@abi-software/flatmapvuer 0.5.10 → 0.6.0-vue3-0

package/src/components/FlatmapVuer.vue

@@ -1,2070 +1,2117 @@
-<template>
-  <div
-    class="flatmap-container"
-    ref="flatmapContainer"
-    v-loading="loading"
-    element-loading-text="Loading..."
-    element-loading-spinner="el-icon-loading"
-    element-loading-background="rgba(0, 0, 0, 0.3)"
-  >
-    <map-svg-sprite-color />
-    <div
-      style="height: 100%; width: 100%; position: relative; overflow-y: none"
-    >
-      <div style="height: 100%; width: 100%" ref="display"></div>
-      <div class="beta-popovers">
-        <div>
-          <el-popover
-            placement="right"
-            :appendToBody="false"
-            trigger="manual"
-            popper-class="warning-popper flatmap-popper right-popper"
-            v-model="hoverVisibilities[6].value"
-            ref="warningPopover"
-          >
-            <p
-              v-if="isLegacy"
-              @mouseover="showToolitip(6)"
-              @mouseout="hideToolitip(6)"
-            >
-              This is a legacy map, you may view the latest map instead.
-            </p>
-            <p
-              v-else-if="isFC"
-              @mouseover="showToolitip(6)"
-              @mouseout="hideToolitip(6)"
-            >
-              This map displays the connectivity of individual neurons.
-              Specifically, those which align with (parts of) the neuron
-              populations from the
-              <a
-                href="https://sparc.science/resources/1ZUKXU2YmLcn2reCyXjlew"
-                target="_blank"
-              >
-                ApiNATOMY
-              </a>
-              models available in
-              <a
-                href="https://sparc.science/resources/6eg3VpJbwQR4B84CjrvmyD"
-                target="_blank"
-              >
-                SCKAN </a
-              >.
-            </p>
-            <p v-else @mouseover="showToolitip(6)" @mouseout="hideToolitip(6)">
-              This map displays the connectivity of neuron populations.
-              Specifically, those from the primarily rat-based
-              <a
-                href="https://sparc.science/resources/1ZUKXU2YmLcn2reCyXjlew"
-                target="_blank"
-              >
-                ApiNATOMY
-              </a>
-              models available in
-              <a
-                href="https://sparc.science/resources/6eg3VpJbwQR4B84CjrvmyD"
-                target="_blank"
-              >
-                SCKAN </a
-              >. New connectivity and species specificity will be added as the
-              SPARC program progresses.
-            </p>
-          </el-popover>
-          <i
-            class="el-icon-warning warning-icon"
-            v-if="displayWarning"
-            @mouseover="showToolitip(6)"
-            @mouseout="hideToolitip(6)"
-            v-popover:warningPopover
-          >
-            <template v-if="isLegacy">
-              <span class="warning-text">Legacy Map</span>
-              <div class="latest-map-text" @click="viewLatestMap">
-                Click here for the latest map
-              </div>
-            </template>
-            <template v-else>
-              <span class="warning-text">Beta</span>
-            </template>
-          </i>
-        </div>
-        <el-popover
-          placement="right"
-          v-if="displayLatestChanges"
-          :appendToBody="false"
-          trigger="manual"
-          popper-class="warning-popper flatmap-popper right-popper"
-          v-model="hoverVisibilities[7].value"
-          ref="latestChangesPopover"
-        >
-          <template #reference> 
-            <i
-              class="el-icon-warning latest-changesicon"
-              v-if="displayLatestChanges"
-              @mouseover="showToolitip(7)"
-              @mouseout="hideToolitip(7)"
-              v-popover:latestChangesPopover
-            >
-              <span class="warning-text">What's new?</span>
-            </i>
-          </template>
-          <template #default>
-            <b>Network discovery mode</b>
-            <p>
-              You can now view the network of neurons connected to a selected
-              neuron. This mode is located in the settings at the bottom right.
-              Once discovery mode is on, click on a neuron to see its connections.
-            </p>
-            <b>Now can display up to 6 panes</b>
-            <p>
-              You can now display up to 6 panes in the flatmap. This allows you to
-              compare between different datasets and/or different views of the
-              same dataset.
-            </p>
-          </template>
-        </el-popover>
-      </div>
-
-      <!-- The element below is placed onto the flatmap when it is ready -->
-      <i
-        class="el-icon-arrow-down minimap-resize"
-        :class="{ enlarge: minimapSmall, shrink: !minimapSmall }"
-        ref="minimapResize"
-        v-show="minimapResizeShow"
-        @click="closeMinimap"
-      ></i>
-
-      <div class="bottom-right-control">
-        <el-popover
-          content="Zoom in"
-          placement="left"
-          :appendToBody="false"
-          trigger="manual"
-          popper-class="flatmap-popper left-popper"
-          v-model="hoverVisibilities[0].value"
-        >
-          <map-svg-icon
-            icon="zoomIn"
-            class="icon-button zoomIn"
-            slot="reference"
-            @click.native="zoomIn()"
-            @mouseover.native="showToolitip(0)"
-            @mouseout.native="hideToolitip(0)"
-          />
-        </el-popover>
-        <el-popover
-          content="Zoom out"
-          placement="top-end"
-          :appendToBody="false"
-          trigger="manual"
-          popper-class="flatmap-popper popper-zoomout"
-          v-model="hoverVisibilities[1].value"
-        >
-          <map-svg-icon
-            icon="zoomOut"
-            class="icon-button zoomOut"
-            slot="reference"
-            @click.native="zoomOut()"
-            @mouseover.native="showToolitip(1)"
-            @mouseout.native="hideToolitip(1)"
-          />
-        </el-popover>
-        <el-popover
-          content="Reset"
-          placement="top"
-          :appendToBody="false"
-          trigger="manual"
-          popper-class="flatmap-popper"
-          v-model="hoverVisibilities[2].value"
-        >
-          <div>
-            Fit to
-            <br />
-            window
-          </div>
-          <map-svg-icon
-            slot="reference"
-            icon="fitWindow"
-            class="icon-button fitWindow"
-            @click.native="resetView()"
-            @mouseover.native="showToolitip(2)"
-            @mouseout.native="hideToolitip(2)"
-          />
-        </el-popover>
-      </div>
-      <el-popover
-        content="Change pathway visibility"
-        placement="right"
-        :appendToBody="false"
-        trigger="manual"
-        popper-class="flatmap-popper right-popper"
-        v-model="hoverVisibilities[4].value"
-        ref="checkBoxPopover"
-      />
-      <div
-        class="pathway-location"
-        :class="{ open: drawerOpen, close: !drawerOpen }"
-      >
-        <div
-          class="pathway-container"
-          :class="{ open: drawerOpen, close: !drawerOpen }"
-          :style="{ 'max-height' : pathwaysMaxHeight + 'px' }"
-          v-if="pathControls"
-          v-popover:checkBoxPopover
-        >
-          <svg-legends v-if="!isFC" class="svg-legends-container" />
-          <el-popover
-            content="Location of the featured dataset"
-            placement="right"
-            :appendToBody="false"
-            trigger="hover"
-            popper-class="flatmap-popper popper-bump-right right-popper"
-            v-model="hoverVisibilities[9].value"
-            ref="featuredMarkerPopover"
-          >
-          </el-popover>
-          <div v-show="showStarInLegend" v-popover:featuredMarkerPopover class="yellow-star-legend" v-html="yellowstar"></div>
-          <!-- The line below places the yellowstar svg on the left, and the text "Featured markers on the right" with css so they are both centered in the div -->
-
-          <el-popover
-            content="Find these markers for data"
-            placement="right"
-            :appendToBody="false"
-            trigger="manual"
-            popper-class="flatmap-popper popper-bump-right  right-popper"
-            v-model="hoverVisibilities[5].value"
-            ref="markerPopover"
-          ></el-popover>
-          <div
-            v-show="hoverVisibilities[5].value"
-            class="flatmap-marker-help"
-            v-html="flatmapMarker"
-            v-popover:markerPopover
-          ></div>
-          <tree-controls
-            v-if="isFC && systems && systems.length > 0"
-            :active="currentActive"
-            :hover="currentHover"
-            :tree-data="systems"
-            ref="treeControls"
-            @changed="systemSelected"
-            @checkAll="checkAllSystems"
-            @change-active="ftuSelected"
-          />
-          <selections-group
-            v-if="!isFC && centreLines && centreLines.length > 0"
-            title="Nerves"
-            labelKey="label"
-            identifierKey="key"
-            :selections="centreLines"
-            @changed="centreLinesSelected"
-            ref="centrelinesSelection"
-            key="centrelinesSelection"
-          />
-          <!--
-          <selections-group
-            v-if="isFC && sckanDisplay && sckanDisplay.length > 0"
-            title="SCKAN"
-            labelKey="label"
-            identifierKey="key"
-            :selections="sckanDisplay"
-            @changed="sckanSelected"
-            @checkAll="checkAllSCKAN"
-            ref="skcanSelection"
-            key="skcanSelection"
-          />
-          <selections-group
-            v-if="layers && layers.length > 0"
-            title="Layers"
-            labelKey="description"
-            identifierKey="id"
-            :selections="layers"
-            @changed="layersSelected"
-            @checkAll="checkAllLayers"
-            ref="layersSelection"
-            key="layersSelection"
-          />
-          -->
-          <selections-group
-            v-if="!isFC && taxonConnectivity && taxonConnectivity.length > 0"
-            title="Observed in"
-            labelKey="label"
-            identifierKey="taxon"
-            :selections="taxonConnectivity"
-            @changed="taxonsSelected"
-            @checkAll="checkAllTaxons"
-            ref="taxonSelection"
