BI-2372 Create Deltabreed List Controller

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

@@ -1,5 +1,6 @@
 package org.breedinginsight.brapi.v2;
 
+import com.drew.lang.annotations.Nullable;
 import io.micronaut.context.annotation.Property;
 import io.micronaut.http.HttpHeaders;
 import io.micronaut.http.HttpResponse;
@@ -19,10 +20,11 @@
 import org.brapi.v2.model.BrAPIIndexPagination;
 import org.brapi.v2.model.BrAPIMetadata;
 import org.brapi.v2.model.BrAPIStatus;
-import org.brapi.v2.model.core.BrAPITrial;
 import org.brapi.v2.model.germ.*;
 import org.brapi.v2.model.germ.request.BrAPIGermplasmSearchRequest;
-import org.brapi.v2.model.germ.response.*;
+import org.brapi.v2.model.germ.response.BrAPIGermplasmListResponse;
+import org.brapi.v2.model.germ.response.BrAPIGermplasmPedigreeResponse;
+import org.brapi.v2.model.germ.response.BrAPIGermplasmProgenyResponse;
 import org.breedinginsight.api.auth.ProgramSecured;
 import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
 import org.breedinginsight.api.model.v1.request.query.SearchRequest;
@@ -33,27 +35,25 @@
 import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
 import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
-import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
-import org.breedinginsight.model.Program;
-import org.breedinginsight.services.ProgramService;
-import org.breedinginsight.utilities.Utilities;
-import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper;
 import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
 import org.breedinginsight.brapps.importer.model.exports.FileType;
 import org.breedinginsight.daos.ProgramDAO;
 import org.breedinginsight.model.DownloadFile;
 import org.breedinginsight.model.GermplasmGenotype;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
 import org.breedinginsight.services.exceptions.AuthorizationException;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.services.geno.GenotypeService;
+import org.breedinginsight.utilities.Utilities;
 import org.breedinginsight.utilities.response.ResponseUtils;
+import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper;
 
 import javax.inject.Inject;
 import javax.validation.Valid;
 import java.util.*;
 import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 
 @Slf4j
 @Controller("/${micronaut.bi.api.version}")
@@ -209,7 +209,8 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
                 germplasmQueryMapper.setDateDisplayFormat(dateFormatParam);
             }
 
-            List<BrAPIGermplasm> germplasm = germplasmService.getGermplasm(programId);
+            // Fetch all germplasm in the program unless a list id is supplied to return only germplasm in that collection
+            List<BrAPIGermplasm> germplasm = queryParams.getListDbId() == null ? germplasmService.getGermplasm(programId) : germplasmService.getGermplasmByList(programId, queryParams.getListDbId());
             SearchRequest searchRequest = queryParams.constructSearchRequest();
             return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams, searchRequest);
         } catch (ApiException e) {
@@ -221,52 +222,17 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
         }
     }
 
-    @Get("/programs/{programId}/germplasm/lists/{listDbId}/records{?queryParams*}")
-    @Produces(MediaType.APPLICATION_JSON)
-    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
-    public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasmListRecords(
-        @PathVariable("programId") UUID programId,
-        @PathVariable("listDbId") String listDbId,
-        @QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid GermplasmQuery queryParams) {
-        try {
-            List<BrAPIGermplasm> germplasm = germplasmService.getGermplasmByList(programId, listDbId);
-            SearchRequest searchRequest = queryParams.constructSearchRequest();
-            return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams, searchRequest);
-        } catch (Exception e) {
-            log.info(e.getMessage(), e);
-            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving germplasm list records");
-        }
-    }
-
-    @Get("/programs/{programId}/germplasm/lists/{listDbId}/export{?fileExtension}")
-    @Produces(value = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
-    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
-    public HttpResponse<StreamedFile> germplasmListExport(
-            @PathVariable("programId") UUID programId, @PathVariable("listDbId") String listDbId, @QueryValue(defaultValue = "XLSX") String fileExtension) {
-        String downloadErrorMessage = "An error occurred while generating the download file. Contact the development team at bidevteam@cornell.edu.";
-        try {
-            FileType extension = Enum.valueOf(FileType.class, fileExtension);
-            DownloadFile germplasmListFile = germplasmService.exportGermplasmList(programId, listDbId, extension);
-            HttpResponse<StreamedFile> germplasmListExport = HttpResponse.ok(germplasmListFile.getStreamedFile()).header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename="+germplasmListFile.getFileName()+extension.getExtension());
-            return germplasmListExport;
-        }
-        catch (Exception e) {
-            log.info(e.getMessage(), e);
-            e.printStackTrace();
-            HttpResponse response = HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, downloadErrorMessage).contentType(MediaType.TEXT_PLAIN).body(downloadErrorMessage);
-            return response;
-        }
-    }
-
-    @Get("/programs/{programId}/germplasm/export{?fileExtension}")
+    @Get("/programs/{programId}/germplasm/export{?fileExtension,list}")
     @Produces(value = "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
     @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
     public HttpResponse<StreamedFile> germplasmExport(
-            @PathVariable("programId") UUID programId, @QueryValue(defaultValue = "XLSX") String fileExtension) {
+            @PathVariable("programId") UUID programId,
+            @QueryValue(defaultValue = "XLSX") String fileExtension,
+            @QueryValue Optional<String> list) {
         String downloadErrorMessage = "An error occurred while generating the download file. Contact the development team at bidevteam@cornell.edu.";
         try {
             FileType extension = Enum.valueOf(FileType.class, fileExtension);
-            DownloadFile germplasmListFile = germplasmService.exportGermplasm(programId, extension);
+            DownloadFile germplasmListFile = list.isEmpty() ? germplasmService.exportGermplasm(programId, extension) : germplasmService.exportGermplasmList(programId, list.get(), extension);
             HttpResponse<StreamedFile> germplasmExport = HttpResponse.ok(germplasmListFile.getStreamedFile()).header(HttpHeaders.CONTENT_DISPOSITION, "attachment;filename="+germplasmListFile.getFileName()+extension.getExtension());
             return germplasmExport;
         }

