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Merge pull request #421 from Breeding-Insight/bug/BI-2344
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BI-2344 - merging into develop
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@mlm483
mlm483 authored Oct 30, 2024
2 parents 9d4f7c7 + ee5a46a commit a98bbf8
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Showing 4 changed files with 41 additions and 35 deletions.
15 changes: 8 additions & 7 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -95,13 +95,14 @@ public HttpResponse<BrAPIPedigreeListResponse> pedigreeGet(@PathVariable("progra
try {
List<BrAPIPedigreeNode> pedigree = pedigreeDAO.getPedigree(
program.get(),
Optional.ofNullable(includeParents),
Optional.ofNullable(includeSiblings),
Optional.ofNullable(includeProgeny),
Optional.ofNullable(includeFullTree),
Optional.ofNullable(pedigreeDepth),
Optional.ofNullable(progenyDepth),
Optional.ofNullable(germplasmName));
includeParents,
includeSiblings,
includeProgeny,
includeFullTree,
pedigreeDepth,
progenyDepth,
germplasmName,
accessionNumber);

return HttpResponse.ok(
new BrAPIPedigreeListResponse()
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30 changes: 16 additions & 14 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java
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Expand Up @@ -73,13 +73,14 @@ public BrAPIPedigreeDAO(ProgramDAO programDAO, BrAPIDAOUtil brAPIDAOUtil,
*/
public List<BrAPIPedigreeNode> getPedigree(
Program program,
Optional<Boolean> includeParents,
Optional<Boolean> includeSiblings,
Optional<Boolean> includeProgeny,
Optional<Boolean> includeFullTree,
Optional<Integer> pedigreeDepth,
Optional<Integer> progenyDepth,
Optional<String> germplasmName
Boolean includeParents,
Boolean includeSiblings,
Boolean includeProgeny,
Boolean includeFullTree,
Integer pedigreeDepth,
Integer progenyDepth,
String germplasmName,
String accessionNumber
) throws ApiException {

PedigreeQueryParams pedigreeRequest = new PedigreeQueryParams();
Expand All @@ -94,13 +95,14 @@ public List<BrAPIPedigreeNode> getPedigree(
pedigreeRequest.externalReferenceId(extRefId);
pedigreeRequest.externalReferenceSource(extRefSrc);

includeParents.ifPresent(pedigreeRequest::includeParents);
includeSiblings.ifPresent(pedigreeRequest::includeSiblings);
includeProgeny.ifPresent(pedigreeRequest::includeProgeny);
includeFullTree.ifPresent(pedigreeRequest::includeFullTree);
pedigreeDepth.ifPresent(pedigreeRequest::pedigreeDepth);
progenyDepth.ifPresent(pedigreeRequest::progenyDepth);
germplasmName.ifPresent(pedigreeRequest::germplasmName);
if (includeParents != null) pedigreeRequest.includeParents(includeParents);
if (includeSiblings != null) pedigreeRequest.includeSiblings(includeSiblings);
if (includeProgeny != null) pedigreeRequest.includeProgeny(includeProgeny);
if (includeFullTree != null) pedigreeRequest.includeFullTree(includeFullTree);
if (pedigreeDepth != null) pedigreeRequest.pedigreeDepth(pedigreeDepth);
if (progenyDepth != null) pedigreeRequest.progenyDepth(progenyDepth);
if (germplasmName != null) pedigreeRequest.germplasmName(germplasmName);
if (accessionNumber != null) pedigreeRequest.accessionNumber(accessionNumber);
// TODO: other parameters

// TODO: write utility to do paging instead of hardcoding
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30 changes: 16 additions & 14 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 @@ -82,10 +82,15 @@ public Optional<BrAPIGermplasm> getGermplasmByDBID(UUID programId, String germpl
return germplasmDAO.getGermplasmByDBID(germplasmId, programId);
}

public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm, BrAPIListDetails germplasmList){
public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm, BrAPIListDetails germplasmList, Program program){
Map<String, BrAPIGermplasm> germplasmByName = new HashMap<>();
for (BrAPIGermplasm g: germplasm) {
germplasmByName.put(g.getGermplasmName(), g);
// Use the full, unique germplasmName with programKey and accessionNumber (GID) for 2 reasons:
// 1. the BrAPI list items are full names, and
// 2. germplasmNames alone are not unique within a program, this led to unexpected behavior, see BI-2344.
String uniqueGermplasmName = String.format("%s [%s-%s]", g.getGermplasmName(), program.getKey(), g.getAccessionNumber());
g.setGermplasmName(uniqueGermplasmName); // Mutate the germplasmName in place for later use.
germplasmByName.put(uniqueGermplasmName, g);
}

