From 4232f15c048e908c5804b84a95486615be22a8d3 Mon Sep 17 00:00:00 2001
From: lana-k <skochetova89@gmail.com>
Date: Sun, 17 Aug 2025 21:21:21 +0200
Subject: [PATCH] autostart, reset and fixes

---
 jsconfig.json                                 |   2 +-
 .../AdvancedForceAtlasLayoutSettings.vue      | 117 ++++++++
 .../Graph/ForceAtlasLayoutSettings.vue        |  90 +-----
 src/lib/graphHelper.js                        |   5 +-
 .../Tabs/Tab/DataView/Graph/GraphEditor.vue   | 256 ++++++++++++------
 .../Tabs/Tab/DataView/Graph/index.vue         |   6 +-
 6 files changed, 303 insertions(+), 173 deletions(-)
 create mode 100644 src/components/Graph/AdvancedForceAtlasLayoutSettings.vue

diff --git a/jsconfig.json b/jsconfig.json
index c806975..770f83f 100644
--- a/jsconfig.json
+++ b/jsconfig.json
@@ -4,7 +4,7 @@
   "compilerOptions": {
     "baseUrl": "./",
     "paths": {
-      "@*": ["./src/*"]
+      "@\/*": ["./src/*"]
     }
   }
 }
diff --git a/src/components/Graph/AdvancedForceAtlasLayoutSettings.vue b/src/components/Graph/AdvancedForceAtlasLayoutSettings.vue
new file mode 100644
index 0000000..0f2902f
--- /dev/null
+++ b/src/components/Graph/AdvancedForceAtlasLayoutSettings.vue
@@ -0,0 +1,117 @@
+<template>
+  <Field label="Adjust sizes">
+    <RadioBlocks
+      :options="booleanOptions"
+      :activeOption="modelValue.adjustSizes"
+      @option-change="update('adjustSizes', $event)"
+    />
+  </Field>
+
+  <Field label="Barnes-Hut optimize">
+    <RadioBlocks
+      :options="booleanOptions"
+      :activeOption="modelValue.barnesHutOptimize"
+      @option-change="update('barnesHutOptimize', $event)"
+    />
+  </Field>
+
+  <Field v-show="modelValue.barnesHutOptimize" label="Barnes-Hut Theta">
+    <NumericInput
+      :value="modelValue.barnesHutTheta"
+      @update="update('barnesHutTheta', $event)"
+    />
+  </Field>
+
+  <Field label="Gravity">
+    <NumericInput
+      :value="modelValue.gravity"
+      @update="update('gravity', $event)"
+    />
+  </Field>
+
+  <Field label="Strong gravity mode">
+    <RadioBlocks
+      :options="booleanOptions"
+      :activeOption="modelValue.strongGravityMode"
+      @option-change="update('strongGravityMode', $event)"
+    />
+  </Field>
+
+  <Field label="Noack's LinLog model">
+    <RadioBlocks
+      :options="booleanOptions"
+      :activeOption="modelValue.linLogMode"
+      @option-change="update('linLogMode', $event)"
+    />
+  </Field>
+
+  <Field label="Out bound attraction distribution">
+    <RadioBlocks
+      :options="booleanOptions"
+      :activeOption="modelValue.outboundAttractionDistribution"
+      @option-change="update('outboundAttractionDistribution', $event)"
+    />
+  </Field>
+
+  <Field label="Slow down">
+    <NumericInput
+      :value="modelValue.slowDown"
+      :min="0"
+      @update="update('slowDown', $event)"
+    />
+  </Field>
+
+  <Field label="Edge weight">
+    <Dropdown
+      :options="keyOptions"
+      :value="modelValue.weightSource"
+      @change="update('weightSource', $event)"
+    />
+  </Field>
+  <Field v-show="modelValue.weightSource" label="Edge weight influence">
+    <NumericInput
