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[BI-2751] - Germplasm entry number weirdness #494

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[BI-2751] - Germplasm entry number weirdness #494

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86 changes: 47 additions & 39 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 @@ -91,7 +91,7 @@ public class GermplasmProcessor implements Processor {

public static String missingGIDsMsg = "The following GIDs were not found in the database: %s";
public static String missingParentalGIDsMsg = "The following parental GIDs were not found in the database: %s";
public static String missingParentalEntryNoMsg = "The following parental entry numbers were not found in the database: %s";
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 missingEntryNumbersMsg = "Either all or none of the germplasm must have entry numbers";
Expand Down Expand Up @@ -137,14 +137,17 @@ public void getExistingBrapiData(List<BrAPIImport> importRows, Program program)
BrAPIImport germplasmImport = importRows.get(i);
Germplasm germplasm = germplasmImport.getGermplasm();
if (germplasm != null) {

//Ignore this if germplasm already has a pedigree in the database
// 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 (!databaseGermplasmHasPedigree(germplasm)) {
if (germplasm.getFemaleParentAccessionNumber() != null) {
germplasmAccessionNumbers.put(germplasm.getFemaleParentAccessionNumber(), true);
}
if (germplasm.getMaleParentAccessionNumber() != null) {
germplasmAccessionNumbers.put(germplasm.getMaleParentAccessionNumber(), true);
}
}

if (germplasm.getAccessionNumber() != null) {
germplasmAccessionNumbers.put(germplasm.getAccessionNumber(), false);
}
Expand Down Expand Up @@ -223,27 +226,31 @@ public void getExistingBrapiData(List<BrAPIImport> importRows, Program program)
arrayOfStringFormatter.apply(missingAccessionNumbers)));
}

List<String> missingEntryNumbers = new ArrayList<>();
for (BrAPIImport importRow: importRows) {
Germplasm germplasm = importRow.getGermplasm();
// Check Female Parent
if (germplasm.getFemaleParentEntryNo() != null) {
if ((!germplasmIndexByEntryNo.containsKey(germplasm.getFemaleParentEntryNo())) && !(germplasm.getFemaleParentEntryNo().equals("0"))) {
missingEntryNumbers.add(germplasm.getFemaleParentEntryNo());
List<String> missingEntryNumbers = new ArrayList<>();
for (BrAPIImport importRow : importRows) {
Germplasm germplasm = importRow.getGermplasm();

//If germplasm already has a pedigree, pedigree cannot be overwritten and file values for pedigree will be ignored
boolean pedigreeExists = databaseGermplasmHasPedigree(germplasm);

// Check Female Parent
if (germplasm.getFemaleParentEntryNo() != null && !pedigreeExists) {
if ((!germplasmIndexByEntryNo.containsKey(germplasm.getFemaleParentEntryNo())) && !(germplasm.getFemaleParentEntryNo().equals("0"))) {
missingEntryNumbers.add(germplasm.getFemaleParentEntryNo());
}
}
}
// Check Male Parent
if (germplasm.getMaleParentEntryNo() != null) {
if ((!germplasmIndexByEntryNo.containsKey(germplasm.getMaleParentEntryNo())) && !(germplasm.getMaleParentEntryNo().equals("0"))) {
missingEntryNumbers.add(germplasm.getMaleParentEntryNo());
// Check Male Parent
if (germplasm.getMaleParentEntryNo() != null && !pedigreeExists) {
if ((!germplasmIndexByEntryNo.containsKey(germplasm.getMaleParentEntryNo())) && !(germplasm.getMaleParentEntryNo().equals("0"))) {
missingEntryNumbers.add(germplasm.getMaleParentEntryNo());
}
}
}
}
if (missingEntryNumbers.size() > 0) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY,
String.format(missingParentalEntryNoMsg,
arrayOfStringFormatter.apply(missingEntryNumbers)));
}
if (missingEntryNumbers.size() > 0) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY,
String.format(missingParentalEntryNoMsg,
arrayOfStringFormatter.apply(missingEntryNumbers)));
}

if (listNameDup) {
throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY, listNameAlreadyExists);
Expand Down Expand Up @@ -405,21 +412,8 @@ private boolean processExistingGermplasm(Germplasm germplasm, ValidationErrors v
return false;
}

// 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)) {
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;
}
}

// if no existing pedigree and file has pedigree then validate and update
// if pedigree exists, file pedigree information should be ignored
if(germplasm.pedigreeExists() && !hasPedigree(existingGermplasm)) {
validatePedigree(germplasm, rowIndex + 2, validationErrors);
updatePedigree = true;
Expand Down Expand Up @@ -460,6 +454,16 @@ 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, if so, pedigree information in file should be ignored
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 @@ -793,6 +797,8 @@ else if (germplasmIndexByEntryNo.containsKey(germplasm.getFemaleParentEntryNo())
if (commit) {
if (femaleParentFound) {
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID, femaleParent.getAccessionNumber());
//entry number no longer needed for figuring out parentage, can remove (since same germplasm can have different entry numbers across multiple lists)
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_ENTRY_NO, null);
// Add femaleParentUUID to additionalInfo.
Optional<BrAPIExternalReference> femaleParentUUID = Utilities.getExternalReference(femaleParent.getExternalReferences(), BRAPI_REFERENCE_SOURCE);
if (femaleParentUUID.isPresent()) {
Expand All @@ -802,6 +808,8 @@ else if (germplasmIndexByEntryNo.containsKey(germplasm.getFemaleParentEntryNo())

if (maleParent != null) {
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParent.getAccessionNumber());
//entry number no longer needed for figuring out parentage, can remove (since same germplasm can have different entry numbers across multiple lists)
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_ENTRY_NO, null);
// Add maleParentUUID to additionalInfo.
Optional<BrAPIExternalReference> maleParentUUID = Utilities.getExternalReference(maleParent.getExternalReferences(), BRAPI_REFERENCE_SOURCE);
if (maleParentUUID.isPresent()) {
Expand Down
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