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BI-1864 - Experiment Export doesn't consistently work #276

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Merged
timparsons merged 1 commit into from
Jul 28, 2023
Merged

BI-1864 - Experiment Export doesn't consistently work #276

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2 changes: 2 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentExportQuery.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import io.micronaut.core.annotation.Introspected;
import lombok.Getter;
import lombok.ToString;
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;
Expand All @@ -14,6 +15,7 @@

@Getter
@Introspected
@ToString
public class ExperimentExportQuery {
private FileType fileExtension;
private String dataset;
Expand Down
37 changes: 29 additions & 8 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 @@ -32,6 +32,7 @@
import java.time.OffsetDateTime;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;

@Slf4j
Expand Down Expand Up @@ -99,6 +100,8 @@ public DownloadFile exportObservations(
Program program,
UUID experimentId,
ExperimentExportQuery params) throws IOException, DoesNotExistException, ApiException {
String logHash = UUID.randomUUID().toString();
log.debug(logHash + ": exporting experiment: "+experimentId+", params: " + params);
StreamedFile downloadFile;
boolean isDataset = false;
List<BrAPIObservation> dataset = new ArrayList<>();
Expand All @@ -110,6 +113,7 @@ public DownloadFile exportObservations(
FileType fileType = params.getFileExtension();

// get requested environments for the experiment
log.debug(logHash + ": fetching environments for export");
List<BrAPIStudy> expStudies = studyDAO.getStudiesByExperimentID(experimentId, program);
if (!requestedEnvIds.isEmpty()) {
expStudies = expStudies
Expand All @@ -120,6 +124,7 @@ public DownloadFile exportObservations(
expStudies.forEach(study -> studyByDbId.putIfAbsent(study.getStudyDbId(), study));

// get the OUs for the requested environments
log.debug(logHash + ": fetching OUs for export");
List<BrAPIObservationUnit> ous = new ArrayList<>();
Map<String, BrAPIObservationUnit> ouByOUDbId = new HashMap<>();
try {
Expand All @@ -129,21 +134,23 @@ public DownloadFile exportObservations(
ous.addAll(studyOUs);
}
} catch (ApiException err) {
log.error("Error fetching observation units for a study by its DbId" +
log.error(logHash + ": Error fetching observation units for a study by its DbId" +
Utilities.generateApiExceptionLogMessage(err), err);
}

// make columns present in all exports
List<Column> columns = ExperimentFileColumns.getOrderedColumns();

// add columns for requested dataset obsvars and timestamps
log.debug(logHash + ": fetching experiment for export");
BrAPITrial experiment = getExperiment(program, experimentId);
if ((StringUtils.isBlank(params.getDataset()) || "observations".equalsIgnoreCase(params.getDataset())) &&
experiment.getAdditionalInfo().getAsJsonObject().get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID) != null) {
String obsDatasetId = experiment
.getAdditionalInfo().getAsJsonObject()
.get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID).getAsString();
isDataset = true;
log.debug(logHash + ": fetching dataset observation variables for export");
obsVars = getDatasetObsVars(obsDatasetId, program);

// make additional columns in the export for each obs variable and obs variable timestamp
Expand All @@ -153,12 +160,19 @@ public DownloadFile exportObservations(

// make export rows from any observations
if (isDataset) {
log.debug(logHash + ": fetching observations for export");
dataset = observationDAO.getObservationsByTrialDbId(List.of(experiment.getTrialDbId()), program);
}
if (!requestedEnvIds.isEmpty()) {
log.debug(logHash + ": filtering observations to only requested environments for export");
dataset = filterDatasetByEnvironment(dataset, requestedEnvIds, studyByDbId);
}

log.debug(logHash + ": fetching program's germplasm for export");
List<BrAPIGermplasm> programGermplasm = germplasmDAO.getGermplasmsByDBID(ouByOUDbId.values().stream().map(BrAPIObservationUnit::getGermplasmDbId).collect(Collectors.toList()), program.getId());
Map<String, BrAPIGermplasm> programGermplasmByDbId = programGermplasm.stream().collect(Collectors.toMap(BrAPIGermplasm::getGermplasmDbId, Function.identity()));

log.debug(logHash + ": populating rows for export");
// update rowByOUId
addBrAPIObsToRecords(
dataset,
Expand All @@ -168,19 +182,21 @@ public DownloadFile exportObservations(
studyByDbId,
rowByOUId,
params.isIncludeTimestamps(),
obsVars
obsVars,
programGermplasmByDbId
);

