Skip to content

[BI-1960-2] Exp import proceeds with multiple exp names & error message improvement #316

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dmeidlin merged 2 commits into from
Dec 6, 2023
Merged

[BI-1960-2] Exp import proceeds with multiple exp names & error message improvement #316

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ac8d844
add check for multiple exp titles in import
dmeidlin Nov 28, 2023
a433556
handle exception in exp processor public method
dmeidlin Dec 1, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 11 additions & 3 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,7 @@
import org.breedinginsight.services.ProgramLocationService;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.services.exceptions.MissingRequiredInfoException;
import org.breedinginsight.services.exceptions.UnprocessableEntityException;
import org.breedinginsight.services.exceptions.ValidatorException;
import org.breedinginsight.utilities.Utilities;
import org.jooq.DSLContext;
Expand All @@ -85,6 +86,7 @@ public class ExperimentProcessor implements Processor {
"If you’re trying to add these units to the experiment, please create a new environment" +
" with all appropriate experiment units (NOTE: this will generate new Observation Unit Ids " +
"for each experiment unit).";
private static final String MULTIPLE_EXP_TITLES = "File contains more than one Experiment Title";
private static final String MIDNIGHT = "T00:00:00-00:00";
private static final String TIMESTAMP_PREFIX = "TS:";
private static final String TIMESTAMP_REGEX = "^"+TIMESTAMP_PREFIX+"\\s*";
Expand Down Expand Up @@ -476,7 +478,12 @@ private void initNewBrapiData(List<BrAPIImport> importRows, List<Column<?>> phen
for (int rowNum = 0; rowNum < importRows.size(); rowNum++) {
ExperimentObservation importRow = (ExperimentObservation) importRows.get(rowNum);

PendingImportObject<BrAPITrial> trialPIO = fetchOrCreateTrialPIO(program, user, commit, importRow, expNextVal);
PendingImportObject<BrAPITrial> trialPIO = null;
try {
trialPIO = fetchOrCreateTrialPIO(program, user, commit, importRow, expNextVal);
} catch (UnprocessableEntityException e) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
}

String expSeqValue = null;
if (commit) {
Expand Down Expand Up @@ -552,7 +559,6 @@ private ValidationErrors validateFields(List<BrAPIImport> importRows, Validation
for (int rowNum = 0; rowNum < importRows.size(); rowNum++) {
ExperimentObservation importRow = (ExperimentObservation) importRows.get(rowNum);
PendingImport mappedImportRow = mappedBrAPIImport.get(rowNum);

if (StringUtils.isNotBlank(importRow.getGid())) { // if GID is blank, don't bother to check if it is valid.
validateGermplasm(importRow, validationErrors, rowNum, mappedImportRow.getGermplasm());
}
Expand Down Expand Up @@ -981,10 +987,12 @@ private PendingImportObject<ProgramLocation> fetchOrCreateLocationPIO(Experiment
return pio;
}

private PendingImportObject<BrAPITrial> fetchOrCreateTrialPIO(Program program, User user, boolean commit, ExperimentObservation importRow, Supplier<BigInteger> expNextVal) {
private PendingImportObject<BrAPITrial> fetchOrCreateTrialPIO(Program program, User user, boolean commit, ExperimentObservation importRow, Supplier<BigInteger> expNextVal) throws UnprocessableEntityException {
PendingImportObject<BrAPITrial> pio;
if (trialByNameNoScope.containsKey(importRow.getExpTitle())) {
pio = trialByNameNoScope.get(importRow.getExpTitle());
} else if (!trialByNameNoScope.isEmpty()) {
throw new UnprocessableEntityException(MULTIPLE_EXP_TITLES);
} else {
UUID id = UUID.randomUUID();
String expSeqValue = null;
Expand Down