Merge branch 'v2-alpha' into gh-981-gafferpy-fishbowl-maintain

.github/workflows/continuous-integration.yaml

@@ -111,7 +111,9 @@ jobs:
     env:
       MAVEN_OPTS: -Dmaven.wagon.http.retryHandler.count=3 -Dmaven.wagon.httpconnectionManager.ttlSeconds=25
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
 
     - name: Setup JDK
       uses: actions/setup-java@v2
@@ -133,5 +135,9 @@ jobs:
     - name: Test
       run: mvn verify -B -P coverage -pl ${{matrix.modules}}
 
+    - name: Check Copyright Headers
+      if: github.event_name == 'pull_request'
+      run: mvn -B -q spotless:check -pl ${{matrix.modules}}
+
     - name: Upload Coverage
       uses: codecov/codecov-action@v2

code-style/checkstyle.xml

@@ -33,10 +33,6 @@
         <property name="id" value="fileTabChar"/>
         <property name="eachLine" value="true"/>
     </module>
-    <module name="RegexpHeader">
-        <property name="id" value="headerCheck"/>
-        <property name="headerFile" value="${checkstyle.header.file}"/>
-    </module>
 
     <module name="RegexpSingleline">
         <property name="id" value="trailingSpaces"/>

code-style/licence-header-java.txt

@@ -0,0 +1,16 @@
+/*
+ * Copyright $YEAR Crown Copyright
+ *
+ * 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.
+ */
+

code-style/licence-header-pom.txt

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  ~ Copyright $YEAR Crown Copyright
+  ~
+  ~ 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.
+  -->
+

pom.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  ~ Copyright 2016-2019 Crown Copyright
+  ~ Copyright 2016-2022 Crown Copyright
   ~
   ~ Licensed under the Apache License, Version 2.0 (the "License");
   ~ you may not use this file except in compliance with the License.
@@ -85,8 +85,6 @@
                     <encoding>UTF-8</encoding>
                     <consoleOutput>true</consoleOutput>
                     <failsOnError>true</failsOnError>
-                    <headerLocation>code-style/licenseHeader.txt
-                    </headerLocation>
                     <excludes>**/generated/**/*</excludes>
                     <sourceDirectories>
                         <sourceDirectory>${project.build.sourceDirectory}
@@ -105,8 +103,6 @@
                             <encoding>UTF-8</encoding>
                             <consoleOutput>true</consoleOutput>
                             <failsOnError>true</failsOnError>
-                            <headerLocation>code-style/licenseHeader.txt
-                            </headerLocation>
                         </configuration>
                         <goals>
                             <goal>check</goal>

ui/src/main/webapp/app/graph/graph-component.js

@@ -140,6 +140,7 @@ function GraphController($q, graph, config, error, loading, query, operationOpti
         events.unsubscribe('resultsCleared', vm.reset);
 
         if (cytoscapeGraph) {
+            saveGraph();
             cytoscapeGraph.destroy();
         }
     }
@@ -151,15 +152,35 @@ function GraphController($q, graph, config, error, loading, query, operationOpti
         createCytoscapeGraph().then(function(cy) {
             cytoscapeGraph = cy;
             generateStylesheets();
-            vm.reset()
+
+            if(graph.hasGraphJson()) {
+                restoreGraph();
+                cytoscapeGraph.elements().lock();
+                vm.update(results.get());
+                cytoscapeGraph.elements().unlock();
+            } else {
+                vm.reset();
+            }
             vm.graphLoading = false;
             var searchTerm = graph.getSearchTerm();
-
             if (searchTerm !== null && searchTerm !== undefined && searchTerm !== "") {
                 vm.filter(searchTerm)
             }
         });
     }
+
+    var saveGraph = function() {
+        if(cytoscapeGraph) {
+            graph.setGraphJson(cytoscapeGraph.json());
+        }
+    }
+
+    var restoreGraph = function() {
+        if(graph.hasGraphJson() && cytoscapeGraph && (results.get().edges || results.get().entities)) {
+            cytoscapeGraph.json(graph.getGraphJson());
+            cytoscapeGraph.nodes().removeClass("filtered"); // seems to be a bug in cytoscape json
+        }
+    }
 
     /**
      * Loads cytoscape graph onto an element containing the "graphCy" id. It also registers the
@@ -416,6 +437,7 @@ function GraphController($q, graph, config, error, loading, query, operationOpti
                 cytoscapeGraph.getElementById(id).data(elementsToMergeData[id]);
             }
 
+            removePreviouslyRemovedElements();
             vm.redraw();
         });
 
@@ -598,6 +620,8 @@ function GraphController($q, graph, config, error, loading, query, operationOpti
      */
     vm.reset = function() {
         vm.clear();
+        graph.setRemovedElements([]);
+        saveGraph();
         vm.update(results.get());
     }
 
@@ -610,7 +634,7 @@ function GraphController($q, graph, config, error, loading, query, operationOpti
         searchTerm = searchTerm.toLowerCase();
         cytoscapeGraph.batch(function() {
             var nodes = cytoscapeGraph.nodes();
-            for(var i in nodes) {
+            for(var i = 0; i < nodes.length; i++) {
                 if(nodes[i].data && nodes[i].data('id')) {
                     if(nodes[i].data('id').toLowerCase().indexOf(searchTerm) === -1) {
                         nodes[i].addClass("filtered");
@@ -630,9 +654,21 @@ function GraphController($q, graph, config, error, loading, query, operationOpti
      * Removes every selected element in the graph.
      */
     vm.removeSelected = function() {
-        cytoscapeGraph.filter(":selected").remove();
+        var removedElements = cytoscapeGraph.filter(":selected").remove().toArray();
+        graph.setRemovedElements(graph.getRemovedElements().concat(removedElements));
+
         cytoscapeGraph.elements().unselect();
         vm.selectedElements.entities = [];
         vm.selectedElements.edges = [];
     }
+
+    var removePreviouslyRemovedElements = function() {
+        var elements = cytoscapeGraph.elements();
+        graph.getRemovedElements().forEach(function(removedElement) {
+            var element = elements.getElementById(removedElement.id());
+            if(element && element.id()) {
+                element.remove();
+            }
+        });
+    }
 }

ui/src/main/webapp/app/graph/graph-service.js

@@ -24,6 +24,9 @@ angular.module('app').factory('graph', function() {
 
     var graphConfiguration = null;
 
