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BI-2789 - Create Germplasm: loosen breeding method and source requirement #513

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Merged
davedrp merged 4 commits into from
May 4, 2026
Merged

BI-2789 - Create Germplasm: loosen breeding method and source requirement #513

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2bf7ca0
BI-2789: Updated code to add custom validations for breeding method a…
humsika Apr 26, 2026
896f6d5
Merge remote-tracking branch 'origin/develop' into feature/BI-2789
humsika Apr 26, 2026
de1fbe3
BI-2789: Addressed comments and also cleaned up some existing code to…
humsika Apr 30, 2026
6f0dd36
Merge branch 'develop' into feature/BI-2789
davedrp May 4, 2026
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35 changes: 31 additions & 4 deletions src/main/java/org/breedinginsight/brapps/importer/model/base/Germplasm.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,12 +57,10 @@ public class Germplasm implements BrAPIObject {
private String germplasmName;

@ImportFieldType(type= ImportFieldTypeEnum.TEXT)
@ImportMappingRequired
@ImportFieldMetadata(id="breedingMethod", name="Breeding Method", description = "The breeding method name or code")
private String breedingMethod;

@ImportFieldType(type= ImportFieldTypeEnum.TEXT)
@ImportMappingRequired
@ImportFieldMetadata(id="germplasmSource", name="Source", description = "The germplasm origin. If External UID present, assumed to be the source associated with the External UID.")
private String germplasmSource;

Expand Down Expand Up @@ -160,12 +158,12 @@ public static String constructGermplasmListName(String listName, Program program
*
* @param germplasm germplasm object
* @param program program
* @param listId list id
* @param commit flag indicating if commit changes should be made
* @param updatePedigree flag indicating if pedigree should be updated
* @return mutated indicator
*/
public boolean updateBrAPIGermplasm(BrAPIGermplasm germplasm, Program program, UUID listId, boolean commit, boolean updatePedigree) {
public boolean updateBrAPIGermplasm(BrAPIGermplasm germplasm, Program program, boolean commit,
boolean updatePedigree, ProgramBreedingMethodEntity breedingMethod) {

boolean mutated = false;

Expand All @@ -185,6 +183,27 @@ public boolean updateBrAPIGermplasm(BrAPIGermplasm germplasm, Program program, U
mutated = true;
}

// Append Source only when DB value is blank
if (StringUtils.isBlank(germplasm.getSeedSource()) && StringUtils.isNotBlank(getGermplasmSource())) {
germplasm.setSeedSource(getGermplasmSource());
mutated = true;
}

// Append Breeding Method only when DB field is blank
if (breedingMethod != null) {
boolean hasBreedingMethodId = hasDateInAdditionalInfo(germplasm, BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD_ID);
boolean hasBreedingMethodName = hasDateInAdditionalInfo(germplasm, BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD);

if (!hasBreedingMethodId) {
germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD_ID, breedingMethod.getId().toString());
mutated = true;
}
if (!hasBreedingMethodName) {
germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD, breedingMethod.getName());
mutated = true;
}
}

// Append synonyms to germplasm that don't already exist
// Synonym comparison is based on name and type
if (synonyms != null) {
Expand All @@ -211,6 +230,14 @@ public boolean updateBrAPIGermplasm(BrAPIGermplasm germplasm, Program program, U
return mutated;
}