+      :value="modelValue.edgeWeightInfluence"
+      @update="update('edgeWeightInfluence', $event)"
+    />
+  </Field>
+</template>
+
+<script>
+import { markRaw } from 'vue'
+import { applyPureReactInVue } from 'veaury'
+import Field from 'react-chart-editor/lib/components/fields/Field'
+import RadioBlocks from 'react-chart-editor/lib/components/widgets/RadioBlocks'
+import NumericInput from 'react-chart-editor/lib/components/widgets/NumericInput'
+import Dropdown from 'react-chart-editor/lib/components/widgets/Dropdown'
+import 'react-chart-editor/lib/react-chart-editor.css'
+
+export default {
+  components: {
+    Field: applyPureReactInVue(Field),
+    RadioBlocks: applyPureReactInVue(RadioBlocks),
+    Dropdown: applyPureReactInVue(Dropdown),
+    NumericInput: applyPureReactInVue(NumericInput)
+  },
+  props: {
+    modelValue: Object,
+    keyOptions: Array
+  },
+  emits: ['update:modelValue'],
+  data() {
+    return {
+      booleanOptions: markRaw([
+        { label: 'Yes', value: true },
+        { label: 'No', value: false }
+      ])
+    }
+  },
+  methods: {
+    update(attributeName, value) {
+      this.$emit('update:modelValue', {
+        ...this.modelValue,
+        [attributeName]: value
+      })
+    }
+  }
+}
+</script>
diff --git a/src/components/Graph/ForceAtlasLayoutSettings.vue b/src/components/Graph/ForceAtlasLayoutSettings.vue
index b3575c1..0261543 100644
--- a/src/components/Graph/ForceAtlasLayoutSettings.vue
+++ b/src/components/Graph/ForceAtlasLayoutSettings.vue
@@ -1,55 +1,9 @@
 <template>
-  <Field label="Adjust sizes">
-    <RadioBlocks
-      :options="booleanOptions"
-      :activeOption="modelValue.adjustSizes"
-      @option-change="update('adjustSizes', $event)"
-    />
-  </Field>
-
-  <Field label="Barnes-Hut optimize">
-    <RadioBlocks
-      :options="booleanOptions"
-      :activeOption="modelValue.barnesHutOptimize"
-      @option-change="update('barnesHutOptimize', $event)"
-    />
-  </Field>
-
-  <Field v-show="modelValue.barnesHutOptimize" label="Barnes-Hut Theta">
+  <Field label="Initial iterations">
     <NumericInput
-      :value="modelValue.barnesHutTheta"
-      @update="update('barnesHutTheta', $event)"
-    />
-  </Field>
-
-  <Field label="Gravity">
-    <NumericInput
-      :value="modelValue.gravity"
-      @update="update('gravity', $event)"
-    />
-  </Field>
-
-  <Field label="Strong gravity mode">
-    <RadioBlocks
-      :options="booleanOptions"
-      :activeOption="modelValue.strongGravityMode"
-      @option-change="update('strongGravityMode', $event)"
-    />
-  </Field>
-
-  <Field label="Noack's LinLog model">
-    <RadioBlocks
-      :options="booleanOptions"
-      :activeOption="modelValue.linLogMode"
-      @option-change="update('linLogMode', $event)"
-    />
-  </Field>
-
-  <Field label="Out bound attraction distribution">
-    <RadioBlocks
-      :options="booleanOptions"
-      :activeOption="modelValue.outboundAttractionDistribution"
-      @option-change="update('outboundAttractionDistribution', $event)"
+      :value="modelValue.initialIterationsAmount"
+      :min="1"
+      @update="update('initialIterationsAmount', $event)"
     />
   </Field>
 
