[BI-1606] Allow germplasm records to be in multiple lists

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

@@ -106,10 +106,10 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
     @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
     public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasmListRecords(
         @PathVariable("programId") UUID programId,
-        @PathVariable("listDbId") String listId,
+        @PathVariable("listDbId") String listDbId,
         @QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid GermplasmQuery queryParams) {
         try {
-            List<BrAPIGermplasm> germplasm = germplasmService.getGermplasmByList(programId, listId);
+            List<BrAPIGermplasm> germplasm = germplasmService.getGermplasmByList(programId, listDbId);
             SearchRequest searchRequest = queryParams.constructSearchRequest();
             return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams, searchRequest);
         } catch (Exception e) {

src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java

@@ -18,6 +18,8 @@
 package org.breedinginsight.brapi.v2.constants;
 
 public final class BrAPIAdditionalInfoFields {
+    public static final String GERMPLASM_LIST_ENTRY_NUMBERS = "listEntryNumbers";
+    public static final String GERMPLASM_LIST_ID = "listId";
     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";

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

@@ -9,11 +9,10 @@
 import lombok.extern.slf4j.Slf4j;
 import org.brapi.v2.model.core.BrAPIListSummary;
 import org.brapi.v2.model.core.BrAPIListTypes;
+import org.brapi.v2.model.core.request.BrAPIListNewRequest;
 import org.brapi.v2.model.core.response.BrAPIListDetails;
-import org.brapi.v2.model.core.response.BrAPIListsListResponse;
 import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
 import org.brapi.v2.model.germ.BrAPIGermplasm;
-import org.brapi.v2.model.germ.BrAPIGermplasmSynonyms;
 import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapps.importer.daos.BrAPIListDAO;
 import org.breedinginsight.brapps.importer.model.exports.FileType;
@@ -35,6 +34,7 @@
 import java.time.OffsetDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.*;
+import java.util.function.ToIntFunction;
 import java.util.stream.Collectors;
 
 @Slf4j
@@ -112,18 +112,25 @@ public List<BrAPIListSummary> getGermplasmListsByProgramId(UUID programId, HttpR
         }
     }
 
-    public List<Map<String, Object>> processData(List<BrAPIGermplasm> germplasm){
+    public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm, UUID germplasmListId){
         List<Map<String, Object>> processedData =  new ArrayList<>();
 
         for (BrAPIGermplasm germplasmEntry: germplasm) {
             HashMap<String, Object> row = new HashMap<>();
             row.put("GID", Integer.valueOf(germplasmEntry.getAccessionNumber()));
             row.put("Name", germplasmEntry.getGermplasmName());
-            row.put("Entry No", germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsInt());
             row.put("Breeding Method", germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD).getAsString());
             String source = germplasmEntry.getSeedSource();
             row.put("Source", source);
 
+            // Use the entry number in the list map if generated
+            if(new UUID(0,0).compareTo(germplasmListId) == 0) {
+                row.put("Entry No", germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsInt());
+            } else {
+                row.put("Entry No", germplasmEntry.getAdditionalInfo()
+                        .getAsJsonObject(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ENTRY_NUMBERS).get(germplasmListId.toString()).getAsInt());
+            }
+
             //If germplasm was imported with an external UID, it will be stored in external reference with same source as seed source
             List<BrAPIExternalReference> externalReferences = germplasmEntry.getExternalReferences();
             for (BrAPIExternalReference reference: externalReferences){
@@ -156,17 +163,24 @@ public List<Map<String, Object>> processData(List<BrAPIGermplasm> germplasm){
         return processedData;
     }
 
-    public List<BrAPIGermplasm> getGermplasmByList(UUID programId, String listId) throws ApiException {
+    public List<BrAPIGermplasm> getGermplasmByList(UUID programId, String listDbId) throws ApiException {
         // get list germplasm names
-        BrAPIListsSingleResponse listResponse = brAPIListDAO.getListById(listId, programId);
+        BrAPIListsSingleResponse listResponse = brAPIListDAO.getListById(listDbId, programId);
         if(Objects.nonNull(listResponse) && Objects.nonNull(listResponse.getResult())) {
-            List<String> germplasmNames = listResponse.getResult().getData();
+
+            // get the list ID stored in the list external references
+            UUID listId = getGermplasmListId(listResponse.getResult());
 
