fix lint

package-lock.json

@@ -1,12 +1,13 @@
 {
   "name": "sqliteviz",
-  "version": "0.28.2",
+  "version": "0.29.0",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "sqliteviz",
-      "version": "0.28.2",
+      "version": "0.29.0",
+      "hasInstallScript": true,
       "license": "Apache-2.0",
       "dependencies": {
         "@sigma/export-image": "^3.0.0",
@@ -29,7 +30,7 @@
         "react-chart-editor": "^0.46.1",
         "react-dom": "^16.14.0",
         "seedrandom": "^3.0.5",
-        "sigma": "^3.0.1",
+        "sigma": "3.0.2",
         "sql.js": "file:./lib/sql-js",
         "tiny-emitter": "^2.1.0",
         "tinycolor2": "^1.4.2",
@@ -64,6 +65,8 @@
         "karma-spec-reporter": "^0.0.36",
         "karma-vite": "^1.0.5",
         "mocha": "^5.2.0",
+        "patch-package": "^8.0.1",
+        "postinstall-postinstall": "^2.1.0",
         "prettier": "3.5.3",
         "process": "^0.11.10",
         "url-loader": "^4.1.1",
@@ -3093,6 +3096,12 @@
       "license": "Apache-2.0",
       "peer": true
     },
+    "node_modules/@yarnpkg/lockfile": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/@yarnpkg/lockfile/-/lockfile-1.1.0.tgz",
+      "integrity": "sha512-GpSwvyXOcOOlV70vbnzjj4fW5xW/FdUF6nQEt1ENy7m4ZCczi1+/buVUPAqmGfqznsORNFzUMjctTIp8a9tuCQ==",
+      "dev": true
+    },
     "node_modules/abbrev": {
       "version": "2.0.0",
       "license": "ISC",
@@ -4776,6 +4785,21 @@
         "node": ">=6.0"
       }
     },
+    "node_modules/ci-info": {
+      "version": "3.9.0",
+      "resolved": "https://registry.npmjs.org/ci-info/-/ci-info-3.9.0.tgz",
+      "integrity": "sha512-NIxF55hv4nSqQswkAeiOi1r83xy8JldOFDTWiug55KBu9Jnblncd2U6ViHmYgHf01TPZS77NJBhBMKdWj9HQMQ==",
+      "dev": true,
+      "funding": [
+        {
+          "type": "github",
+          "url": "https://github.com/sponsors/sibiraj-s"
+        }
+      ],
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/cipher-base": {
       "version": "1.0.6",
       "dev": true,
@@ -7809,6 +7833,15 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/find-yarn-workspace-root": {
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/find-yarn-workspace-root/-/find-yarn-workspace-root-2.0.0.tgz",
+      "integrity": "sha512-1IMnbjt4KzsQfnhnzNd8wUEgXZ44IzZaZmnLYx7D5FZlaHt2gW20Cri8Q+E/t5tIj4+epTBub+2Zxu/vNILzqQ==",
+      "dev": true,
+      "dependencies": {
+        "micromatch": "^4.0.2"
+      }
+    },
     "node_modules/flat-cache": {
       "version": "3.2.0",
       "dev": true,
@@ -10358,11 +10391,36 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/json-stable-stringify": {
+      "version": "1.3.0",
+      "resolved": "https://registry.npmjs.org/json-stable-stringify/-/json-stable-stringify-1.3.0.tgz",
+      "integrity": "sha512-qtYiSSFlwot9XHtF9bD9c7rwKjr+RecWT//ZnPvSmEjpV5mmPOCN4j8UjY5hbjNkOwZ/jQv3J6R1/pL7RwgMsg==",
+      "dev": true,
+      "dependencies": {
+        "call-bind": "^1.0.8",
+        "call-bound": "^1.0.4",
+        "isarray": "^2.0.5",
+        "jsonify": "^0.0.1",
+        "object-keys": "^1.1.1"
+      },
+      "engines": {
+        "node": ">= 0.4"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
     "node_modules/json-stable-stringify-without-jsonify": {
       "version": "1.0.1",
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/json-stable-stringify/node_modules/isarray": {
+      "version": "2.0.5",
+      "resolved": "https://registry.npmjs.org/isarray/-/isarray-2.0.5.tgz",
+      "integrity": "sha512-xHjhDr3cNBK0BzdUJSPXZntQUx/mwMS5Rw4A7lPJ90XGAO6ISP/ePDNuo0vhqOZU+UD5JoodwCAAoZQd3FeAKw==",
+      "dev": true
+    },
     "node_modules/json-stringify-pretty-compact": {
       "version": "4.0.0",
       "license": "MIT"
@@ -10385,6 +10443,15 @@
         "graceful-fs": "^4.1.6"
       }
     },
+    "node_modules/jsonify": {
+      "version": "0.0.1",
+      "resolved": "https://registry.npmjs.org/jsonify/-/jsonify-0.0.1.tgz",
+      "integrity": "sha512-2/Ki0GcmuqSrgFyelQq9M05y7PS0mEwuIzrf3f1fPqkVDVRvZrPZtVSMHxdgo8Aq0sxAOb/cr2aqqA3LeWHVPg==",
+      "dev": true,
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
     "node_modules/jsonpointer": {
       "version": "5.0.1",
       "dev": true,
@@ -10683,6 +10750,15 @@
         "node": ">=0.10.0"
       }
     },
+    "node_modules/klaw-sync": {
+      "version": "6.0.0",
+      "resolved": "https://registry.npmjs.org/klaw-sync/-/klaw-sync-6.0.0.tgz",
+      "integrity": "sha512-nIeuVSzdCCs6TDPTqI8w1Yre34sSq7AkZ4B3sfOBbI2CgVSB4Du4aLQijFU2+lhAFCwt9+42Hel6lQNIv6AntQ==",
+      "dev": true,
+      "dependencies": {
+        "graceful-fs": "^4.1.11"
+      }
+    },
     "node_modules/lazy-cache": {
       "version": "1.0.4",
       "dev": true,
@@ -12318,6 +12394,22 @@
         "wrappy": "1"
       }
     },
+    "node_modules/open": {
+      "version": "7.4.2",
+      "resolved": "https://registry.npmjs.org/open/-/open-7.4.2.tgz",
+      "integrity": "sha512-MVHddDVweXZF3awtlAS+6pgKLlm/JgxZ90+/NBurBoQctVOOB/zDdVjcyPzQ+0laDGbsWgrRkflI65sQeOgT9Q==",
+      "dev": true,
+      "dependencies": {
+        "is-docker": "^2.0.0",
+        "is-wsl": "^2.1.1"
+      },
+      "engines": {
+        "node": ">=8"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/optimist": {
       "version": "0.6.1",
       "dev": true,
@@ -12550,6 +12642,106 @@
         "node": ">=0.10.0"
       }
     },
+    "node_modules/patch-package": {
+      "version": "8.0.1",
+      "resolved": "https://registry.npmjs.org/patch-package/-/patch-package-8.0.1.tgz",
+      "integrity": "sha512-VsKRIA8f5uqHQ7NGhwIna6Bx6D9s/1iXlA1hthBVBEbkq+t4kXD0HHt+rJhf/Z+Ci0F/HCB2hvn0qLdLG+Qxlw==",
+      "dev": true,
+      "dependencies": {
+        "@yarnpkg/lockfile": "^1.1.0",
+        "chalk": "^4.1.2",
+        "ci-info": "^3.7.0",
+        "cross-spawn": "^7.0.3",
+        "find-yarn-workspace-root": "^2.0.0",
+        "fs-extra": "^10.0.0",
+        "json-stable-stringify": "^1.0.2",
+        "klaw-sync": "^6.0.0",
+        "minimist": "^1.2.6",
+        "open": "^7.4.2",
+        "semver": "^7.5.3",
+        "slash": "^2.0.0",
+        "tmp": "^0.2.4",
+        "yaml": "^2.2.2"
+      },
+      "bin": {
+        "patch-package": "index.js"
+      },
+      "engines": {
+        "node": ">=14",
+        "npm": ">5"
+      }
+    },
+    "node_modules/patch-package/node_modules/fs-extra": {
+      "version": "10.1.0",
+      "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-10.1.0.tgz",
+      "integrity": "sha512-oRXApq54ETRj4eMiFzGnHWGy+zo5raudjuxN0b8H7s/RU2oW0Wvsx9O0ACRN/kRq9E8Vu/ReskGB5o3ji+FzHQ==",
+      "dev": true,
+      "dependencies": {
+        "graceful-fs": "^4.2.0",
+        "jsonfile": "^6.0.1",
+        "universalify": "^2.0.0"
+      },
+      "engines": {
+        "node": ">=12"
+      }
+    },
+    "node_modules/patch-package/node_modules/jsonfile": {
+      "version": "6.2.0",
+      "resolved": "https://registry.npmjs.org/jsonfile/-/jsonfile-6.2.0.tgz",
+      "integrity": "sha512-FGuPw30AdOIUTRMC2OMRtQV+jkVj2cfPqSeWXv1NEAJ1qZ5zb1X6z1mFhbfOB/iy3ssJCD+3KuZ8r8C3uVFlAg==",
+      "dev": true,
+      "dependencies": {
+        "universalify": "^2.0.0"
+      },
+      "optionalDependencies": {
+        "graceful-fs": "^4.1.6"
+      }
+    },
+    "node_modules/patch-package/node_modules/minimist": {
+      "version": "1.2.8",
+      "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz",
+      "integrity": "sha512-2yyAR8qBkN3YuheJanUpWC5U3bb5osDywNB8RzDVlDwDHbocAJveqqj1u8+SVD7jkWT4yvsHCpWqqWqAxb0zCA==",
+      "dev": true,
+      "funding": {
+        "url": "https://github.com/sponsors/ljharb"
+      }
+    },
+    "node_modules/patch-package/node_modules/semver": {
+      "version": "7.7.4",
+      "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.4.tgz",
+      "integrity": "sha512-vFKC2IEtQnVhpT78h1Yp8wzwrf8CM+MzKMHGJZfBtzhZNycRFnXsHk6E5TxIkkMsgNS7mdX3AGB7x2QM2di4lA==",
+      "dev": true,
+      "bin": {
+        "semver": "bin/semver.js"
+      },
+      "engines": {
+        "node": ">=10"
+      }
+    },
+    "node_modules/patch-package/node_modules/universalify": {
+      "version": "2.0.1",
+      "resolved": "https://registry.npmjs.org/universalify/-/universalify-2.0.1.tgz",
+      "integrity": "sha512-gptHNQghINnc/vTGIk0SOFGFNXw7JVrlRUtConJRlvaw6DuX0wO5Jeko9sWrMBhh+PsYAZ7oXAiOnf/UKogyiw==",
+      "dev": true,
+      "engines": {
+        "node": ">= 10.0.0"
+      }
+    },
+    "node_modules/patch-package/node_modules/yaml": {
+      "version": "2.8.3",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.3.tgz",
+      "integrity": "sha512-AvbaCLOO2Otw/lW5bmh9d/WEdcDFdQp2Z2ZUH3pX9U2ihyUY0nvLv7J6TrWowklRGPYbB/IuIMfYgxaCPg5Bpg==",
+      "dev": true,
+      "bin": {
+        "yaml": "bin.mjs"
+      },
+      "engines": {
+        "node": ">= 14.6"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/eemeli"
+      }
+    },
     "node_modules/path-browserify": {
       "version": "1.0.1",
       "dev": true,
@@ -12994,6 +13186,13 @@
       "version": "4.2.0",
       "license": "MIT"
     },
+    "node_modules/postinstall-postinstall": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/postinstall-postinstall/-/postinstall-postinstall-2.1.0.tgz",
+      "integrity": "sha512-7hQX6ZlZXIoRiWNrbMQaLzUUfH+sSx39u8EJ9HYuDc1kLo9IXKWjM5RSquZN1ad5GnH8CGFM78fsAAQi3OKEEQ==",
+      "dev": true,
+      "hasInstallScript": true
+    },
     "node_modules/potpack": {
       "version": "1.0.2",
       "license": "ISC"
@@ -14454,6 +14653,15 @@
         "node": ">=4"
       }
     },
+    "node_modules/slash": {
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/slash/-/slash-2.0.0.tgz",
+      "integrity": "sha512-ZYKh3Wh2z1PpEXWr0MpSBZ0V6mZHAQfYevttO11c51CaWjGTaadiKZ+wVt1PbMlDV5qhMFslpZCemhwOK7C89A==",
+      "dev": true,
+      "engines": {
+        "node": ">=6"
+      }
+    },
     "node_modules/smob": {
       "version": "1.5.0",
       "dev": true,
@@ -15571,9 +15779,10 @@
       "license": "ISC"
     },
     "node_modules/tmp": {
-      "version": "0.2.3",
+      "version": "0.2.5",
+      "resolved": "https://registry.npmjs.org/tmp/-/tmp-0.2.5.tgz",
+      "integrity": "sha512-voyz6MApa1rQGUxT3E+BK7/ROe8itEx7vD8/HEvt4xwXucvQ5G5oeEiHkmHZJuBO21RpOf+YYm9MOivj709jow==",
       "dev": true,
-      "license": "MIT",
       "engines": {
         "node": ">=14.14"
       }