-            key="taxonSelection"
-          />
-          <selections-group
-            v-if="pathways && pathways.length > 0"
-            title="Pathways"
-            labelKey="label"
-            identifierKey="type"
-            colourStyle="line"
-            :selections="pathways"
-            @changed="pathwaysSelected"
-            @checkAll="checkAllPathways"
-            ref="pathwaysSelection"
-            key="pathwaysSelection"
-          />
-        </div>
-        <div
-          @click="toggleDrawer"
-          class="drawer-button"
-          :class="{ open: drawerOpen, close: !drawerOpen }"
-        >
-          <i class="el-icon-arrow-left"></i>
-        </div>
-      </div>
-      <el-popover
-        ref="open-map-popover"
-        placement="top-start"
-        width="128"
-        :append-to-body="false"
-        trigger="click"
-        popper-class="open-map-popper non-selectable"
-      >
-        <el-row v-for="item in openMapOptions" :key="item.key">
-          <el-button type="primary" plain @click="$emit('open-map', item.key)">
-            {{ item.display }}
-          </el-button>
-        </el-row>
-      </el-popover>
-      <el-popover
-        ref="backgroundPopover"
-        placement="top-start"
-        width="175"
-        :appendToBody="false"
-        trigger="click"
-        popper-class="background-popper"
-      >
-        <el-row class="backgroundText">Viewing Mode</el-row>
-        <el-row class="backgroundControl">
-          <el-select
-            :popper-append-to-body="false"
-            v-model="viewingMode"
-            placeholder="Select"
-            class="select-box"
-            popper-class="flatmap_dropdown"
-          >
-            <el-option
-              v-for="item in viewingModes"
-              :key="item"
-              :label="item"
-              :value="item"
-            >
-              <el-row>
-                <el-col :span="12">{{ item }}</el-col>
-              </el-row>
-            </el-option>
-          </el-select>
-        </el-row>
-        <el-row class="backgroundSpacer"></el-row>
-        <el-row class="backgroundText">Organs display</el-row>
-        <el-row class="backgroundControl">
-          <el-radio-group
-            v-model="colourRadio"
-            class="flatmap-radio"
-            @change="setColour"
-          >
-            <el-radio :label="true">Colour</el-radio>
-            <el-radio :label="false">Greyscale</el-radio>
-          </el-radio-group>
-        </el-row>
-        <el-row class="backgroundSpacer"></el-row>
-        <el-row class="backgroundText">Outlines display</el-row>
-        <el-row class="backgroundControl">
-          <el-radio-group
-            v-model="outlinesRadio"
-            class="flatmap-radio"
-            @change="setOutlines"
-          >
-            <el-radio :label="true">Show</el-radio>
-            <el-radio :label="false">Hide</el-radio>
-          </el-radio-group>
-        </el-row>
-        <el-row class="backgroundSpacer"></el-row>
-        <el-row class="backgroundText">Change background</el-row>
-        <el-row class="backgroundControl">
-          <div
-            v-for="item in availableBackground"
-            :key="item"
-            :class="[
-              'backgroundChoice',
-              item,
-              item == currentBackground ? 'active' : '',
-            ]"
-            @click="backgroundChangeCallback(item)"
-          />
-        </el-row>
-      </el-popover>
-      <div
-        class="settings-group"
-        :class="{ open: drawerOpen, close: !drawerOpen }"
-      >
-        <el-row>
-          <el-popover
-            v-model="hoverVisibilities[8].value"
-            content="Open new map"
-            placement="right"
-            :append-to-body="false"
-            trigger="manual"
-            popper-class="flatmap-popper right-popper"
-          >
-            <map-svg-icon
-              v-if="enableOpenMapUI && openMapOptions.length > 0"
-              slot="reference"
-              v-popover:open-map-popover
-              icon="openMap"
-              class="icon-button"
-              @mouseover.native="showToolitip(8)"
-              @mouseout.native="hideToolitip(8)"
-            />
-          </el-popover>
-        </el-row>
-        <el-row>
-          <el-popover
-            content="Change settings"
-            placement="right"
-            v-model="hoverVisibilities[3].value"
-            :appendToBody="false"
-            trigger="manual"
-            popper-class="flatmap-popper right-popper"
-          >
-            <map-svg-icon
-              v-popover:backgroundPopover
-              icon="changeBckgd"
-              class="icon-button"
-              slot="reference"
-              @mouseover.native="showToolitip(3)"
-              @mouseout.native="hideToolitip(3)"
-            />
-          </el-popover>
-        </el-row>
-      </div>
-      <Tooltip
-        ref="tooltip"
-        class="tooltip"
-        :annotationEntry="annotationEntry"
-        :entry="tooltipEntry"
-        :annotationDisplay="viewingMode === 'Annotation'"
-      />
-    </div>
-  </div>
-</template>
-
-<script>
-/* eslint-disable no-alert, no-console */
-import Vue from "vue";
-import Tooltip from "./Tooltip";
-import SelectionsGroup from "./SelectionsGroup";
-import TreeControls from "./TreeControls";
-import { MapSvgIcon, MapSvgSpriteColor } from "@abi-software/svg-sprite";
-import SvgLegends from "./legends/SvgLegends";
-import {
-  Button,
-  Col,
-  Loading,
-  Radio,
-  RadioGroup,
-  Row,
-  Select,
-} from "element-ui";
-import lang from "element-ui/lib/locale/lang/en";
-import locale from "element-ui/lib/locale";
-import flatmapMarker from "../icons/flatmap-marker";
-import {FlatmapQueries, findTaxonomyLabel} from "../services/flatmapQueries.js";
-import yellowstar from "../icons/yellowstar";
-
-locale.use(lang);
-Vue.use(Button);
-Vue.use(Col);
-Vue.use(Loading.directive);
-Vue.use(Radio);
-Vue.use(RadioGroup);
-Vue.use(Row);
-Vue.use(Select);
-const ResizeSensor = require("css-element-queries/src/ResizeSensor");
-
-const processTaxon = (flatmapAPI, taxonIdentifiers) => {
-  let processed = [];
-  taxonIdentifiers.forEach((taxon) => {
-    findTaxonomyLabel(flatmapAPI, taxon).then((value) => {
-      const item = { taxon, label: value };
-      processed.push(item);
-    });
-  });
-
-  return processed;
-};
-
-const processFTUs = (parent, key) => {
-  const ftus = [];
-  let items = parent.organs ? parent.organs : parent.ftus;
-  const children = items
-    ? items.filter(
-        (obj, index) =>
-          items.findIndex((item) => item.label === obj.label) === index
-      )
-    : undefined;
-  if (children) {
-    children.forEach((child) => {
-      const data = {
-        label: child.label,
-        models: child.models,
-        key: `${key}.${child.label}`,
-      };
-      const grandChildren = processFTUs(child, data.key);
-      if (grandChildren.length > 0) {
-        data.children = grandChildren;
-      }
-      ftus.push(data);
-    });
-  }
-  return ftus;
-};
-
-const processSystems = (systems) => {
-  const allSystems = [];
-  if (systems && systems.length > 0) {
-    const data = { label: "All", key: "All", children: [] };
-    systems.forEach((system) => {
-      const child = {
-        colour: system.colour,
-        enabled: system.enabled,
-        label: system.id,
-        key: system.id,
-      };
-      const children = processFTUs(system, child.key);
-      if (children.length > 0) child.children = children;
-      data.children.push(child);
-    });
-
-    allSystems.push(data);
-  }
-
-  return allSystems;
-};
-
-const createUnfilledTooltipData = function () {
-  return {
-    destinations: [],
-    origins: [],
-    components: [],
-    destinationsWithDatasets: [],
-    originsWithDatasets: [],
-    componentsWithDatasets: [],
-    resource: undefined,
-  };
-};
-
-export default {
-  name: "FlatmapVuer",
-  components: {
-    MapSvgIcon,
-    MapSvgSpriteColor,
-    Tooltip,
-    TreeControls,
-    SelectionsGroup,
-    SvgLegends,
-  },
-  beforeCreate: function () {
-    this.mapManager = undefined;
-    this.mapImp = undefined;
-    //The state watcher may triggered before
-    //created causing issue, This flag will
-    //resolve this issue.
-    this.setStateRequired = false;
-  },
-  methods: {
-    viewLatestMap: function () {
-      let biologicalSex = this.biologicalSex ? this.biologicalSex : undefined;
-      //Human requires special handling
-      if (this.entry === "NCBITaxon:9606") {
-        biologicalSex = "PATO:0000384";
-      }
-      const state = {
-        entry: this.entry,
-        biologicalSex,
-        viewport: this.mapImp.getState(),
-      };
-      this.$emit("view-latest-map", state);
-    },
-    backgroundChangeCallback: function (colour) {
-      this.currentBackground = colour;
-      if (this.mapImp) {
-        this.mapImp.setBackgroundColour(this.currentBackground, 1);
-      }
-    },
-    toggleDrawer: function () {
-      this.drawerOpen = !this.drawerOpen;
-    },
-    /**
-     * Function to toggle colour/greyscale of organs.
-     */
-    setColour: function (flag) {
-      this.colourRadio = flag;
-      if (this.mapImp) {
-        this.mapImp.setColour({ colour: flag, outline: this.outlinesRadio });
-      }
-    },
-    /**
-     * Function to toggle outlines f organs.
-     */
-    setOutlines: function (flag) {
-      this.outlineRadio = flag;
-      if (this.mapImp) {
-        this.mapImp.setColour({ colour: this.colourRadio, outline: flag });
-      }
-    },
-    /**
-     * Function to toggle paths to default.
-     * Also called when the associated button is pressed.
-     */
-    resetView: function () {
-      if (this.mapImp) {
-        this.mapImp.resetMap();
-        if (this.$refs.centrelinesSelection) {
-          this.$refs.centrelinesSelection.reset();
-        }
-        if (this.$refs.skcanSelection) {
-          this.$refs.skcanSelection.reset();
-        }
-        if (this.$refs.layersSelection) {
-          this.$refs.layersSelection.reset();
-        }
-        if (this.$refs.systemsSelection) {
-          this.$refs.pathwaysSelection.reset();
-        }
-        if (this.$refs.pathwaysSelection) {
-          this.$refs.pathwaysSelection.reset();
-        }
-      }
-    },
-    /**
-     * Function to zoom in.
-     * Also called when the associated button is pressed.
-     */
-    zoomIn: function () {
-      if (this.mapImp) {
-        this.mapImp.zoomIn();
-      }
-    },
-    /**
-     * Function to zoom out.
-     * Also called when the associated button is pressed.