//Method to check whether breeding method already exists in DB additionalInfo
private boolean hasDateInAdditionalInfo(BrAPIGermplasm germplasm, String key) {
JsonObject additionalInfo = germplasm.getAdditionalInfo();
return additionalInfo != null
&& additionalInfo.has(key)
&& !additionalInfo.get(key).isJsonNull()
&& StringUtils.isNotBlank(additionalInfo.get(key).getAsString());
}

public void setUpdateCommitFields(BrAPIGermplasm germplasm, String programKey) {

Expand Down
114 changes: 67 additions & 47 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 @@ -94,6 +93,7 @@ public class GermplasmProcessor implements Processor {
public static String missingParentalEntryNoMsg = "The following parental entry numbers were not found in the file: %s";
public static String badBreedMethodsMsg = "Invalid breeding method";
public static String badGermplasmNameMsg = "Germplasm name cannot contain /";
public static String missingBreedingMethodForParentalGIDorEntryNo = "Required field \"Breeding Method\" cannot contain empty values when parent(s) are specified";
public static String missingEntryNumbersMsg = "Either all or none of the germplasm must have entry numbers";
public static String duplicateEntryNoMsg = "Entry numbers must be unique. Duplicated entry numbers found: %s";
public static String circularDependency = "Circular dependency in the pedigree tree";
Expand Down Expand Up @@ -160,17 +160,16 @@ public void getExistingBrapiData(List<BrAPIImport> importRows, Program program)
});

// 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);
}
}
}

Expand Down Expand Up @@ -269,7 +268,7 @@ public Map<String, ImportPreviewStatistics> process(ImportUpload upload, List<Br
// Method for generating accession number
String germplasmSequenceName = program.getGermplasmSequence();
if (germplasmSequenceName == null) {
log.error(String.format("Program, %s, is missing a value in the germplasm sequence column.", program.getName()));
log.error("Program, {}, is missing a value in the germplasm sequence column.", program.getName());
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY, "Program is not properly configured for germplasm import");
}
Supplier<BigInteger> nextVal = () -> dsl.nextval(germplasmSequenceName.toLowerCase());
Expand All @@ -285,14 +284,13 @@ 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<>();
ValidationErrors validationErrors = new ValidationErrors();

for (int i = 0; i < importRows.size(); i++) {
log.debug("processing germplasm row: " + (i+1));
log.debug("processing germplasm row: {}", i + 1);
BrAPIImport brapiImport = importRows.get(i);
PendingImport mappedImportRow = mappedBrAPIImport.getOrDefault(i, new PendingImport());

Expand All @@ -315,28 +313,28 @@ public Map<String, ImportPreviewStatistics> process(ImportUpload upload, List<Br
//TODO maybe make separate method for cleanliness
// Have GID so updating an existing germplasm record
if (germplasm.getAccessionNumber() != null) {
processExistingGermplasm(germplasm, validationErrors, importRows, program, importListId, commit, mappedImportRow, i);
processExistingGermplasm(germplasm, validationErrors, importRows, breedingMethods, badBreedingMethods, program, commit, mappedImportRow, i);
} else {
processNewGermplasm(germplasm, validationErrors, breedingMethods, badBreedingMethods, program, importListId, commit, mappedImportRow, i, user, nextVal);
}
mappedBrAPIImport.put(i, mappedImportRow);
}
if (validationErrors.hasErrors() ){
if (validationErrors.hasErrors()) {
throw new ValidatorException(validationErrors);
}

// 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);
}

// Check for duplicate entry numbers
if (entryNumberCounts.size() < importRows.size()) {
List<String> dups = entryNumberCounts.keySet().stream()
.filter(key -> entryNumberCounts.get(key) > 1)
.collect(Collectors.toList());
.filter(key -> entryNumberCounts.get(key) > 1)
.collect(Collectors.toList());
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY,
String.format(duplicateEntryNoMsg, arrayOfStringFormatter.apply(dups)));
String.format(duplicateEntryNoMsg, arrayOfStringFormatter.apply(dups)));
}

