BI-1845 - add listType parameter to GET /lists calls

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

@@ -79,9 +79,6 @@ public HttpResponse<Response<DataResponse<Object>>> getLists(
 
             // get germplasm lists by default
             BrAPIListTypes type = BrAPIListTypes.fromValue(queryParams.getListType());
-            if (type == null) {
-                type = BrAPIListTypes.GERMPLASM;
-            }
             String source = null;
             String id = null;
             if (queryParams.getExternalReferenceSource() != null && !queryParams.getExternalReferenceSource().isEmpty()) {

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

@@ -72,19 +72,20 @@ public List<BrAPIListSummary> getListSummariesByTypeAndXref(
             // set the owner of the list items as the list owner
             BrAPIListsSingleResponse listDetails = listDAO.getListById(list.getListDbId(), program.getId());
             List<String> listItemNames = listDetails.getResult().getData();
-            switch (type) {
-                case OBSERVATIONVARIABLES:
-                    break;
-                case GERMPLASM:
-                default:
-                    String createdBy = germplasmDAO.getGermplasmByRawName(listItemNames, program.getId()).get(0)
-                            .getAdditionalInfo()
-                            .getAsJsonObject("createdBy")
-                            .get("userName")
-                            .getAsString();
-                    list.setListOwnerName(createdBy);
+            if (type != null) {
+                switch (type) {
+                    case GERMPLASM:
+                        String createdBy = germplasmDAO.getGermplasmByRawName(listItemNames, program.getId()).get(0)
+                                .getAdditionalInfo()
+                                .getAsJsonObject("createdBy")
+                                .get("userName")
+                                .getAsString();
+                        list.setListOwnerName(createdBy);
+                    case OBSERVATIONVARIABLES:
+                    default:
+                        break;
+                }
             }
-
         }
 
         return programLists;

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

@@ -210,7 +210,7 @@ public void getPaginatedSuccess() {
     @SneakyThrows
     public void getAllGermplasmListsSuccess() {
         Flowable<HttpResponse<String>> call = client.exchange(
-                GET(String.format("/programs/%s/brapi/v2/lists",validProgram.getId().toString()))
+                GET(String.format("/programs/%s/brapi/v2/lists?listType=germplasm",validProgram.getId().toString()))
                         .cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
         );
 