-     */
-    zoomOut: function () {
-      if (this.mapImp) {
-        this.mapImp.zoomOut();
-      }
-    },
-    centreLinesSelected: function (payload) {
-      if (this.mapImp) {
-        this.mapImp.enableCentrelines(payload.value);
-      }
-    },
-    sckanSelected: function (payload) {
-      if (this.mapImp) {
-        this.mapImp.enableSckanPath(payload.key, payload.value);
-      }
-    },
-    checkAllSCKAN: function (payload) {
-      if (this.mapImp) {
-        payload.keys.forEach((key) =>
-          this.mapImp.enableSckanPath(key, payload.value));
-      }
-    },
-    highlightConnectedPaths: function (payload) {
-      if (this.mapImp) {
-        let paths = [...this.mapImp.pathModelNodes(payload)];
-        // The line below matches the paths to the annIdToFeatureId map to get the feature ids
-
-        let pathFeatures = paths.map(p=>this.mapImp.featureProperties(p));
-        let toHighlight = [];
-        pathFeatures.forEach(p=>{
-          this.mapImp.nodePathModels(p.featureId).forEach(f=>{
-            toHighlight.push(f);
-          })
-        })
-        // display connected paths
-        this.mapImp.zoomToFeatures(toHighlight, {noZoomIn: true});
-      }
-    },
-    systemSelected: function (payload) {
-      if (this.mapImp) {
-        this.mapImp.enableSystem(payload.key, payload.value);
-      }
-    },
-    checkAllSystems: function (flag) {
-      if (this.mapImp) {
-        this.systems[0].children.forEach((key) =>
-          this.mapImp.enableSystem(key.label, flag)
-        );
-      }
-    },
-    ftuSelected: function (models) {
-      this.searchAndShowResult(models, true);
-    },
-    layersSelected: function (payload) {
-      if (this.mapImp) {
-        this.mapImp.enableLayer(payload.key, payload.value);
-      }
-    },
-    checkAllLayers: function (payload) {
-      if (this.mapImp) {
-        payload.keys.forEach((key) =>
-          this.mapImp.enableLayer(key, payload.value)
-        );
-      }
-    },
-    taxonsSelected: function (payload) {
-      if (this.mapImp) {
-        this.mapImp.enableConnectivityByTaxonIds(payload.key, payload.value);
-      }
-    },
-    checkAllTaxons: function (payload) {
-      if (this.mapImp) {
-        payload.keys.forEach((key) =>
-          this.mapImp.enableConnectivityByTaxonIds(key, payload.value)
-        );
-      }
-    },
-    pathwaysSelected: function (payload) {
-      if (this.mapImp) {
-        this.mapImp.enablePath(payload.key, payload.value);
-      }
-    },
-    checkAllPathways: function (payload) {
-      if (this.mapImp) {
-        payload.keys.forEach((key) =>
-          this.mapImp.enablePath(key, payload.value)
-        );
-      }
-    },
-    enablePanZoomEvents: function (flag) {
-      this.mapImp.enablePanZoomEvents(flag);
-    },
-    eventCallback: function () {
-      return (eventType, data, ...args) => {
-        if (eventType !== "pan-zoom") {
-          const label = data.label;
-          const resource = [data.models];
-          const taxonomy = this.entry;
-          const biologicalSex = this.biologicalSex;
-          const payload = {
-            dataset: data.dataset,
-            biologicalSex: biologicalSex,
-            taxonomy: taxonomy,
-            resource: resource,
-            label: label,
-            feature: data,
-            userData: args,
-            eventType: eventType,
-            provenanceTaxonomy: data.taxons
-              ? JSON.parse(data.taxons)
-              : undefined,
-          };
-          if (eventType === "click") {
-            if (this.viewingMode === "Network Discovery") {
-              this.highlightConnectedPaths([data.models]);
-            } else {
-              this.currentActive = data.models ? data.models : "";
-            }
-          } else if (eventType === "mouseenter" && 
-          !(this.viewingMode === "Network Discovery")) {
-            this.currentHover = data.models ? data.models : "";
-          }
-          if (
-            data &&
-            data.type !== "marker" &&
-            eventType === "click" &&
-            !(this.viewingMode === "Network Discovery")
-          ) {
-            this.checkAndCreatePopups(payload);
-          }
-          this.$emit("resource-selected", payload);
-        } else {
-          this.$emit("pan-zoom-callback", data);
-        }
-      };
-    },
-    // checkNeuronClicked shows a neuron path pop up if a path was recently clicked
-    checkAndCreatePopups: async function (data) {
-      // Call flatmap database to get the connection data
-      if (this.viewingMode  === "Annotation") {
-        if (data.feature && data.feature.featureId && data.feature.models) {
-          this.annotationEntry = { ...data.feature, resourceId: this.serverUUID };
-          this.displayTooltip(data.feature.models);
-        } else {
-          this.annotation = {};
-        }
-      } else {
-        let results =
-          await this.flatmapQueries.retrieveFlatmapKnowledgeForEvent(data);
-        // The line below only creates the tooltip if some data was found on the path
-        // result 0 is the connection, result 1 is the pubmed results from flatmap
-        if (
-          results[0] ||
-          results[1] ||
-          (data.feature.hyperlinks && data.feature.hyperlinks.length > 0)
-        ) {
-          this.resourceForTooltip = data.resource[0];
-          data.resourceForTooltip = this.resourceForTooltip;
-          this.createTooltipFromNeuronCuration(data);
-        }
-      }
-    },
-    popUpCssHacks: function () {
-      // Below is a hack to remove flatmap tooltips while popup is open
-      let ftooltip = document.querySelector(".flatmap-tooltip-popup");
-      if (ftooltip) ftooltip.style.display = "none";
-      document.querySelector(".maplibregl-popup-close-button").style.display =
-        "block";
-      this.$refs.tooltip.$el.style.display = "flex";
-      document.querySelector(".maplibregl-popup-close-button").onclick = () => {
-        document.querySelector(".flatmap-tooltip-popup").style.display =
-          "block";
-      };
-    },
-    closeTooltip: function () {
-      this.$refs.tooltip.$el.style.display = "none";
-      document.querySelectorAll(".maplibregl-popup").forEach((item) => {
-        item.style.display = "none";
-      });
-    },
-    createTooltipFromNeuronCuration: async function (data) {
-      this.tooltipEntry = await this.flatmapQueries.createTooltipData(data);
-      this.displayTooltip(data.resource[0]);
-    },
-    // Keeping this as an API
-    showPopup: function (featureId, node, options) {
-      let myOptions = options;
-      if (this.mapImp) {
-        if (myOptions) {
-          if (!myOptions.className) myOptions.className = "custom-popup";
-        } else {
-          myOptions = { className: "custom-popup", positionAtLastClick: true };
-        }
-        this.mapImp.showPopup(featureId, node, myOptions);
-      }
-    },
-    showMarkerPopup: function (featureId, node, options) {
-      if (this.mapImp) {
-        this.mapImp.showMarkerPopup(featureId, node, options);
-      }
-    },
-    closeMinimap: function () {
-      let minimapEl = this.$refs.flatmapContainer.querySelector(
-        ".maplibregl-ctrl-minimap"
-      ); // find minimap
-      if (this.minimapSmall) {
-        //switch the classes on the minimap
-        minimapEl.classList.add("enlarge");
-        minimapEl.classList.remove("shrink");
-      } else {
-        minimapEl.classList.add("shrink");
-        minimapEl.classList.remove("enlarge");
-      }
-      this.minimapSmall = !this.minimapSmall;
-    },
-    addResizeButtonToMinimap: function () {
-      let minimapEl = this.$refs.flatmapContainer.querySelector(
-        ".maplibregl-ctrl-minimap"
-      );
-      if (minimapEl) {
-        this.$refs.minimapResize.parentNode.removeChild(
-          this.$refs.minimapResize
-        );
-        minimapEl.appendChild(this.$refs.minimapResize);
-        this.minimapResizeShow = true;
-      }
-    },
-    setHelpMode: function (helpMode) {
-      if (helpMode) {
-        this.inHelp = true;
-        this.hoverVisibilities.forEach((item) => {
-          item.value = true;
-        });
-        this.openFlatmapHelpPopup();
-      } else {
-        this.inHelp = false;
-        this.hoverVisibilities.forEach((item) => {
-          item.value = false;
-        });
-        this.closeFlatmapHelpPopup();
-      }
-    },
-    showToolitip: function (tooltipNumber) {
-      if (!this.inHelp) {
-        clearTimeout(this.tooltipWait[tooltipNumber]);
-        this.tooltipWait[tooltipNumber] = setTimeout(() => {
-          this.hoverVisibilities[tooltipNumber].value = true;
-        }, 500);
-      }
-    },
-    hideToolitip: function (tooltipNumber) {
-      if (!this.inHelp) {
-        clearTimeout(this.tooltipWait[tooltipNumber]);
-        this.tooltipWait[tooltipNumber] = setTimeout(() => {
-          this.hoverVisibilities[tooltipNumber].value = false;
-        }, 500);
-      }
-    },
-    displayTooltip: function (feature) {
-      this.mapImp.showPopup(
-        this.mapImp.modelFeatureIds(feature)[0],
-        this.$refs.tooltip.$el,
-        { className: "flatmapvuer-popover", positionAtLastClick: true }
-      );
-      this.popUpCssHacks();
-    },
-    openFlatmapHelpPopup: function () {
-      if (this.mapImp) {
-        let heartId = this.mapImp.featureIdsForModel("UBERON:0000948")[0];
-        const elm = "Click for more information";
-        this.mapImp.showPopup(heartId, elm, {
-          anchor: "top",
-          className: "flatmap-popup-popper",
-        });
-      }
-    },
-    closeFlatmapHelpPopup: function () {
-      this.$el
-        .querySelectorAll(".maplibregl-popup-close-button")
-        .forEach((item) => {
-          item.click();
-        });
-    },
-    getLabels: function () {
-      let labels = [];
-      if (this.mapImp) {
-        let annotations = this.mapImp.annotations;
-        for (let value of annotations.values()) {
-          if (value.label) labels.push(value.label);
-        }
-        return Array.from(new Set(labels));
-      }
-    },
-    getState: function () {
-      if (this.mapImp) {
-        let state = {
-          entry: this.entry,
-          viewport: this.mapImp.getState(),
-        };
-        const identifier = this.mapImp.getIdentifier();
-        if (this.biologicalSex) state["biologicalSex"] = this.biologicalSex;
-        else if (identifier && identifier.biologicalSex)
-          state["biologicalSex"] = identifier.biologicalSex;
-        if (identifier && identifier.uuid) state["uuid"] = identifier.uuid;
-        return state;
-      }
-      return undefined;
-    },
-    setState: function (state) {
-      if (state) {
-        if (
-          this.mapImp &&
-          state.entry &&
-          this.entry == state.entry &&
-          (!state.biologicalSex || state.biologicalSex === this.biologicalSex)
-        ) {
-          if (state.viewport) {
-            this.mapImp.setState(state.viewport);
-          }
-        } else {
-          this.createFlatmap(state);
-        }
-        this.setStateRequired = false;
-      }
-    },
-    restoreMapState: function (state) {
-      if (state) {
-        if (state.viewport) this.mapImp.setState(state.viewport);
-        if (state.searchTerm) this.searchAndShowResult(state.searchTerm, true);
-      }
-    },
-    createFlatmap: function (state) {
-      if (!this.mapImp && !this.loading) {
-        this.loading = true;
-        let minimap = false;
-        if (this.displayMinimap) {
-          minimap = { position: "top-right" };
-        }
-
-        //As for flatmap-viewer@2.2.7, see below for the documentation
-        //for the identifier:
-
-        //@arg identifier {string|Object}
-        // A string or object identifying the map to load. If a string its
-        // value can be either the map's ``uuid``, assigned at generation time,
-        // or taxon and biological sex identifiers of the species that the map
-        // represents. The latest version of a map is loaded unless it has been
-        // identified using a ``uuid`` (see below).
