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[BI-1147] 2.0 Experimental Data Preview Universal Elements #219

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Merged
dmeidlin merged 2 commits into from
Oct 31, 2022
Merged

[BI-1147] 2.0 Experimental Data Preview Universal Elements #219

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6c77566
add createdBy and createdDate to imported Trial additionalInfo
dmeidlin Oct 18, 2022
ef6199b
[BI-1147] - Updating date format for experiment created date to ISO f…
timparsons Oct 19, 2022
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28 changes: 22 additions & 6 deletions ...inginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,9 +29,12 @@
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.model.BrAPIConstants;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.User;
import org.breedinginsight.utilities.Utilities;

import java.math.BigInteger;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.function.Supplier;

Expand Down Expand Up @@ -110,14 +113,11 @@ public class ExperimentObservation implements BrAPIImport {
@ImportFieldMetadata(id="obsUnitID", name="Observation Unit ID", description = "A database generated unique identifier for experimental observation units")
private String obsUnitID;

public BrAPITrial constructBrAPITrial(Program program, boolean commit, String referenceSource, UUID id, String expSeqValue) {
public BrAPITrial constructBrAPITrial(Program program, User user, boolean commit, String referenceSource, UUID id, String expSeqValue) {
BrAPIProgram brapiProgram = program.getBrapiProgram();
BrAPITrial trial = new BrAPITrial();
if( commit ){
trial.setTrialName( Utilities.appendProgramKey(getExpTitle(), program.getKey() ));

// Set external reference
trial.setExternalReferences(getTrialExternalReferences(program, referenceSource, id));
if (commit) {
setBrAPITrialCommitFields(program, trial, referenceSource, id);
}
else{
trial.setTrialName( getExpTitle() );
Expand All @@ -127,13 +127,29 @@ public BrAPITrial constructBrAPITrial(Program program, boolean commit, String re
trial.setProgramDbId(brapiProgram.getProgramDbId());
trial.setProgramName(brapiProgram.getProgramName());

Map<String, String> createdBy = new HashMap<>();
createdBy.put(BrAPIAdditionalInfoFields.CREATED_BY_USER_ID, user.getId().toString());
createdBy.put(BrAPIAdditionalInfoFields.CREATED_BY_USER_NAME, user.getName());
trial.putAdditionalInfoItem(BrAPIAdditionalInfoFields.CREATED_BY, createdBy);
trial.putAdditionalInfoItem( BrAPIAdditionalInfoFields.DEFAULT_OBSERVATION_LEVEL, getExpUnit());
trial.putAdditionalInfoItem( BrAPIAdditionalInfoFields.EXPERIMENT_TYPE, getExpType());
trial.putAdditionalInfoItem( BrAPIAdditionalInfoFields.EXPERIMENT_NUMBER, expSeqValue);

return trial;
}

private void setBrAPITrialCommitFields(Program program, BrAPITrial trial, String referenceSource, UUID id) {
trial.setTrialName( Utilities.appendProgramKey(getExpTitle(), program.getKey() ));

// Set external reference
trial.setExternalReferences(getTrialExternalReferences(program, referenceSource, id));

// Set createdDate field
LocalDateTime now = LocalDateTime.now();
trial.putAdditionalInfoItem(BrAPIAdditionalInfoFields.CREATED_DATE, DateTimeFormatter.ISO_LOCAL_DATE.format(now));

}

public BrAPILocation constructBrAPILocation() {
BrAPILocation location = new BrAPILocation();
location.setLocationName(getEnvLocation());
Expand Down
10 changes: 5 additions & 5 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Expand Up @@ -153,7 +153,7 @@ public Map<String, ImportPreviewStatistics> process(
ValidationErrors validationErrors = new ValidationErrors();

// add "New" pending data to the BrapiData objects
getNewBrapiData(importRows, program, commit);
getNewBrapiData(importRows, program, user, commit);

// For each import row
for (int i = 0; i < importRows.size(); i++) {
Expand Down Expand Up @@ -191,7 +191,7 @@ public Map<String, ImportPreviewStatistics> process(
return getStatisticsMap(importRows);
}

private void getNewBrapiData(List<BrAPIImport> importRows, Program program, boolean commit) {
private void getNewBrapiData(List<BrAPIImport> importRows, Program program, User user, boolean commit) {

String expSequenceName = program.getExpSequence();
if (expSequenceName == null) {
Expand All @@ -210,7 +210,7 @@ private void getNewBrapiData(List<BrAPIImport> importRows, Program program, bool
for (BrAPIImport row : importRows) {
ExperimentObservation importRow = (ExperimentObservation) row;

PendingImportObject<BrAPITrial> trialPIO = createTrialPIO(program, commit, importRow, expNextVal);
PendingImportObject<BrAPITrial> trialPIO = createTrialPIO(program, user, commit, importRow, expNextVal);
this.trialByNameNoScope.put(importRow.getExpTitle(), trialPIO);

String expSeqValue = null;
Expand Down Expand Up @@ -442,7 +442,7 @@ private PendingImportObject<BrAPILocation> createLocationPIO(ExperimentObservati
return pio;
}

private PendingImportObject<BrAPITrial> createTrialPIO(Program program, boolean commit, ExperimentObservation importRow, Supplier<BigInteger> expNextVal) {
private PendingImportObject<BrAPITrial> createTrialPIO(Program program, User user, boolean commit, ExperimentObservation importRow, Supplier<BigInteger> expNextVal) {
PendingImportObject<BrAPITrial> pio = null;
if( trialByNameNoScope.containsKey( importRow.getExpTitle()) ) {
pio = trialByNameNoScope.get( importRow.getExpTitle() ) ;
Expand All @@ -453,7 +453,7 @@ private PendingImportObject<BrAPITrial> createTrialPIO(Program program, boolean
if(commit){
expSeqValue = expNextVal.get().toString();
}
BrAPITrial newTrial = importRow.constructBrAPITrial(program, commit, BRAPI_REFERENCE_SOURCE, id, expSeqValue);
BrAPITrial newTrial = importRow.constructBrAPITrial(program, user, commit, BRAPI_REFERENCE_SOURCE, id, expSeqValue);
pio = new PendingImportObject<>(ImportObjectState.NEW, newTrial, id);
}
return pio;
Expand Down