package.json

@@ -10,7 +10,8 @@
     "serve": "vite preview",
     "test": "karma start karma.conf.cjs",
     "lint": "eslint --ext .js,.vue --ignore-path .gitignore --fix src",
-    "format": "prettier .  --write"
+    "format": "prettier .  --write",
+    "postinstall": "patch-package"
   },
   "dependencies": {
     "@sigma/export-image": "^3.0.0",
@@ -33,7 +34,7 @@
     "react-chart-editor": "^0.46.1",
     "react-dom": "^16.14.0",
     "seedrandom": "^3.0.5",
-    "sigma": "^3.0.1",
+    "sigma": "3.0.2",
     "sql.js": "file:./lib/sql-js",
     "tiny-emitter": "^2.1.0",
     "tinycolor2": "^1.4.2",
@@ -68,6 +69,8 @@
     "karma-spec-reporter": "^0.0.36",
     "karma-vite": "^1.0.5",
     "mocha": "^5.2.0",
+    "patch-package": "^8.0.1",
+    "postinstall-postinstall": "^2.1.0",
     "prettier": "3.5.3",
     "process": "^0.11.10",
     "url-loader": "^4.1.1",

patches/sigma+3.0.2.patch

@@ -0,0 +1,24 @@
+diff --git a/node_modules/sigma/dist/colors-beb06eb2.esm.js b/node_modules/sigma/dist/colors-beb06eb2.esm.js
+index b7130d1..bf101b6 100644
+--- a/node_modules/sigma/dist/colors-beb06eb2.esm.js
++++ b/node_modules/sigma/dist/colors-beb06eb2.esm.js
+@@ -51,7 +51,6 @@ function _nonIterableRest() {
+ function _slicedToArray(r, e) {
+   return _arrayWithHoles(r) || _iterableToArrayLimit(r, e) || _unsupportedIterableToArray(r, e) || _nonIterableRest();
+ }
+-
+ var HTML_COLORS = {
+   black: "#000000",
+   silver: "#C0C0C0",
+@@ -267,7 +266,10 @@ for (var htmlColor in HTML_COLORS) {
+   FLOAT_COLOR_CACHE[HTML_COLORS[htmlColor]] = FLOAT_COLOR_CACHE[htmlColor];
+ }
+ function rgbaToFloat(r, g, b, a, masking) {
+-  INT32[0] = a << 24 | b << 16 | g << 8 | r;
++  const r_= Math.floor(r * a / 255)
++  const g_= Math.floor(g * a / 255)
++  const b_= Math.floor(b * a / 255)
++  INT32[0] = a << 24 | b_ << 16 | g_ << 8 | r_;
+   if (masking) INT32[0] = INT32[0] & 0xfeffffff;
+   return FLOAT32[0];
+ }