-        // @arg identifier.taxon {string} The taxon identifier of the species
-        //  represented by the map. This is specified as metadata in the map's source file.
-        // @arg identifier.biologicalSex {string} The biological sex of the species
-        // represented by the map. This is specified as metadatain the map's source file.
-        // @arg identifier.uuid {string} The unique uuid the flatmap. If given then this exact map will
-        //  be loaded, overriding ``taxon`` and ``biologicalSex``.
-
-        let identifier = { taxon: this.entry };
-        if (this.uuid) {
-          identifier.uuid = this.uuid;
-        }
-        //This now handle the uses of uuid when resuming states
-        if (state) {
-          if (state.uuid) {
-            identifier = { uuid: state.uuid };
-          } else if (state.entry) {
-            identifier.taxon = state.entry;
-            if (state.biologicalSex) {
-              identifier["biologicalSex"] = state.biologicalSex;
-            } else if (identifier.taxon === "NCBITaxon:9606") {
-              //For backward compatibility
-              identifier["biologicalSex"] = "PATO:0000384";
-            }
-          }
-        } else {
-          // Set the bioloicalSex now if map is not resumed from
-          // a saved state
-          if (this.biologicalSex) {
-            identifier["biologicalSex"] = this.biologicalSex;
-          }
-        }
-
-        let promise1 = this.mapManager.loadMap(
-          identifier,
-          this.$refs.display,
-          this.eventCallback(),
-          {
-            //fullscreenControl: false,
-            //annotatable: false,
-            //debug: true,
-            featureInfo: this.featureInfo,
-            "min-zoom": this.minZoom,
-            layerControl: true,
-            pathControls: true,
-            searchable: this.searchable,
-            tooltips: this.tooltips,
-            minimap: minimap,
-          }
-        );
-        promise1.then((returnedObject) => {
-          this.mapImp = returnedObject;
-          this.serverUUID = this.mapImp.getIdentifier().uuid;
-          this.onFlatmapReady();
-          if (this._stateToBeSet) this.restoreMapState(this._stateToBeSet);
-          else {
-            this.restoreMapState(state);
-          }
-        });
-      } else if (state) {
-        this._stateToBeSet = {
-          viewport: state.viewport,
-          searchTerm: state.searchTerm,
-        };
-        if (this.mapImp && !this.loading)
-          this.restoreMapState(this._stateToBeSet);
-      }
-    },
-    computePathControlsMaximumHeight() {
-      const elem = this.$refs.display;
-      if (elem) {
-        const computed = getComputedStyle(elem);
-        const padding =
-          parseInt(computed.paddingTop) + parseInt(computed.paddingBottom);
-        const height = elem.clientHeight - padding;
-        this.pathwaysMaxHeight = height - 170;
-      }
-    },
-    mapResize: function () {
-      try {
-        this.computePathControlsMaximumHeight();
-        if (this.mapImp) {
-          this.mapImp.resize();
-          this.showMinimap(this.displayMinimap);
-          if (this.mapImp._minimap) {
-            this.mapImp._minimap.resize();
-          }
-        }
-      } catch {
-        console.error("Map resize error");
-      }
-    },
-    onFlatmapReady: function () {
-      // onFlatmapReady is used for functions that need to run immediately after the flatmap is loaded
-      this.sensor = new ResizeSensor(this.$refs.display, this.mapResize);
-      if (this.mapImp.options && this.mapImp.options.style === "functional") {
-        this.isFC = true;
-      }
-      this.mapImp.setBackgroundOpacity(1);
-      this.backgroundChangeCallback(this.currentBackground);
-      this.pathways = this.mapImp.pathTypes();
-      this.mapImp.enableCentrelines(false);
-      //Disable layers for now
-      //this.layers = this.mapImp.getLayers();
-      this.systems = processSystems(this.mapImp.getSystems());
-      this.taxonConnectivity = processTaxon(
-        this.flatmapAPI,
-        this.mapImp.taxonIdentifiers
-      );
-      this.addResizeButtonToMinimap();
-      this.loading = false;
-      this.computePathControlsMaximumHeight();
-      this.drawerOpen = true;
-      this.mapResize();
-      this.$emit("ready", this);
-    },
-    showMinimap: function (flag) {
-      if (this.mapImp) this.mapImp.showMinimap(flag);
-    },
-    showPathwaysDrawer: function (flag) {
-      this.drawerOpen = flag;
-    },
-    /**
-     * Function to display features with annotation matching the provided term,
-     * with the option to display the label using displayLabel flag.
-     */
-    searchAndShowResult: function (term, displayLabel) {
-      if (this.mapImp) {
-        if (term === undefined || term === "") {
-          this.mapImp.clearSearchResults();
-          return true;
-        } else {
-          const searchResults = this.mapImp.search(term);
-          if (
-            searchResults &&
-            searchResults.results &&
-            searchResults.results.length > 0
-          ) {
-            this.mapImp.showSearchResults(searchResults);
-            if (
-              displayLabel &&
-              searchResults.results[0].featureId &&
-              searchResults.results[0].text
-            ) {
-              const annotation = this.mapImp.annotation(
-                searchResults.results[0].featureId
-              );
-              this.mapImp.showPopup(
-                searchResults.results[0].featureId,
-                annotation.label,
-                {
-                  className: "custom-popup",
-                  positionAtLastClick: false,
-                  preserveSelection: true,
-                }
-              );
-            }
-            return true;
-          } else this.mapImp.clearSearchResults();
-        }
-      }
-      return false;
-    },
-    /**
-     * Get the list of suggested terms
-     */
-    searchSuggestions: function (term) {
-      if (this.mapImp) return this.mapImp.search(term);
-      return [];
-    },
-  },
-  props: {
-    entry: String,
-    uuid: String,
-    biologicalSex: {
-      type: String,
-      default: "",
-    },
-    featureInfo: {
-      type: Boolean,
-      default: false,
-    },
-    minZoom: {
-      type: Number,
-      default: 4,
-    },
-    pathControls: {
-      type: Boolean,
-      default: false,
-    },
-    searchable: {
-      type: Boolean,
-      default: false,
-    },
-    layerControl: {
-      type: Boolean,
-      default: false,
-    },
-    tooltips: {
-      type: Boolean,
-      default: true,
-    },
-    helpMode: {
-      type: Boolean,
-      default: false,
-    },
-    renderAtMounted: {
-      type: Boolean,
-      default: true,
-    },
-    displayMinimap: {
-      type: Boolean,
-      default: false,
-    },
-    displayWarning: {
-      type: Boolean,
-      default: false,
-    },
-    /**
-     * Flag to determine rather open map UI should be
-     * presented or not.
-     */
-    enableOpenMapUI: {
-      type: Boolean,
-      default: false,
-    },
-    openMapOptions: {
-      type: Array,
-      default: function () {
-        return [
-          {
-            display: "Open AC Map",
-            key: "AC",
-          },
-          {
-            display: "Open FC Map",
-            key: "FC",
-          },
-          {
-            display: "Open 3D Human Map",
-            key: "3D",
-          },
-        ];
-      },
-    },
-    showStarInLegend: {
-      type: Boolean,
-      default: false
-    },
-    isLegacy: {
-      type: Boolean,
-      default: false,
-    },
-    displayLatestChanges: {
-      type: Boolean,
-      default: false,
-    },
-    /**
-     * State containing state of the flatmap.
-     */
-    state: {
-      type: Object,
-      default: undefined,
-    },
-    /**
-     * Specify the endpoint of the flatmap server.
-     */
-    flatmapAPI: {
-      type: String,
-      default: "https://mapcore-demo.org/current/flatmap/v3/",
-    },
-    sparcAPI: {
-      type: String,
-      default: "https://api.sparc.science/",
-    },
-  },
-  provide() {
-    return {
-      flatmapAPI: this.flatmapAPI,
-      sparcAPI: this.sparcAPI,
-    };
-  },
-  data: function () {
-    return {
-      annotationEntry: {},
-      serverUUID: undefined,
-      layers: [],
-      pathways: [],
-      sckanDisplay: [
-        {
-          label: "Display Path with SCKAN",
-          key: "VALID",
-        },
-      ],
-      centreLines: [
-        {
-          label: "Display Nerves",
-          key: "centrelines",
-          enabled: false,
-        },
-      ],
-      systems: [],
-      taxonConnectivity: [],
-      pathwaysMaxHeight: 1000,
-      hoverVisibilities: [
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-      ],
-      yellowstar: yellowstar,
-      isFC: false,
-      inHelp: false,
-      currentBackground: "white",
-      availableBackground: ["white", "lightskyblue", "black"],
-      loading: false,
-      flatmapMarker: flatmapMarker,
-      tooltipEntry: createUnfilledTooltipData(),
-      connectivityTooltipVisible: false,
-      drawerOpen: false,
-      annotationRadio: false,
-      colourRadio: true,
-      outlinesRadio: true,
-      minimapResizeShow: false,
-      minimapSmall: false,
-      currentActive: "",
-      currentHover: "",
-      viewingMode: "Exploration",
-      viewingModes: ["Annotation", "Exploration", "Network Discovery"],
-    };
-  },
-  watch: {
-    entry: function () {
-      if (!this.state) this.createFlatmap();
-    },
-    helpMode: function (val) {
-      this.setHelpMode(val);
-    },
-    state: {
-      handler: function (state) {
-        if (this.mapManager) {