// Construct pedigree
Expand All @@ -351,25 +349,12 @@ private void processNewGermplasm(Germplasm germplasm, ValidationErrors validatio
List<String> badBreedingMethods,
Program program, UUID importListId, boolean commit, PendingImport mappedImportRow, int i, User user, Supplier<BigInteger> nextVal) {
germplasm = removeBreedingMethodBlanks(germplasm);
//Validating if Breeding Method exists for valid parent entries
validateGermplasmBreedingMethod(germplasm, i + 2, validationErrors);
// Get the breeding method database object
ProgramBreedingMethodEntity breedingMethod = null;
if (germplasm.getBreedingMethod() != null) {
if (breedingMethods.containsKey(germplasm.getBreedingMethod())) {
breedingMethod = breedingMethods.get(germplasm.getBreedingMethod());
} else {
List<ProgramBreedingMethodEntity> breedingMethodResults = breedingMethodDAO.findByNameOrAbbreviation(germplasm.getBreedingMethod(), program.getId());
if (breedingMethodResults.size() > 0) {
breedingMethods.put(germplasm.getBreedingMethod(), breedingMethodResults.get(0));
breedingMethod = breedingMethods.get(germplasm.getBreedingMethod());
} else {
ValidationError ve = new ValidationError("Breeding Method", badBreedMethodsMsg, HttpStatus.UNPROCESSABLE_ENTITY);
validationErrors.addError(i + 2, ve); // +2 instead of +1 to account for the column header row.
badBreedingMethods.add(germplasm.getBreedingMethod());
}
}
}
ProgramBreedingMethodEntity breedingMethod = resolveBreedingMethod(germplasm, validationErrors, breedingMethods, badBreedingMethods, program, i + 2);

validateGermplasmName(germplasm, i+2, validationErrors);
validateGermplasmName(germplasm, i + 2, validationErrors);
validatePedigree(germplasm, i + 2, validationErrors);

if (germplasm.pedigreeExists()) {
Expand All @@ -391,16 +376,17 @@ private void processNewGermplasm(Germplasm germplasm, ValidationErrors validatio

// Removes leading and trailing blanks from the germplasm breedingMethod
private Germplasm removeBreedingMethodBlanks(Germplasm germplasm) {
if(germplasm.getBreedingMethod() != null ) {
if (germplasm.getBreedingMethod() != null) {
germplasm.setBreedingMethod(germplasm.getBreedingMethod().strip());
}
return germplasm;
}

private boolean processExistingGermplasm(Germplasm germplasm, ValidationErrors validationErrors, List<BrAPIImport> importRows, Program program, UUID importListId, boolean commit, PendingImport mappedImportRow, int rowIndex) {
private void processExistingGermplasm(Germplasm germplasm, ValidationErrors validationErrors, List<BrAPIImport> importRows, Map<String, ProgramBreedingMethodEntity> breedingMethods,
List<String> badBreedingMethods, Program program, boolean commit, PendingImport mappedImportRow, int rowIndex) {
BrAPIGermplasm existingGermplasm;
String gid = germplasm.getAccessionNumber();
boolean mutated = false;
boolean mutated;
boolean updatePedigree = false;

if (germplasmByAccessionNumber.containsKey(gid)) {
Expand All @@ -410,31 +396,37 @@ private boolean processExistingGermplasm(Germplasm germplasm, ValidationErrors v
} else {
//should be caught in getExistingBrapiData
ValidationError ve = new ValidationError("GID", String.format(missingGID, gid), HttpStatus.NOT_FOUND);
validationErrors.addError(rowIndex+2, ve ); // +2 instead of +1 to account for the column header row.
return false;
validationErrors.addError(rowIndex + 2, ve); // +2 instead of +1 to account for the column header row.
return;
}

germplasm = removeBreedingMethodBlanks(germplasm);
//Validating if Breeding Method exists for valid parent entries
validateGermplasmBreedingMethod(germplasm, rowIndex + 2, validationErrors);
// Get the breeding method database object
ProgramBreedingMethodEntity breedingMethod = resolveBreedingMethod(germplasm, validationErrors, breedingMethods, badBreedingMethods, program, rowIndex + 2);