             // get list BrAPI germplasm variables
-            return germplasmDAO.getGermplasmByRawName(germplasmNames, programId);
+            List<String> germplasmNames = listResponse.getResult().getData();
+            List<BrAPIGermplasm> germplasm = germplasmDAO.getGermplasmByRawName(germplasmNames, programId);
+
+            // set the list ID in the germplasm additional info
+             germplasm.forEach(g -> g.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ID, listId));
+            return germplasm;
         } else throw new ApiException();
     }
-    public DownloadFile exportGermplasmList(UUID programId, String listId, FileType fileExtension) throws ApiException, IOException {
+    public DownloadFile exportGermplasmList(UUID programId, String listId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException {
         List<Column> columns = GermplasmFileColumns.getOrderedColumns();
 
         //Retrieve germplasm list data
@@ -175,8 +189,10 @@ public DownloadFile exportGermplasmList(UUID programId, String listId, FileType
         //Retrieve germplasm data
         List<String> germplasmNames = listData.getData();
         List<BrAPIGermplasm> germplasm = germplasmDAO.getGermplasmByRawName(germplasmNames, programId);
+
         //processGermplasmForDisplay, numbers
-        germplasm.sort(Comparator.comparingInt(g -> g.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsInt()));
+        UUID germplasmListId = getGermplasmListId(listData);
+        germplasm.sort(Comparator.comparingInt(getEntryNumber(germplasmListId)));
 
         String listName = listData.getListName();
         Optional<Program> optionalProgram = programService.getById(programId);
@@ -187,7 +203,7 @@ public DownloadFile exportGermplasmList(UUID programId, String listId, FileType
         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 =  processData(germplasm);
+        List<Map<String, Object>> processedData =  processListData(germplasm, germplasmListId);
 
         if (fileExtension == FileType.CSV){
             downloadFile = CSVWriter.writeToDownload(columns, processedData, fileExtension);
@@ -198,6 +214,57 @@ public DownloadFile exportGermplasmList(UUID programId, String listId, FileType
         return new DownloadFile(fileName, downloadFile);
     }
 
+    public UUID getGermplasmListId(BrAPIListDetails listData) {
+        if(Objects.nonNull(listData.getExternalReferences()) && hasListExternalReference(listData.getExternalReferences())) {
+            return UUID.fromString(listData.getExternalReferences().stream()
+                    .filter(e -> referenceSource.concat("/lists").equals(e.getReferenceSource()))
+                    .map(e -> e.getReferenceID()).findAny().orElse("00000000-0000-0000-000000000000"));
+        } else {
+            return new UUID(0,0);
+        }
+    }
+
+    public UUID getGermplasmListId(BrAPIListNewRequest importList) {
+        if(Objects.nonNull(importList.getExternalReferences()) && hasListExternalReference(importList.getExternalReferences())) {
+            return UUID.fromString(importList.getExternalReferences().stream()
+                    .filter(e -> referenceSource.concat("/lists").equals(e.getReferenceSource()))
+                    .map(e -> e.getReferenceID()).findAny().orElse("00000000-0000-0000-000000000000"));
+        } else {
+            return new UUID(0,0);
+        }
+    }
+
+    private boolean hasListExternalReference(List<BrAPIExternalReference> refs) throws IllegalArgumentException {
+        if (refs == null) throw new IllegalArgumentException();
+        return refs.stream().anyMatch(e -> referenceSource.concat("/lists").equals(e.getReferenceSource()));
+    }
+
+    private ToIntFunction<BrAPIGermplasm> getEntryNumber(UUID germplasmListId) throws IllegalArgumentException {
+        if(germplasmListId.compareTo(new UUID(0,0)) == 0) {
+            return this::getImportEntryNumber;
+        } else {
+            return g -> getGermplasmListEntryNumber(g, germplasmListId);
+        }
+    }
+
+    private Integer getImportEntryNumber(BrAPIGermplasm g) throws IllegalArgumentException {
+        if(Objects.nonNull(g.getAdditionalInfo()) &&
+                g.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER)) {
+            return g.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsInt();
+        } else {
+            throw new IllegalArgumentException();
+        }
+    }
+    private Integer getGermplasmListEntryNumber(BrAPIGermplasm g, UUID germplasmListId) throws IllegalArgumentException {
+        if(Objects.nonNull(g.getAdditionalInfo()) &&
+                g.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ENTRY_NUMBERS)) {
+            return g.getAdditionalInfo().getAsJsonObject(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ENTRY_NUMBERS)
+                .get(germplasmListId.toString()).getAsInt();
+        } else {
+            throw new IllegalArgumentException();
+        }
+    }
+
     private String createFileName(BrAPIListDetails listData, String listName) {
         //TODO change timestamp to edit date when editing functionality is added
         String timestamp;