src/components/Graph/ForceAtlasSeedLayoutSettings.vue

@@ -0,0 +1,86 @@
+<template>
+  <Field label="Initial algorithm">
+    <Dropdown
+      :options="layoutOptions"
+      :value="modelValue.initialAlgorithm"
+      :clearable="false"
+      className="test_fa2_initial_layout_algorithm_select"
+      @change="updateInitialAlgorithm"
+    />
+  </Field>
+
+  <component
+    :is="layoutSettingsComponentMap[modelValue.initialAlgorithm]"
+    v-if="modelValue.initialAlgorithm !== 'circular'"
+    :modelValue="modelValue"
+    :keyOptions="keyOptions"
+    @update:model-value="$emit('update:modelValue', $event)"
+  />
+</template>
+
+<script>
+import { markRaw } from 'vue'
+import { applyPureReactInVue } from 'veaury'
+import Field from 'react-chart-editor/lib/components/fields/Field'
+import NumericInput from 'react-chart-editor/lib/components/widgets/NumericInput'
+import Dropdown from 'react-chart-editor/lib/components/widgets/Dropdown'
+import 'react-chart-editor/lib/react-chart-editor.css'
+import CirclePackLayoutSettings from '@/components/Graph/CirclePackLayoutSettings.vue'
+import RandomLayoutSettings from '@/components/Graph/RandomLayoutSettings.vue'
+
+export default {
+  components: {
+    Field: applyPureReactInVue(Field),
+    Dropdown: applyPureReactInVue(Dropdown),
+    NumericInput: applyPureReactInVue(NumericInput),
+    RandomLayoutSettings,
+    CirclePackLayoutSettings
+  },
+  props: {
+    modelValue: Object,
+    keyOptions: Array
+  },
+  emits: ['update:modelValue'],
+  data() {
+    return {
+      layoutOptions: markRaw([
+        { label: 'Circular', value: 'circular' },
+        { label: 'Random', value: 'random' },
+        { label: 'Circle pack', value: 'circlepack' }
+      ]),
+      layoutSettingsComponentMap: markRaw({
+        random: RandomLayoutSettings,
+        circlepack: CirclePackLayoutSettings
+      }),
+      defaultSeedLayoutSettings: {
+        circular: { initialAlgorithm: 'circular' },
+        random: { initialAlgorithm: 'random', seedValue: 1 },
+        circlepack: {
+          initialAlgorithm: 'circlepack',
+          hierarchyAttributes: [],
+          seedValue: 1
+        }
+      }
+    }
+  },
+  methods: {
+    updateInitialAlgorithm(newAlgorithm) {
+      const newSettings = {
+        ...this.modelValue
+      }
+
+      const prevAlgorithmSettings =
+        this.defaultSeedLayoutSettings[this.modelValue.initialAlgorithm]
+      Object.keys(prevAlgorithmSettings).forEach(key => {
+        delete newSettings[key]
+        prevAlgorithmSettings[key] = this.modelValue[key]
+      })
+
+      this.$emit('update:modelValue', {
+        ...newSettings,
+        ...this.defaultSeedLayoutSettings[newAlgorithm]
+      })
+    }
+  }
+}
+</script>

src/components/Graph/GraphEditor.vue

@@ -171,6 +171,17 @@
             />
           </Fold>
           <template v-if="settings.layout.type === 'forceAtlas2'">
+            <Fold name="Seed layout">
+              <Field>
+                If you already built a graph using another layout, the initial
+                algorithm doesn't apply unless you restart it.
+              </Field>
+              <ForceAtlasSeedLayoutSettings
+                v-model="settings.layout.options"
+                :keyOptions="keysOptions"
+                @update:model-value="updateLayout(settings.layout.type)"
+              />
+            </Fold>
             <Fold name="Advanced layout settings">
               <AdvancedForceAtlasLayoutSettings
                 v-model="settings.layout.options"
@@ -182,6 +193,7 @@
               <Button
                 variant="secondary"
                 class="test_fa2_reset"
+                title="Set the settings to default or previously saved ones."
                 @click="resetFA2LayoutSettings"
               >
                 Reset
@@ -192,16 +204,25 @@
                 @click="toggleFA2Layout"
               >
                 <template #node:icon>
-                  <div
+                  <div>
-                    :style="{
-                      padding: '0 3px'
-                    }"
-                  >
                     <RunIcon v-if="!fa2Running" />
-                    <StopIcon v-else />
+                    <PauseIcon v-else />
                   </div>
                 </template>
-                {{ fa2Running ? 'Stop' : 'Start' }}
+                {{ fa2Running ? 'Pause' : 'Continue' }}
+              </Button>
+              <Button
+                variant="primary"
+                class="test_fa2_restart"
+                title="Clear node coordinates and run the layout algorithm anew."
+                @click="restartFA2Layout"
+              >
+                <template #node:icon>
+                  <div>
+                    <RestartIcon />
+                  </div>
+                </template>
+                Restart
               </Button>
             </div>
           </template>
@@ -234,13 +255,15 @@ 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 ForceAtlasSeedLayoutSettings from '@/components/Graph/ForceAtlasSeedLayoutSettings.vue'
 // eslint-disable-next-line max-len
 import AdvancedForceAtlasLayoutSettings from '@/components/Graph/AdvancedForceAtlasLayoutSettings.vue'
 import CirclePackLayoutSettings from '@/components/Graph/CirclePackLayoutSettings.vue'
 import FA2Layout from 'graphology-layout-forceatlas2/worker'
 import * as forceAtlas2 from 'graphology-layout-forceatlas2'
 import RunIcon from '@/components/svg/run.vue'
-import StopIcon from '@/components/svg/stop.vue'
+import RestartIcon from '@/components/svg/restart.vue'
+import PauseIcon from '@/components/svg/pause.vue'
 import { downloadAsPNG, drawOnCanvas } from '@sigma/export-image'
 import {
   buildNodes,
@@ -248,7 +271,8 @@ import {
   updateNodes,
   updateEdges,
   reduceNodes,
-  reduceEdges
+  reduceEdges,
+  clearNodeCoordinates
 } from '@/lib/graphHelper'
 import Graph from 'graphology'
 import { circular, random, circlepack } from 'graphology-layout'
@@ -273,14 +297,16 @@ export default {
     Button: applyPureReactInVue(Button),
     ColorPicker: applyPureReactInVue(ColorPicker),
     RunIcon,
-    StopIcon,
+    RestartIcon,
+    PauseIcon,
     RandomLayoutSettings,
     CirclePackLayoutSettings,
     NodeColorSettings,
     NodeSizeSettings,
     EdgeSizeSettings,
     EdgeColorSettings,
-    AdvancedForceAtlasLayoutSettings
+    AdvancedForceAtlasLayoutSettings,
+    ForceAtlasSeedLayoutSettings
   },
   inject: ['tabLayout'],
   props: {
@@ -311,6 +337,12 @@ export default {
         circlepack: CirclePackLayoutSettings,
         forceAtlas2: ForceAtlasLayoutSettings
       }),
+      layoutMethodMap: markRaw({
+        circular: this.applyCircularLayout,
+        random: this.applyRandomLayout,
+        circlepack: this.applyCirclePackLayout,
+        forceAtlas2: this.applyFA2Layout
+      }),
       selectedNodeId: undefined,
       hoveredNodeId: undefined,
       selectedEdgeId: undefined,
@@ -642,19 +674,21 @@ export default {
         this.fa2Layout.kill()
       }
 
