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Merge pull request #443 from Breeding-Insight/feature/BI-2047
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BI-2047 - Pull Existing Observation Values For An Experiment Into Field-Book
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@mlm483
mlm483 authored Feb 18, 2025
2 parents e57120c + 7aed5ac commit 487aedb
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Showing 4 changed files with 278 additions and 15 deletions.
112 changes: 108 additions & 4 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIObservationsController.java
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Expand Up @@ -28,13 +28,17 @@
import org.brapi.client.v2.ApiResponse;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.client.v2.modules.phenotype.ObservationsApi;
import org.brapi.v2.model.BrAPIIndexPagination;
import org.brapi.v2.model.BrAPIMetadata;
import org.brapi.v2.model.BrAPIStatus;
import org.brapi.v2.model.BrAPIWSMIMEDataTypes;
import org.brapi.v2.model.core.BrAPIStudy;
import org.brapi.v2.model.pheno.BrAPIObservation;
import org.brapi.v2.model.pheno.response.BrAPIObservationTableResponse;
import org.brapi.v2.model.pheno.response.*;
import org.breedinginsight.api.auth.ProgramSecured;
import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
import org.breedinginsight.brapi.v1.controller.BrapiVersion;
import org.breedinginsight.brapi.v2.dao.BrAPIObservationDAO;
import org.breedinginsight.brapi.v2.dao.BrAPIStudyDAO;
import org.breedinginsight.brapi.v2.model.request.query.ObservationQuery;
import org.breedinginsight.daos.ProgramDAO;
Expand All @@ -47,6 +51,8 @@
import javax.annotation.Nullable;
import javax.inject.Inject;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;

@Slf4j
@Controller("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2)
Expand All @@ -57,13 +63,20 @@ public class BrAPIObservationsController {
private final ProgramDAO programDAO;
private final BrAPIStudyDAO brAPIStudyDAO;
private final BrAPIEndpointProvider brAPIEndpointProvider;
private final BrAPIObservationDAO observationDAO;

@Inject
public BrAPIObservationsController(ProgramService programService, ProgramDAO programDAO, ProgramDAO programDAO1, BrAPIStudyDAO brAPIStudyDAO, BrAPIEndpointProvider brAPIEndpointProvider) {
public BrAPIObservationsController(ProgramService programService,
ProgramDAO programDAO,
ProgramDAO programDAO1,
BrAPIStudyDAO brAPIStudyDAO,
BrAPIEndpointProvider brAPIEndpointProvider,
BrAPIObservationDAO brAPIObservationDAO) {
this.programService = programService;
this.programDAO = programDAO1;
this.brAPIStudyDAO = brAPIStudyDAO;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.observationDAO = brAPIObservationDAO;
}

@Get("/observations")
Expand Down Expand Up @@ -93,8 +106,99 @@ public HttpResponse observationsGet(@PathVariable("programId") UUID programId,
@Nullable @QueryValue("externalReferenceSource") String externalReferenceSource,
@Nullable @QueryValue("page") Integer page,
@Nullable @QueryValue("pageSize") Integer pageSize) {
//TODO
return HttpResponse.notFound();
log.debug("observationsGet: fetching observations by filters");
Optional<Program> program = programService.getById(programId);
if(program.isEmpty()) {
log.warn("Program id: " + programId + " not found");
return HttpResponse.notFound();
}

try {

// TODO: BI-2506 - implement support for all query parameters.
List<Object> unsupportedParams = Stream.of(
observationDbId,
observationUnitDbId,
observationVariableDbId,
locationDbId,
seasonDbId,
observationTimeStampRangeStart,
observationTimeStampRangeEnd,
observationUnitLevelName,
observationUnitLevelOrder,
observationUnitLevelCode,
observationUnitLevelRelationshipName,
observationUnitLevelRelationshipOrder,
observationUnitLevelRelationshipCode,
observationUnitLevelRelationshipDbId,
commonCropName,
programDbId,
trialDbId,
germplasmDbId,
externalReferenceID,
externalReferenceId,
externalReferenceSource
).filter(Objects::nonNull).collect(Collectors.toList());

if (!unsupportedParams.isEmpty()) {
return HttpResponse.status(HttpStatus.NOT_IMPLEMENTED).body(
new BrAPIObservationListResponse().metadata(new BrAPIMetadata().status(List.of(new BrAPIStatus().messageType(BrAPIStatus.MessageTypeEnum.ERROR)
.message("Unsupported query parameter. Only studyDbId, page, and pageSize are supported."))))
);
}

