[BI-1191] Germplasm Search

src/main/java/org/breedinginsight/api/model/v1/request/query/SearchRequest.java

@@ -26,6 +26,8 @@
 @Getter
 @Setter
 @Introspected
+@AllArgsConstructor
+@NoArgsConstructor
 public class SearchRequest {
     private List<FilterRequest> filters = new ArrayList<>();
 }

src/main/java/org/breedinginsight/brapi/v1/model/request/query/BrapiQuery.java

@@ -20,6 +20,7 @@
 import lombok.Getter;
 import lombok.NoArgsConstructor;
 import lombok.Setter;
+import org.breedinginsight.api.model.v1.request.query.FilterRequest;
 import org.breedinginsight.api.model.v1.request.query.PaginationParams;
 import org.breedinginsight.api.v1.controller.metadata.SortOrder;
 
@@ -50,4 +51,11 @@ public Integer getDefaultPage() {
     public Integer getDefaultPageSize() {
         return DEFAULT_PAGE_SIZE;
     }
+
+    protected FilterRequest constructFilterRequest(String field, String value) {
+        return FilterRequest.builder()
+                .field(field)
+                .value(value)
+                .build();
+    }
 }

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

@@ -14,11 +14,14 @@
 import org.brapi.v2.model.germ.BrAPIGermplasm;
 import org.breedinginsight.api.auth.ProgramSecured;
 import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
+import org.breedinginsight.api.model.v1.request.query.SearchRequest;
 import org.breedinginsight.api.model.v1.response.DataResponse;
 import org.breedinginsight.api.model.v1.response.Response;
 import org.breedinginsight.api.model.v1.validators.QueryValid;
+import org.breedinginsight.api.model.v1.validators.SearchValid;
 import org.breedinginsight.brapi.v1.controller.BrapiVersion;
 import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
+import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
 import org.breedinginsight.brapi.v2.model.response.mappers.GermplasmQueryMapper;
 import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
 import org.breedinginsight.brapps.importer.model.exports.FileType;
@@ -46,18 +49,39 @@ public GermplasmController(BrAPIGermplasmService germplasmService, GermplasmQuer
         this.germplasmQueryMapper = germplasmQueryMapper;
     }
 
+    @Post("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/search/germplasm{?queryParams*}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> searchGermplasm(
+            @PathVariable("programId") UUID programId,
+            @QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid BrapiQuery queryParams,
+            @Body @SearchValid(using = GermplasmQueryMapper.class) SearchRequest searchRequest) {
+        try {
+            log.debug("fetching germ for program: " + programId);
+            List<BrAPIGermplasm> germplasm = germplasmService.getGermplasm(programId);
+            queryParams.setSortField(germplasmQueryMapper.getDefaultSortField());
+            queryParams.setSortOrder(germplasmQueryMapper.getDefaultSortOrder());
+            return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams, searchRequest);
+        } catch (ApiException e) {
+            log.info(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving germplasm");
+        }
+    }
+
     @Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/germplasm{?queryParams*}")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
     public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
             @PathVariable("programId") UUID programId,
-            @QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid BrapiQuery queryParams) {
+            @QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid GermplasmQuery queryParams) {
         try {
             log.debug("fetching germ for program: " + programId);
+
             List<BrAPIGermplasm> germplasm = germplasmService.getGermplasm(programId);
             queryParams.setSortField(germplasmQueryMapper.getDefaultSortField());
             queryParams.setSortOrder(germplasmQueryMapper.getDefaultSortOrder());
-            return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams);
+            SearchRequest searchRequest = queryParams.constructSearchRequest();
+            return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams, searchRequest);
         } catch (ApiException e) {
             log.info(e.getMessage(), e);
             return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving germplasm");

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

@@ -21,4 +21,15 @@ public final class BrAPIAdditionalInfoFields {
     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";
+    public static final String GERMPLASM_IMPORT_ENTRY_NUMBER = "importEntryNumber";
+    public static final String GERMPLASM_FEMALE_PARENT_GID = "femaleParentGid";
+    public static final String GERMPLASM_MALE_PARENT_GID = "maleParentGid";
+    public static final String GERMPLASM_FEMALE_PARENT_ENTRY_NO = "femaleParentEntryNo";
+    public static final String GERMPLASM_MALE_PARENT_ENTRY_NO = "maleParentEntryNo";
+    public static final String CREATED_BY = "createdBy";
+    public static final String CREATED_BY_USER_ID = "userId";
+    public static final String CREATED_BY_USER_NAME = "userName";
+    public static final String GERMPLASM_BREEDING_METHOD_ID = "breedingMethodId";
+    public static final String GERMPLASM_BREEDING_METHOD = "breedingMethod";
+    public static final String CREATED_DATE = "createdDate";
 }