-      if (layoutType === 'circular') {
+      this.layoutMethodMap[layoutType]()
-        circular.assign(this.graph)
-        return
-      }
 
-      if (layoutType === 'random') {
+      if (layoutType === 'forceAtlas2' && layoutType !== prevLayout) {
+        this.autoRunFA2Layout()
+      }
+    },
+    applyCircularLayout() {
+      circular.assign(this.graph)
+    },
+    applyRandomLayout() {
       random.assign(this.graph, {
         rng: seedrandom(this.settings.layout.options.seedValue)
       })
-        return
+    },
-      }
+    applyCirclePackLayout() {
-
-      if (layoutType === 'circlepack') {
       this.graph.forEachNode(nodeId => {
         this.graph.updateNode(nodeId, attributes => {
           const newAttributes = { ...attributes }
@@ -684,33 +718,32 @@ export default {
           ) || [],
         rng: seedrandom(this.settings.layout.options.seedValue)
       })
-        return
+    },
-      }
+    applyFA2Layout() {
-
-      if (layoutType === 'forceAtlas2') {
       if (
         !this.graph.someNode(
           (nodeKey, attributes) =>
-              typeof attributes.x === 'number' &&
+            typeof attributes.x === 'number' && typeof attributes.y === 'number'
-              typeof attributes.y === 'number'
         )
       ) {
-          circular.assign(this.graph)
+        this.layoutMethodMap[this.settings.layout.options.initialAlgorithm]()
       }
 
+      const fa2settings = { ...this.settings.layout.options }
+      // delete all custom settings because they can break the algorithm running
+      delete fa2settings.initialAlgorithm
+      delete fa2settings.seedValue
+      delete fa2settings.initialIterationsAmount
+      delete fa2settings.hierarchyAttributes
       this.fa2Layout = markRaw(
         new FA2Layout(this.graph, {
           getEdgeWeight: (_, attr) =>
             this.settings.layout.options.weightSource
               ? attr.data[this.settings.layout.options.weightSource]
               : 1,
-            settings: this.settings.layout.options
+          settings: fa2settings
         })
       )
-        if (layoutType !== prevLayout) {
-          this.autoRunFA2Layout()
-        }
-      }
     },
     toggleFA2Layout() {
       if (this.fa2Layout.isRunning()) {
@@ -731,6 +764,15 @@ export default {
         this.checkIteration = null
       }
     },
+    restartFA2Layout() {
+      if (this.fa2Layout.isRunning()) {
+        this.stopFA2Layout()
+      }
+      this.fa2Layout.kill()
+      clearNodeCoordinates(this.graph)
+      this.applyFA2Layout()
+      this.autoRunFA2Layout()
+    },
     autoRunFA2Layout() {
       let iteration = 1
       this.checkIteration = () => {
@@ -748,6 +790,7 @@ export default {
     setRecommendedFA2Settings() {
       const sensibleSettings = forceAtlas2.default.inferSettings(this.graph)
       this.settings.layout.options = {
+        initialAlgorithm: 'circular',
         initialIterationsAmount: 50,
         adjustSizes: false,
         barnesHutOptimize: false,
@@ -809,4 +852,8 @@ export default {
   flex-grow: 1;
   flex-basis: 0;
 }
+
+.force-atlas-buttons :deep(.button__icon > div) {
+  padding: 0 3px;
+}
 </style>

src/components/Graph/RandomLayoutSettings.vue

@@ -1,5 +1,5 @@
 <template>
-  <Field label="Seed value">
+  <Field label="Seed value" fieldContainerClassName="test_seed_value">
     <NumericInput
       :value="modelValue.seedValue"
       @update="update('seedValue', $event)"

src/components/svg/pause.vue

@@ -0,0 +1,27 @@
+<template>
+  <svg
+    width="18"
+    height="18"
+    viewBox="0 0 18 18"
+    fill="none"
+    xmlns="http://www.w3.org/2000/svg"
+  >
+    <path
+      d="M3 4C3 3.44772 3.14924 3 3.33333 3H6.66667C6.85076 3 7 3.44772 7 
+      4V14C7 14.5523 6.85076 15 6.66667 15H3.33333C3.14924 15 3 14.5523 3 14V4Z"
+      fill="#A2B1C6"
+    />
+    <path
+      d="M11 4C11 3.44772 11.1492 3 11.3333 3H14.6667C14.8508 3 15 3.44772 15 
+      4V14C15 14.5523 14.8508 15 14.6667 15H11.3333C11.1492 15 11 14.5523 11 
+      14V4Z"
+      fill="#A2B1C6"
+    />
+  </svg>
+</template>
+
+<script>
+export default {
+  name: 'PauseIcon'
+}
+</script>

src/components/svg/restart.vue

@@ -0,0 +1,36 @@
+<template>
+  <svg
+    width="18"
+    height="18"
+    viewBox="0 0 18 18"
+    fill="none"
+    xmlns="http://www.w3.org/2000/svg"
+  >
+    <path
+      d="M7.34708 3.32922C8.63088 2.90468 10.017 2.90308 11.3022 
+      3.32434C11.9084 3.52308 12.4768 3.8114 12.9906 4.1759V3.34387C12.9906 
+      2.79159 13.4384 2.34387 13.9906 2.34387C14.5429 2.34387 14.9906 2.79159 
+      14.9906 3.34387V6.67102C14.9906 7.22331 14.5429 7.67102 13.9906 
+      7.67102H10.6635C10.1112 7.67102 9.66349 7.22331 9.66349 6.67102C9.66351 
+      6.11876 10.1112 5.67102 10.6635 5.67102H11.6313C11.3351 5.4851 11.0154 
+      5.33498 10.6791 5.22473C9.80069 4.93681 8.85289 4.93738 7.97501 
+      5.22766C7.09726 5.51795 6.33574 6.08228 5.80216 6.83704C5.26867 
+      7.59191 4.99088 8.49846 5.01017 9.42297C5.02954 10.3475 5.34482 
+      11.2417 5.90958 11.9738C6.47435 12.7058 7.25871 13.237 8.14787 
+      13.4904C9.03716 13.7437 9.9843 13.7055 10.85 13.381C11.7157 13.0565 
+      12.4548 12.463 12.9584 11.6876C13.2592 11.2244 13.879 11.0929 14.3422 
+      11.3937C14.805 11.6945 14.9366 12.3135 14.6361 12.7765C13.8996 13.9106 
+      12.8185 14.7794 11.5522 15.254C10.2859 15.7287 8.90058 15.7846 7.60001 
+      15.4142C6.2994 15.0437 5.15167 14.2661 4.3256 13.1954C3.49956 12.1247 
+      3.03849 10.8169 3.01017 9.46497C2.98191 8.1131 3.38782 6.7872 4.16837 
+      5.68274C4.94892 4.57842 6.06331 3.75379 7.34708 3.32922Z"
+      fill="#A2B1C6"
+    />
+  </svg>
+</template>
+
+<script>
+export default {
+  name: 'RestartIcon'
+}
+</script>