-          this.setState(state);
-        } else {
-          //this component has not been mounted yet
-          this.setStateRequired = true;
-        }
-      },
-      immediate: true,
-      deep: true,
-    },
-  },
-  mounted: function () {
-    const flatmap = require("@abi-software/flatmap-viewer");
-    this.tooltipWait = [];
-    this.tooltipWait.length = this.hoverVisibilities.length;
-    this.mapManager = new flatmap.MapManager(this.flatmapAPI);
-    this.flatmapQueries = new FlatmapQueries();
-    this.flatmapQueries.initialise(this.flatmapAPI);
-    if (this.state) {
-      //State is set and require to set the state
-      if (this.setStateRequired) {
-        this.setState(this.state);
-      }
-    } else if (this.renderAtMounted) {
-      this.createFlatmap();
-    }
-  },
-};
-</script>
-
-<!-- Add "scoped" attribute to limit CSS to this component only -->
-<style scoped lang="scss">
-@import "~element-ui/packages/theme-chalk/src/button";
-@import "~element-ui/packages/theme-chalk/src/loading";
-@import "~element-ui/packages/theme-chalk/src/row";
-@import "~element-ui/packages/theme-chalk/src/select";
-
-.beta-popovers {
-  position: absolute;
-  top: 90px;
-  left: 16px;
-  text-align: left;
-  font-size: 25px;
-}
-
-.warning-icon {
-  color: $warning;
-
-  &:hover {
-    cursor: pointer;
-  }
-}
-
-.warning-text {
-  font-family: Asap, sans-serif;
-  font-size: 15px;
-  vertical-align: 5px;
-}
-
-.latest-map-text {
-  color: $app-primary-color;
-  font-family: Asap, sans-serif;
-  font-size: 12px;
-  margin-top: 5px;
-  vertical-align: 10px;
-  cursor: pointer;
-}
-
-.latest-changesicon {
-  color: $success;
-
-  &:hover {
-    cursor: pointer;
-  }
-}
-
-.latest-changestext {
-  font-family: Asap, sans-serif;
-  font-size: 15px;
-  vertical-align: 5px;
-}
-
-.flatmap-container {
-  height: 100%;
-  width: 100%;
-}
-
-.pathway-location {
-  position: absolute;
-  bottom: 0px;
-  transition: all 1s ease;
-  &.open {
-    left: 0px;
-  }
-  &.close {
-    left: -298px;
-  }
-}
-
-.svg-legends-container {
-  width: 70%;
-  height: auto;
-  position: relative;
-  max-height: 140px;
-}
-
-.pathway-container {
-  float: left;
-  padding-left: 16px;
-  padding-right: 18px;
-  text-align: left;
-  overflow: auto;
-  border: 1px solid rgb(220, 223, 230);
-  padding-bottom: 16px;
-  background: #ffffff;
-  overflow-x: hidden;
-  scrollbar-width: thin;
-
-  transition: all 1s ease;
-  &.open {
-    opacity: 1;
-  }
-  &.close {
-    opacity: 0;
-  }
-
-  &::-webkit-scrollbar {
-    width: 4px;
-  }
-
-  &::-webkit-scrollbar-thumb {
-    border-radius: 10px;
-    box-shadow: inset 0 0 6px #c0c4cc;
-  }
-}
-
-.flatmap-marker-help {
-  display: inline-block;
-}
-
-::v-deep .popper-bump-right {
-  left: 30px;
-}
-
-.el-dropdown-link {
-  cursor: pointer;
-  color: #409eff;
-}
-.el-icon-arrow-down {
-  font-size: 12px;
-}
-.demonstration {
-  display: block;
-  color: #8492a6;
-  font-size: 14px;
-  margin-bottom: 20px;
-}
-
-.tooltip {
-  display: none;
-}
-
-::v-deep .maplibregl-popup {
-  max-width: 300px !important;
-}
-
-::v-deep .flatmap-tooltip-popup {
-  &.maplibregl-popup-anchor-bottom {
-    .maplibregl-popup-content {
-      margin-bottom: 12px;
-      &::after,
-      &::before {
-        top: 100%;
-        border-width: 12px;
-      }
-      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
-      &::after {
-        margin-top: -1px;
-        border-color: rgb(255, 255, 255) transparent transparent transparent;
-      }
-      /* this border color controlls the outside, thin border */
-      &::before {
-        margin: 0 auto;
-        border-color: $app-primary-color transparent transparent transparent;
-      }
-    }
-  }
-  &.maplibregl-popup-anchor-top {
-    .maplibregl-popup-content {
-      margin-top: 18px;
-      &::after,
-      &::before {
-        top: calc(-100% + 6px);
-        border-width: 12px;
-      }
-      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
-      &::after {
-        margin-top: 1px;
-        border-color: transparent transparent rgb(255, 255, 255) transparent;
-      }
-      &::before {
-        margin: 0 auto;
-        border-color: transparent transparent $app-primary-color transparent;
-      }
-    }
-  }
-  .maplibregl-popup-content {
-    border-radius: 4px;
-    box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);
-    pointer-events: none;
-    display: none;
-    background: #fff;
-    border: 1px solid $app-primary-color;
-    padding-left: 6px;
-    padding-right: 6px;
-    display: flex;
-    justify-content: center;
-    align-items: center;
-    &::after,
-    &::before {
-      content: "";
-      display: block;
-      position: absolute;
-      width: 0;
-      height: 0;
-      border-style: solid;
-      flex-shrink: 0;
-    }
-  }
-  .maplibregl-popup-tip {
-    display: none;
-  }
-}
-
-::v-deep .maplibregl-popup {
-  &.flatmap-marker-popup {
-    box-shadow: 1px 1px 2px rgba(0, 0, 0, 0.1);
-    pointer-events: auto;
-    background: #fff;
-  }
-}
-
-/* Fix for chrome bug where under triangle pops up above one on top of it  */
-.selector:not(*:root),
-::v-deep.flatmap-tooltip-popup {
-  .maplibregl-popup-content::after {
-    top: 99.9%;
-  }
-}
-
-::v-deep .flatmap-tooltip-dialog {
-  .maplibregl-popup-tip {
-    display: none;
-  }
-}
-
-::v-deep .flatmap-marker-popup {
-  .maplibregl-popup-content {
-    padding: 0px;
-  }
-}
-
-::v-deep .flatmapvuer-popover {
-  .maplibregl-popup-close-button {
-    position: absolute;
-    right: 0.5em;
-    top: 0;
-    border: 0;
-    border-radius: 0 3px 0 0;
-    cursor: pointer;
-    background-color: transparent;
-    font-size: 2.5em;
-    color: grey;
-    top: 0.95em;
-  }
-}
-
-.zoomOut {
-  padding-left: 8px;
-}
-
-.fitWindow {
-  padding-left: 8px;
-}
-
-.yellow-star-legend {
-  width: 130px;
-  cursor: pointer;
-}
-
-.settings-group {
-  bottom: 16px;
-  position: absolute;
-  transition: all 1s ease;
-  &.open {
-    left: 322px;
-  }
-  &.close {
-    left: 24px;
-  }
-}
-
-::v-deep .background-popper {
-  padding: 5px 12px;
-  background-color: #ffffff;
-  border: 1px solid $app-primary-color;
-  box-shadow: 0px 2px 12px 0px rgba(0, 0, 0, 0.06);
-  height: 270px;
-  width: 175px;
-  min-width: 175px;
-  &.el-popper[x-placement^="top"] {
-    .popper__arrow {
-      border-top-color: $app-primary-color !important;
-      &::after {
-        border-top-color: #fff !important;
-      }
-    }
-  }
-}
-
-::v-deep .open-map-popper {
-  padding-top: 5px;
-  padding-bottom: 5px;
-  background-color: #ffffff;
-  border: 1px solid $app-primary-color;
-  box-shadow: 0px 2px 12px 0px rgba(0, 0, 0, 0.06);
-  width: 178px;
-  min-width: 178px;
-
-  .el-row ~ .el-row {
-    margin-top: 8px;
-  }
-
-  .el-button {
-    padding-top: 5px;
-    padding-bottom: 5px;
-  }
-
-  &.el-popper[x-placement^="top"] {
-    .popper__arrow {
-      border-top-color: $app-primary-color !important;
-      &:after {
-        border-top-color: #fff !important;
-      }
-    }
-  }
-}
-
-.backgroundText {
-  color: rgb(48, 49, 51);
-  font-size: 14px;
-  font-weight: normal;
-  line-height: 20px;
-}
-
-.backgroundControl {
-  display: flex;
-  margin-top: 12px;
-}
-
-.backgroundChoice {
-  width: 20px;
-  height: 20px;
-  border: 1px solid rgb(144, 147, 153);
-  margin-left: 20px;
-  &.active {
-    border: 2px solid $app-primary-color;
-  }
-  &:hover {
-    cursor: pointer;
-  }
-  &.white {
-    background-color: white;
-    margin-left: 10px;
-  }
-  &.black {
-    background-color: black;
-  }
-  &.lightskyblue {
-    background-color: lightskyblue;
-  }
-}
-
-.icon-button {
-  height: 24px !important;
-  width: 24px !important;
-  color: $app-primary-color;
-  &:hover {
-    cursor: pointer;
-  }
-}
-
-::v-deep .maplibregl-ctrl-minimap {
-  transform-origin: top right;
-  @media (max-width: 1250px) {
-    height: 125px !important; // important is needed here as we are over-riding the style set by the flatmap
-    width: 180px !important;
-    >>> .maplibregl-canvas .maplibregl-canvas {
-      height: 125px !important;
-      width: 180px !important;
-    }
-  }
-  @media (min-width: 1251px) {
-    height: 190px !important;
-    width: 300px !important;
-    >>> .maplibregl-canvas .maplibregl-canvas {
-      height: 190px !important;
-      width: 300px !important;
-    }
-  }
-  transition: all 1s ease;
-  &.shrink {
-    transform: scale(0.5);
-    transform: scale(0.5);
-  }
-}
-
-.minimap-resize {
-  position: absolute;
-  pointer-events: all;
-  cursor: pointer;
-  top: 0;
-  right: 0;
-  padding-top: 3px; // needed as icon is offset
-  width: 20px;
-  height: 14px;
-  z-index: 9;
-  transition: all 1s ease;
-  &.shrink {
-    transform: rotate(0deg);
-  }
-  &.enlarge {
-    transform: rotate(180deg) scale(2);
-    padding-bottom: 5px; // note padding is added to the opposite side since it is rotated
-    padding-left: 5px;
-  }
-}
-
-::v-deep .flatmap-popper {
-  padding: 6px 4px;
-  font-size: 12px;
-  color: rgb(48, 49, 51);
-  background-color: #f3ecf6;
-  border: 1px solid $app-primary-color;
-  white-space: nowrap;
-  min-width: unset;
-  &.warning-popper {
-    min-width: 150px;
-    max-width: 400px;
-    word-break: keep-all;
-    white-space: unset;
-  }
-  &.left-popper {
-    .popper__arrow {
-      border-left-color: $app-primary-color !important;
-      &::after {
-        border-left-color: #f3ecf6 !important;
-      }
-    }
-  }
-  &.right-popper {
-    .popper__arrow {
-      border-right-color: $app-primary-color !important;
-      &:after {
-        border-right-color: #f3ecf6 !important;
-      }
-    }
-  }
-  &.el-popper[x-placement^="top"] {
-    .popper__arrow {
-      border-top-color: $app-primary-color !important;
-      &:after {