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

@@ -49,8 +49,6 @@
 @Context
 public class BrAPIGermplasmDAO {
 
-    private final String BREEDING_METHOD_ID_KEY = "breedingMethodId";
-
     private final ProgramDAO programDAO;
     private final ImportDAO importDAO;
 
@@ -143,8 +141,8 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
             programGermplasmByFullName.put(germplasm.getGermplasmName(), germplasm);
 
             JsonObject additionalInfo = germplasm.getAdditionalInfo();
-            if (additionalInfo != null && additionalInfo.has(BREEDING_METHOD_ID_KEY)) {
-                germplasm.setBreedingMethodDbId(additionalInfo.get(BREEDING_METHOD_ID_KEY).getAsString());
+            if (additionalInfo != null && additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD_ID)) {
+                germplasm.setBreedingMethodDbId(additionalInfo.get(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD_ID).getAsString());
             }
 
             if (germplasm.getDefaultDisplayName() != null) {
@@ -175,20 +173,24 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
                 List<String> parents = Arrays.asList(germplasm.getPedigree().split("/"));
                 if (parents.size() >= 1) {
                     if (programGermplasmByFullName.containsKey(parents.get(0))) {
-                        newPedigreeString = programGermplasmByFullName.get(parents.get(0)).getAccessionNumber();
+                        String femaleParentAccessionNumber = programGermplasmByFullName.get(parents.get(0)).getAccessionNumber();
+                        newPedigreeString = femaleParentAccessionNumber;
                         namePedigreeString = programGermplasmByFullName.get(parents.get(0)).getDefaultDisplayName();
                         uuidPedigreeString = programGermplasmByFullName.get(parents.get(0)).getExternalReferences().
                                 stream().filter(ref -> ref.getReferenceSource().equals(referenceSource)).
                                 map(ref -> ref.getReferenceID()).findFirst().orElse("");
+                        additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID, femaleParentAccessionNumber);
                     }
                 }
                 if (parents.size() == 2) {
                     if (programGermplasmByFullName.containsKey(parents.get(1))) {
-                        newPedigreeString += "/" + programGermplasmByFullName.get(parents.get(1)).getAccessionNumber();
+                        String maleParentAccessionNumber = programGermplasmByFullName.get(parents.get(1)).getAccessionNumber();
+                        newPedigreeString += "/" + maleParentAccessionNumber;
                         namePedigreeString += "/" + programGermplasmByFullName.get(parents.get(1)).getDefaultDisplayName();
                         uuidPedigreeString += "/" + programGermplasmByFullName.get(parents.get(1)).getExternalReferences().
                                 stream().filter(ref -> ref.getReferenceSource().equals(referenceSource)).
                                 map(ref -> ref.getReferenceID()).findFirst().orElse("");
+                        additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParentAccessionNumber);
                     }
                 }
                 //For use in individual germplasm display

src/main/java/org/breedinginsight/brapi/v2/model/request/query/GermplasmQuery.java

@@ -0,0 +1,39 @@
+package org.breedinginsight.brapi.v2.model.request.query;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.Getter;
+import org.breedinginsight.api.model.v1.request.query.FilterRequest;
+import org.breedinginsight.api.model.v1.request.query.SearchRequest;
+import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
+import org.jooq.tools.StringUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Getter
+@Introspected
+public class GermplasmQuery extends BrapiQuery {
+    private String accessionNumber;
+    private String defaultDisplayName;
+    private String breedingMethod;
+    private String seedSource;
+    private String femaleParentGID;
+    private String maleParentGID;
+    private String createdDate;
+    private String createdByUserName;
+    private String synonym;
+
+    public SearchRequest constructSearchRequest() {
+        List<FilterRequest> filters = new ArrayList<>();
+        if (!StringUtils.isBlank(getAccessionNumber())) filters.add(constructFilterRequest("accessionNumber", getAccessionNumber()));
+        if (!StringUtils.isBlank(getDefaultDisplayName())) filters.add(constructFilterRequest("defaultDisplayName", getDefaultDisplayName()));
+        if (!StringUtils.isBlank(getBreedingMethod())) filters.add(constructFilterRequest("breedingMethod", getBreedingMethod()));
+        if (!StringUtils.isBlank(getSeedSource())) filters.add(constructFilterRequest("seedSource", getSeedSource()));
+        if (!StringUtils.isBlank(getFemaleParentGID())) filters.add(constructFilterRequest("femaleParentGID", getFemaleParentGID()));
+        if (!StringUtils.isBlank(getMaleParentGID())) filters.add(constructFilterRequest("maleParentGID", getMaleParentGID()));
+        if (!StringUtils.isBlank(getCreatedDate())) filters.add(constructFilterRequest("createdDate", getCreatedDate()));
+        if (!StringUtils.isBlank(getCreatedByUserName())) filters.add(constructFilterRequest("createdByUserName", getCreatedByUserName()));
+        if (!StringUtils.isBlank(getSynonym())) filters.add(constructFilterRequest("synonym", getSynonym()));
+        return new SearchRequest(filters);
+    }
+}

