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BI-1881 - Store Parent UUIDs in Germplasm AdditionalInfo #290

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Merged
mlm483 merged 9 commits into from
Sep 22, 2023
Merged

BI-1881 - Store Parent UUIDs in Germplasm AdditionalInfo #290

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9a38c0f
[BI-1881] - work in progress
mlm483 Sep 18, 2023
dcd0a48
[BI-1881] - fixed failing test
mlm483 Sep 19, 2023
f6d060a
[BI-1881] - added logging
mlm483 Sep 19, 2023
df489f1
Merge branch 'develop' into bug/BI-1881-mlm483
mlm483 Sep 20, 2023
edc00a6
[BI-1881] - updated comments and messages
mlm483 Sep 20, 2023
6521943
[BI-1881] - imported constants, simplified usages
mlm483 Sep 20, 2023
9add27a
[BI-1847] - revert to passing only putBrAPIGermplasmList
mlm483 Sep 21, 2023
2e34aa1
[BI-1847] - use result of putBrAPIGermplasmList
mlm483 Sep 21, 2023
0939586
[BI-1881] - changes based on review
mlm483 Sep 22, 2023
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2 changes: 2 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java
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Expand Up @@ -23,6 +23,8 @@ public final class BrAPIAdditionalInfoFields {
public static final String GERMPLASM_RAW_PEDIGREE = "rawPedigree";
public static final String GERMPLASM_PEDIGREE_BY_NAME = "pedigreeByName";
public static final String GERMPLASM_PEDIGREE_BY_UUID = "pedigreeByUUID";
public static final String GERMPLASM_FEMALE_PARENT_UUID = "femaleParentUUID";
public static final String GERMPLASM_MALE_PARENT_UUID = "maleParentUUID";
public static final String GERMPLASM_IMPORT_ENTRY_NUMBER = "importEntryNumber";
public static final String GERMPLASM_FEMALE_PARENT_GID = "femaleParentGid";
public static final String GERMPLASM_MALE_PARENT_GID = "maleParentGid";
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96 changes: 58 additions & 38 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
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Expand Up @@ -158,9 +158,7 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
// Process the germplasm
Map<String, BrAPIGermplasm> programGermplasmMap = new HashMap<>();
log.trace("processing germ for display: " + programGermplasm);
Map<String, BrAPIGermplasm> programGermplasmByFullName = new HashMap<>();
for (BrAPIGermplasm germplasm: programGermplasm) {
programGermplasmByFullName.put(germplasm.getGermplasmName(), germplasm);

JsonObject additionalInfo = germplasm.getAdditionalInfo();
if (additionalInfo != null && additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD_ID)) {
Expand Down Expand Up @@ -192,46 +190,70 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
String pedigree = processBreedbasePedigree(germplasm.getPedigree());
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE, pedigree);

String newPedigreeString = "";
String gidPedigreeString = "";
String namePedigreeString = "";
String uuidPedigreeString = "";
List<String> parents = Arrays.asList("","");
if (germplasm.getPedigree() != null) {
parents = Arrays.asList(germplasm.getPedigree().split("/"));
}
if (parents.size() >= 1) {
if (programGermplasmByFullName.containsKey(parents.get(0))) {
String femaleParentAccessionNumber = programGermplasmByFullName.get(parents.get(0)).getAccessionNumber();
newPedigreeString = femaleParentAccessionNumber;
namePedigreeString = programGermplasmByFullName.get(parents.get(0)).getDefaultDisplayName();
uuidPedigreeString = programGermplasmByFullName.get(parents.get(0)).getExternalReferences().
stream().filter(ref -> ref.getReferenceSource().equals(referenceSource)).
map(ref -> ref.getReferenceID()).findFirst().orElse("");
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID, femaleParentAccessionNumber);
} else if (additionalInfo.has(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN) && additionalInfo.get(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN).getAsBoolean()) {
namePedigreeString = "Unknown";