@@ -59,45 +13,17 @@
       @update="update('scalingRatio', $event)"
     />
   </Field>
-
-  <Field label="Slow down">
-    <NumericInput
-      :value="modelValue.slowDown"
-      :min="1"
-      @update="update('slowDown', $event)"
-    />
-  </Field>
-
-  <Field label="Edge weight influence">
-    <NumericInput
-      :value="modelValue.edgeWeightInfluence"
-      @update="update('edgeWeightInfluence', $event)"
-    />
-  </Field>
-
-  <Field label="Edge weight">
-    <Dropdown
-      :options="keyOptions"
-      :value="modelValue.weightSource"
-      @change="update('weightSource', $event)"
-    />
-  </Field>
 </template>
 
 <script>
-import { markRaw } from 'vue'
 import { applyPureReactInVue } from 'veaury'
 import Field from 'react-chart-editor/lib/components/fields/Field'
-import RadioBlocks from 'react-chart-editor/lib/components/widgets/RadioBlocks'
 import NumericInput from 'react-chart-editor/lib/components/widgets/NumericInput'
-import Dropdown from 'react-chart-editor/lib/components/widgets/Dropdown'
 import 'react-chart-editor/lib/react-chart-editor.css'
 
 export default {
   components: {
     Field: applyPureReactInVue(Field),
-    RadioBlocks: applyPureReactInVue(RadioBlocks),
-    Dropdown: applyPureReactInVue(Dropdown),
     NumericInput: applyPureReactInVue(NumericInput)
   },
   props: {
@@ -105,14 +31,6 @@ export default {
     keyOptions: Array
   },
   emits: ['update:modelValue'],
-  data() {
-    return {
-      booleanOptions: markRaw([
-        { label: 'Yes', value: true },
-        { label: 'No', value: false }
-      ])
-    }
-  },
   methods: {
     update(attributeName, value) {
       this.$emit('update:modelValue', {
diff --git a/src/lib/graphHelper.js b/src/lib/graphHelper.js
index b0358d2..6e8303e 100644
--- a/src/lib/graphHelper.js
+++ b/src/lib/graphHelper.js
@@ -13,7 +13,6 @@ export function buildNodes(graph, dataSources, options) {
     const nodes = dataSources[docColumn]
       .map(json => JSON.parse(json))
       .filter(item => item[objectType] === TYPE_NODE)
-
     nodes.forEach(node => {
       graph.addNode(node[nodeId], {
         data: node,
@@ -89,8 +88,8 @@ export function updateEdges(graph, attributeUpdates) {
   }
 
   graph.forEachEdge((edgeId, attributes, source, target) => {
-    graph.updateEdge(source, target, attributes => {
-      const newAttributes = { ...attributes }
+    graph.updateEdgeWithKey(edgeId, source, target, attr => {
+      const newAttributes = { ...attr }
       changeMethods.forEach(method => method(newAttributes, edgeId))
       return newAttributes
     })
diff --git a/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/GraphEditor.vue b/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/GraphEditor.vue
index 1031578..00e21b4 100644
--- a/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/GraphEditor.vue
+++ b/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/GraphEditor.vue
@@ -133,8 +133,19 @@
               :keyOptions="keysOptions"
               @update:model-value="updateLayout(settings.layout.type)"
             />
-
-            <Field v-if="settings.layout.type === 'forceAtlas2'">
+          </Fold>
+          <template v-if="settings.layout.type === 'forceAtlas2'">
+            <Fold name="Advanced layout settings">
+              <AdvancedForceAtlasLayoutSettings
+                v-model="settings.layout.options"
+                :keyOptions="keysOptions"
+                @update:model-value="updateLayout(settings.layout.type)"
+              />
+            </Fold>
+            <div class="force-atlas-buttons">
+              <Button variant="secondary" @click="resetFA2LayoutSettings">
+                Reset
+              </Button>
               <Button variant="primary" @click="toggleFA2Layout">
                 <template #node:icon>
                   <div
@@ -143,12 +154,13 @@
                     }"
                   >
                     <RunIcon v-if="!fa2Running" />
-                    <StopIcon v-else /></div
-                ></template>
+                    <StopIcon v-else />
+                  </div>
+                </template>
                 {{ fa2Running ? 'Stop' : 'Start' }}
               </Button>
-            </Field>
-          </Fold>
+            </div>
+          </template>
         </Panel>
       </PanelMenuWrapper>
     </GraphEditorControls>
@@ -176,6 +188,7 @@ import Button from 'react-chart-editor/lib/components/widgets/Button'
 import Field from 'react-chart-editor/lib/components/fields/Field'
 import RandomLayoutSettings from '@/components/Graph/RandomLayoutSettings.vue'
 import ForceAtlasLayoutSettings from '@/components/Graph/ForceAtlasLayoutSettings.vue'
+import AdvancedForceAtlasLayoutSettings from '@/components/Graph/AdvancedForceAtlasLayoutSettings.vue'
 import CirclePackLayoutSettings from '@/components/Graph/CirclePackLayoutSettings.vue'
 import FA2Layout from 'graphology-layout-forceatlas2/worker'
 import forceAtlas2 from 'graphology-layout-forceatlas2'
@@ -216,7 +229,8 @@ export default {
     NodeColorSettings,
     NodeSizeSettings,
     EdgeSizeSettings,
-    EdgeColorSettings
+    EdgeColorSettings,
+    AdvancedForceAtlasLayoutSettings
   },
   inject: ['tabLayout'],
   props: {
@@ -226,10 +240,11 @@ export default {
   emits: ['update'],
   data() {
     return {
-      graph: new Graph(),
+      graph: new Graph({ multi: true, allowSelfLoops: true }),
       renderer: null,
       fa2Layout: null,
       fa2Running: false,
+      checkIteration: null,
       visibilityOptions: markRaw([
         { label: 'Show', value: true },
         { label: 'Hide', value: false }
@@ -246,50 +261,52 @@ export default {
         forceAtlas2: ForceAtlasLayoutSettings
       }),
 