src/main/java/org/breedinginsight/brapps/importer/model/base/Germplasm.java

@@ -27,6 +27,7 @@
 import org.brapi.v2.model.germ.BrAPIGermplasmSynonyms;
 import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapps.importer.model.config.*;
+import org.breedinginsight.dao.db.tables.pojos.BreedingMethodEntity;
 import org.breedinginsight.dao.db.tables.pojos.ProgramBreedingMethodEntity;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.model.User;
@@ -131,25 +132,29 @@ public BrAPIListNewRequest constructBrAPIList(Program program, String referenceS
         brapiList.setListName(constructGermplasmListName(listName, program));
         brapiList.setListDescription(this.listDescription);
         brapiList.listType(BrAPIListTypes.GERMPLASM);
-        // Set external reference
-        BrAPIExternalReference reference = new BrAPIExternalReference();
-        reference.setReferenceSource(String.format("%s/programs", referenceSource));
-        reference.setReferenceID(program.getId().toString());
-        brapiList.setExternalReferences(List.of(reference));
+
+        // Set external references
+        BrAPIExternalReference programReference = new BrAPIExternalReference();
+        programReference.setReferenceSource(String.format("%s/programs", referenceSource));
+        programReference.setReferenceID(program.getId().toString());
+        BrAPIExternalReference listReference = new BrAPIExternalReference();
+        listReference.setReferenceSource(String.format("%s/lists", referenceSource));
+        listReference.setReferenceID(UUID.randomUUID().toString());
+        brapiList.setExternalReferences(List.of(programReference, listReference));
+
         return brapiList;
     }
 
     public static String constructGermplasmListName(String listName, Program program) {
         return String.format("%s [%s-germplasm]", listName, program.getKey());
     }
 
-    private BrAPIGermplasm constructBrAPIGermplasm(ProgramBreedingMethodEntity breedingMethod, User user) {
+    public BrAPIGermplasm constructBrAPIGermplasm(ProgramBreedingMethodEntity breedingMethod, User user, UUID listId) {
         BrAPIGermplasm germplasm = new BrAPIGermplasm();
         germplasm.setGermplasmName(getGermplasmName());
         germplasm.setDefaultDisplayName(getGermplasmName());
         germplasm.setGermplasmPUI(getGermplasmPUI());
         germplasm.setCollection(getCollection());
-        germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER, entryNo);
         germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID, getFemaleParentDBID());
         germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, getMaleParentDBID());
         germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_ENTRY_NO, getFemaleParentEntryNo());
@@ -158,6 +163,9 @@ private BrAPIGermplasm constructBrAPIGermplasm(ProgramBreedingMethodEntity breed
         createdBy.put(BrAPIAdditionalInfoFields.CREATED_BY_USER_ID, user.getId().toString());
         createdBy.put(BrAPIAdditionalInfoFields.CREATED_BY_USER_NAME, user.getName());
         germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.CREATED_BY, createdBy);
+        Map<UUID, String> listEntryNumbers = new HashMap<>();
+        listEntryNumbers.put(listId, entryNo);
+        germplasm.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ENTRY_NUMBERS, listEntryNumbers);
         //TODO: Need to check that the acquisition date it in date format
         //brAPIGermplasm.setAcquisitionDate(pedigreeImport.getGermplasm().getAcquisitionDate());
         germplasm.setCountryOfOriginCode(getCountryOfOrigin());
@@ -246,8 +254,8 @@ private void setBrAPIGermplasmCommitFields(BrAPIGermplasm germplasm, String prog
         }
     }
 