src/components/svg/stop.vue

@@ -1,21 +0,0 @@
-<template>
-  <svg
-    width="18"
-    height="18"
-    viewBox="0 0 18 18"
-    fill="none"
-    xmlns="http://www.w3.org/2000/svg"
-  >
-    <path
-      d="M3 4C3 3.44772 3.44772 3 4 3H14C14.5523 3 15 3.44772 15 4V14C15 
-      14.5523 14.5523 15 14 15H4C3.44772 15 3 14.5523 3 14V4Z"
-      fill="#A2B1C6"
-    />
-  </svg>
-</template>
-
-<script>
-export default {
-  name: 'StopIcon'
-}
-</script>

src/lib/graphHelper.js

@@ -36,6 +36,13 @@ export function dataSourceIsValid(dataSources) {
   }
 }
 
+export function clearNodeCoordinates(graph) {
+  graph.forEachNode((nodeId, attributes) => {
+    attributes.x = undefined
+    attributes.y = undefined
+  })
+}
+
 export function buildNodes(graph, dataSources, options) {
   const docColumn = Object.keys(dataSources)[0]
   const { objectType, nodeId } = options.structure
@@ -144,6 +151,9 @@ export function reduceNodes(nodeId, nodeData, interactionState, settings) {
   if (selectedNodeId || hoveredNodeId || hoveredEdgeId || selectedEdgeId) {
     res.zIndex = 2
     res.highlighted = nodeId === selectedNodeId || nodeId === hoveredNodeId
+    if (res.highlighted) {
+      res.labelColor = 'black'
+    }
 
     const isInHoveredFamily =
       nodeId === hoveredNodeId ||

src/lib/storedInquiries/_migrations.js

@@ -17,6 +17,17 @@ export default {
       })
     }
 
+    if (installedVersion < 4) {
+      inquiries.forEach(inquiry => {
+        if (
+          inquiry.viewType === 'graph' &&
+          inquiry.viewOptions.layout.type === 'forceAtlas2'
+        ) {
+          inquiry.viewOptions.layout.options.initialAlgorithm = 'circular'
+        }
+      })
+    }
+
     return inquiries
   }
 }

src/lib/storedInquiries/index.js

@@ -5,9 +5,10 @@ import migration from './_migrations'
 
 const migrate = migration._migrate
 const myInquiriesKey = 'myInquiries'
+const latestVersion = 4
 
 export default {
-  version: 3,
+  version: latestVersion,
   myInquiriesKey,
   getStoredInquiries() {
     let myInquiries = JSON.parse(localStorage.getItem(myInquiriesKey))
@@ -21,8 +22,8 @@ export default {
       return []
     }
 
-    if (myInquiries.version === 2) {
+    if (myInquiries.version < latestVersion) {
-      myInquiries = migrate(2, myInquiries.inquiries)
+      myInquiries = migrate(myInquiries.version, myInquiries.inquiries)
       this.updateStorage(myInquiries)
       return myInquiries
     }
@@ -69,8 +70,8 @@ export default {
       // Turn data into array if they are not
       inquiryList = !Array.isArray(inquiries) ? [inquiries] : inquiries
       inquiryList = migrate(1, inquiryList)
-    } else if (inquiries.version === 2) {
+    } else if (inquiries.version < latestVersion) {
-      inquiryList = migrate(2, inquiries.inquiries)
+      inquiryList = migrate(inquiries.version, inquiries.inquiries)
     } else {
       inquiryList = inquiries.inquiries || []
     }
@@ -110,8 +111,8 @@ export default {
 
     if (!data.version) {
       return data.length > 0 ? migrate(1, data) : []
-    } else if (data.version === 2) {
+    } else if (data.version < latestVersion) {
-      return migrate(2, data.inquiries)
+      return migrate(data.version, data.inquiries)
     } else {
       return data.inquiries
     }

tests/components/Graph/GraphEditor.spec.js

@@ -1309,7 +1309,7 @@ describe('GraphEditor', () => {
 
     expect(startSpy.calledOnce).to.equal(true)
     await waitCondition(() => stopSpy.callCount === 1)
-    expect(wrapper.text()).to.contain('Start')
+    expect(wrapper.text()).to.contain('Continue')
 
     const coordinates = graph
       .export()
@@ -1349,6 +1349,7 @@ describe('GraphEditor', () => {
           layout: {
             type: 'forceAtlas2',
             options: {
+              initialAlgorithm: 'circular',
               initialIterationsAmount: 55,
               gravity: 1.5,
               scalingRatio: 1.2,
@@ -1383,7 +1384,7 @@ describe('GraphEditor', () => {
 
     expect(startSpy.calledOnce).to.equal(true)
     await waitCondition(() => stopSpy.callCount === 1)
-    expect(wrapper.text()).to.contain('Start')
+    expect(wrapper.text()).to.contain('Continue')
 
     const initialCoordinates = graph
       .export()
@@ -1397,7 +1398,7 @@ describe('GraphEditor', () => {
       new Event('blur', { bubbles: true })
     )
     // Call nextTick after setting number input,
-    // otherwise the value will be changed beck to initial for some reason
+    // otherwise the value will be changed back to initial for some reason
     await nextTick()
 
     expect(wrapper.vm.settings.layout.options.gravity).to.equal(12)
@@ -1405,6 +1406,30 @@ describe('GraphEditor', () => {
     // Algorithm wasn't called
     expect(startSpy.calledOnce).to.equal(true)
 
+    // Change initial algorithm
+    await wrapper
+      .find(
+        '.test_fa2_initial_layout_algorithm_select .dropdown-container .Select__indicator'
+      )
+      .wrapperElement.dispatchEvent(
+        new MouseEvent('mousedown', { bubbles: true })
+      )
+
+    await wrapper.findAll('.Select__menu .Select__option')[1].trigger('click')
+    await nextTick()
+    expect(wrapper.vm.settings.layout.options.initialAlgorithm).to.equal(
+      'random'
+    )
+
+    // Change seed value
+    const seedValueInput = wrapper.find('.test_seed_value input')
+    await seedValueInput.setValue(123)
+    seedValueInput.wrapperElement.dispatchEvent(
+      new Event('blur', { bubbles: true })
+    )
+    await nextTick()
+    expect(wrapper.vm.settings.layout.options.seedValue).to.equal(123)
+
     // Change scaling ratio
     const scalingInput = wrapper.find('.test_fa2_scaling input')
     await scalingInput.setValue(2)
@@ -1493,13 +1518,13 @@ describe('GraphEditor', () => {
       false
     )
 
-    // Click Start
+    // Click Continue
     const toggleButton = wrapper.find('button.test_fa2_toggle')
     await toggleButton.trigger('click')
-    expect(toggleButton.text()).to.contain('Stop')
+    expect(toggleButton.text()).to.contain('Pause')
     expect(startSpy.callCount).to.equal(2)
 
-    // Wait a bit and click Stop
+    // Wait a bit and click Pause
     await time.sleep(500)
     await toggleButton.trigger('click')
     expect(stopSpy.callCount).to.equal(2)
@@ -1513,9 +1538,10 @@ describe('GraphEditor', () => {
 
     // Click Reset
     await wrapper.find('button.test_fa2_reset').trigger('click')
-    expect(toggleButton.text()).to.contain('Start')
+    expect(toggleButton.text()).to.contain('Continue')
     expect(startSpy.callCount).to.equal(2)
     expect(wrapper.vm.settings.layout.options).to.eql({
+      initialAlgorithm: 'circular',
       initialIterationsAmount: 55,
       gravity: 1.5,
       scalingRatio: 1.2,
@@ -1533,6 +1559,148 @@ describe('GraphEditor', () => {
     wrapper.unmount()
   })
 
