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BI-2783 Logic In Germplasm Import Dependent on Name Lookup #504

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BI-2783 Logic In Germplasm Import Dependent on Name Lookup #504

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6c715d8
[BI-2783] replase lookup germplasm by name with loolkup germplasm by GID
Mar 26, 2026
fba0f42
[BI-2783] Cleaned up code
Mar 26, 2026
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20 changes: 10 additions & 10 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -350,16 +350,16 @@ public List<BrAPIGermplasm> getRawGermplasmByAccessionNumber(ArrayList<String> g
}
return resultGermplasm;
}

public List<BrAPIGermplasm> getGermplasmByDisplayName(List<String> germplasmDisplayNames, UUID programId) throws ApiException {
List<BrAPIGermplasm> allGermplasm = getGermplasm(programId);
HashSet<String> requestedNames = new HashSet<>(germplasmDisplayNames);
List<BrAPIGermplasm> matchingGermplasm = new ArrayList<>();
for (BrAPIGermplasm germplasm: allGermplasm) {
if (requestedNames.contains(germplasm.getDefaultDisplayName())) {
matchingGermplasm.add(germplasm);
}

public List<BrAPIGermplasm> getGermplasmByGID(List<String> germplasmGIDs, UUID programId) throws ApiException {
List<BrAPIGermplasm> allGermplasm = getGermplasm(programId);
HashSet<String> requestedGIDs = new HashSet<>(germplasmGIDs);
List<BrAPIGermplasm> matchingGermplasm = new ArrayList<>();
for (BrAPIGermplasm germplasm: allGermplasm) {
if (requestedGIDs.contains(germplasm.getAccessionNumber())) {
matchingGermplasm.add(germplasm);
}
return matchingGermplasm;
}
return matchingGermplasm;
}
}
74 changes: 29 additions & 45 deletions ...org/breedinginsight/brapps/importer/services/processors/germplasm/GermplasmProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@
package org.breedinginsight.brapps.importer.services.processors.germplasm;

import com.google.gson.Gson;
import com.google.gson.JsonElement;
import io.micronaut.context.annotation.Property;
import io.micronaut.context.annotation.Prototype;
import io.micronaut.http.HttpStatus;
Expand Down Expand Up @@ -68,15 +67,16 @@ public class GermplasmProcessor implements Processor {
@Property(name = "brapi.server.reference-source")
private String BRAPI_REFERENCE_SOURCE;

private BrAPIGermplasmService brAPIGermplasmService;
private final BrAPIGermplasmService brAPIGermplasmService;
private final BreedingMethodDAO breedingMethodDAO;
private final BrAPIListDAO brAPIListDAO;
private final DSLContext dsl;
private final BrAPIGermplasmDAO brAPIGermplasmDAO;
private final Gson gson = new Gson();

Map<String, PendingImportObject<BrAPIGermplasm>> germplasmByAccessionNumber = new HashMap<>();
Map<String, Integer> fileGermplasmByName = new HashMap<>();
Map<String, Integer> fileGermplasmByGID = new HashMap<>();

Map<String, BrAPIGermplasm> dbGermplasmByName = new HashMap<>();
Map<String, BrAPIGermplasm> dbGermplasmByAccessionNo = new HashMap<>();
Map<String, Integer> germplasmIndexByEntryNo = new HashMap<>();
Expand Down Expand Up @@ -110,7 +110,6 @@ public class GermplasmProcessor implements Processor {

@Inject
public GermplasmProcessor(BrAPIGermplasmService brAPIGermplasmService, DSLContext dsl, BreedingMethodDAO breedingMethodDAO, BrAPIListDAO brAPIListDAO, BrAPIGermplasmDAO brAPIGermplasmDAO) {
this.brAPIGermplasmService = brAPIGermplasmService;
this.dsl = dsl;
this.breedingMethodDAO = breedingMethodDAO;
this.brAPIGermplasmDAO = brAPIGermplasmDAO;
Expand Down Expand Up @@ -146,65 +145,63 @@ public void getExistingBrapiData(List<BrAPIImport> importRows, Program program)
germplasmIndexByEntryNo.put(germplasm.getEntryNo(), i);
}

Integer count = fileGermplasmByName.getOrDefault(germplasm.getGermplasmName(), 0);
fileGermplasmByName.put(germplasm.getGermplasmName(), count+1);
Integer count = fileGermplasmByGID.getOrDefault(germplasm.getAccessionNumber(), 0);
fileGermplasmByGID.put(germplasm.getAccessionNumber(), count+1);
}
}

// Get existing germplasm names
List<BrAPIGermplasm> dbGermplasm = brAPIGermplasmService.getGermplasmByDisplayName(new ArrayList<>(fileGermplasmByName.keySet()), program.getId());
List<BrAPIGermplasm> dbGermplasm = brAPIGermplasmService.getGermplasmByGID(new ArrayList<>(fileGermplasmByGID.keySet()), program.getId());
dbGermplasm.forEach(germplasm -> {
dbGermplasmByName.put(germplasm.getDefaultDisplayName(), germplasm);
dbGermplasmByAccessionNo.put(germplasm.getAccessionNumber(), germplasm);
});

