrapiQuery> void setPagination(T brapiSearchRequest, U biSearchQuery) {
/**
* Sets three generic search parameters for an outgoing BrAPI Search Query:
* - Sorting
* - Filtering
* - Pagination
*/
public <T extends BrAPISearchRequestParametersPaging, U extends BrapiQuery> void setGenericSearchParameters(T brapiSearchRequest, U biSearchQuery) {
// Set SortBy
List<BrAPISortBy> brAPISortBy = new ArrayList<>();

Map<String, String> brapiColNameByBiColName = biSearchQuery.getBrAPIColumnNamesByBiColumnName();

if (StringUtils.isNotBlank(biSearchQuery.getSortField()) && brapiColNameByBiColName.containsKey(biSearchQuery.getSortField())) {
brAPISortBy.add(constructSortBy(brapiColNameByBiColName.get(biSearchQuery.getSortField()), biSearchQuery.getSortOrder().toString()));
}

if (!brAPISortBy.isEmpty()) {
brapiSearchRequest.setSortBy(brAPISortBy);
}

// Set FilterBy
List<BrAPIFilterBy> brAPIFilterBy = new ArrayList<>();

Map<String, String> filterValuesByBrAPIColName = biSearchQuery.getFilterValuesByBrAPIColumnName();

filterValuesByBrAPIColName.forEach((brapiColumnName, value) -> {
if (StringUtils.isNotBlank(value)) {
brAPIFilterBy.add(constructFilterBy(brapiColumnName, value));
}
});

if (!brAPIFilterBy.isEmpty()) {
brapiSearchRequest.setFilterBy(brAPIFilterBy);
}

// Set Pagination
if (biSearchQuery.getPage() == null) {
brapiSearchRequest.setPage(biSearchQuery.getDefaultPage());
} else {
Expand Down
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