Issue #731 Metabolic pathways

server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/Page.java

@@ -0,0 +1,36 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2022 EPAM Systems
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+package com.epam.ngb.cli.entity;
+
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.List;
+
+@Getter
+@Setter
+public class Page<T> {
+    List<T> items;
+    long totalCount;
+}

server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pathway/PathwayListHandler.java

@@ -26,6 +26,7 @@
 
 import com.epam.ngb.cli.app.ApplicationOptions;
 import com.epam.ngb.cli.constants.MessageConstants;
+import com.epam.ngb.cli.entity.Page;
 import com.epam.ngb.cli.entity.ResponseResult;
 import com.epam.ngb.cli.entity.pathway.Pathway;
 import com.epam.ngb.cli.exception.ApplicationException;
@@ -63,24 +64,24 @@ public void parseAndVerifyArguments(List<String> arguments, ApplicationOptions o
     @Override public int runCommand() {
         final HttpRequestBase request = getRequest(getRequestUrl());
         final String result = RequestManager.executeRequest(request);
-        final ResponseResult<List<Pathway>> responseResult;
+        final ResponseResult<Page<Pathway>> responseResult;
         try {
             responseResult = getMapper().readValue(result,
                     getMapper().getTypeFactory().constructParametrizedType(
                             ResponseResult.class, ResponseResult.class,
-                            getMapper().getTypeFactory().constructParametrizedType(
-                                    List.class, List.class, Pathway.class)));
+                            getMapper().getTypeFactory()
+                                    .constructParametrizedType(Page.class, Page.class, Pathway.class)));
         } catch (IOException e) {
             throw new ApplicationException(e.getMessage(), e);
         }
         if (!SUCCESS_STATUS.equals(responseResult.getStatus())) {
             throw new ApplicationException(responseResult.getMessage());
         }
         if (responseResult.getPayload() == null ||
-                responseResult.getPayload().isEmpty()) {
+                responseResult.getPayload().getItems().isEmpty()) {
             log.info("No metabolic pathways registered on the server.");
         } else {
-            List<Pathway> pathways = responseResult.getPayload();
+            List<Pathway> pathways = responseResult.getPayload().getItems();
             AbstractResultPrinter printer = AbstractResultPrinter
                     .getPrinter(printTable, pathways.get(0).getFormatString(pathways));
             printer.printHeader(pathways.get(0));

server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pathway/PathwayRegistrationHandler.java

@@ -27,7 +27,6 @@
 import com.epam.ngb.cli.app.ApplicationOptions;
 import com.epam.ngb.cli.constants.MessageConstants;
 import com.epam.ngb.cli.entity.ResponseResult;
-import com.epam.ngb.cli.entity.lineage.LineageTree;
 import com.epam.ngb.cli.entity.pathway.Pathway;
 import com.epam.ngb.cli.entity.pathway.PathwayRegistrationRequest;
 import com.epam.ngb.cli.exception.ApplicationException;