List<Map<String, Object>> processedData = new ArrayList<>();
Expand All @@ -107,14 +112,13 @@ public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm,
for (String germplasmName: orderedGermplasmNames) {
// Increment entryNumber.
++entryNumber;
// Strip program key and accession number from germplasm name.
germplasmName = Utilities.removeUnknownProgramKey(germplasmName); // TODO: could move to the germplasmList != null codepath.
// Lookup the BrAPI germplasm in the map.
BrAPIGermplasm germplasmEntry = germplasmByName.get(germplasmName);

HashMap<String, Object> row = new HashMap<>();
row.put("GID", Integer.valueOf(germplasmEntry.getAccessionNumber()));
row.put("Germplasm Name", germplasmEntry.getGermplasmName());
// Strip programKey and accessionNumber from germplasmName for the file output.
row.put("Germplasm Name", Utilities.removeProgramKeyAnyAccession(germplasmEntry.getGermplasmName(), program.getKey()));
row.put("Breeding Method", germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD).getAsString());
String source = germplasmEntry.getSeedSource();
row.put("Source", source);
Expand Down Expand Up @@ -217,7 +221,7 @@ private BrAPIGermplasm cloneBrAPIGermplasm(BrAPIGermplasm germplasm) {
return (BrAPIGermplasm) gson.fromJson(gson.toJson(germplasm), BrAPIGermplasm.class);
}

public DownloadFile exportGermplasm(UUID programId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException {
public DownloadFile exportGermplasm(UUID programId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException, DoesNotExistException {
List<Column> columns = GermplasmFileColumns.getOrderedColumns();

//Retrieve germplasm list data
Expand All @@ -238,7 +242,8 @@ public DownloadFile exportGermplasm(UUID programId, FileType fileExtension) thro

StreamedFile downloadFile;
//Convert list data to List<Map<String, Object>> data to pass into file writer
List<Map<String, Object>> processedData = processListData(germplasm, null);
Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Could not find program: " + programId));
List<Map<String, Object>> processedData = processListData(germplasm, null, program);

if (fileExtension == FileType.CSV){
downloadFile = CSVWriter.writeToDownload(columns, processedData, fileExtension);
Expand All @@ -249,7 +254,7 @@ public DownloadFile exportGermplasm(UUID programId, FileType fileExtension) thro
return new DownloadFile(fileName, downloadFile);
}

public DownloadFile exportGermplasmList(UUID programId, String listId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException {
public DownloadFile exportGermplasmList(UUID programId, String listId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException, DoesNotExistException {
List<Column> columns = GermplasmFileColumns.getOrderedColumns();

//Retrieve germplasm list data
Expand All @@ -260,15 +265,12 @@ public DownloadFile exportGermplasmList(UUID programId, String listId, FileType
List<BrAPIGermplasm> germplasm = germplasmDAO.getGermplasmByRawName(germplasmNames, programId);

String listName = listData.getListName();
Optional<Program> optionalProgram = programService.getById(programId);
if (optionalProgram.isPresent()) {
Program program = optionalProgram.get();
listName = removeAppendedKey(listName, program.getKey());
}
Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Could not find program: " + programId));
listName = removeAppendedKey(listName, program.getKey());
String fileName = createFileName(listData, listName);
StreamedFile downloadFile;
//Convert list data to List<Map<String, Object>> data to pass into file writer
List<Map<String, Object>> processedData = processListData(germplasm, listData);
List<Map<String, Object>> processedData = processListData(germplasm, listData, program);

if (fileExtension == FileType.CSV){
downloadFile = CSVWriter.writeToDownload(columns, processedData, fileExtension);
Expand Down
1 change: 1 addition & 0 deletions src/main/resources/version.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -14,5 +14,6 @@
# limitations under the License.
#


version=v1.1.0+852
versionInfo=https://github.com/Breeding-Insight/bi-api/commit/3fbb75f662c5600da816270d53699aa1192777b9

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