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

@@ -1,29 +1,15 @@
-/*
- * See the NOTICE file distributed with this work for additional information
- * regarding copyright ownership.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
 package org.breedinginsight.brapi.v2;
 
+import io.micronaut.http.HttpRequest;
 import io.micronaut.http.HttpResponse;
 import io.micronaut.http.HttpStatus;
 import io.micronaut.http.MediaType;
 import io.micronaut.http.annotation.*;
 import io.micronaut.security.annotation.Secured;
 import io.micronaut.security.rules.SecurityRule;
+import io.reactivex.rxjava3.core.Single;
 import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.lang3.tuple.Pair;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.v2.model.core.BrAPIListSummary;
 import org.brapi.v2.model.core.BrAPIListTypes;
@@ -41,31 +27,35 @@
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.utilities.response.ResponseUtils;
 import org.breedinginsight.utilities.response.mappers.ListQueryMapper;
+import reactor.core.publisher.Mono;
+import reactor.util.function.Tuples;
 
 import javax.inject.Inject;
 import javax.validation.Valid;
+import javax.validation.Validator;
 import java.util.List;
+import java.util.Optional;
 import java.util.UUID;
 
 @Slf4j
-@Controller
+@Controller("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2)
 @Secured(SecurityRule.IS_AUTHENTICATED)
 public class BrAPIListController {
-
     private final ProgramService programService;
-    private final BrAPIListService listService;
+    private final BrAPIListService brapiListService;
     private final ListQueryMapper listQueryMapper;
+    private final Validator validator;
 
     @Inject
-    public BrAPIListController(ProgramService programService, BrAPIListService listService,
-                               ListQueryMapper listQueryMapper) {
+    public BrAPIListController(ProgramService programService, BrAPIListService brapiListService,
+                               ListQueryMapper listQueryMapper, Validator validator) {
         this.programService = programService;
-        this.listService = listService;
+        this.brapiListService = brapiListService;
         this.listQueryMapper = listQueryMapper;
+        this.validator = validator;
     }
 
-    //@Get(BrapiVersion.BRAPI_V2 + "/lists")
-    @Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/lists{?queryParams*}")
+    @Get("/lists{?queryParams*}")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
     public HttpResponse<Response<DataResponse<Object>>> getLists(
@@ -77,7 +67,6 @@ public HttpResponse<Response<DataResponse<Object>>> getLists(
                     .getById(programId)
                     .orElseThrow(() -> new DoesNotExistException("Program does not exist"));
 
-            // get germplasm lists by default
             BrAPIListTypes type = BrAPIListTypes.fromValue(queryParams.getListType());
             String source = null;
             String id = null;
@@ -93,7 +82,7 @@ public HttpResponse<Response<DataResponse<Object>>> getLists(
             if (dateFormatParam != null) {
                 listQueryMapper.setDateDisplayFormat(dateFormatParam);
             }
-            List<BrAPIListSummary> brapiLists = listService.getListSummariesByTypeAndXref(type, source, id, program);
+            List<BrAPIListSummary> brapiLists = brapiListService.getListSummariesByTypeAndXref(type, source, id, program);
             SearchRequest searchRequest = queryParams.constructSearchRequest();
 
             return ResponseUtils.getBrapiQueryResponse(brapiLists, listQueryMapper, queryParams, searchRequest);
@@ -105,4 +94,25 @@ public HttpResponse<Response<DataResponse<Object>>> getLists(
             throw new RuntimeException(e);
         }
     }
+
+    @Delete("/lists/{listDbId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
+    public HttpResponse deleteListById(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("listDbId") String listDbId,
+            HttpRequest<Void> request
+    ) {
+        boolean hardDelete = false;
+        if (request.getParameters().contains("hardDelete")) {
+            String paramValue = request.getParameters().get("hardDelete");
+            hardDelete = "true".equals(paramValue);
+        }
+        try {
+            return brapiListService.deleteBrAPIList(listDbId, programId, hardDelete);
+        } catch (Exception e) {
+            log.info(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error deleting germplasm list");
+        }
+    }
 }