-    public BrAPIGermplasm constructBrAPIGermplasm(Program program, ProgramBreedingMethodEntity breedingMethod, User user, boolean commit, String referenceSource, Supplier<BigInteger> nextVal) {
-        BrAPIGermplasm germplasm = constructBrAPIGermplasm(breedingMethod, user);
+    public BrAPIGermplasm constructBrAPIGermplasm(Program program, ProgramBreedingMethodEntity breedingMethod, User user, boolean commit, String referenceSource, Supplier<BigInteger> nextVal, UUID listId) {
+        BrAPIGermplasm germplasm = constructBrAPIGermplasm(breedingMethod, user, listId);
         if (commit) {
             setBrAPIGermplasmCommitFields(germplasm, program.getKey(), referenceSource, nextVal);
         }
@@ -261,4 +269,4 @@ public BrAPIGermplasm constructBrAPIGermplasm(Program program, ProgramBreedingMe
 
         return germplasm;
     }
-}
+}

src/main/java/org/breedinginsight/brapps/importer/services/processors/GermplasmProcessor.java

@@ -273,7 +273,9 @@ public Map<String, ImportPreviewStatistics> process(List<BrAPIImport> importRows
                 entryNumberCounts.put(germplasm.getEntryNo(),
                                       entryNumberCounts.containsKey(germplasm.getEntryNo()) ? entryNumberCounts.get(germplasm.getEntryNo()) + 1 : 1);
 
-                BrAPIGermplasm newGermplasm = germplasm.constructBrAPIGermplasm(program, breedingMethod, user, commit, BRAPI_REFERENCE_SOURCE, nextVal);
+                UUID importListId = brAPIGermplasmService.getGermplasmListId(importList);
+
+                BrAPIGermplasm newGermplasm = germplasm.constructBrAPIGermplasm(program, breedingMethod, user, commit, BRAPI_REFERENCE_SOURCE, nextVal, importListId);
 
                 newGermplasmList.add(newGermplasm);
                 // Assign status of the germplasm

src/main/java/org/breedinginsight/utilities/response/mappers/GermplasmQueryMapper.java

@@ -2,6 +2,7 @@
 
 import com.google.gson.JsonObject;
 import lombok.Getter;
+import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
 import org.brapi.v2.model.germ.BrAPIGermplasm;
 import org.breedinginsight.api.v1.controller.metadata.SortOrder;
 import org.breedinginsight.brapi.v1.model.ObservationVariable;
@@ -24,10 +25,24 @@ public class GermplasmQueryMapper extends AbstractQueryMapper {
 
     public GermplasmQueryMapper() {
         fields = Map.ofEntries(
-                Map.entry("importEntryNumber", (germplasm) ->
-                        germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER) ?
-                        germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsString() :
-                        null),
+                Map.entry("importEntryNumber", (germplasm) ->{
+                    String entryNumber = null;
+                        if (germplasm.getAdditionalInfo() != null) {
+                            // if additionalInfo contains the importEntryNumber key then return the value
+                            if (germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER)) {
+                                entryNumber = germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsString();
+                            }
+
+                            // if additionalInfo has both listEntryNumbers and listId keys then return the entry number
+                            // mapped to the listId
+                            if (germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ENTRY_NUMBERS)
+                                && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ID)) {
+                                String listId = germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ID).getAsString();
+                                entryNumber = germplasm.getAdditionalInfo().getAsJsonObject(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ENTRY_NUMBERS).get(listId).getAsString();
+                            }
+                        }
+                    return entryNumber;
+                }),
                 Map.entry("accessionNumber", BrAPIGermplasm::getAccessionNumber),
                 Map.entry("defaultDisplayName", BrAPIGermplasm::getDefaultDisplayName),
                 Map.entry("breedingMethod", (germplasm) ->