// Get parental accession nos in file
for (int i = 0; i < importRows.size(); i++) {
BrAPIImport germplasmImport = importRows.get(i);
for (BrAPIImport germplasmImport : importRows) {
Germplasm germplasm = germplasmImport.getGermplasm();
if (germplasm != null) {
// Retrieve parent accession numbers to assess if already in db
if (germplasm.getFemaleParentAccessionNumber() != null) {
germplasmAccessionNumbers.put(germplasm.getFemaleParentAccessionNumber(), true);
}
if (germplasm.getMaleParentAccessionNumber() != null) {
germplasmAccessionNumbers.put(germplasm.getMaleParentAccessionNumber(), true);
}
if (germplasm.getFemaleParentAccessionNumber() != null) {
germplasmAccessionNumbers.put(germplasm.getFemaleParentAccessionNumber(), true);
}
if (germplasm.getMaleParentAccessionNumber() != null) {
germplasmAccessionNumbers.put(germplasm.getMaleParentAccessionNumber(), true);
}
}
}

// If a parental accession number is present, it should exist in the database.
existingGermplasm = new ArrayList<>();
List<String> missingParentalAccessionNumbers = germplasmAccessionNumbers.entrySet().stream().filter(Map.Entry::getValue).map(Map.Entry::getKey).collect(Collectors.toList());
List<String> missingAccessionNumbers = germplasmAccessionNumbers.entrySet().stream().filter(entry -> !entry.getValue()).map(Map.Entry::getKey).collect(Collectors.toList());
if (germplasmAccessionNumbers.size() > 0) {
if (!germplasmAccessionNumbers.isEmpty()) {
try {
existingGermplasm = brAPIGermplasmService.getRawGermplasmByAccessionNumber(new ArrayList<>(germplasmAccessionNumbers.keySet()), program.getId());
List<String> existingAccessionNumbers = existingGermplasm.stream()
.map(germplasm -> germplasm.getAccessionNumber())
.map(BrAPIGermplasm::getAccessionNumber)
.collect(Collectors.toList());
missingParentalAccessionNumbers.removeAll(existingAccessionNumbers);
missingAccessionNumbers.removeAll(existingAccessionNumbers);

existingGermplasm.forEach(existingGermplasm -> {
germplasmByAccessionNumber.put(existingGermplasm.getAccessionNumber(), new PendingImportObject<>(ImportObjectState.EXISTING, existingGermplasm));
});
existingGermplasm.forEach(existingGermplasm -> germplasmByAccessionNumber.put(existingGermplasm.getAccessionNumber(), new PendingImportObject<>(ImportObjectState.EXISTING, existingGermplasm)));
} catch (ApiException e) {
// We shouldn't get an error back from our services. If we do, nothing the user can do about it
throw new InternalServerException(e.toString(), e);
}
}

// Check for existing germplasm lists
Boolean listNameDup = false;
if (importRows.size() > 0 && importRows.get(0).getGermplasm().getListName() != null) {
boolean listNameDup = false;
if (!importRows.isEmpty() && importRows.get(0).getGermplasm().getListName() != null) {
try {
Germplasm row = importRows.get(0).getGermplasm();
String listName = Germplasm.constructGermplasmListName(row.getListName(), program);
List<BrAPIListSummary> existingLists = brAPIListDAO.getListsByName(List.of(listName), program.getId());
for (BrAPIListSummary existingList: existingLists) {
if (existingList.getListName().equals(listName)) {
listNameDup = true;
break;
}
}
} catch (ApiException e) {
Expand All @@ -217,14 +214,14 @@ public void getExistingBrapiData(List<BrAPIImport> importRows, Program program)
missingAccessionNumbers.remove("0");

// Parent reference checks
if (missingParentalAccessionNumbers.size() > 0) {
if (!missingParentalAccessionNumbers.isEmpty()) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY,
String.format(missingParentalGIDsMsg,
arrayOfStringFormatter.apply(missingParentalAccessionNumbers)));
}

//GID existence check
if (missingAccessionNumbers.size() > 0) {
if (!missingAccessionNumbers.isEmpty()) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY,
String.format(missingGIDsMsg,
arrayOfStringFormatter.apply(missingAccessionNumbers)));
Expand All @@ -247,7 +244,7 @@ public void getExistingBrapiData(List<BrAPIImport> importRows, Program program)
}
}
}
if (missingEntryNumbers.size() > 0) {
if (!missingEntryNumbers.isEmpty()) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY,
String.format(missingParentalEntryNoMsg,
arrayOfStringFormatter.apply(missingEntryNumbers)));
Expand Down Expand Up @@ -284,7 +281,6 @@ public Map<String, ImportPreviewStatistics> process(ImportUpload upload, List<Br
newGermplasmList = new ArrayList<>();
updatedGermplasmList = new ArrayList<>();
Map<String, ProgramBreedingMethodEntity> breedingMethods = new HashMap<>();
Boolean nullEntryNotFound = false;
List<String> badBreedingMethods = new ArrayList<>();
Map<String, Integer> entryNumberCounts = new HashMap<>();
List<String> userProvidedEntryNumbers = new ArrayList<>();
Expand Down Expand Up @@ -325,7 +321,7 @@ public Map<String, ImportPreviewStatistics> process(ImportUpload upload, List<Br
}