+  it('FA2: restarts and applies selected initial layout', async () => {
+    const stopSpy = sinon.spy(FA2Layout.prototype, 'stop')
+    const startSpy = sinon.spy(FA2Layout.prototype, 'start')
+    const wrapper = mount(GraphEditor, {
+      attachTo: document.body,
+      props: {
+        dataSources: {
+          doc: [
+            '{"type": 0, "node_id": 1, "size": 20}',
+            '{"type": 0, "node_id": 2, "size": 2}',
+            '{"type": 0, "node_id": 3, "size": 2}',
+            '{"type": 0, "node_id": 4, "size": 2}',
+            '{"type": 1, "source": 1, "target": 3, "wgt": 20}',
+            '{"type": 1, "source": 1, "target": 2, "wgt": 15}',
+            '{"type": 1, "source": 1, "target": 4, "wgt": 5}'
+          ]
+        },
+        initOptions: {
+          ...defaultInitOptions,
+          structure: {
+            nodeId: 'node_id',
+            objectType: 'type',
+            edgeSource: 'source',
+            edgeTarget: 'target'
+          },
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialAlgorithm: 'circular',
+              initialIterationsAmount: 55,
+              gravity: 1.5,
+              scalingRatio: 1.2,
+              adjustSizes: true,
+              barnesHutOptimize: true,
+              barnesHutTheta: 0.5,
+              strongGravityMode: false,
+              linLogMode: true,
+              outboundAttractionDistribution: false,
+              slowDown: 1,
+              weightSource: 'wgt',
+              edgeWeightInfluence: 0.5
+            }
+          }
+        },
+        showViewSettings: true
+      },
+      global: {
+        provide: {
+          tabLayout: { dataView: 'above' }
+        }
+      }
+    })
+
+    const graph = wrapper.vm.graph
+
+    const styleMenuItem = wrapper.findAll('.sidebar__group__title')[1]
+    await styleMenuItem.trigger('click')
+
+    const layoutMenuItem = wrapper.findAll('.sidebar__item')[4]
+    await layoutMenuItem.trigger('click')
+
+    expect(startSpy.calledOnce).to.equal(true)
+    await waitCondition(() => stopSpy.callCount === 1)
+
+    const initialCoordinates = graph
+      .export()
+      .nodes.map(node => `x:${node.attributes.x},y:${node.attributes.y}`)
+      .join()
+
+    // Change initial algorithm
+    await wrapper
+      .find(
+        '.test_fa2_initial_layout_algorithm_select .dropdown-container .Select__indicator'
+      )
+      .wrapperElement.dispatchEvent(
+        new MouseEvent('mousedown', { bubbles: true })
+      )
+
+    await wrapper.findAll('.Select__menu .Select__option')[1].trigger('click')
+    await nextTick()
+
+    // Click Restart
+    const restartButton = wrapper.find('button.test_fa2_restart')
+    await restartButton.trigger('click')
+    const toggleButton = wrapper.find('button.test_fa2_toggle')
+    expect(toggleButton.text()).to.contain('Pause')
+    expect(startSpy.callCount).to.equal(2)
+
+    // Wait until restarting finished
+    await waitCondition(() => stopSpy.callCount === 2)
+
+    const randomCoordinates1 = graph
+      .export()
+      .nodes.map(node => `x:${node.attributes.x},y:${node.attributes.y}`)
+      .join()
+
+    // Change seed value
+    const seedValueInput = wrapper.find('.test_seed_value input')
+    await seedValueInput.setValue(123)
+    seedValueInput.wrapperElement.dispatchEvent(
+      new Event('blur', { bubbles: true })
+    )
+    await nextTick()
+
+    // Click Restart
+    await restartButton.trigger('click')
+    expect(toggleButton.text()).to.contain('Pause')
+    expect(startSpy.callCount).to.equal(3)
+
+    // Wait until restarting finished
+    await waitCondition(() => stopSpy.callCount === 3)
+
+    const randomCoordinates2 = graph
+      .export()
+      .nodes.map(node => `x:${node.attributes.x},y:${node.attributes.y}`)
+      .join()
+
+    // Change seed value back to 1
+    await seedValueInput.setValue(1)
+    seedValueInput.wrapperElement.dispatchEvent(
+      new Event('blur', { bubbles: true })
+    )
+    await nextTick()
+
+    // Click Restart
+    await restartButton.trigger('click')
+
+    // Wait until restarting finished
+    await waitCondition(() => stopSpy.callCount === 4)
+
+    const randomCoordinates1After = graph
+      .export()
+      .nodes.map(node => `x:${node.attributes.x},y:${node.attributes.y}`)
+      .join()
+
+    expect(initialCoordinates).not.to.equal(randomCoordinates1)
+    expect(randomCoordinates1).not.to.equal(randomCoordinates2)
+    expect(randomCoordinates1).to.equal(randomCoordinates1After)
+
+    wrapper.unmount()
+  })
+
   it('FA2: resets parameters to default', async () => {
     const wrapper = mount(GraphEditor, {
       attachTo: document.body,
@@ -1603,6 +1771,26 @@ describe('GraphEditor', () => {
     )
     await nextTick()
 
+    // Change initial algorithm
+    await wrapper
+      .find(
+        '.test_fa2_initial_layout_algorithm_select .dropdown-container .Select__indicator'
+      )
+      .wrapperElement.dispatchEvent(
+        new MouseEvent('mousedown', { bubbles: true })
+      )
+
+    await wrapper.findAll('.Select__menu .Select__option')[1].trigger('click')
+    await nextTick()
+
+    // Change seed value
+    const seedValueInput = wrapper.find('.test_seed_value input')
+    await seedValueInput.setValue(123)
+    seedValueInput.wrapperElement.dispatchEvent(
+      new Event('blur', { bubbles: true })
+    )
+    await nextTick()
+
     // Change scaling ratio
     const scalingInput = wrapper.find('.test_fa2_scaling input')
     await scalingInput.setValue(2)
@@ -1671,6 +1859,8 @@ describe('GraphEditor', () => {
     await nextTick()
 
     expect(wrapper.vm.settings.layout.options).to.eql({
+      initialAlgorithm: 'random',
+      seedValue: 123,
       initialIterationsAmount: 120,
       gravity: 12,
       scalingRatio: 2,
@@ -1756,6 +1946,7 @@ describe('GraphEditor', () => {
           layout: {
             type: 'forceAtlas2',
             options: {
+              initialAlgorithm: 'circular',
               initialIterationsAmount: 50,
               gravity: 1.5,
               scalingRatio: 1.2,
@@ -1788,7 +1979,7 @@ describe('GraphEditor', () => {
     expect(startSpy.calledOnce).to.equal(true)
     await waitCondition(() => stopSpy.callCount === 1)
 
-    // Click Start
+    // Click Continue
     const toggleButton = wrapper.find('button.test_fa2_toggle')
     await toggleButton.trigger('click')
     expect(startSpy.callCount).to.equal(2)
@@ -1884,7 +2075,7 @@ describe('GraphEditor', () => {
 
     expect(startSpy.calledOnce).to.equal(true)
     await waitCondition(() => stopSpy.callCount === 1)
-    expect(wrapper.text()).to.contain('Start')
+    expect(wrapper.text()).to.contain('Continue')
 
     const coordinates = graph
       .export()

tests/lib/graphHelper.spec.js

@@ -2,6 +2,7 @@ import { expect } from 'chai'
 import sinon from 'sinon'
 import * as graphHelper from '@/lib/graphHelper'
 import Graph from 'graphology'
+import { random } from 'graphology-layout'
 
 describe('graphHelper.js', () => {
   afterEach(() => {
@@ -1231,7 +1232,11 @@ describe('graphHelper.js', () => {
       }
     }
 
