[BI-1086] - Germplasm lists table

src/main/java/org/breedinginsight/brapi/v2/BrAPIV2Controller.java

@@ -27,13 +27,17 @@
 import io.micronaut.security.rules.SecurityRule;
 import lombok.extern.slf4j.Slf4j;
 import okhttp3.*;
+import org.brapi.client.v2.JSON;
+import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.v2.model.core.BrAPIServerInfo;
+import org.brapi.v2.model.core.response.BrAPIListsListResponse;
 import org.brapi.v2.model.core.response.BrAPIServerInfoResponse;
 import org.breedinginsight.api.auth.AuthenticatedUser;
 import org.breedinginsight.api.auth.ProgramSecured;
 import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
 import org.breedinginsight.api.auth.SecurityService;
 import org.breedinginsight.brapi.v1.controller.BrapiVersion;
+import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
 import org.breedinginsight.model.ProgramBrAPIEndpoints;
 import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
@@ -51,11 +55,13 @@ public class BrAPIV2Controller {
 
     private final SecurityService securityService;
     private final ProgramService programService;
+    private final BrAPIGermplasmService germplasmService;
 
     @Inject
-    public BrAPIV2Controller(SecurityService securityService, ProgramService programService) {
+    public BrAPIV2Controller(SecurityService securityService, ProgramService programService, BrAPIGermplasmService germplasmService) {
         this.securityService = securityService;
         this.programService = programService;
+        this.germplasmService = germplasmService;
     }
 
 
@@ -72,6 +78,17 @@ public BrAPIServerInfoResponse serverinfo() {
         return new BrAPIServerInfoResponse().result(serverInfo);
     }
 
+    //@Get(BrapiVersion.BRAPI_V2 + "/lists")
+    @Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/lists")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse getLists(@PathVariable("programId") UUID programId, HttpRequest<String> request) throws DoesNotExistException, ApiException {
+        BrAPIListsListResponse response = germplasmService.getGermplasmListsByProgramId(programId, request);
+
+        String respBody = new JSON().getGson().toJson(response);
+        return HttpResponse.ok(respBody);
+    }
+
     @Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/{+path}")
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})

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

@@ -2,13 +2,20 @@
 
 import com.google.gson.JsonObject;
 import io.micronaut.context.annotation.Property;
+import io.micronaut.http.HttpRequest;
 import io.micronaut.http.server.exceptions.InternalServerException;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.client.v2.modules.germplasm.GermplasmApi;
+import org.brapi.v2.model.core.BrAPIListTypes;
+import org.brapi.v2.model.core.response.BrAPIListsListResponse;
 import org.brapi.v2.model.germ.BrAPIGermplasm;
 import org.brapi.v2.model.germ.request.BrAPIGermplasmSearchRequest;
+import org.breedinginsight.brapps.importer.daos.BrAPIListDAO;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.brapi.BrAPIClientType;
 import org.breedinginsight.services.brapi.BrAPIProvider;
+import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.utilities.BrAPIDAOUtil;
 
 import javax.inject.Inject;
@@ -23,10 +30,14 @@ public class BrAPIGermplasmService {
     private String referenceSource;
     private final String BREEDING_METHOD_ID_KEY = "breedingMethodId";
     private final String GERMPLASM_NAME_REGEX = "^(.*\\b) \\[([A-Z]{2,6})-(\\d+)\\]$";
+    private ProgramService programService;
+    private BrAPIListDAO brAPIListDAO;
 
     @Inject
-    public BrAPIGermplasmService(BrAPIProvider brAPIProvider) {
+    public BrAPIGermplasmService(BrAPIProvider brAPIProvider, BrAPIListDAO brAPIListDAO, ProgramService programService) {
         this.brAPIProvider = brAPIProvider;
+        this.brAPIListDAO = brAPIListDAO;
+        this.programService = programService;
     }
 
     public List<BrAPIGermplasm> getGermplasm(UUID programId) {
@@ -79,4 +90,35 @@ public List<BrAPIGermplasm> getGermplasm(UUID programId) {
 
         return germplasmList;
     }
+
+    public BrAPIListsListResponse getGermplasmListsByProgramId(UUID programId, HttpRequest<String> request) throws DoesNotExistException, ApiException {
+
+        if (!programService.exists(programId)) {
+            throw new DoesNotExistException("Program does not exist");
+        }
+
+        Optional<Program> optionalProgram = programService.getById(programId);
+        if(optionalProgram.isPresent()) {
+            Program program = optionalProgram.get();
+            String appendedKey = String.format(" [%s-germplasm]", program.getKey());
+
+            BrAPIListsListResponse germplasmLists = brAPIListDAO.getListByTypeAndExternalRef(BrAPIListTypes.GERMPLASM, programId, referenceSource + "/programs", programId);
+
+            //Remove key appended to listName for brapi
+            String listName;
+            String newListName;
+            int listLength = germplasmLists.getResult().getData().size();
+            for (int i=0; i<listLength; i++) {
+                listName = germplasmLists.getResult().getData().get(i).getListName();
+                newListName = listName.replace(appendedKey, "");
+                germplasmLists.getResult().getData().get(i).setListName(newListName);
+            }
+
+            return germplasmLists;
+        }
+        else {
+            throw new DoesNotExistException("Program does not exist");
+        }
+    }
+
 }

