Untangle/Hack Pedigree UUID scheme so links work on fe

.env.template

@@ -79,3 +79,5 @@ TRIAL_START_DELAY=15s
 TRAIT_START_DELAY=20s
 OBSERVATION_START_DELAY=25s
 OBSERVATION_UNIT_START_DELAY=30s
+
+DATA_TABLE_MAX_SIZE=200

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

@@ -226,6 +226,7 @@ private void setDbIds(BrAPIObservationUnit ou) {
         ou.programDbId(Utilities.getExternalReference(ou.getExternalReferences(), Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS))
                                    .orElseThrow(() -> new IllegalStateException("No BI external reference found"))
                                    .getReferenceID());
+        // TODO: Remove this as part of [BI-3006]
         if (ou.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_UUID)) {
             ou.setGermplasmDbId(ou.getAdditionalInfo()
                                   .get(BrAPIAdditionalInfoFields.GERMPLASM_UUID)

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

@@ -316,7 +316,7 @@ public List<BrAPIObservationUnit> getObservationUnits(Program program,
                                                .orElse(true);
 
             //adding filter for germplasmDbId because we can't easily search that in the stored data object
-            // TODO: Add search on accessionNumber once it's been added to prod server and brapi client [BI-2978]
+            // TODO: Add search on germplasmDbId directly in search request [BI-3006]
             return matches && germplasmId.map(id -> id.equals(ou.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_UUID).getAsString())).orElse(true);
         }).collect(Collectors.toList());
     }
@@ -382,7 +382,7 @@ private void processObservationUnits(Program program, List<BrAPIObservationUnit>
 
     	HashMap<String, BrAPIGermplasm> germplasmByDbId = new HashMap<>();
     	if( withGID ){
-            // TODO: Optimize this to use germplasm information directly in BrAPIObservationUnit by adding accession num/GID there via the prodserver/client [BI-2978]
+            // TODO: Optimize this to use germplasm information directly in BrAPIObservationUnit by searching on ou.germplasmDbIds in a GermplasmSearchRequest [BI-3006]
             this.germplasmService.getGermplasm(program.getId()).forEach((germplasm -> germplasmByDbId.put(germplasm.getGermplasmDbId(), germplasm)));
         }
 

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

@@ -85,7 +85,7 @@ public List<BrAPIPedigreeNode> getPedigree(
 
         PedigreeQueryParams pedigreeRequest = new PedigreeQueryParams();
 
-        // TODO: Issue with BrAPI server programDbId filtering, think germplasm are linked to program through observation
+        // TODO: Issue with BrAPI server programDbId filtering, think germplasm are linked to program through observation [BI-
         // units and doesn't work if don't have any loaded
         // use external refs instead for now
         //pedigreeSearchRequest.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));

src/main/resources/application.yml

@@ -237,3 +237,5 @@ startup:
     trait: ${TRAIT_START_DELAY:2s}
     observation: ${OBSERVATION_START_DELAY:3s}
     observation_unit: ${OBSERVATION_UNIT_START_DELAY:3s}
+data-table:
+  max-size: ${DATA_TABLE_MAX_SIZE:200}

src/test/java/org/breedinginsight/services/BrAPIGermplasmServiceUnitTest.java

@@ -155,6 +155,7 @@ public void getGermplasmListExport() {
         when(programDAO.getProgramBrAPI(any())).thenReturn(brapiProgram);
         when(brAPIDAOUtil.get(any(Function.class),
                 any(GermplasmQueryParams.class))).thenReturn(germplasm);
+        when(brAPIDAOUtil.getBrAPIProgramDbId(any())).thenReturn(brapiProgramDbId);
 
         //Create germplasm cache of stub data
         Method setupMethod = BrAPIGermplasmDAO.class.getDeclaredMethod("setup");