-        border-top-color: #f3ecf6 !important;
-      }
-    }
-  }
-}
-
-::v-deep .el-loading-spinner {
-  i,
-  .el-loading-text {
-    color: $app-primary-color;
-  }
-}
-
-::v-deep .flatmap-popup-popper {
-  .maplibregl-popup-tip {
-    border-bottom-color: $app-primary-color;
-  }
-  .maplibregl-popup-content {
-    padding: 6px 4px;
-    font-size: 12px;
-    color: rgb(48, 49, 51);
-    background-color: #f3ecf6;
-    border: 1px solid $app-primary-color;
-    white-space: nowrap;
-    min-width: unset;
-    .maplibregl-popup-close-button {
-      display: none;
-    }
-  }
-}
-
-::v-deep .popper-zoomout {
-  padding-right: 13px !important;
-  left: -21px !important;
-}
-
-::v-deep .popper-zoomout {
-  .popper__arrow {
-    left: 53px !important;
-  }
-}
-
-::v-deep .maplibregl-popup-content {
-  padding: 0px;
-}
-
-.bottom-right-control {
-  position: absolute;
-  right: 16px;
-  bottom: 16px;
-}
-
-::v-deep .my-drawer {
-  background: rgba(0, 0, 0, 0);
-  box-shadow: none;
-}
-
-.drawer {
-  ::v-deep .el-drawer:focus {
-    outline: none;
-  }
-}
-
-.open-drawer,
-.drawer-button {
-  z-index: 8;
-  width: 20px;
-  height: 40px;
-  border: solid 1px $app-primary-color;
-  text-align: center;
-  vertical-align: middle;
-  cursor: pointer;
-  pointer-events: auto;
-}
-
-.open-drawer {
-  position: absolute;
-  left: 0px;
-  background-color: #f7faff;
-  box-shadow: 0 2px 12px 0 rgba(0, 0, 0, 0.06);
-}
-
-.drawer-button {
-  float: left;
-  margin-top: calc(50% - 36px);
-  background-color: #f9f2fc;
-
-  i {
-    font-weight: 600;
-    margin-top: 12px;
-    color: $app-primary-color;
-    transition-delay: 0.9s;
-  }
-  &.open {
-    i {
-      transform: rotate(0deg) scaleY(2);
-    }
-  }
-  &.close {
-    i {
-      transform: rotate(180deg) scaleY(2);
-    }
-  }
-}
-
-::v-deep .maplibregl-canvas-container {
-  canvas {
-    outline: none;
-  }
-}
-
-.backgroundSpacer {
-  border-bottom: 1px solid #e4e7ed;
-  margin-bottom: 10px;
-}
-
-.flatmap-radio {
-  ::v-deep label {
-    margin-right: 20px;
-    &:last-child {
-      margin-right: 0px;
-    }
-  }
-  ::v-deep .el-radio__input {
-    &.is-checked {
-      & + .el-radio__label {
-        color: $app-primary-color;
-      }
-      .el-radio__inner {
-        border-color: $app-primary-color;
-        background: $app-primary-color;
-      }
-    }
-    .el-radio__inner:hover {
-      border-color: $app-primary-color;
-    }
-  }
-}
-
-::v-deep .custom-popup {
-  .maplibregl-popup-tip {
-    display: none;
-  }
-  .maplibregl-popup-content {
-    border-radius: 4px;
-    box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);
-    pointer-events: none;
-    display: none;
-    background: #fff;
-    font-family: "Asap", sans-serif;
-    font-size: 12pt;
-    color: $app-primary-color;
-    border: 1px solid $app-primary-color;
-    padding-left: 6px;
-    padding-right: 6px;
-    padding-top: 6px;
-    padding-bottom: 6px;
-    display: flex;
-    justify-content: center;
-    align-items: center;
-    &::after,
-    &::before {
-      content: "";
-      display: block;
-      position: absolute;
-      width: 0;
-      height: 0;
-      border-style: solid;
-      flex-shrink: 0;
-    }
-    .maplibregl-popup-close-button {
-      display: none;
-    }
-  }
-  &.maplibregl-popup-anchor-bottom {
-    .maplibregl-popup-content {
-      margin-bottom: 12px;
-      &::after,
-      &::before {
-        top: 100%;
-        border-width: 12px;
-      }
-      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
-      &::after {
-        margin-top: -1px;
-        border-color: rgb(255, 255, 255) transparent transparent transparent;
-      }
-      /* this border color controlls the outside, thin border */
-      &::before {
-        margin: 0 auto;
-        border-color: $app-primary-color transparent transparent transparent;
-      }
-    }
-  }
-  &.maplibregl-popup-anchor-top {
-    .maplibregl-popup-content {
-      margin-top: 18px;
-      &::after,
-      &::before {
-        top: calc(-100% + 6px);
-        border-width: 12px;
-      }
-      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
-      &::after {
-        margin-top: 1px;
-        border-color: transparent transparent rgb(255, 255, 255) transparent;
-      }
-      &::before {
-        margin: 0 auto;
-        border-color: transparent transparent $app-primary-color transparent;
-      }
-    }
-  }
-}
-
-.select-box {
-  border-radius: 4px;
-  border: 1px solid rgb(144, 147, 153);
-  background-color: var(--white);
-  font-weight: 500;
-  color: rgb(48, 49, 51);
-  ::v-deep .el-input__inner {
-    height: 30px;
-    color: rgb(48, 49, 51);
-  }
-  ::v-deep .el-input__inner {
-    &is-focus,
-    &:focus {
-      border: 1px solid $app-primary-color;
-    }
-  }
-  ::v-deep .el-input__icon {
-    line-height: 30px;
-  }
-}
-
-::v-deep .flatmap_dropdown {
-  min-width: 160px !important;
-  .el-select-dropdown__item {
-    white-space: nowrap;
-    text-align: left;
-    &.selected {
-      color: $app-primary-color;
-      font-weight: normal;
-    }
-  }
-}
-</style>
-
+<template>
+  <div
+    class="flatmap-container"
+    ref="flatmapContainer"
+    v-loading="loading"
+    element-loading-text="Loading..."
+    element-loading-background="rgba(0, 0, 0, 0.3)"
+  >
+    <map-svg-sprite-color />
+    <div
+      style="height: 100%; width: 100%; position: relative; overflow-y: none"
+    >
+      <div style="height: 100%; width: 100%" ref="display"></div>
+      <div class="beta-popovers">
+        <div>
+          <el-popover
+            placement="right"
+            popper-class="warning-popper flatmap-popper"
+            :teleported="false"
+            :visible="hoverVisibilities[6].value"
+            ref="warningPopover"
+          >
+            <p
+              v-if="isLegacy"
+              @mouseover="showToolitip(6)"
+              @mouseout="hideToolitip(6)"
+            >
+              This is a legacy map, you may view the latest map instead.
+            </p>
+            <p
+              v-else-if="isFC"
+              @mouseover="showToolitip(6)"
+              @mouseout="hideToolitip(6)"
+            >
+              This map displays the connectivity of individual neurons.
+              Specifically, those which align with (parts of) the neuron
+              populations from the
+              <a
+                href="https://sparc.science/resources/1ZUKXU2YmLcn2reCyXjlew"
+                target="_blank"
+              >
+                ApiNATOMY
+              </a>
+              models available in
+              <a
+                href="https://sparc.science/resources/6eg3VpJbwQR4B84CjrvmyD"
+                target="_blank"
+              >
+                SCKAN </a
+              >.
+            </p>
+            <p v-else @mouseover="showToolitip(6)" @mouseout="hideToolitip(6)">
+              This map displays the connectivity of neuron populations.
+              Specifically, those from the primarily rat-based
+              <a
+                href="https://sparc.science/resources/1ZUKXU2YmLcn2reCyXjlew"
+                target="_blank"
+              >
+                ApiNATOMY
+              </a>
+              models available in
+              <a
+                href="https://sparc.science/resources/6eg3VpJbwQR4B84CjrvmyD"
+                target="_blank"
+              >
+                SCKAN </a
+              >. New connectivity and species specificity will be added as the
+              SPARC program progresses.
+            </p>
+            <template #reference>
+              <div
+                class="el-icon-warning warning-icon"
+                v-if="displayWarning"
+                @mouseover="showToolitip(6)"
+                @mouseout="hideToolitip(6)"
+                v-popover:warningPopover
+              >
+                <el-icon><el-icon-warning-filled /></el-icon>
+                <template v-if="isLegacy">
+                  <span class="warning-text">Legacy Map</span>
+                  <div class="latest-map-text" @click="viewLatestMap">
+                    Click here for the latest map
+                  </div>
+                </template>
+                <template v-else>
+                  <span class="warning-text">Beta</span>
+                </template>
+              </div>
+            </template>
+          </el-popover>
+        </div>
+        <el-popover
+          placement="right"
+          v-if="displayLatestChanges"
+          :teleported="false"
+          trigger="manual"
+          popper-class="warning-popper flatmap-popper"
+          :visible="hoverVisibilities[7].value"
+          ref="latestChangesPopover"
+        >
+          <template #reference>
+            <div
+              class="latest-changesicon"
+              v-if="displayLatestChanges"
+              @mouseover="showToolitip(7)"
+              @mouseout="hideToolitip(7)"
+              v-popover:latestChangesPopover
+            >
+              <el-icon><el-icon-warning-filled /></el-icon>
+              <span class="warning-text">What's new?</span>
+            </div>
+          </template>
+          <template #default>
+            <b>Network discovery mode</b>
+            <p>
+              You can now view the network of neurons connected to a selected
+              neuron. This mode is located in the settings at the bottom right.
+              Once discovery mode is on, click on a neuron to see its
+              connections.
+            </p>
+            <b>Now can display up to 6 panes</b>
+            <p>
+              You can now display up to 6 panes in the flatmap. This allows you
+              to compare between different datasets and/or different views of
+              the same dataset.