// Get a filtered list of observations.
List<BrAPIObservation> observations = observationDAO.getObservationsByFilters(program.get(), studyDbId);

// If page is not provided, set it to the default value 0.
if (page == null) page = 0;
// If pageSize is not provided, set it to the default value 1000.
if (pageSize == null) pageSize = 1000;

// Total number of records in the unpaged super set.
int totalCount = observations.size();
// The least of pageSize and totalCount, unless pageSize is zero, in which case use totalCount.
int requestedPageSize = pageSize > 0 ? Math.min(pageSize, totalCount) : totalCount;
// Integer division and round up.
int totalPages = totalCount / requestedPageSize + ((totalCount % requestedPageSize == 0) ? 0 : 1);
log.info("(Pagination) totalCount: " + totalCount + " page (0-indexed): " + page + " requestedPageSize: " + requestedPageSize + " totalPages: " + totalPages);

// Determine validity of pagination query parameters.
boolean pageSizeValid = pageSize > 0;
boolean pageValid = page >= 0 && page < totalPages;

// Only paginate if valid pagination values were sent.
if (pageSizeValid && pageValid) {
int start = page * requestedPageSize;
// Account for last page, which may have fewer than requestedPageSize items, or exactly requestedPageSize items.
int end = (page == (totalPages - 1) && totalCount % requestedPageSize != 0) ? (start + (totalCount % requestedPageSize)) : Math.min(((page + 1) * requestedPageSize), totalCount);
log.info("(Pagination) start " + start + " end " + end);
// Sort observations so that paging is consistent and coherent.
observations.sort(Comparator.comparing(BrAPIObservation::getObservationDbId));
// Paginate response.
observations = observations.subList(start, end);
} else {
String errorMessage = "Invalid query parameters: page, pageSize";
return HttpResponse.badRequest(new BrAPIObservationListResponse().metadata(new BrAPIMetadata().status(List.of(new BrAPIStatus().messageType(BrAPIStatus.MessageTypeEnum.ERROR)
.message(errorMessage)))));
}

return HttpResponse.ok(new BrAPIObservationListResponse().metadata(new BrAPIMetadata().pagination(new BrAPIIndexPagination()
.currentPage(page)
.totalPages(totalPages)
.pageSize(observations.size())
.totalCount(totalCount)))
.result(new BrAPIObservationListResponseResult().data(observations)));

} catch (ApiException e) {
log.error(Utilities.generateApiExceptionLogMessage(e), e);
return HttpResponse.serverError(new BrAPIObservationListResponse().metadata(new BrAPIMetadata().status(List.of(new BrAPIStatus().messageType(BrAPIStatus.MessageTypeEnum.ERROR)
.message("Error fetching observations")))));
} catch (Exception e) {
log.error("Error fetching Observations", e);
return HttpResponse.serverError(new BrAPIObservationListResponse().metadata(new BrAPIMetadata().status(List.of(new BrAPIStatus().messageType(BrAPIStatus.MessageTypeEnum.ERROR)
.message("Error fetching observations")))));
}
}

@Get("/observations/{observationDbId}")
Expand Down
43 changes: 42 additions & 1 deletion 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 @@ -38,7 +38,10 @@
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.daos.cache.ProgramCacheProvider;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.Trait;
import org.breedinginsight.services.TraitService;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.utilities.BrAPIDAOUtil;
import org.breedinginsight.utilities.Utilities;
import org.jetbrains.annotations.NotNull;
Expand All @@ -62,6 +65,7 @@ public class BrAPIObservationDAO extends BrAPICachedDAO<BrAPIObservation> {
private final BrAPIEndpointProvider brAPIEndpointProvider;
private final String referenceSource;
private boolean runScheduledTasks;
private final TraitService traitService;

@Inject
public BrAPIObservationDAO(ProgramDAO programDAO,
Expand All @@ -71,14 +75,15 @@ public BrAPIObservationDAO(ProgramDAO programDAO,
BrAPIEndpointProvider brAPIEndpointProvider,
@Property(name = "brapi.server.reference-source") String referenceSource,
@Property(name = "micronaut.bi.api.run-scheduled-tasks") boolean runScheduledTasks,
ProgramCacheProvider programCacheProvider) {
ProgramCacheProvider programCacheProvider, 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);
}