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

@@ -0,0 +1,190 @@
+/*
+ * 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 com.google.gson.*;
+import io.kowalski.fannypack.FannyPack;
+import io.micronaut.http.HttpResponse;
+import io.micronaut.http.HttpStatus;
+import io.micronaut.http.client.RxHttpClient;
+import io.micronaut.http.client.annotation.Client;
+import io.micronaut.http.netty.cookies.NettyCookie;
+import io.micronaut.test.extensions.junit5.annotation.MicronautTest;
+import io.reactivex.Flowable;
+import junit.framework.AssertionFailedError;
+import lombok.SneakyThrows;
+import org.breedinginsight.BrAPITest;
+import org.breedinginsight.TestUtils;
+import org.breedinginsight.api.auth.AuthenticatedUser;
+import org.breedinginsight.brapps.importer.ImportTestUtils;
+import org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentObservation;
+import org.breedinginsight.model.Trait;
+import org.breedinginsight.services.OntologyService;
+import org.breedinginsight.services.exceptions.ValidatorException;
+import org.breedinginsight.dao.db.tables.pojos.BiUserEntity;
+import org.breedinginsight.daos.UserDAO;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.services.SpeciesService;
+import org.jooq.DSLContext;
+import org.junit.jupiter.api.*;
+
+import javax.inject.Inject;
+
+import java.io.File;
+import java.time.OffsetDateTime;
+import java.util.*;
+
+import static io.micronaut.http.HttpRequest.GET;
+import static org.junit.jupiter.api.Assertions.*;
+
+@MicronautTest
+@TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
+public class ListControllerIntegrationTest extends BrAPITest {
+
+    private Program program;
+    private String germplasmImportId;
+    private ImportTestUtils importTestUtils;
+    private String mappingId;
+    private BiUserEntity testUser;
+
+
+    @Inject
+    private SpeciesService speciesService;
+    @Inject
+    @Client("/${micronaut.bi.api.version}")
+    RxHttpClient client;
+    @Inject
+    private UserDAO userDAO;
+    @Inject
+    private DSLContext dsl;
+
+    private Gson gson = new GsonBuilder().registerTypeAdapter(OffsetDateTime.class, (JsonDeserializer<OffsetDateTime>)
+                    (json, type, context) -> OffsetDateTime.parse(json.getAsString()))
+            .create();
+
+    private final String germplasmListName = "Program List";
+    private final String germplasmListDesc = "Program List";
+
+    @Inject
+    private OntologyService ontologyService;
+
+    @BeforeAll
+    @SneakyThrows
+    public void setup() {
+        importTestUtils = new ImportTestUtils();
+        Map<String, Object> setupObjects = importTestUtils.setup(client, gson, dsl, speciesService, userDAO, super.getBrapiDsl(), "ExperimentsTemplateMap");
+        mappingId = (String) setupObjects.get("mappingId");
+        program = (Program) setupObjects.get("program");
+        testUser = (BiUserEntity) setupObjects.get("testUser");
+        FannyPack securityFp = (FannyPack) setupObjects.get("securityFp");
+
+        dsl.execute(securityFp.get("InsertSystemRoleAdmin"), testUser.getId().toString());
+
+        // Generate traits and persist them.
+        List<Trait> traits = importTestUtils.createTraits(1);
+        AuthenticatedUser user = new AuthenticatedUser(testUser.getName(), new ArrayList<>(), testUser.getId(), new ArrayList<>());
+        try {
+            ontologyService.createTraits(program.getId(), traits, user, false);
+        } catch (ValidatorException e) {
+            System.err.println(e.getErrors());
+            throw e;
+        }
+
+        // Get germplasm system import.
+        Flowable<HttpResponse<String>> call = client.exchange(
+                GET("/import/mappings?importName=germplasmtemplatemap").cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
+        );
+        HttpResponse<String> response = call.blockingFirst();
+        germplasmImportId = JsonParser.parseString(response.body()).getAsJsonObject()
+                .getAsJsonObject("result")
+                .getAsJsonArray("data")
+                .get(0).getAsJsonObject().get("id").getAsString();
+
+        // Insert program germplasm.
+        File file = new File("src/test/resources/files/germplasm_import/minimal_germplasm_import.csv");
+        Map<String, String> germplasmListInfo = Map.ofEntries(
+                Map.entry("germplasmListName", germplasmListName),
+                Map.entry("germplasmListDescription", germplasmListDesc)
+        );
+        TestUtils.uploadDataFile(client, program.getId(), germplasmImportId, germplasmListInfo, file);
+
+        // Make test experiment import.
+        Map<String, Object> newExp = new HashMap<>();
+        newExp.put(ExperimentObservation.Columns.GERMPLASM_GID, "1");
+        newExp.put(ExperimentObservation.Columns.TEST_CHECK, "T");
+        newExp.put(ExperimentObservation.Columns.EXP_TITLE, "Test Exp");
+        newExp.put(ExperimentObservation.Columns.EXP_UNIT, "Plot");
+        newExp.put(ExperimentObservation.Columns.EXP_TYPE, "Phenotyping");
+        newExp.put(ExperimentObservation.Columns.ENV, "New Env");
+        newExp.put(ExperimentObservation.Columns.ENV_LOCATION, "Location A");
+        newExp.put(ExperimentObservation.Columns.ENV_YEAR, "2023");
+        newExp.put(ExperimentObservation.Columns.EXP_UNIT_ID, "a-1");
+        newExp.put(ExperimentObservation.Columns.REP_NUM, "1");
+        newExp.put(ExperimentObservation.Columns.BLOCK_NUM, "1");
+        newExp.put(ExperimentObservation.Columns.ROW, "1");
+        newExp.put(ExperimentObservation.Columns.COLUMN, "1");
+        newExp.put(traits.get(0).getObservationVariableName(), "1");
+
+        JsonObject result = importTestUtils.uploadAndFetch(
+                importTestUtils.writeDataToFile(List.of(newExp), traits), null, true, client, program, mappingId
+        );
+
+    }
+
+    @Test
+    @SneakyThrows
+    public void getAllListsSuccess() {
+        // A GET request to the brapi/v2/lists endpoint with no query params should return all lists.
+        Flowable<HttpResponse<String>> call = client.exchange(
+                GET(String.format("/programs/%s/brapi/v2/lists", program.getId().toString()))
+                        .cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
+        );
+
+        // Ensure 200 OK response.
+        HttpResponse<String> response = call.blockingFirst();
+        assertEquals(HttpStatus.OK, response.getStatus());
+
+        // Parse result.
+        JsonObject result = JsonParser.parseString(response.body()).getAsJsonObject().getAsJsonObject("result");
+        JsonArray data = result.getAsJsonArray("data");
+
+        // Ensure all lists are returned.
+        assertEquals(2, data.size(), "Wrong number of lists were returned");
+
+        // Ensure the list names and types are as expected.
+        List<String> listNames = List.of(germplasmListName, "Observation Dataset");
+        List<String> listTypes = List.of("germplasm", "observationVariables");
+        for (JsonElement element: data) {
+            JsonObject list = element.getAsJsonObject();
+            if (listNames.contains(list.get("listName").getAsString())) {
+                int index = listNames.indexOf(list.get("listName").getAsString());
+                assertEquals(list.get("listName").getAsString(), listNames.get(index), "List name incorrect");
+            } else {
+                throw new AssertionFailedError("List name not found");
+            }
+            if (listTypes.contains(list.get("listType").getAsString())) {
+                int index = listTypes.indexOf(list.get("listType").getAsString());
+                assertEquals(list.get("listType").getAsString(), listTypes.get(index), "List type incorrect");
+            } else {
+                throw new AssertionFailedError("List type not found");
+            }
+        }
+    }
+
+}