-    const nodeData = { color: '#FF0000CC', label: 'Node label' }
+    const nodeData = {
+      color: '#FF0000CC',
+      label: 'Node label',
+      labelColor: 'blue'
+    }
 
     let interactionState = {
       selectedNodeId: 'node-1',
@@ -1249,6 +1254,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'black',
       zIndex: 2,
       highlighted: true,
       forceLabel: true
@@ -1258,6 +1264,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'black',
       zIndex: 2,
       highlighted: true,
       forceLabel: true
@@ -1268,6 +1275,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1278,6 +1286,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1288,6 +1297,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#3300cc',
       label: '',
+      labelColor: 'blue',
       zIndex: 1,
       highlighted: false
     })
@@ -1308,6 +1318,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'black',
       zIndex: 2,
       highlighted: true,
       forceLabel: true
@@ -1318,6 +1329,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1328,6 +1340,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1338,6 +1351,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1348,6 +1362,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#3300cc',
       label: '',
+      labelColor: 'blue',
       zIndex: 1,
       highlighted: false
     })
@@ -1368,6 +1383,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1377,6 +1393,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1386,6 +1403,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1395,6 +1413,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1405,6 +1424,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#3300cc',
       label: '',
+      labelColor: 'blue',
       zIndex: 1,
       highlighted: false
     })
@@ -1425,6 +1445,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1434,6 +1455,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'black',
       zIndex: 2,
       highlighted: true,
       forceLabel: true
@@ -1443,6 +1465,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1452,6 +1475,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#FF0000CC',
       label: 'Node label',
+      labelColor: 'blue',
       zIndex: 2,
       highlighted: false,
       forceLabel: true
@@ -1462,6 +1486,7 @@ describe('graphHelper.js', () => {
     ).to.eql({
       color: '#3300cc',
       label: '',
+      labelColor: 'blue',
       zIndex: 1,
       highlighted: false
     })
@@ -1481,32 +1506,37 @@ describe('graphHelper.js', () => {
       graphHelper.reduceNodes('node-1', nodeData, interactionState, settings)
     ).to.eql({
       color: '#FF0000CC',
-      label: 'Node label'
+      label: 'Node label',
+      labelColor: 'blue'
     })
     expect(
       graphHelper.reduceNodes('node-2', nodeData, interactionState, settings)
     ).to.eql({
       color: '#FF0000CC',
-      label: 'Node label'
+      label: 'Node label',
+      labelColor: 'blue'
     })
     expect(
       graphHelper.reduceNodes('node-1.1', nodeData, interactionState, settings)
     ).to.eql({
       color: '#FF0000CC',
-      label: 'Node label'
+      label: 'Node label',
+      labelColor: 'blue'
     })
     expect(
       graphHelper.reduceNodes('node-2.1', nodeData, interactionState, settings)
     ).to.eql({
       color: '#FF0000CC',
-      label: 'Node label'
+      label: 'Node label',
+      labelColor: 'blue'
     })
 
     expect(
       graphHelper.reduceNodes('node-3', nodeData, interactionState, settings)
     ).to.eql({
       color: '#FF0000CC',
-      label: 'Node label'
+      label: 'Node label',
+      labelColor: 'blue'
     })
   })
 
@@ -2193,4 +2223,44 @@ describe('graphHelper.js', () => {
       )
     ).to.eql(edgeData)
   })
+
+  it('clearNodeCoordinates', () => {
+    const dataSources = {
+      doc: [
+        '{"type": 0, "node_id": 1, "label": "cat"}',
+        '{"type": 0, "node_id": 2, "label": "dog"}'
+      ]
+    }
+    const graph = new Graph()
+    const options = {
+      structure: {
+        nodeId: 'node_id',
+        objectType: 'type',
+        edgeSource: null,
+        edgeTarget: null
+      }
+    }
+
+    graphHelper.buildNodes(graph, dataSources, options)
+    random.assign(graph)
+    graphHelper.clearNodeCoordinates(graph)
+    expect(graph.export().nodes).to.eql([
+      {
+        key: '1',
+        attributes: {
+          data: { type: 0, node_id: 1, label: 'cat' },
+          x: undefined,
+          y: undefined
+        }
+      },
+      {
+        key: '2',
+        attributes: {
+          data: { type: 0, node_id: 2, label: 'dog' },
+          x: undefined,
+          y: undefined
+        }
+      }
+    ])
+  })
 })

tests/lib/storedInquiries/_migrations.spec.js

@@ -82,7 +82,22 @@ describe('_migrations.js', () => {
               label: { source: null, color: '#a2b1c6' }
             }
           },
-          layout: { type: 'circular', options: null }
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialIterationsAmount: 50,
+              adjustSizes: false,
+              barnesHutOptimize: false,
+              barnesHutTheta: 0.5,
+              edgeWeightInfluence: 0,
+              gravity: 1,
+              linLogMode: false,
+              outboundAttractionDistribution: false,
+              scalingRatio: 1,
+              slowDown: 1,
+              strongGravityMode: false
+            }
+          }
         },
         createdAt: '2021-05-07T11:05:50.877Z'
       }
@@ -130,7 +145,153 @@ describe('_migrations.js', () => {
               label: { source: null, color: '#a2b1c6' }
             }
           },
-          layout: { type: 'circular', options: null }
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialAlgorithm: 'circular',
+              initialIterationsAmount: 50,
+              adjustSizes: false,
+              barnesHutOptimize: false,
+              barnesHutTheta: 0.5,
+              edgeWeightInfluence: 0,
+              gravity: 1,
+              linLogMode: false,
+              outboundAttractionDistribution: false,
+              scalingRatio: 1,
+              slowDown: 1,
+              strongGravityMode: false
+            }
+          }
+        },
+        createdAt: '2021-05-07T11:05:50.877Z'
+      }
+    ])
+  })
+
+  it('migrates from version 3 to the current', () => {
+    const oldInquiries = [
+      {
+        id: '123',
+        name: 'foo',
+        query: 'SELECT * FROM foo',
+        viewType: 'chart',
+        viewOptions: { here_are: 'foo chart settings' },
+        createdAt: '2021-05-06T11:05:50.877Z'
+      },
+      {
+        id: '456',
+        name: 'bar',
+        query: 'SELECT * FROM bar',
+        viewType: 'graph',
+        viewOptions: {
+          structure: {
+            nodeId: 'node_id',
+            objectType: 'object_type',
+            edgeSource: 'source',
+            edgeTarget: 'target'
+          },
+          style: {
+            backgroundColor: 'white',
+            highlightMode: 'node_and_neighbors',
+            nodes: {
+              size: { type: 'constant', value: 10 },
+              color: {
+                type: 'calculated',
+                method: 'degree',
+                colorscale: null,
+                mode: 'continious',
+                colorscaleDirection: 'reversed',
+                opacity: 100
+              },
+              label: { source: 'label', color: '#444444' }
+            },
+            edges: {
+              showDirection: true,
+              size: { type: 'constant', value: 2 },
+              color: { type: 'constant', value: '#a2b1c6' },
+              label: { source: null, color: '#a2b1c6' }
+            }
+          },
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialIterationsAmount: 50,
+              adjustSizes: false,
+              barnesHutOptimize: false,
+              barnesHutTheta: 0.5,
+              edgeWeightInfluence: 0,
+              gravity: 1,
+              linLogMode: false,
+              outboundAttractionDistribution: false,
+              scalingRatio: 1,
+              slowDown: 1,
+              strongGravityMode: false
+            }
+          }
+        },
+        createdAt: '2021-05-07T11:05:50.877Z'
+      }
+    ]
+    expect(migrations._migrate(3, oldInquiries)).to.eql([
+      {
+        id: '123',
+        name: 'foo',
+        query: 'SELECT * FROM foo',
+        viewType: 'chart',
+        viewOptions: { here_are: 'foo chart settings' },
+        createdAt: '2021-05-06T11:05:50.877Z'
+      },
+      {
+        id: '456',
+        name: 'bar',
+        query: 'SELECT * FROM bar',
+        viewType: 'graph',
+        viewOptions: {
+          structure: {
+            nodeId: 'node_id',
+            objectType: 'object_type',
+            edgeSource: 'source',
+            edgeTarget: 'target'
+          },
+          style: {
+            backgroundColor: 'white',
+            highlightMode: 'node_and_neighbors',
+            nodes: {
+              size: { type: 'constant', value: 10 },
+              color: {
+                type: 'calculated',
+                method: 'degree',
+                colorscale: null,
+                mode: 'continious',
+                colorscaleDirection: 'reversed',
+                opacity: 100
+              },
+              label: { source: 'label', color: '#444444' }
+            },
+            edges: {
+              showDirection: true,
+              size: { type: 'constant', value: 2 },
+              color: { type: 'constant', value: '#a2b1c6' },
+              label: { source: null, color: '#a2b1c6' }
+            }
+          },
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialAlgorithm: 'circular',
+              initialIterationsAmount: 50,
+              adjustSizes: false,
+              barnesHutOptimize: false,
+              barnesHutTheta: 0.5,
+              edgeWeightInfluence: 0,
+              gravity: 1,
+              linLogMode: false,
+              outboundAttractionDistribution: false,
+              scalingRatio: 1,
+              slowDown: 1,
+              strongGravityMode: false
+            }
+          }
         },
         createdAt: '2021-05-07T11:05:50.877Z'
       }