-      settings: this.initOptions || {
-        structure: {
-          nodeId: null,
-          objectType: null,
-          edgeSource: null,
-          edgeTarget: null
-        },
-        style: {
-          backgroundColor: 'white',
-          nodes: {
-            size: {
-              type: 'constant',
-              value: 4
+      settings: this.initOptions
+        ? JSON.parse(JSON.stringify(this.initOptions))
+        : {
+            structure: {
+              nodeId: null,
+              objectType: null,
+              edgeSource: null,
+              edgeTarget: null
             },
-            color: {
-              type: 'constant',
-              value: '#1F77B4'
+            style: {
+              backgroundColor: 'white',
+              nodes: {
+                size: {
+                  type: 'constant',
+                  value: 4
+                },
+                color: {
+                  type: 'constant',
+                  value: '#1F77B4'
+                },
+                label: {
+                  source: null,
+                  color: '#444444'
+                }
+              },
+              edges: {
+                showDirection: true,
+                size: {
+                  type: 'constant',
+                  value: 2
+                },
+                color: {
+                  type: 'constant',
+                  value: '#a2b1c6'
+                },
+                label: {
+                  source: null,
+                  color: '#a2b1c6'
+                }
+              }
             },
-            label: {
-              source: null,
-              color: '#444444'
+            layout: {
+              type: 'circular',
+              options: null
             }
           },
-          edges: {
-            showDirection: true,
-            size: {
-              type: 'constant',
-              value: 2
-            },
-            color: {
-              type: 'constant',
-              value: '#a2b1c6'
-            },
-            label: {
-              source: null,
-              color: '#a2b1c6'
-            }
-          }
-        },
-        layout: {
-          type: 'circular',
-          options: null
-        }
-      },
       layoutOptionsArchive: {
         random: null,
         circlepack: null,
@@ -370,13 +387,16 @@ export default {
       updateNodes(this.graph, this.settings.style.nodes)
       updateEdges(this.graph, this.settings.style.edges)
 
-      circular.assign(this.graph)
+      this.updateLayout(this.settings.layout.type)
       this.renderer = new Sigma(this.graph, this.$refs.graph, {
         renderEdgeLabels: true,
         allowInvalidContainer: true,
         labelColor: { attribute: 'labelColor', color: '#444444' },
         edgeLabelColor: { attribute: 'labelColor', color: '#a2b1c6' }
       })
+      if (this.settings.layout.type === 'forceAtlas2') {
+        this.autoRunFA2Layout()
+      }
     },
     updateStructure(attributeName, value) {
       this.settings.structure[attributeName] = value
@@ -410,41 +430,33 @@ export default {
       })
     },
     updateLayout(layoutType) {
-      if (layoutType !== this.settings.layout.type) {
-        const prevLayout = this.settings.layout.type
+      const prevLayout = this.settings.layout.type
+
+      // Change layout type? - restore layout settings or set default settings
+      if (layoutType !== prevLayout) {
         this.layoutOptionsArchive[prevLayout] = this.settings.layout.options
         this.settings.layout.options = this.layoutOptionsArchive[layoutType]
 
-        if (layoutType === 'forceAtlas2' && !this.settings.layout.options) {
-          const sensibleSettings = forceAtlas2.inferSettings(this.graph)
-          this.settings.layout.options = {
-            adjustSizes: false,
-            barnesHutOptimize: false,
-            barnesHutTheta: 0.5,
-            edgeWeightInfluence: 1,
-            gravity: 1,
-            linLogMode: false,
-            outboundAttractionDistribution: false,
-            scalingRatio: 1,
-            slowDown: 1,
-            strongGravityMode: false,
-            ...sensibleSettings
-          }
-        } else if (layoutType === 'random' && !this.settings.layout.options) {
-          this.settings.layout.options = {
-            seedValue: 1
-          }
-        } else if (
-          layoutType === 'circlepack' &&
-          !this.settings.layout.options
-        ) {
-          this.settings.layout.options = {
-            seedValue: 1
+        if (!this.settings.layout.options) {
+          if (layoutType === 'forceAtlas2') {
+            this.setRecommendedFA2Settings()
+          } else if (['random', 'circlepack'].includes(layoutType)) {
+            this.settings.layout.options = {
+              seedValue: 1
+            }
           }
         }
         this.settings.layout.type = layoutType
       }
 