// Check for missing entry numbers
if (userProvidedEntryNumbers.size() > 0 && userProvidedEntryNumbers.size() < importRows.size()) {
if (!userProvidedEntryNumbers.isEmpty() && userProvidedEntryNumbers.size() < importRows.size()) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY, missingEntryNumbersMsg);
}

Expand Down Expand Up @@ -357,7 +353,7 @@ private void processNewGermplasm(Germplasm germplasm, ValidationErrors validatio
breedingMethod = breedingMethods.get(germplasm.getBreedingMethod());
} else {
List<ProgramBreedingMethodEntity> breedingMethodResults = breedingMethodDAO.findByNameOrAbbreviation(germplasm.getBreedingMethod(), program.getId());
if (breedingMethodResults.size() > 0) {
if (!breedingMethodResults.isEmpty()) {
breedingMethods.put(germplasm.getBreedingMethod(), breedingMethodResults.get(0));
breedingMethod = breedingMethods.get(germplasm.getBreedingMethod());
} else {
Expand All @@ -379,7 +375,7 @@ private void processNewGermplasm(Germplasm germplasm, ValidationErrors validatio

newGermplasmList.add(newGermplasm);
// Assign status of the germplasm
if (fileGermplasmByName.get(newGermplasm.getDefaultDisplayName()) > 1 || dbGermplasmByName.containsKey(newGermplasm.getDefaultDisplayName())) {
if (fileGermplasmByGID.get(newGermplasm.getAccessionNumber()) > 1 || dbGermplasmByAccessionNo.containsKey(newGermplasm.getAccessionNumber())) {
mappedImportRow.setGermplasm(new PendingImportObject<>(ImportObjectState.EXISTING, newGermplasm));
} else {
mappedImportRow.setGermplasm(new PendingImportObject<>(ImportObjectState.NEW, newGermplasm));
Expand Down Expand Up @@ -468,16 +464,6 @@ private boolean hasPedigree(BrAPIGermplasm germplasm) {
germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN).getAsBoolean());
}

//Used to check if germplasm already has a pedigree in the database
private boolean databaseGermplasmHasPedigree(Germplasm germplasm) {
if (germplasm.getAccessionNumber() == null || dbGermplasmByAccessionNo.get(germplasm.getAccessionNumber()) == null) {
return false;
} else {
BrAPIGermplasm dbGermplasm = dbGermplasmByAccessionNo.get(germplasm.getAccessionNumber());
return hasPedigree(dbGermplasm);
}
}

/**
* Compare an existing germplasm's pedigree to the incoming germplasm's pedigree to ensure they are the same.<br><br>
* Assumes that an empty value for a given parent in the incoming germplasm is equal to the existing germplasm.<br><br>
Expand Down Expand Up @@ -527,7 +513,7 @@ private boolean arePedigreesEqual(BrAPIGermplasm existingGermplasm, Germplasm ge
germplasmPedigreeGIDString.append(existingMalePedigree);
}

return existingPedigreeGIDString.toString().equals(germplasmPedigreeGIDString.toString());
return existingPedigreeGIDString.toString().contentEquals(germplasmPedigreeGIDString);
} else {
return true;
}
Expand Down Expand Up @@ -656,7 +642,7 @@ private void createPostOrder() {
}

totalRecorded += createList.size();
if (createList.size() > 0) {
if (!createList.isEmpty()) {
created.addAll(createList.stream().map(GermplasmImportIdUtils::getImportId).collect(Collectors.toList()));
postOrder.add(createList);
} else if (totalRecorded < newGermplasmList.size()) {
Expand All @@ -667,7 +653,7 @@ private void createPostOrder() {
}

@Override
public void validateDependencies(Map<Integer, PendingImport> mappedBrAPIImport) throws ValidatorException {
public void validateDependencies(Map<Integer, PendingImport> mappedBrAPIImport) {
// TODO
}

Expand Down Expand Up @@ -706,9 +692,7 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program

// Update our records with what is returned
Map<String, BrAPIGermplasm> createdGermplasmMap = new HashMap<>();
createdGermplasm.forEach(germplasm -> {
createdGermplasmMap.put(germplasm.getGermplasmName(), germplasm);
});
createdGermplasm.forEach(germplasm -> createdGermplasmMap.put(germplasm.getGermplasmName(), germplasm));
for (Map.Entry<Integer,PendingImport> entry : mappedBrAPIImport.entrySet()) {
String germplasmName = entry.getValue().getGermplasm().getBrAPIObject().getGermplasmName();
if (createdGermplasmMap.containsKey(germplasmName)) {
Expand Down
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