// Get parent germplasm names without program key.
// This is designed so that pedigree="female/" will result in parentNames=["female", ""]
// and pedigree="/male" will result in parentNames=["", "male"];
// pedigree=null or pedigree="" will result in parentNames=[].
List<String> parentNames = new ArrayList<>();
if (pedigree != null) {
// Note: split with limit=-1 applies pattern as many times as possible, allowing capture of leading or trailing empty strings.
for (String name : pedigree.split("/", -1)) {
if (!name.isEmpty())
{
// Strip program key.
name = Utilities.removeProgramKeyAndUnknownAdditionalData(name, programKey);
}
parentNames.add(name);
}
if (parents.size() == 2) {
if (programGermplasmByFullName.containsKey(parents.get(1))) {
String maleParentAccessionNumber = programGermplasmByFullName.get(parents.get(1)).getAccessionNumber();
newPedigreeString += "/" + maleParentAccessionNumber;
namePedigreeString += "/" + programGermplasmByFullName.get(parents.get(1)).getDefaultDisplayName();
uuidPedigreeString += "/" + programGermplasmByFullName.get(parents.get(1)).getExternalReferences().
stream().filter(ref -> ref.getReferenceSource().equals(referenceSource)).
map(ref -> ref.getReferenceID()).findFirst().orElse("");
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParentAccessionNumber);
}

// Update pedigree info for female parent.
if (parentNames.size() >= 1 && !parentNames.get(0).isEmpty())
{
gidPedigreeString = additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID) ? additionalInfo.get(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID).getAsString() : "";
namePedigreeString = parentNames.get(0);
uuidPedigreeString = additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_UUID) ? additionalInfo.get(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_UUID).getAsString() : "";
// Throw a descriptive error if femaleParentUUID is absent.
if (!additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_UUID)) {
String programId = "unknown program";
Optional<BrAPIExternalReference> exRef = Utilities.getExternalReference(germplasm.getExternalReferences(), referenceSource + "/programs");
if (exRef.isPresent()) {
programId = exRef.get().getReferenceID();
}
log.debug("The germplasm data for program " + programId + " needs to be updated: https://github.com/Breeding-Insight/bi-api/pull/290");
throw new InternalServerException("Germplasm (" + germplasm.getGermplasmName() + ") has a female parent but femaleParentUUID is missing (Pedigree: " + germplasm.getPedigree() + ").");
}
//Add Unknown germplasm for display
if (additionalInfo.has(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN) && additionalInfo.get(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN).getAsBoolean()) {
namePedigreeString += "/Unknown";
} else if (additionalInfo.has(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN) && additionalInfo.get(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN).getAsBoolean()) {
namePedigreeString = "Unknown";
}
// Update pedigree info for male parent.
if (parentNames.size() == 2 && !parentNames.get(1).isEmpty())
{
gidPedigreeString += "/" + (additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID) ? additionalInfo.get(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID).getAsString() : "");
namePedigreeString += "/" + parentNames.get(1);
uuidPedigreeString += "/" + (additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_UUID) ? additionalInfo.get(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_UUID).getAsString() : "");
// Throw a descriptive error if maleParentUUID is absent.
if (!additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_UUID)) {
String programId = "unknown program";
Optional<BrAPIExternalReference> exRef = Utilities.getExternalReference(germplasm.getExternalReferences(), referenceSource + "/programs");
if (exRef.isPresent()) {
programId = exRef.get().getReferenceID();
}
log.debug("The germplasm data for program " + programId + " needs to be updated: https://github.com/Breeding-Insight/bi-api/pull/290");
throw new InternalServerException("Germplasm (" + germplasm.getGermplasmName() + ") has a male parent but maleParentUUID is missing (Pedigree: " + germplasm.getPedigree() + ").");
}
//For use in individual germplasm display
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME, namePedigreeString);
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_UUID, uuidPedigreeString);
} else if (additionalInfo.has(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN) && additionalInfo.get(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN).getAsBoolean()) {
namePedigreeString += "/Unknown";
}
//For use in individual germplasm display
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME, namePedigreeString);
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_UUID, uuidPedigreeString);

germplasm.setPedigree(newPedigreeString);
germplasm.setPedigree(gidPedigreeString);

BrAPIExternalReference extRef = germplasm.getExternalReferences().stream().filter(reference -> referenceSource.equals(reference.getReferenceSource())).findFirst().orElseThrow(() -> new IllegalStateException("No BI external reference found"));
String germplasmId = extRef.getReferenceID();
Expand Down Expand Up @@ -293,10 +315,8 @@ public List<BrAPIGermplasm> updateBrAPIGermplasm(List<BrAPIGermplasm> putBrAPIGe
try {
if (!putBrAPIGermplasmList.isEmpty()) {
postFunction = () -> {
putGermplasm(putBrAPIGermplasmList, api);
// Need all program germplasm for processGermplasmForDisplay parents pedigree
List<BrAPIGermplasm> germplasm = getRawGermplasm(programId);
return processGermplasmForDisplay(germplasm, program.getKey());
List<BrAPIGermplasm> putResponse = putGermplasm(putBrAPIGermplasmList, api);
return processGermplasmForDisplay(putResponse, program.getKey());
};
}
return programGermplasmCache.post(programId, postFunction);
Expand Down
13 changes: 12 additions & 1 deletion ...main/java/org/breedinginsight/brapps/importer/services/processors/GermplasmProcessor.java
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Expand Up @@ -24,6 +24,7 @@
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIListSummary;
import org.brapi.v2.model.core.request.BrAPIListNewRequest;
import org.brapi.v2.model.germ.BrAPIGermplasm;
Expand All @@ -45,6 +46,7 @@
import org.breedinginsight.model.Program;
import org.breedinginsight.model.User;
import org.breedinginsight.services.exceptions.ValidatorException;
import org.breedinginsight.utilities.Utilities;
import org.jooq.DSLContext;
import tech.tablesaw.api.Table;