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPIListDAO.java

@@ -2,12 +2,15 @@
 
 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.BrAPIResponse;
 import org.brapi.v2.model.BrAPIResponseResult;
 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.request.BrAPIListSearchRequest;
+import org.brapi.v2.model.core.response.BrAPIListsListResponse;
 import org.brapi.v2.model.pheno.BrAPIObservation;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.daos.ProgramDAO;
@@ -39,6 +42,17 @@ public List<BrAPIListSummary> getListByName(List<String> listNames, UUID program
         );
     }
 
+    public BrAPIListsListResponse getListByTypeAndExternalRef(BrAPIListTypes listType, UUID programId, String externalReferenceSource, UUID externalReferenceId) throws ApiException {
+        ListQueryParams getParams = new ListQueryParams()
+                .externalReferenceID(externalReferenceId.toString())
+                .externalReferenceSource(externalReferenceSource)
+                .listType(listType);
+
+        ListsApi api = new ListsApi(programDAO.getCoreClient(programId));
+        ApiResponse<BrAPIListsListResponse> apiGetResponse = api.listsGet(getParams);
+        return apiGetResponse.getBody();
+    }
+
     public List<BrAPIObservation> createBrAPILists(List<BrAPIListNewRequest> brapiLists, UUID programId, ImportUpload upload) throws ApiException {
         ListsApi api = new ListsApi(programDAO.getCoreClient(programId));
         // Do manually, it doesn't like List<Object> to List<BrAPIListNewRequest> for some reason

src/test/java/org/breedinginsight/brapi/v2/GermplasmControllerIntegrationTest.java

@@ -57,6 +57,9 @@ public class GermplasmControllerIntegrationTest extends BrAPITest {
             (json, type, context) -> OffsetDateTime.parse(json.getAsString()))
             .create();
 
+    private final String germplasmListName = "Program List";
+    private final String germplasmListDesc = "Program List";
+
     @AfterAll
     public void finish() { super.stopContainers(); }
 
@@ -114,16 +117,16 @@ public void setup() {
         // Insert other program germplasm
         File otherFile = new File("src/test/resources/files/germplasm_import/minimal_germplasm_import.csv");
         Map<String, String> otherListInfo = Map.ofEntries(
-                Map.entry("germplasmListName", "Program List"),
-                Map.entry("germplasmListDescription", "Program List")
+                Map.entry("germplasmListName", germplasmListName),
+                Map.entry("germplasmListDescription", germplasmListDesc)
         );
         TestUtils.uploadDataFile(client, otherValidProgram.getId(), germplasmImportId, otherListInfo, otherFile);
 
         // Insert program germplasm
         File file = new File("src/test/resources/files/germplasm_import/full_import.csv");
         Map<String, String> germplasmListInfo = Map.ofEntries(
-                Map.entry("germplasmListName", "Program List"),
-                Map.entry("germplasmListDescription", "Program List")
+                Map.entry("germplasmListName", germplasmListName),
+                Map.entry("germplasmListDescription", germplasmListDesc)
         );
         TestUtils.uploadDataFile(client, validProgram.getId(), germplasmImportId, germplasmListInfo, file);
     }
@@ -173,4 +176,27 @@ public void getPaginatedSuccess() {
 
         assertEquals(1, data.size(), "Wrong number of germplasm were returned");
     }
+
+    @Test
+    @SneakyThrows
+    public void getAllGermplasmListsSuccess() {
+        Flowable<HttpResponse<String>> call = client.exchange(
+                GET(String.format("/programs/%s/brapi/v2/lists",validProgram.getId().toString()))
+                        .cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
+        );
+
+        HttpResponse<String> response = call.blockingFirst();
+        assertEquals(HttpStatus.OK, response.getStatus());
+
+        JsonObject result = JsonParser.parseString(response.body()).getAsJsonObject().getAsJsonObject("result");
+
+        JsonArray data = result.getAsJsonArray("data");
+
+        assertEquals(1, data.size(), "Wrong number of germplasm lists were returned");
+        JsonObject exampleGermplasmList = data.get(0).getAsJsonObject();
+        assertEquals(exampleGermplasmList.get("listName").getAsString(), germplasmListName, "Germplasm list name incorrect");
+        assertEquals(exampleGermplasmList.get("listDescription").getAsString(), germplasmListDesc, "Germplasm list description incorrect");
+        assertEquals(exampleGermplasmList.get("listSize").getAsInt(), 3, "Germplasm list displays incorrect total entries ");
+    }
+
 }