+    var removedElements = [];
+    var graphJson = {};
+
     var selectedElements = {
         entities: [],
         edges: []
@@ -76,6 +79,43 @@ angular.module('app').factory('graph', function() {
         searchTerm = angular.copy(search);
     }
 
+    /**
+     * Gets the removed elements.
+     */
+    service.getRemovedElements = function() {
+        return removedElements;
+    }
+
+    /**
+     * Sets the removed elements.
+     * @param removedElements;
+     */
+    service.setRemovedElements = function(newRemovedElements) {
+        removedElements = newRemovedElements
+    }
+
+    /**
+     * Checks if the graph json has been set.
+     */
+    service.hasGraphJson = function() {
+        return graphJson && Object.keys(graphJson).length > 0 && Object.keys(graphJson.elements).length > 0;
+    }
+
+    /**
+     * Gets the graph json.
+     */
+    service.getGraphJson = function() {
+        return graphJson;
+    }
+
+    /**
+     * Sets the graph json.
+     * @param graphJson;
+     */
+    service.setGraphJson = function(newGraphJson) {
+        graphJson = newGraphJson;
+    }
+
     /**
      * Resets the value of the selected elements
      */

ui/src/main/webapp/app/toolbar/toolbar-component.js

@@ -26,7 +26,7 @@ function toolbar() {
     };
 }
 
-function ToolbarController($rootScope, $mdDialog, operationService, results, query, config, loading, events, properties, error, $mdToast, $cookies) {
+function ToolbarController($rootScope, $mdDialog, operationService, results, query, config, loading, events, properties, error, $mdToast, $cookies, graph) {
     var vm = this;
     vm.addMultipleSeeds = false;
     vm.appTitle;
@@ -165,6 +165,7 @@ function ToolbarController($rootScope, $mdDialog, operationService, results, que
 
     vm.executeAll = function() {
         var ops = query.getOperations();
+        graph.setGraphJson(null);
         if (ops.length > 0) {
             results.clear(false);
             loading.load();
@@ -175,6 +176,7 @@ function ToolbarController($rootScope, $mdDialog, operationService, results, que
     }
 
     vm.clearResults = function() {
+        graph.setGraphJson(null);
         results.clear();
     }
 

ui/src/test/webapp/app/graph/graph-component-spec.js

@@ -308,6 +308,24 @@ describe("The Graph Component", function() {
             expect(ctrl.update).toHaveBeenCalled();
         })
 
+        it('should load the graph from the saved graph json when it exists', function() {
+            var graphJson = {elements: [1,2]};
+            spyOn(ctrl, 'update').and.stub();
+            $httpBackend.whenGET('config/config.json').respond(200, {});
+            graph.setGraphJson(graphJson);
+            spyOn(injectableCytoscape, 'json')
+
+            ctrl.$onInit();
+
+            $httpBackend.flush();
+            jasmine.clock().tick(101);
+
+            scope.$digest();
+
+            expect(injectableCytoscape.json).toHaveBeenCalledWith(graphJson);
+            expect(ctrl.update).toHaveBeenCalled();
+        })
+
         it('should run the filter once loaded if the service holds a filter', function() {
             spyOn(ctrl, 'filter').and.stub();
             spyOn(ctrl, 'update').and.stub();
@@ -447,7 +465,16 @@ describe("The Graph Component", function() {
 
                 expect(events.unsubscribe).toHaveBeenCalledWith("incomingResults", jasmine.any(Function));
             });
-
+
+            it('should save the graph json', function() {
+                var graphJson = {elements: [1,2]};
+                spyOn(injectableCytoscape, 'json').and.returnValue(graphJson);
+
+                ctrl.$onDestroy();
+                expect(injectableCytoscape.json).toHaveBeenCalled();
+                expect(graph.getGraphJson()).toEqual(graphJson);
+            });
+
             it('should destroy the cytoscape graph cleanly', function() {    
                 spyOn(injectableCytoscape, 'destroy');
 
@@ -649,7 +676,15 @@ describe("The Graph Component", function() {
 
                 expect(injectableCytoscape.nodes().size()).toEqual(1);
             });
-
+
+            it('should save the removed elements', function() {
+                graph.setRemovedElements([]);
+                ctrl.removeSelected();
+
+                expect(injectableCytoscape.nodes().size()).toEqual(1);
+                expect(graph.getRemovedElements().length).toEqual(2);
+            });
+
             it('should unselect all the elements', function() {
                 expect(injectableCytoscape.elements(':selected').size()).toEqual(1);
 
@@ -680,6 +715,13 @@ describe("The Graph Component", function() {
                 expect(injectableCytoscape.elements().size()).toEqual(3);
             });
 
+            it('should remove previously removed elements from the results', function() {
+                graph.setRemovedElements([{id: function(){return "\"foo\""}}]);
+                injectableCytoscape.elements().restore();
+                ctrl.update(elements);
+                expect(injectableCytoscape.elements().size()).toEqual(1);
+            });
+
             it('should not error when vertex type is unknown', function() {
                 entityVertexType = undefined;