Expand Down Expand Up @@ -717,11 +719,20 @@ else if (germplasmIndexByEntryNo.containsKey(germplasm.getFemaleParentEntryNo())
if (commit) {
if (femaleParentFound) {
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID, femaleParent.getAccessionNumber());
// Add femaleParentUUID to additionalInfo.
Optional<BrAPIExternalReference> femaleParentUUID = Utilities.getExternalReference(femaleParent.getExternalReferences(), BRAPI_REFERENCE_SOURCE);
if (femaleParentUUID.isPresent()) {
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_UUID, femaleParentUUID.get().getReferenceID());
}
}

if (maleParent != null) {
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParent.getAccessionNumber());
}
// Add maleParentUUID to additionalInfo.
Optional<BrAPIExternalReference> maleParentUUID = Utilities.getExternalReference(maleParent.getExternalReferences(), BRAPI_REFERENCE_SOURCE);
if (maleParentUUID.isPresent()) {
brAPIGermplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_UUID, maleParentUUID.get().getReferenceID());
} }
}
}
}
Expand Down
13 changes: 8 additions & 5 deletions src/test/java/org/breedinginsight/services/BrAPIGermplasmServiceUnitTest.java
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Expand Up @@ -36,6 +36,7 @@
import java.util.*;
import java.util.stream.Collectors;

import static org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.Mockito.*;

Expand Down Expand Up @@ -92,20 +93,21 @@ public void getGermplasmListExport() {
listResponse.setResult(listDetails);

//Create Germplasm
String parentUuid = UUID.randomUUID().toString();
List<BrAPIGermplasm> germplasm = new ArrayList();
BrAPIGermplasm testGermplasm = new BrAPIGermplasm();
testGermplasm.setGermplasmName("Germplasm A [TEST-1]");
testGermplasm.setSeedSource("Wild");
testGermplasm.setAccessionNumber("1");
testGermplasm.setDefaultDisplayName("Germplasm A");
JsonObject additionalInfo = new JsonObject();
additionalInfo.addProperty("importEntryNumber", "2");
additionalInfo.addProperty("breedingMethod", "Allopolyploid");
additionalInfo.addProperty(GERMPLASM_IMPORT_ENTRY_NUMBER, "2");
additionalInfo.addProperty(GERMPLASM_BREEDING_METHOD, "Allopolyploid");
testGermplasm.setAdditionalInfo(additionalInfo);
List<BrAPIExternalReference> externalRef = new ArrayList<>();
BrAPIExternalReference testReference = new BrAPIExternalReference();
testReference.setReferenceSource(referenceSource);
testReference.setReferenceID(UUID.randomUUID().toString());
testReference.setReferenceID(parentUuid);
externalRef.add(testReference);
testGermplasm.setExternalReferences(externalRef);
germplasm.add(testGermplasm);
Expand All @@ -117,8 +119,9 @@ public void getGermplasmListExport() {
testGermplasm.setDefaultDisplayName("Germplasm B");
testGermplasm.setPedigree("Germplasm A [TEST-1]");
additionalInfo = new JsonObject();
additionalInfo.addProperty("importEntryNumber", "3");
additionalInfo.addProperty("breedingMethod", "Autopolyploid");
additionalInfo.addProperty(GERMPLASM_IMPORT_ENTRY_NUMBER, "3");
additionalInfo.addProperty(GERMPLASM_BREEDING_METHOD, "Autopolyploid");
additionalInfo.addProperty(GERMPLASM_FEMALE_PARENT_UUID, parentUuid);
testGermplasm.setAdditionalInfo(additionalInfo);
testReference = new BrAPIExternalReference();
testReference.setReferenceSource(referenceSource);
Expand Down