// Error conditions:
// has existing pedigree and file pedigree is different and not empty
// Valid conditions:
// no existing pedigree and file different pedigree
// existing pedigree and file pedigree same
// existing pedigree and file pedigree empty
if(hasPedigree(existingGermplasm) && germplasm.pedigreeExists()) {
if(!arePedigreesEqual(existingGermplasm, germplasm, importRows)) {
if (hasPedigree(existingGermplasm) && germplasm.pedigreeExists()) {
if (!arePedigreesEqual(existingGermplasm, germplasm, importRows)) {
ValidationError ve = new ValidationError("Pedigree", pedigreeAlreadyExists, HttpStatus.UNPROCESSABLE_ENTITY);
validationErrors.addError(rowIndex + 2, ve); // +2 instead of +1 to account for the column header row.
return false;
return;
}
}

// if no existing pedigree and file has pedigree then validate and update
if(germplasm.pedigreeExists() && !hasPedigree(existingGermplasm)) {
if (germplasm.pedigreeExists() && !hasPedigree(existingGermplasm)) {
validatePedigree(germplasm, rowIndex + 2, validationErrors);
updatePedigree = true;
}

mutated = germplasm.updateBrAPIGermplasm(existingGermplasm, program, importListId, commit, updatePedigree);
mutated = germplasm.updateBrAPIGermplasm(existingGermplasm, program, commit, updatePedigree, breedingMethod);

if (mutated) {
updatedGermplasmList.add(existingGermplasm);
Expand All @@ -448,7 +440,6 @@ private boolean processExistingGermplasm(Germplasm germplasm, ValidationErrors v

// add to list regardless of mutated or not
importList.addDataItem(existingGermplasm.getGermplasmName());
return true;
}

private boolean canUpdatePedigree(BrAPIGermplasm existingGermplasm, Germplasm germplasm) {
Expand Down Expand Up @@ -604,6 +595,35 @@ private void validateGermplasmName(Germplasm germplasm, Integer rowNumber, Valid
}
}

private void validateGermplasmBreedingMethod(Germplasm germplasm, Integer rowNumber, ValidationErrors validationErrors) {
if (germplasm.pedigreeExists() && StringUtils.isBlank(germplasm.getBreedingMethod())) {
ValidationError error = new ValidationError("Breeding Method", missingBreedingMethodForParentalGIDorEntryNo, HttpStatus.UNPROCESSABLE_ENTITY);
validationErrors.addError(rowNumber, error);
}
}

//shared Breeding Method lookup for create and update processes
private ProgramBreedingMethodEntity resolveBreedingMethod(Germplasm germplasm, ValidationErrors validationErrors,
Map<String, ProgramBreedingMethodEntity> breedingMethods,
List<String> badBreedingMethods, Program program, int rowNumber) {
if (germplasm.getBreedingMethod() == null) {
return null;
}
if (breedingMethods.containsKey(germplasm.getBreedingMethod())) {
return breedingMethods.get(germplasm.getBreedingMethod());
}
List<ProgramBreedingMethodEntity> breedingMethodResults = breedingMethodDAO.findByNameOrAbbreviation(germplasm.getBreedingMethod(), program.getId());

if (breedingMethodResults.isEmpty()) {
ValidationError ve = new ValidationError("Breeding Method", badBreedMethodsMsg, HttpStatus.UNPROCESSABLE_ENTITY);
validationErrors.addError(rowNumber, ve);
badBreedingMethods.add(germplasm.getBreedingMethod());
return null;
}
breedingMethods.put(germplasm.getBreedingMethod(), breedingMethodResults.get(0));
return breedingMethods.get(germplasm.getBreedingMethod());
}

private void validatePedigree(Germplasm germplasm, Integer rowNumber, ValidationErrors validationErrors) {
String femaleParentEntryNo = germplasm.getFemaleParentEntryNo();
String maleParentEntryNo = germplasm.getMaleParentEntryNo();
Expand Down Expand Up @@ -657,7 +677,7 @@ 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 Down
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