tests/lib/storedInquiries/storedInquiries.spec.js

@@ -92,9 +92,24 @@ describe('storedInquiries.js', () => {
                   label: { source: null, color: '#a2b1c6' }
                 }
               },
-              layout: { type: 'circular', options: null }
+              layout: {
+                type: 'forceAtlas2',
+                options: {
+                  initialIterationsAmount: 50,
+                  adjustSizes: false,
+                  barnesHutOptimize: false,
+                  barnesHutTheta: 0.5,
+                  edgeWeightInfluence: 0,
+                  gravity: 1,
+                  linLogMode: false,
+                  outboundAttractionDistribution: false,
+                  scalingRatio: 1,
+                  slowDown: 1,
+                  strongGravityMode: false
+                }
+              }
             },
-            name: 'student graph',
+            name: 'student graph FA2',
             updatedAt: '2026-01-19T21:49:40.708Z',
             createdAt: '2026-01-19T21:46:13.899Z'
           },
@@ -145,9 +160,25 @@ describe('storedInquiries.js', () => {
               label: { source: null, color: '#a2b1c6' }
             }
           },
-          layout: { type: 'circular', options: null }
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialAlgorithm: 'circular',
+              initialIterationsAmount: 50,
+              adjustSizes: false,
+              barnesHutOptimize: false,
+              barnesHutTheta: 0.5,
+              edgeWeightInfluence: 0,
+              gravity: 1,
+              linLogMode: false,
+              outboundAttractionDistribution: false,
+              scalingRatio: 1,
+              slowDown: 1,
+              strongGravityMode: false
+            }
+          }
         },
-        name: 'student graph',
+        name: 'student graph FA2',
         updatedAt: '2026-01-19T21:49:40.708Z',
         createdAt: '2026-01-19T21:46:13.899Z'
       },
@@ -244,7 +275,7 @@ describe('storedInquiries.js', () => {
     const str = storedInquiries.serialiseInquiries(inquiryList)
     const parsedJson = JSON.parse(str)
 
-    expect(parsedJson.version).to.equal(3)
+    expect(parsedJson.version).to.equal(4)
     expect(parsedJson.inquiries).to.have.lengthOf(2)
     expect(parsedJson.inquiries[1]).to.eql(inquiryList[1])
     expect(parsedJson.inquiries[0]).to.eql({
@@ -339,7 +370,22 @@ describe('storedInquiries.js', () => {
                 "label": { "source": null, "color": "#a2b1c6" }
               }
             },
-            "layout": { "type": "circular", "options": null }
+            "layout": {
+                "type": "forceAtlas2",
+                "options": {
+                  "initialIterationsAmount": 50,
+                  "adjustSizes": false,
+                  "barnesHutOptimize": false,
+                  "barnesHutTheta": 0.5,
+                  "edgeWeightInfluence": 0,
+                  "gravity": 1,
+                  "linLogMode": false,
+                  "outboundAttractionDistribution": false,
+                  "scalingRatio": 1,
+                  "slowDown": 1,
+                  "strongGravityMode": false
+                }
+              }
           },
           "name": "student graph",
           "createdAt": "2026-01-19T21:46:13.899Z"
@@ -391,7 +437,23 @@ describe('storedInquiries.js', () => {
               label: { source: null, color: '#a2b1c6' }
             }
           },
-          layout: { type: 'circular', options: null }
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialAlgorithm: 'circular',
+              initialIterationsAmount: 50,
+              adjustSizes: false,
+              barnesHutOptimize: false,
+              barnesHutTheta: 0.5,
+              edgeWeightInfluence: 0,
+              gravity: 1,
+              linLogMode: false,
+              outboundAttractionDistribution: false,
+              scalingRatio: 1,
+              slowDown: 1,
+              strongGravityMode: false
+            }
+          }
         },
         name: 'student graph',
         createdAt: '2026-01-19T21:46:13.899Z'
@@ -486,7 +548,7 @@ describe('storedInquiries.js', () => {
 
   it('importInquiries', async () => {
     const str = `{
-      "version": 3,
+      "version": 4,
       "inquiries": [{
         "id": 1,
         "name": "foo",
@@ -579,7 +641,22 @@ describe('storedInquiries.js', () => {
                 "label": { "source": null, "color": "#a2b1c6" }
               }
             },
-            "layout": { "type": "circular", "options": null }
+            "layout": {
+                "type": "forceAtlas2",
+                "options": {
+                  "initialIterationsAmount": 50,
+                  "adjustSizes": false,
+                  "barnesHutOptimize": false,
+                  "barnesHutTheta": 0.5,
+                  "edgeWeightInfluence": 0,
+                  "gravity": 1,
+                  "linLogMode": false,
+                  "outboundAttractionDistribution": false,
+                  "scalingRatio": 1,
+                  "slowDown": 1,
+                  "strongGravityMode": false
+                }
+              }
           },
           "name": "student graph",
           "createdAt": "2026-01-19T21:46:13.899Z"
@@ -632,7 +709,23 @@ describe('storedInquiries.js', () => {
               label: { source: null, color: '#a2b1c6' }
             }
           },
-          layout: { type: 'circular', options: null }
+          layout: {
+            type: 'forceAtlas2',
+            options: {
+              initialAlgorithm: 'circular',
+              initialIterationsAmount: 50,
+              adjustSizes: false,
+              barnesHutOptimize: false,
+              barnesHutTheta: 0.5,
+              edgeWeightInfluence: 0,
+              gravity: 1,
+              linLogMode: false,
+              outboundAttractionDistribution: false,
+              scalingRatio: 1,
+              slowDown: 1,
+              strongGravityMode: false
+            }
+          }
         },
         name: 'student graph',
         createdAt: '2026-01-19T21:46:13.899Z'
@@ -642,7 +735,7 @@ describe('storedInquiries.js', () => {
 
   it('readPredefinedInquiries', async () => {
     const str = `{
-      "version": 3,
+      "version": 4,
       "inquiries": [
         {
           "id": 1,