+            </p>
+          </template>
+        </el-popover>
+      </div>
+
+      <!-- The element below is placed onto the flatmap when it is ready -->
+      <el-icon
+        class="minimap-resize"
+        :class="{ enlarge: minimapSmall, shrink: !minimapSmall }"
+        ref="minimapResize"
+        v-show="minimapResizeShow"
+        @click="closeMinimap"
+      >
+        <el-icon-arrow-down />
+      </el-icon>
+
+      <div class="bottom-right-control">
+        <el-popover
+          content="Zoom in"
+          placement="left"
+          :teleported="false"
+          trigger="manual"
+          width="70"
+          popper-class="flatmap-popper"
+          :visible="hoverVisibilities[0].value"
+        >
+          <template #reference>
+            <map-svg-icon
+              icon="zoomIn"
+              class="icon-button zoomIn"
+              @click.native="zoomIn()"
+              @mouseover.native="showToolitip(0)"
+              @mouseout.native="hideToolitip(0)"
+            />
+          </template>
+        </el-popover>
+        <el-popover
+          content="Zoom out"
+          placement="top-end"
+          :teleported="false"
+          trigger="manual"
+          width="70"
+          popper-class="flatmap-popper popper-zoomout"
+          :visible="hoverVisibilities[1].value"
+        >
+          <template #reference>
+            <map-svg-icon
+              icon="zoomOut"
+              class="icon-button zoomOut"
+              @click.native="zoomOut()"
+              @mouseover.native="showToolitip(1)"
+              @mouseout.native="hideToolitip(1)"
+            />
+          </template>
+        </el-popover>
+        <el-popover
+          content="Reset"
+          placement="top"
+          :teleported="false"
+          trigger="manual"
+          width="70"
+          popper-class="flatmap-popper"
+          :visible="hoverVisibilities[2].value"
+        >
+          <div>
+            Fit to
+            <br />
+            window
+          </div>
+          <template #reference>
+            <map-svg-icon
+              icon="fitWindow"
+              class="icon-button fitWindow"
+              @click.native="resetView()"
+              @mouseover.native="showToolitip(2)"
+              @mouseout.native="hideToolitip(2)"
+            />
+          </template>
+        </el-popover>
+      </div>
+      <el-popover
+        content="Change pathway visibility"
+        placement="right"
+        :teleported="false"
+        trigger="manual"
+        popper-class="flatmap-popper"
+        :visible="hoverVisibilities[4].value"
+        ref="checkBoxPopover"
+      >
+        <template #reference>
+          <div
+            class="pathway-location"
+            :class="{ open: drawerOpen, close: !drawerOpen }"
+          >
+            <div
+              class="pathway-container"
+              :class="{ open: drawerOpen, close: !drawerOpen }"
+              :style="{ 'max-height': pathwaysMaxHeight + 'px' }"
+              v-if="pathControls"
+              v-popover:checkBoxPopover
+            >
+              <svg-legends v-if="!isFC" class="svg-legends-container" />
+              <el-popover
+                content="Location of the featured dataset"
+                placement="right"
+                :teleported="false"
+                trigger="hover"
+                popper-class="flatmap-popper popper-bump-right"
+                :visible="hoverVisibilities[9].value"
+                ref="featuredMarkerPopover"
+              >
+                <template #reference>
+                  <div
+                    v-show="showStarInLegend"
+                    v-popover:featuredMarkerPopover
+                    class="yellow-star-legend"
+                    v-html="yellowstar"
+                  ></div>
+                </template>
+              </el-popover>
+              <!-- The line below places the yellowstar svg on the left, and the text "Featured markers on the right" with css so they are both centered in the div -->
+
+              <el-popover
+                content="Find these markers for data"
+                placement="right"
+                :teleported="false"
+                trigger="manual"
+                popper-class="flatmap-popper popper-bump-right"
+                :visible="hoverVisibilities[5].value"
+                ref="markerPopover"
+              >
+                <template #reference>
+                  <div
+                    v-show="hoverVisibilities[5].value"
+                    class="flatmap-marker-help"
+                    v-html="flatmapMarker"
+                    v-popover:markerPopover
+                  ></div>
+                </template>
+              </el-popover>
+              <tree-controls
+                v-if="isFC && systems && systems.length > 0"
+                :active="currentActive"
+                :hover="currentHover"
+                :tree-data="systems"
+                ref="treeControls"
+                @changed="systemSelected"
+                @checkAll="checkAllSystems"
+                @change-active="ftuSelected"
+              />
+              <selections-group
+                v-if="!isFC && centreLines && centreLines.length > 0"
+                title="Nerves"
+                labelKey="label"
+                identifierKey="key"
+                :selections="centreLines"
+                @changed="centreLinesSelected"
+                ref="centrelinesSelection"
+                key="centrelinesSelection"
+              />
+              <!--             
+                <selections-group
+                  v-if="isFC && sckanDisplay && sckanDisplay.length > 0"
+                  title="SCKAN"
+                  labelKey="label"
+                  identifierKey="key"
+                  :selections="sckanDisplay"
+                  @changed="sckanSelected"
+                  @checkAll="checkAllSCKAN"
+                  ref="skcanSelection"
+                  key="skcanSelection"
+                />
+                <selections-group
+                  v-if="layers && layers.length > 0"
+                  title="Layers"
+                  labelKey="description"
+                  identifierKey="id"
+                  :selections="layers"
+                  @changed="layersSelected"
+                  @checkAll="checkAllLayers"
+                  ref="layersSelection"
+                  key="layersSelection"
+                />
+              -->
+              <selections-group
+                v-if="!isFC && taxonConnectivity && taxonConnectivity.length > 0"
+                title="Observed in"
+                labelKey="label"
+                identifierKey="taxon"
+                :selections="taxonConnectivity"
+                @changed="taxonsSelected"
+                @checkAll="checkAllTaxons"
+                ref="taxonSelection"
+                key="taxonSelection"
+              />
+              <selections-group
+                v-if="pathways && pathways.length > 0"
+                title="Pathways"
+                labelKey="label"
+                identifierKey="type"
+                colourStyle="line"
+                :selections="pathways"
+                @changed="pathwaysSelected"
+                @checkAll="checkAllPathways"
+                ref="pathwaysSelection"
+                key="pathwaysSelection"
+              />
+            </div>
+            <div
+              @click="toggleDrawer"
+              class="drawer-button"
+              :class="{ open: drawerOpen, close: !drawerOpen }"
+            >
+              <el-icon><el-icon-arrow-left /></el-icon>
+            </div>
+          </div>
+        </template>
+      </el-popover>
+      <el-popover
+        v-if="openMapRef"
+        ref="open-map-popover"
+        :virtual-ref="openMapRef"
+        placement="top-start"
+        width="136"
+        :teleported="false"
+        trigger="click"
+        popper-class="open-map-popper non-selectable"
+        virtual-triggering
+      >
+        <div>
+          <el-row v-for="item in openMapOptions" :key="item.key">
+            <el-button type="primary" plain @click="$emit('open-map', item.key)">
+              {{ item.display }}
+            </el-button>
+          </el-row>
+        </div>
+      </el-popover>
+      <el-popover
+        ref="backgroundPopover"
+        :virtual-ref="backgroundIconRef"
+        placement="top-start"
+        width="200"
+        :teleported="false"
+        trigger="click"
+        popper-class="background-popper"
+        virtual-triggering
+      >
+        <div>
+          <el-row class="backgroundText">Viewing Mode</el-row>
+          <el-row class="backgroundControl">
+            <el-select
+              :teleported="false"
+              v-model="viewingMode"
+              placeholder="Select"
+              class="select-box"
+              popper-class="flatmap_dropdown"
+            >
+              <el-option
+                v-for="item in viewingModes"
+                :key="item"
+                :label="item"
+                :value="item"
+              >
+                <el-row>
+                  <el-col :span="12">{{ item }}</el-col>
+                </el-row>
+              </el-option>
+            </el-select>
+          </el-row>
+          <el-row class="backgroundSpacer"></el-row>
+          <el-row class="backgroundText">Organs display</el-row>
+          <el-row class="backgroundControl">
+            <el-radio-group
+              v-model="colourRadio"
+              class="flatmap-radio"
+              @change="setColour"
+            >
+              <el-radio :label="true">Colour</el-radio>
+              <el-radio :label="false">Greyscale</el-radio>
+            </el-radio-group>
+          </el-row>
+          <el-row class="backgroundSpacer"></el-row>
+          <el-row class="backgroundText">Outlines display</el-row>
+          <el-row class="backgroundControl">
+            <el-radio-group
+              v-model="outlinesRadio"
+              class="flatmap-radio"
+              @change="setOutlines"
+            >
+              <el-radio :label="true">Show</el-radio>
+              <el-radio :label="false">Hide</el-radio>
+            </el-radio-group>
+          </el-row>
+          <el-row class="backgroundSpacer"></el-row>
+          <el-row class="backgroundText">Change background</el-row>
+          <el-row class="backgroundControl">
+            <div
+              v-for="item in availableBackground"
+              :key="item"
+              :class="[
+                'backgroundChoice',
+                item,
+                item == currentBackground ? 'active' : '',
+              ]"
+              @click="backgroundChangeCallback(item)"
+            />
+          </el-row>
+        </div>
+      </el-popover>
+      <div
+        class="settings-group"
+        :class="{ open: drawerOpen, close: !drawerOpen }"
+      >
+        <el-row>
+          <el-popover
+            :visible="hoverVisibilities[8].value"
+            content="Open new map"
+            placement="right"
+            :teleported="false"
+            popper-class="flatmap-popper"
+          >
+            <template #reference>
+              <map-svg-icon
+                v-if="enableOpenMapUI && openMapOptions.length > 0"
+                ref="openMapRef"
+                icon="openMap"
+                class="icon-button"
+                @mouseover.native="showToolitip(8)"
+                @mouseout.native="hideToolitip(8)"
+              />
+            </template>
+          </el-popover>
+        </el-row>
+        <el-row>
+          <el-popover
+            content="Change settings"
+            placement="right"
+            :visible="hoverVisibilities[3].value"
+            :teleported="false"
+            trigger="manual"
+            popper-class="flatmap-popper"
+          >
+            <template #reference>
+              <map-svg-icon
+                ref="backgroundIconRef"
+                icon="changeBckgd"
+                class="icon-button"
+                @mouseover.native="showToolitip(3)"
+                @mouseout.native="hideToolitip(3)"
+              />
+            </template>
+          </el-popover>
+        </el-row>
+      </div>
+      <Tooltip
+        ref="tooltip"
+        class="tooltip"
+        :annotationEntry="annotationEntry"
+        :entry="tooltipEntry"
+        :annotationDisplay="viewingMode === 'Annotation'"
+      />
+    </div>
+  </div>
+</template>
+
+<script>
+import { ref } from 'vue'
+import {
+  WarningFilled as ElIconWarningFilled,
+  ArrowDown as ElIconArrowDown,
+  ArrowLeft as ElIconArrowLeft,
+} from '@element-plus/icons-vue'
+/* eslint-disable no-alert, no-console */
+import Tooltip from './Tooltip.vue'
+import SelectionsGroup from './SelectionsGroup.vue'
+import TreeControls from './TreeControls.vue'
+//import { MapSvgIcon, MapSvgSpriteColor } from '@abi-software/svg-sprite'
+import { MapSvgIcon, MapSvgSpriteColor } from 'vue3-component-svg-sprite'
+import SvgLegends from './legends/SvgLegends.vue'
+import {
+  ElButton as Button,
+  ElCol as Col,
+  ElLoading as Loading,
+  ElRadio as Radio,
+  ElRadioGroup as RadioGroup,
+  ElRow as Row,
+  ElSelect as Select,
+} from 'element-plus'
+import flatmapMarker from '../icons/flatmap-marker'
+import {
+  FlatmapQueries,
+  findTaxonomyLabel,
+} from '../services/flatmapQueries.js'
+import yellowstar from '../icons/yellowstar'
+import ResizeSensor from 'css-element-queries/src/ResizeSensor'
+import * as flatmap from '@abi-software/flatmap-viewer'
+
+
+const processFTUs = (parent, key) => {
+  const ftus = []
+  let items = parent.organs ? parent.organs : parent.ftus
+  const children = items
+    ? items.filter(
+        (obj, index) =>
+          items.findIndex((item) => item.label === obj.label) === index
+      )
+    : undefined
+  if (children) {
+    children.forEach((child) => {
+      const data = {
+        label: child.label,
+        models: child.models,
+        key: `${key}.${child.label}`,
+      }
+      const grandChildren = processFTUs(child, data.key)
+      if (grandChildren.length > 0) {
+        data.children = grandChildren
+      }
+      ftus.push(data)
+    })
+  }
+  return ftus
+}
+
+const processSystems = (systems) => {
+  const allSystems = []
+  if (systems && systems.length > 0) {
+    const data = { label: 'All', key: 'All', children: [] }
+    systems.forEach((system) => {
+      const child = {
+        colour: system.colour,
+        enabled: system.enabled,
+        label: system.id,
+        key: system.id,
+      }
+      const children = processFTUs(system, child.key)
+      if (children.length > 0) child.children = children
+      data.children.push(child)
+    })
+
+    allSystems.push(data)
+  }
+
+  return allSystems
+}
+
+const createUnfilledTooltipData = function () {
+  return {
+    destinations: [],
+    origins: [],
+    components: [],
+    destinationsWithDatasets: [],
+    originsWithDatasets: [],
+    componentsWithDatasets: [],
+    resource: undefined,
+  }
+}
+
+export default {
+  name: 'FlatmapVuer',
+  components: {
+    Button,
+    Col,
+    Loading,
+    Radio,
+    RadioGroup,
+    Row,
+    Select,
+    MapSvgIcon,
+    MapSvgSpriteColor,
+    Tooltip,
+    TreeControls,
+    SelectionsGroup,
+    SvgLegends,
+    ElIconWarningFilled,
+    ElIconArrowDown,
+    ElIconArrowLeft,
+  },
+  beforeCreate: function () {
+    this.mapManager = undefined
+    this.mapImp = undefined
+    //The state watcher may triggered before
+    //created causing issue, This flag will
+    //resolve this issue.
