BI-2344 - merging into develop

src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java

@@ -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()

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java

@@ -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();
@@ -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

src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java

@@ -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<>();
@@ -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);
@@ -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
@@ -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);
@@ -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
@@ -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);

src/main/resources/version.properties

@@ -14,5 +14,6 @@
 # limitations under the License.
 #
 
+
 version=v1.1.0+852
 versionInfo=https://github.com/Breeding-Insight/bi-api/commit/3fbb75f662c5600da816270d53699aa1192777b9