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[BI-2911] Remove rest of CRUD operations for ObservationDAO #532

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[BI-2911] Remove rest of CRUD operations for ObservationDAO #532

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e9099ea
Remove rest of cache code from ObservationDAO
jloux-brapi Jul 7, 2026
a5ef826
Fix unit test failures
jloux-brapi Jul 8, 2026
ae20e21
Merge branch 'bug/BI-2944' into feature/BI-2911
jloux-brapi Jul 8, 2026
7997122
Remove referenced to CachedDAO parent class, remove imports
jloux-brapi Jul 8, 2026
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97 changes: 10 additions & 87 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@

import io.micronaut.context.annotation.Property;
import io.micronaut.http.server.exceptions.InternalServerException;
import io.micronaut.scheduling.annotation.Scheduled;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.Pair;
Expand All @@ -33,12 +32,10 @@
import org.brapi.v2.model.pheno.BrAPIObservationUnit;
import org.brapi.v2.model.pheno.request.BrAPIObservationSearchRequest;
import org.brapi.v2.model.pheno.response.BrAPIObservationListResponse;
import org.brapi.v2.model.pheno.response.BrAPIObservationSingleResponse;
import org.breedinginsight.brapps.importer.daos.ImportDAO;
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.daos.cache.ProgramCacheProvider;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.TraitService;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
Expand All @@ -50,22 +47,20 @@
import javax.inject.Inject;
import javax.inject.Singleton;
import java.util.*;
import java.util.concurrent.Callable;
import java.util.stream.Collectors;

import static org.brapi.v2.model.BrAPIWSMIMEDataTypes.APPLICATION_JSON;

@Singleton
@Slf4j
public class BrAPIObservationDAO extends BrAPICachedDAO<BrAPIObservation> {
public class BrAPIObservationDAO {

private ProgramDAO programDAO;
private ImportDAO importDAO;
private BrAPIObservationUnitDAO observationUnitDAO;
private final BrAPIDAOUtil brAPIDAOUtil;
private final BrAPIEndpointProvider brAPIEndpointProvider;
private final String referenceSource;
private boolean runScheduledTasks;
private final TraitService traitService;

private final int brapiMaxPageSize;
Expand All @@ -79,75 +74,17 @@ public BrAPIObservationDAO(ProgramDAO programDAO,
@Property(name = "brapi.server.reference-source") String referenceSource,
@Property(name = "micronaut.bi.api.run-scheduled-tasks") boolean runScheduledTasks,
@Property(name = "brapi.cache.fetch-page-size") int brapiFetchPageSize,
ProgramCacheProvider programCacheProvider, TraitService traitService) {
TraitService traitService) {
this.programDAO = programDAO;
this.importDAO = importDAO;
this.observationUnitDAO = observationUnitDAO;
this.brAPIDAOUtil = brAPIDAOUtil;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.referenceSource = referenceSource;
this.runScheduledTasks = runScheduledTasks;
this.traitService = traitService;
this.programCache = programCacheProvider.getProgramCache(this::fetchProgramObservations, BrAPIObservation.class);
this.brapiMaxPageSize = brapiFetchPageSize;
}

@Scheduled(initialDelay = "${startup.delay.observation}")
public void setup() {
if(!runScheduledTasks) {
return;
}
// Populate the observation cache for all programs on startup.
log.debug("populating observation cache");
List<Program> programs = programDAO.getActive();
if (programs != null) {
programCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
}
}

/**
* Fetch formatted observations for this program.
*/
private Map<String, BrAPIObservation> fetchProgramObservations(UUID programId) throws ApiException {
ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
// Get the program.
List<Program> programs = programDAO.get(programId);
if (programs.size() != 1) {
throw new InternalServerException("Program was not found for given id");
}
Program program = programs.get(0);

// Set query params and make call.
BrAPIObservationSearchRequest observationSearch = new BrAPIObservationSearchRequest();
observationSearch.externalReferenceIds(List.of(programId.toString()));
observationSearch.externalReferenceSources(List.of(Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS)));
return processObservationsForCache(brAPIDAOUtil.search(
api::searchObservationsPost,
api::searchObservationsSearchResultsDbIdGet,
observationSearch
), program.getKey());
}

