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[BI-1761] Error message with the backend code #319

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Merged
dmeidlin merged 5 commits into from
Jan 4, 2024
Merged

[BI-1761] Error message with the backend code #319

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a1d30bc
change OU error message
dmeidlin Dec 6, 2023
34c590b
update message
dmeidlin Dec 7, 2023
219d848
[BI-1761] update and optimize
dmeidlin Dec 12, 2023
9ee4906
[BI-1761] use MissingInformationException
dmeidlin Dec 12, 2023
bded938
update message
dmeidlin Dec 20, 2023
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23 changes: 6 additions & 17 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@
import io.micronaut.http.server.exceptions.InternalServerException;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.collections4.map.CaseInsensitiveMap;
import org.apache.commons.lang3.StringUtils;
import org.brapi.client.v2.JSON;
Expand Down Expand Up @@ -62,7 +61,6 @@
import org.breedinginsight.services.OntologyService;
import org.breedinginsight.services.ProgramLocationService;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.services.exceptions.UnprocessableEntityException;
import org.breedinginsight.services.exceptions.MissingRequiredInfoException;
import org.breedinginsight.services.exceptions.UnprocessableEntityException;
import org.breedinginsight.services.exceptions.ValidatorException;
Expand All @@ -72,7 +70,6 @@
import tech.tablesaw.columns.Column;

import javax.inject.Inject;
import javax.validation.Valid;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.time.OffsetDateTime;
Expand All @@ -87,14 +84,7 @@
public class ExperimentProcessor implements Processor {

private static final String NAME = "Experiment";
private static final String EXISTING_ENV = "Cannot create new observation unit %s for existing environment %s.<br/><br/>" +
"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 MISSING_OBS_UNIT_ID_ERROR = "Experiment Units are missing Observation Unit Id.<br/><br/>" +
"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 MISSING_OBS_UNIT_ID_ERROR = "Experimental entities are missing ObsUnitIDs";
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:";
Expand Down Expand Up @@ -215,7 +205,7 @@ public Map<String, ImportPreviewStatistics> process(
Table data,
Program program,
User user,
boolean commit) throws UnprocessableEntityException, ApiException, ValidatorException {
boolean commit) throws ApiException, ValidatorException, MissingRequiredInfoException {
log.debug("processing experiment import");

ValidationErrors validationErrors = new ValidationErrors();
Expand Down Expand Up @@ -498,7 +488,7 @@ private String getVariableNameFromColumn(Column<?> column) {
return column.name();
}

private void initNewBrapiData(List<BrAPIImport> importRows, List<Column<?>> phenotypeCols, Program program, User user, List<Trait> referencedTraits, boolean commit) throws UnprocessableEntityException, ApiException {
private void initNewBrapiData(List<BrAPIImport> importRows, List<Column<?>> phenotypeCols, Program program, User user, List<Trait> referencedTraits, boolean commit) throws ApiException, MissingRequiredInfoException {

String expSequenceName = program.getExpSequence();
if (expSequenceName == null) {
Expand Down Expand Up @@ -933,7 +923,7 @@ private PendingImportObject<BrAPIGermplasm> getGidPOI(ExperimentObservation impo
return null;
}

private PendingImportObject<BrAPIObservationUnit> fetchOrCreateObsUnitPIO(Program program, boolean commit, String envSeqValue, ExperimentObservation importRow) throws UnprocessableEntityException, ApiException {
private PendingImportObject<BrAPIObservationUnit> fetchOrCreateObsUnitPIO(Program program, boolean commit, String envSeqValue, ExperimentObservation importRow) throws ApiException, MissingRequiredInfoException {
PendingImportObject<BrAPIObservationUnit> pio;
String key = createObservationUnitKey(importRow);
if (this.observationUnitByNameNoScope.containsKey(key)) {
Expand Down Expand Up @@ -963,8 +953,7 @@ private PendingImportObject<BrAPIObservationUnit> fetchOrCreateObsUnitPIO(Progra
List<BrAPIObservationUnit> existingOUs = brAPIObservationUnitDAO.getObservationUnitsForStudyDbId(studyPIO.getBrAPIObject().getStudyDbId(), program);
List<BrAPIObservationUnit> matchingOU = existingOUs.stream().filter(ou -> importRow.getExpUnitId().equals(Utilities.removeProgramKeyAndUnknownAdditionalData(ou.getObservationUnitName(), program.getKey()))).collect(Collectors.toList());
if (matchingOU.isEmpty()) {
throw new UnprocessableEntityException(String.format(EXISTING_ENV, importRow.getExpUnitId(),
Utilities.removeProgramKeyAndUnknownAdditionalData(studyPIO.getBrAPIObject().getStudyName(), program.getKey())));
throw new MissingRequiredInfoException(MISSING_OBS_UNIT_ID_ERROR);
} else {
pio = new PendingImportObject<>(ImportObjectState.EXISTING, (BrAPIObservationUnit) Utilities.formatBrapiObjForDisplay(matchingOU.get(0), BrAPIObservationUnit.class, program));
}
Expand Down Expand Up @@ -1066,7 +1055,7 @@ private void addObsVarsToDatasetDetails(PendingImportObject<BrAPIListDetails> pi
if (trait.getFullName() == null) {
id = trait.getObservationVariableName();
}

if (!details.getData().contains(id) && ImportObjectState.EXISTING != pio.getState()) {
details.getData().add(id);
}
Expand Down
2 changes: 1 addition & 1 deletion src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -604,7 +604,7 @@ public void verifyFailureNewOuExistingEnv(boolean commit) {
JsonObject result = JsonParser.parseString(upload.body()).getAsJsonObject().getAsJsonObject("result");
assertEquals(422, result.getAsJsonObject("progress").get("statuscode").getAsInt(), "Returned data: " + result);

assertTrue(result.getAsJsonObject("progress").get("message").getAsString().startsWith("Cannot create new observation unit"));
assertTrue(result.getAsJsonObject("progress").get("message").getAsString().startsWith("Experimental entities are missing ObsUnitIDs"));
}

@Test
Expand Down