Expand Down Expand Up @@ -242,6 +247,42 @@ public List<BrAPIObservation> getObservationsByObservationUnitsAndStudies(Collec
.collect(Collectors.toList());
}

// TODO: implement other filters in BI-2506.
public List<BrAPIObservation> getObservationsByFilters(Program program, String studyDbId) throws ApiException, DoesNotExistException {

String studySource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.STUDIES);
String observationUnitSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.OBSERVATION_UNITS);
String observationSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.OBSERVATIONS);

// Get all observations for the program.
Collection<BrAPIObservation> observations = getProgramObservations(program.getId()).values();
// Build a hashmap of traits for fast lookup. The key is ObservationVariableDbId, the value is the Trait Id.
HashMap<String, String> traitIdsByObservationVariableDbId = traitService.getIdsByObservationVariableDbIds(program.getId(), observations.stream().map(BrAPIObservation::getObservationVariableDbId).collect(Collectors.toList()));

// Lookup studyDbId.
return observations.stream()
.filter(o -> {
// Short circuit if filter is null.
if (studyDbId == null) return true;
Optional<BrAPIExternalReference> xref = Utilities.getExternalReference(o.getExternalReferences(), studySource);
return xref.filter(brAPIExternalReference -> studyDbId.equals(brAPIExternalReference.getReferenceId())).isPresent();
})
.peek(o -> {
// Translate ObservationVariableDbId.
o.setObservationVariableDbId(traitIdsByObservationVariableDbId.get(o.getObservationVariableDbId()));
// Translate ObservationUnitDbId.
o.setObservationUnitDbId(Utilities.getExternalReference(o.getExternalReferences(), observationUnitSource)
.orElseThrow(() -> new RuntimeException("observationUnit xref not found on observation")).getReferenceId());
// Translate ObservationId.
o.setObservationDbId(Utilities.getExternalReference(o.getExternalReferences(), observationSource)
.orElseThrow(() -> new RuntimeException("observation xref not found on observation")).getReferenceId());
// Translate StudyDbId.
o.setStudyDbId(Utilities.getExternalReference(o.getExternalReferences(), studySource)
.orElseThrow(() -> new RuntimeException("study xref not found on observation")).getReferenceId());
// TODO: consider translating germplasmDbId in BI-2506.
}).collect(Collectors.toList());
}

@NotNull
private ApiResponse<Pair<Optional<BrAPIObservationListResponse>, Optional<BrAPIAcceptedSearchResponse>>> searchObservationsSearchResultsDbIdGet(UUID programId, String searchResultsDbId, Integer page, Integer pageSize) throws ApiException {
ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
Expand Down
25 changes: 25 additions & 0 deletions src/main/java/org/breedinginsight/services/TraitService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -491,4 +491,29 @@ public List<Trait> getByName(UUID programId, List<String> names) throws DoesNotE

return traitDAO.getTraitsByTraitName(programId, names.stream().map(name -> Trait.builder().observationVariableName(name).build()).collect(Collectors.toList()));
}

public Trait getByObservationVariableDbId(UUID programId, String observationVariableDbId) throws DoesNotExistException {
if (!programService.exists(programId)) {
throw new DoesNotExistException("Program does not exist");
}

return traitDAO.getTraitsFullByProgramId(programId).stream()
.filter(t -> t.getObservationVariableDbId().equals(observationVariableDbId))
.findFirst().orElseThrow(() -> new DoesNotExistException("Trait not found for observationVariableDbId: " + observationVariableDbId));

}

public HashMap<String, String> getIdsByObservationVariableDbIds(UUID programId, List<String> observationVariableDbIds) throws DoesNotExistException {
if (!programService.exists(programId)) {
throw new DoesNotExistException("Program does not exist");
}
return traitDAO.getTraitsFullByProgramId(programId).stream()
.filter(t -> observationVariableDbIds.contains(t.getObservationVariableDbId()))
.collect(Collectors.toMap(
Trait::getObservationVariableDbId,
(t) -> t.getId().toString(),
(existing, replacement) -> existing,
HashMap::new
));
}
}
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