/**
* Process a list of observations for insertion into the cache.
*/
private Map<String, BrAPIObservation> processObservationsForCache(List<BrAPIObservation> programObservations, String programKey) {
// Process programObservations in place (strip program key, etc.).
processObservations(programKey, programObservations);
// Build map.
Map<String, BrAPIObservation> programObservationsMap = new HashMap<>();
log.trace("processing observationUnits for cache: " + programObservations);
for (BrAPIObservation observation: programObservations) {
BrAPIExternalReference xref = observation
.getExternalReferences()
.stream()
.filter(reference -> String.format("%s/%s", referenceSource, ExternalReferenceSource.OBSERVATIONS.getName()).equals(reference.getReferenceSource()))
.findFirst().orElseThrow(() -> new IllegalStateException("No BI external reference found"));
programObservationsMap.put(xref.getReferenceId(), observation);
}
return programObservationsMap;
}

/**
* Process BrAPIObservations for use in DeltaBreed (e.g. strip program key).
*/
Expand Down Expand Up @@ -296,11 +233,9 @@ public List<BrAPIObservation> createBrAPIObservations(List<BrAPIObservation> brA
var program = programDAO.fetchOneById(programId);
try {
if (!brAPIObservationList.isEmpty()) {
Callable<Map<String, BrAPIObservation>> postFunction = () -> {
List<BrAPIObservation> postResponse = brAPIDAOUtil.post(brAPIObservationList, upload, api::observationsPost, importDAO::update);
return processObservationsForCache(postResponse, program.getKey());
};
return programCache.post(programId, postFunction);
processObservations(program.getKey(), postResponse);
return postResponse;
}
return new ArrayList<>();
} catch (Exception e) {
Expand Down Expand Up @@ -339,39 +274,27 @@ private List<BrAPIObservation> getBrAPIObservationsUsingBrAPIProgramId(Program p
return result;
}

// This method overloads updateBrAPIObservation(String dbId, BrAPIObservation observation, UUID programId)
// It was added to increase efficiency. It insures that ProgramCache<BrAPIObservation>.populate() is called only once
// not once per observation.
public List<BrAPIObservation> updateBrAPIObservation(Map<String, BrAPIObservation> mutatedObservationByDbId, UUID programId) throws ApiException {
ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
var program = programDAO.fetchOneById(programId);

List <BrAPIObservation> updatedObservations = new ArrayList<>();
try {
// TODO: Instead of a for loop, utilize BrAPI Observations put to do all updates in one request. [BI-2969]
for (Map.Entry<String, BrAPIObservation> entry : mutatedObservationByDbId.entrySet()) {
String dbId = entry.getKey();
BrAPIObservation observation = entry.getValue();
if (observation == null) {
throw new Exception("Null observation");
}

ApiResponse<BrAPIObservationSingleResponse> response = null;
BrAPIObservation updatedObservation;

try {
response = api.observationsObservationDbIdPut(dbId, observation);
updatedObservation = brAPIDAOUtil.put(dbId, observation, api::observationsObservationDbIdPut);
} catch (ApiException e) {
throw new RuntimeException(e);
}
if (response == null) {
throw new ApiException("Response is null", 0, null, null);
}
BrAPIObservationSingleResponse body = response.getBody();
if (body == null) {
throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
}
BrAPIObservation updatedObservation = body.getResult();
if (updatedObservation == null) {
throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
}
updatedObservations.add(updatedObservation);

if (!Objects.equals(observation.getValue(), updatedObservation.getValue())
Expand All @@ -385,8 +308,8 @@ public List<BrAPIObservation> updateBrAPIObservation(Map<String, BrAPIObservatio
throw new Exception(message);
}
}
Map<String, BrAPIObservation> processedObservations = processObservationsForCache(updatedObservations, program.getKey());
return programCache.postThese(programId,processedObservations);
processObservations(program.getKey(), updatedObservations);
return updatedObservations;
} catch (ApiException e) {
log.error("Error updating observation: " + Utilities.generateApiExceptionLogMessage(e), e);
throw e;
Expand Down
1 change: 0 additions & 1 deletion 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 @@ -836,7 +836,6 @@ public int deleteExperiment(Program program, UUID experimentId, boolean hard) th
}
// TODO: if performance is poor, implement more precise invalidation, possibly using hierarchical cache keys.
studyDAO.repopulateCache(program.getId());
observationDAO.repopulateCache(program.getId());
observationUnitDAO.repopulateCache(program.getId());
}

Expand Down
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