// make export rows for OUs without observations
if (rowByOUId.size() < ous.size()) {
for (BrAPIObservationUnit ou: ous) {
String ouId = getOUId(ou);
if (!rowByOUId.containsKey(ouId)) {
rowByOUId.put(ouId, createExportRow(experiment, program, ou, studyByDbId));
rowByOUId.put(ouId, createExportRow(experiment, program, ou, studyByDbId, programGermplasmByDbId));
}
}
}

log.debug(logHash + ": writing data to file for export");
// write export data to requested file format
List<Map<String, Object>> exportRows = new ArrayList<>(rowByOUId.values());
if (fileType.equals(FileType.CSV)){
Expand All @@ -191,7 +207,10 @@ public DownloadFile exportObservations(

String envFilenameFragment = params.getEnvironments() == null ? "All Environments" : params.getEnvironments();
String fileName = makeFileName(experiment, program, envFilenameFragment) + fileType.getExtension();
return new DownloadFile(fileName, downloadFile);
DownloadFile retFile = new DownloadFile(fileName, downloadFile);

log.debug(logHash + ": completed export of experiment: " + experimentId + ", params: " + params);
return retFile;
}

private void addBrAPIObsToRecords(
Expand All @@ -202,7 +221,8 @@ private void addBrAPIObsToRecords(
Map<String, BrAPIStudy> studyByDbId,
Map<String, Map<String, Object>> rowByOUId,
boolean includeTimestamp,
List<BrAPIObservationVariable> obsVars) throws ApiException, DoesNotExistException {
List<BrAPIObservationVariable> obsVars,
Map<String, BrAPIGermplasm> programGermplasmByDbId) throws ApiException, DoesNotExistException {
Map<String, BrAPIObservationVariable> varByDbId = new HashMap<>();
obsVars.forEach(var -> varByDbId.put(var.getObservationVariableDbId(), var));
for (BrAPIObservation obs: dataset) {
Expand All @@ -220,7 +240,7 @@ private void addBrAPIObsToRecords(
} else {

// otherwise make a new row
Map<String, Object> row = createExportRow(experiment, program, ou, studyByDbId);
Map<String, Object> row = createExportRow(experiment, program, ou, studyByDbId, programGermplasmByDbId);
addObsVarDataToRow(row, obs, includeTimestamp, var, program);
rowByOUId.put(ouId, row);
}
Expand Down Expand Up @@ -291,7 +311,8 @@ private Map<String, Object> createExportRow(
BrAPITrial experiment,
Program program,
BrAPIObservationUnit ou,
Map<String, BrAPIStudy> studyByDbId) throws ApiException, DoesNotExistException {
Map<String, BrAPIStudy> studyByDbId,
Map<String, BrAPIGermplasm> programGermplasmByDbId) throws ApiException, DoesNotExistException {
HashMap<String, Object> row = new HashMap<>();

// get OU id, germplasm, and study
Expand All @@ -300,7 +321,7 @@ private Map<String, Object> createExportRow(
String.format("%s/%s", referenceSource, ExternalReferenceSource.OBSERVATION_UNITS.getName()))
.orElseThrow(() -> new RuntimeException("observation unit id not found"));
String ouId = ouXref.getReferenceID();
BrAPIGermplasm germplasm = germplasmDAO.getGermplasmByDBID(ou.getGermplasmDbId(), program.getId())
BrAPIGermplasm germplasm = Optional.ofNullable(programGermplasmByDbId.get(ou.getGermplasmDbId()))
.orElseThrow(() -> new DoesNotExistException("Germplasm not returned from BrAPI service"));
BrAPIStudy study = studyByDbId.get(ou.getStudyDbId());

Expand Down