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

@@ -17,10 +17,15 @@
 
 package org.breedinginsight.brapi.v2.dao;
 
+import io.micronaut.http.HttpResponse;
+import io.micronaut.http.HttpStatus;
+import io.micronaut.http.exceptions.HttpStatusException;
 import lombok.extern.slf4j.Slf4j;
+import okhttp3.HttpUrl;
+import okhttp3.OkHttpClient;
+import okhttp3.Request;
 import org.brapi.client.v2.ApiResponse;
 import org.brapi.client.v2.model.exceptions.ApiException;
-import org.brapi.client.v2.model.queryParams.core.ListQueryParams;
 import org.brapi.client.v2.modules.core.ListsApi;
 import org.brapi.v2.model.BrAPIExternalReference;
 import org.brapi.v2.model.BrAPIResponse;
@@ -29,21 +34,31 @@
 import org.brapi.v2.model.core.BrAPIListTypes;
 import org.brapi.v2.model.core.request.BrAPIListNewRequest;
 import org.brapi.v2.model.core.request.BrAPIListSearchRequest;
-import org.brapi.v2.model.core.response.*;
-import org.brapi.v2.model.pheno.BrAPIObservation;
+import org.brapi.v2.model.core.response.BrAPIListDetails;
+import org.brapi.v2.model.core.response.BrAPIListsListResponse;
+import org.brapi.v2.model.core.response.BrAPIListsListResponseResult;
+import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
+import org.breedinginsight.api.model.v1.response.DataResponse;
+import org.breedinginsight.api.model.v1.response.Response;
+import org.breedinginsight.brapi.v1.controller.BrapiVersion;
 import org.breedinginsight.brapps.importer.daos.ImportDAO;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.daos.ProgramDAO;
+import org.breedinginsight.model.ProgramBrAPIEndpoints;
+import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
+import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.utilities.BrAPIDAOUtil;
 import org.breedinginsight.utilities.Utilities;
 
 import javax.inject.Inject;
 import javax.validation.constraints.NotNull;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.UUID;
+import java.util.concurrent.TimeUnit;
 
 @Slf4j
 public class BrAPIListDAO {
@@ -54,7 +69,10 @@ public class BrAPIListDAO {
     private final BrAPIEndpointProvider brAPIEndpointProvider;
 
     @Inject
-    public BrAPIListDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil brAPIDAOUtil, BrAPIEndpointProvider brAPIEndpointProvider) {
+    public BrAPIListDAO(ProgramDAO programDAO,
+                        ImportDAO importDAO,
+                        BrAPIDAOUtil brAPIDAOUtil,
+                        BrAPIEndpointProvider brAPIEndpointProvider) {
         this.programDAO = programDAO;
         this.importDAO = importDAO;
         this.brAPIDAOUtil = brAPIDAOUtil;
@@ -196,4 +214,19 @@ public List<BrAPIListSummary> createBrAPILists(List<BrAPIListNewRequest> brapiLi
 
         throw new ApiException("No response after creating list");
     }
+
+    public HttpResponse<String> deleteBrAPIList(String listDbId, UUID programId, boolean hardDelete) throws ApiException {
+        // TODO: Switch to using the ListsApi from the BrAPI client library once the delete endpoints from BI-2397 are merged.
+        var programBrAPIBaseUrl = brAPIDAOUtil.getProgramBrAPIBaseUrl(programId);
+        var requestUrl = HttpUrl.parse(programBrAPIBaseUrl + "/lists/" + listDbId).newBuilder();
+        requestUrl.addQueryParameter("hardDelete", Boolean.toString(hardDelete));
+        HttpUrl url = requestUrl.build();
+        var brapiRequest = new Request.Builder().url(url)
+                .method("DELETE", null)
+                .addHeader("Content-Type", "application/json")
+                .build();
+
+        return brAPIDAOUtil.makeCall(brapiRequest);
+    }
+
 }

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

@@ -27,6 +27,9 @@ public class GermplasmQuery extends BrapiQuery {
     // This is a meta-parameter, it describes the display format of any date fields.
     private String dateDisplayFormat;
 
+    // The list id used to get a collection of germplasm
+    private String listDbId;
+
     public SearchRequest constructSearchRequest() {
         List<FilterRequest> filters = new ArrayList<>();
         if (!StringUtils.isBlank(getImportEntryNumber())) {