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BI-1881 (Remove Need to Provide Parents to processGermplasmForDisplay) #288

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BI-1881 (Remove Need to Provide Parents to processGermplasmForDisplay) #288

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[BI-1881] WIP
davedrp Aug 24, 2023
b7a686e
[BI-1881] WIP
davedrp Aug 25, 2023
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56 changes: 41 additions & 15 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
import org.breedinginsight.brapps.importer.daos.ImportDAO;
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.dao.db.tables.pojos.ProgramEntity;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.daos.cache.ProgramCache;
import org.breedinginsight.daos.cache.ProgramCacheProvider;
Expand Down Expand Up @@ -145,21 +146,23 @@ private Map<String, BrAPIGermplasm> fetchProgramGermplasm(UUID programId) throws
api::searchGermplasmPost,
api::searchGermplasmSearchResultsDbIdGet,
germplasmSearch
), program.getKey());
), program);
}

/**
* Process germplasm into a format for display
* @param programGermplasm
* @param germplasmList
* @return Map<Key = string representing germplasm UUID, value = formatted BrAPIGermplasm>
* @throws ApiException
*/
private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplasm> programGermplasm, String programKey) {
private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplasm> germplasmList, ProgramEntity program) throws ApiException {
String programKey = program.getKey();
// Process the germplasm
Map<String, BrAPIGermplasm> programGermplasmMap = new HashMap<>();
log.trace("processing germ for display: " + programGermplasm);
log.trace("processing germ for display: " + germplasmList);
Map<String, BrAPIGermplasm> programGermplasmByFullName = new HashMap<>();
for (BrAPIGermplasm germplasm: programGermplasm) {
boolean isExpanded_programGermplasmByFullName = false;
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@mlm483 mlm483 Aug 28, 2023

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Unless the underscore in the name is part of a convention I don't know about, I would remove it.
isExpandedProgramGermplasmByFullName would be OK with me, something like isMissingParents would be OK too.

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@nickpalladino nickpalladino Aug 29, 2023

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+1

for (BrAPIGermplasm germplasm: germplasmList) {
programGermplasmByFullName.put(germplasm.getGermplasmName(), germplasm);

JsonObject additionalInfo = germplasm.getAdditionalInfo();
Expand All @@ -181,7 +184,7 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
}

// Update pedigree string
for (BrAPIGermplasm germplasm: programGermplasm) {
for (BrAPIGermplasm germplasm: germplasmList) {
JsonObject additionalInfo = germplasm.getAdditionalInfo();
if(additionalInfo == null) {
additionalInfo = new JsonObject();
Expand All @@ -200,6 +203,13 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
parents = Arrays.asList(germplasm.getPedigree().split("/"));
}
if (parents.size() >= 1) {
// if the female parent germplasm is not found in the passed-in germplasmList, then expand the programGermplasmByFullName
// map so we can search all of the program's germplasm for the parent.
if( ! isExpanded_programGermplasmByFullName && !"NA".equals(parents.get(0)) && !programGermplasmByFullName.containsKey(parents.get(0)) ){
if (! additionalInfo.has(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN) || ! additionalInfo.get(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN).getAsBoolean()) {
isExpanded_programGermplasmByFullName = expand_programGermplasmByFullName(program, programGermplasmByFullName);
}
}
if (programGermplasmByFullName.containsKey(parents.get(0))) {
String femaleParentAccessionNumber = programGermplasmByFullName.get(parents.get(0)).getAccessionNumber();
newPedigreeString = femaleParentAccessionNumber;
Expand All @@ -213,11 +223,19 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
}
}
if (parents.size() == 2) {
if (programGermplasmByFullName.containsKey(parents.get(1))) {
String maleParentAccessionNumber = programGermplasmByFullName.get(parents.get(1)).getAccessionNumber();
// if the male parent germplasm is not found in the passed-in germplasmList, then expand the programGermplasmByFullName
// map so we can search all of the program's germplasm for the parent.
String maleParentName = parents.get(1);
if( ! isExpanded_programGermplasmByFullName && !"NA".equals(maleParentName) && !programGermplasmByFullName.containsKey(maleParentName)){
if (!additionalInfo.has(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN) || !additionalInfo.get(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN).getAsBoolean()) {
isExpanded_programGermplasmByFullName = expand_programGermplasmByFullName(program, programGermplasmByFullName);
}
}
if (programGermplasmByFullName.containsKey(maleParentName)) {
String maleParentAccessionNumber = programGermplasmByFullName.get(maleParentName).getAccessionNumber();
newPedigreeString += "/" + maleParentAccessionNumber;
namePedigreeString += "/" + programGermplasmByFullName.get(parents.get(1)).getDefaultDisplayName();
uuidPedigreeString += "/" + programGermplasmByFullName.get(parents.get(1)).getExternalReferences().
namePedigreeString += "/" + programGermplasmByFullName.get(maleParentName).getDefaultDisplayName();
uuidPedigreeString += "/" + programGermplasmByFullName.get(maleParentName).getExternalReferences().
stream().filter(ref -> ref.getReferenceSource().equals(referenceSource)).
map(ref -> ref.getReferenceID()).findFirst().orElse("");
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParentAccessionNumber);
Expand All @@ -241,6 +259,16 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
return programGermplasmMap;
}

private boolean expand_programGermplasmByFullName(ProgramEntity program, Map<String, BrAPIGermplasm> programGermplasmByFullName) throws ApiException {
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@mlm483 mlm483 Aug 28, 2023

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Unless the underscore in the name is part of a convention I don't know about, I would remove it.

List<BrAPIGermplasm> allProgramGermplasm = getRawGermplasm(program.getId());
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@mlm483 mlm483 Aug 28, 2023

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getRawGermplasm hits the cache, calling it from the method processGermplasmForDisplay which is used to populate the cache may be causing the issues I'm seeing locally and in the TAF run.

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@nickpalladino nickpalladino Aug 29, 2023

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I thought the original intent of this card was to grab the accession numbers from the pedigree string [programKey-accessionNumber] and use that to create the newPedigreeString rather than requiring the parent germplasm objects @timparsons? Although I'm not sure how it would create the name and UUID pedigree strings in that case.

for (BrAPIGermplasm programGermplasm: allProgramGermplasm) {
if( ! programGermplasmByFullName.containsKey( programGermplasm.getGermplasmName() ) ){
programGermplasmByFullName.put(programGermplasm.getGermplasmName(), programGermplasm);
}
}
return true;
}

// TODO: hack for now, probably should update breedbase
// Made a JIRA card BI-1883 for this
// Breedbase will return NA/NA for no pedigree or NA/father, mother/NA
Expand Down Expand Up @@ -277,7 +305,7 @@ public List<BrAPIGermplasm> createBrAPIGermplasm(List<BrAPIGermplasm> postBrAPIG
if (!postBrAPIGermplasmList.isEmpty()) {
postFunction = () -> {
List<BrAPIGermplasm> postResponse = brAPIDAOUtil.post(postBrAPIGermplasmList, upload, api::germplasmPost, importDAO::update);
return processGermplasmForDisplay(postResponse, program.getKey());
return processGermplasmForDisplay(postResponse, program);
};
}
return programGermplasmCache.post(programId, postFunction);
Expand All @@ -293,10 +321,8 @@ 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> germplasm = putGermplasm(putBrAPIGermplasmList, api);
return processGermplasmForDisplay(germplasm, program);
};
}
return programGermplasmCache.post(programId, postFunction);
Expand Down