src/main/java/org/breedinginsight/brapi/v2/model/response/mappers/GermplasmQueryMapper.java

@@ -4,11 +4,13 @@
 import org.brapi.v2.model.germ.BrAPIGermplasm;
 import org.breedinginsight.api.v1.controller.metadata.SortOrder;
 import org.breedinginsight.brapi.v1.model.ObservationVariable;
+import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.utilities.response.mappers.AbstractQueryMapper;
 
 import javax.inject.Singleton;
 import java.util.Map;
 import java.util.function.Function;
+import java.util.stream.Collectors;
 
 @Getter
 @Singleton
@@ -21,7 +23,35 @@ public class GermplasmQueryMapper extends AbstractQueryMapper {
 
     public GermplasmQueryMapper() {
         fields = Map.ofEntries(
-                Map.entry("accessionNumber", BrAPIGermplasm::getAccessionNumber)
+                Map.entry("accessionNumber", BrAPIGermplasm::getAccessionNumber),
+                Map.entry("defaultDisplayName", BrAPIGermplasm::getDefaultDisplayName),
+                Map.entry("breedingMethod", (germplasm) ->
+                        germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD) ?
+                                germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD).getAsString() :
+                                null),
+                Map.entry("seedSource", BrAPIGermplasm::getSeedSource),
+                Map.entry("femaleParentGID", (germplasm) ->
+                        germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID) ?
+                                germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID).getAsString() :
+                                null),
+                Map.entry("maleParentGID", (germplasm) ->
+                        germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID) ?
+                                germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID).getAsString() :
+                                null),
+                Map.entry("createdDate", (germplasm) ->
+                        germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.CREATED_DATE) ?
+                                germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.CREATED_DATE).getAsString() :
+                                null),
+                Map.entry("createdByUserName", (germplasm) ->
+                        germplasm.getAdditionalInfo() != null
+                                && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.CREATED_BY)
+                                && germplasm.getAdditionalInfo().getAsJsonObject(BrAPIAdditionalInfoFields.CREATED_BY).has(BrAPIAdditionalInfoFields.CREATED_BY_USER_NAME) ?
+                                germplasm.getAdditionalInfo().getAsJsonObject(BrAPIAdditionalInfoFields.CREATED_BY).get(BrAPIAdditionalInfoFields.CREATED_BY_USER_NAME).getAsString() :
+                                null),
+                Map.entry("synonyms", (germplasm) ->
+                        germplasm.getSynonyms() != null ?
+                                germplasm.getSynonyms().stream().map((synonym) -> synonym.getSynonym())
+                                .collect(Collectors.toList()) : null)
         );
     }
 

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

@@ -13,6 +13,7 @@
 import org.brapi.v2.model.core.response.BrAPIListsListResponse;
 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;
 import org.breedinginsight.model.Column;
@@ -109,8 +110,8 @@ public List<Map<String, Object>> processData(List<BrAPIGermplasm> 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("importEntryNumber").getAsInt());
-            row.put("Breeding Method", germplasmEntry.getAdditionalInfo().get("breedingMethod").getAsString());
+            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);
 
@@ -152,7 +153,7 @@ public DownloadFile exportGermplasmList(UUID programId, String listId, FileType
         List<String> germplasmNames = listData.getData();
         List<BrAPIGermplasm> germplasm = germplasmDAO.getGermplasmByRawName(germplasmNames, programId);
         //processGermplasmForDisplay, numbers
-        germplasm.sort(Comparator.comparingInt(g -> g.getAdditionalInfo().get("importEntryNumber").getAsInt()));
+        germplasm.sort(Comparator.comparingInt(g -> g.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER).getAsInt()));
 
         String listName = listData.getListName();
         Optional<Program> optionalProgram = programService.getById(programId);