+      // In any case kill FA2 if it exists
+      if (this.fa2Layout) {
+        if (this.fa2Layout.isRunning()) {
+          this.stopFA2Layout()
+        }
+        this.fa2Layout.kill()
+      }
+
       if (layoutType === 'circular') {
         circular.assign(this.graph)
         return
@@ -491,27 +503,99 @@ export default {
       }
 
       if (layoutType === 'forceAtlas2') {
-        if (this.fa2Layout) {
-          this.fa2Layout.kill()
+        if (
+          !this.graph.someNode(
+            (nodeKey, attributes) =>
+              typeof attributes.x === 'number' &&
+              typeof attributes.y === 'number'
+          )
+        ) {
+          circular.assign(this.graph)
         }
+
         this.fa2Layout = markRaw(
           new FA2Layout(this.graph, {
             getEdgeWeight: (_, attr) =>
-              attr.data[this.settings.layout.options.weightSource || 'weight'],
+              this.settings.layout.options.weightSource
+                ? attr.data[this.settings.layout.options.weightSource]
+                : 1,
             settings: this.settings.layout.options
           })
         )
+        if (layoutType !== prevLayout) {
+          this.autoRunFA2Layout()
+        }
       }
     },
     toggleFA2Layout() {
       if (this.fa2Layout.isRunning()) {
-        this.fa2Running = false
-        this.fa2Layout.stop()
+        this.stopFA2Layout()
       } else {
         this.fa2Running = true
         this.fa2Layout.start()
       }
     },
+    stopFA2Layout() {
+      this.fa2Running = false
+      this.fa2Layout.stop()
+      if (this.checkIteration) {
+        this.fa2Layout.worker.removeEventListener(
+          'message',
+          this.checkIteration
+        )
+        this.checkIteration = null
+      }
+    },
+    autoRunFA2Layout() {
+      if (this.fa2Layout.isRunning()) {
+        this.stopFA2Layout()
+      }
+
+      let iteration = 1
+      this.checkIteration = () => {
+        if (
+          iteration === this.settings.layout.options.initialIterationsAmount
+        ) {
+          this.stopFA2Layout()
+        }
+        iteration++
+      }
+      this.fa2Layout.worker.addEventListener('message', this.checkIteration)
+      this.fa2Running = true
+      this.fa2Layout.start()
+    },
+    setRecommendedFA2Settings() {
+      const sensibleSettings = forceAtlas2.inferSettings(this.graph)
+      this.settings.layout.options = {
+        initialIterationsAmount: 50,
+        adjustSizes: false,
+        barnesHutOptimize: false,
+        barnesHutTheta: 0.5,
+        edgeWeightInfluence: 0,
+        gravity: 1,
+        linLogMode: false,
+        outboundAttractionDistribution: false,
+        scalingRatio: 1,
+        slowDown: 1,
+        strongGravityMode: false,
+        ...sensibleSettings
+      }
+      if (
+        [Infinity, -Infinity].includes(this.settings.layout.options.slowDown)
+      ) {
+        this.settings.layout.options.slowDown = 1
+      }
+    },
+    resetFA2LayoutSettings() {
+      if (this.initOptions?.layout.type === 'forceAtlas2') {
+        this.settings.layout = JSON.parse(
+          JSON.stringify(this.initOptions.layout)
+        )
+      } else {
+        this.setRecommendedFA2Settings()
+      }
+      this.updateLayout(this.settings.layout.type)
+    },
     saveAsPng() {
       return downloadAsPNG(this.renderer, {
         backgroundColor: this.settings.style.backgroundColor
@@ -534,4 +618,14 @@ export default {
 :deep(.customPickerContainer) {
   float: right;
 }
+.force-atlas-buttons {
+  display: flex;
+  width: 100%;
+  gap: 16px;
+}
+
+.force-atlas-buttons :deep(button) {
+  flex-grow: 1;
+  flex-basis: 0;
+}
 </style>
diff --git a/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/index.vue b/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/index.vue
index 0fd5960..930fe43 100644
--- a/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/index.vue
+++ b/src/views/MainView/Workspace/Tabs/Tab/DataView/Graph/index.vue
@@ -71,8 +71,10 @@ export default {
     },
     async handleResize() {
       const renderer = this.$refs.graphEditor.renderer
-      renderer.refresh()
-      renderer.getCamera().setState({ x: 0.5, y: 0.5 })
+      if (renderer) {
+        renderer.refresh()
+        renderer.getCamera().setState({ x: 0.5, y: 0.5 })
+      }
     }
   }
 }