+    this.setStateRequired = false
+  },
+  methods: {
+    viewLatestMap: function () {
+      let biologicalSex = this.biologicalSex ? this.biologicalSex : undefined
+      //Human requires special handling
+      if (this.entry === 'NCBITaxon:9606') {
+        biologicalSex = 'PATO:0000384'
+      }
+      const state = {
+        entry: this.entry,
+        biologicalSex,
+        viewport: this.mapImp.getState(),
+      }
+      this.$emit('view-latest-map', state)
+    },
+    backgroundChangeCallback: function (colour) {
+      this.currentBackground = colour
+      if (this.mapImp) {
+        this.mapImp.setBackgroundColour(this.currentBackground, 1)
+      }
+    },
+    processSystems: function (systems) {
+      this.systems.length = 0
+      if (systems && systems.length > 0) {
+        const data = { label: 'All', key: 'All', children: [] }
+        systems.forEach((system) => {
+          const child = {
+            colour: system.colour,
+            enabled: system.enabled,
+            label: system.id,
+            key: system.id,
+          }
+          const children = processFTUs(system, child.key)
+          if (children.length > 0) child.children = children
+          data.children.push(child)
+        })
+
+        this.systems.push(data)
+      }
+    },
+    processTaxon: function (flatmapAPI, taxonIdentifiers) {
+      this.taxonConnectivity.length = 0
+      taxonIdentifiers.forEach((taxon) => {
+        findTaxonomyLabel(flatmapAPI, taxon).then((value) => {
+          const item = { taxon, label: value }
+          this.taxonConnectivity.push(item)
+        })
+      })
+    },
+    toggleDrawer: function () {
+      this.drawerOpen = !this.drawerOpen
+    },
+    /**
+     * Function to toggle colour/greyscale of organs.
+     */
+    setColour: function (flag) {
+      this.colourRadio = flag
+      if (this.mapImp) {
+        this.mapImp.setColour({ colour: flag, outline: this.outlinesRadio })
+      }
+    },
+    /**
+     * Function to toggle outlines f organs.
+     */
+    setOutlines: function (flag) {
+      this.outlineRadio = flag
+      if (this.mapImp) {
+        this.mapImp.setColour({ colour: this.colourRadio, outline: flag })
+      }
+    },
+    /**
+     * Function to toggle paths to default.
+     * Also called when the associated button is pressed.
+     */
+    resetView: function () {
+      if (this.mapImp) {
+        this.mapImp.resetMap()
+        if (this.$refs.centrelinesSelection) {
+          this.$refs.centrelinesSelection.reset()
+        }
+        if (this.$refs.skcanSelection) {
+          this.$refs.skcanSelection.reset()
+        }
+        if (this.$refs.layersSelection) {
+          this.$refs.layersSelection.reset()
+        }
+        if (this.$refs.systemsSelection) {
+          this.$refs.pathwaysSelection.reset()
+        }
+        if (this.$refs.pathwaysSelection) {
+          this.$refs.pathwaysSelection.reset()
+        }
+      }
+    },
+    /**
+     * Function to zoom in.
+     * Also called when the associated button is pressed.
+     */
+    zoomIn: function () {
+      if (this.mapImp) {
+        this.mapImp.zoomIn()
+      }
+    },
+    /**
+     * Function to zoom out.
+     * Also called when the associated button is pressed.
+     */
+    zoomOut: function () {
+      if (this.mapImp) {
+        this.mapImp.zoomOut()
+      }
+    },
+    centreLinesSelected: function (payload) {
+      if (this.mapImp) {
+        this.mapImp.enableCentrelines(payload.value)
+      }
+    },
+    sckanSelected: function (payload) {
+      if (this.mapImp) {
+        this.mapImp.enableSckanPath(payload.key, payload.value)
+      }
+    },
+    checkAllSCKAN: function (payload) {
+      if (this.mapImp) {
+        payload.keys.forEach((key) =>
+          this.mapImp.enableSckanPath(key, payload.value)
+        )
+      }
+    },
+    highlightConnectedPaths: function (payload) {
+      if (this.mapImp) {
+        let paths = [...this.mapImp.pathModelNodes(payload)]
+        // The line below matches the paths to the annIdToFeatureId map to get the feature ids
+
+        let pathFeatures = paths.map((p) => this.mapImp.featureProperties(p))
+        let toHighlight = []
+        pathFeatures.forEach((p) => {
+          this.mapImp.nodePathModels(p.featureId).forEach((f) => {
+            toHighlight.push(f)
+          })
+        })
+        // display connected paths
+        this.mapImp.zoomToFeatures(toHighlight, { noZoomIn: true })
+      }
+    },
+    systemSelected: function (payload) {
+      if (this.mapImp) {
+        this.mapImp.enableSystem(payload.key, payload.value)
+      }
+    },
+    checkAllSystems: function (flag) {
+      if (this.mapImp) {
+        this.systems[0].children.forEach((key) =>
+          this.mapImp.enableSystem(key.label, flag)
+        )
+      }
+    },
+    ftuSelected: function (models) {
+      this.searchAndShowResult(models, true)
+    },
+    layersSelected: function (payload) {
+      if (this.mapImp) {
+        this.mapImp.enableLayer(payload.key, payload.value)
+      }
+    },
+    checkAllLayers: function (payload) {
+      if (this.mapImp) {
+        payload.keys.forEach((key) =>
+          this.mapImp.enableLayer(key, payload.value)
+        )
+      }
+    },
+    taxonsSelected: function (payload) {
+      if (this.mapImp) {
+        this.mapImp.enableConnectivityByTaxonIds(payload.key, payload.value)
+      }
+    },
+    checkAllTaxons: function (payload) {
+      if (this.mapImp) {
+        payload.keys.forEach((key) =>
+          this.mapImp.enableConnectivityByTaxonIds(key, payload.value)
+        )
+      }
+    },
+    pathwaysSelected: function (payload) {
+      if (this.mapImp) {
+        this.mapImp.enablePath(payload.key, payload.value)
+      }
+    },
+    checkAllPathways: function (payload) {
+      if (this.mapImp) {
+        payload.keys.forEach((key) =>
+          this.mapImp.enablePath(key, payload.value)
+        )
+      }
+    },
+    enablePanZoomEvents: function (flag) {
+      this.mapImp.enablePanZoomEvents(flag)
+    },
+    eventCallback: function () {
+      return (eventType, data, ...args) => {
+        if (eventType !== 'pan-zoom') {
+          const label = data.label
+          const resource = [data.models]
+          const taxonomy = this.entry
+          const biologicalSex = this.biologicalSex
+          const payload = {
+            dataset: data.dataset,
+            biologicalSex: biologicalSex,
+            taxonomy: taxonomy,
+            resource: resource,
+            label: label,
+            feature: data,
+            userData: args,
+            eventType: eventType,
+            provenanceTaxonomy: data.taxons
+              ? JSON.parse(data.taxons)
+              : undefined,
+          }
+          if (eventType === 'click') {
+            if (this.viewingMode === 'Network Discovery') {
+              this.highlightConnectedPaths([data.models])
+            } else {
+              this.currentActive = data.models ? data.models : ''
+            }
+          } else if (
+            eventType === 'mouseenter' &&
+            !(this.viewingMode === 'Network Discovery')
+          ) {
+            this.currentHover = data.models ? data.models : ''
+          }
+          if (
+            data &&
+            data.type !== 'marker' &&
+            eventType === 'click' &&
+            !(this.viewingMode === 'Network Discovery')
+          ) {
+            this.checkAndCreatePopups(payload)
+          }
+          this.$emit('resource-selected', payload)
+        } else {
+          this.$emit('pan-zoom-callback', data)
+        }
+      }
+    },
+    // checkNeuronClicked shows a neuron path pop up if a path was recently clicked
+    checkAndCreatePopups: async function (data) {
+      // Call flatmap database to get the connection data
+      if (this.viewingMode === 'Annotation') {
+        if (data.feature && data.feature.featureId && data.feature.models) {
+          this.annotationEntry = {
+            ...data.feature,
+            resourceId: this.serverUUID,
+          }
+          this.displayTooltip(data.feature.models)
+        } else {
+          this.annotation = {}
+        }
+      } else {
+        let results =
+          await this.flatmapQueries.retrieveFlatmapKnowledgeForEvent(data)
+        // The line below only creates the tooltip if some data was found on the path
+        // result 0 is the connection, result 1 is the pubmed results from flatmap
+        if (
+          results[0] ||
+          results[1] ||
+          (data.feature.hyperlinks && data.feature.hyperlinks.length > 0)
+        ) {
+          this.resourceForTooltip = data.resource[0]
+          data.resourceForTooltip = this.resourceForTooltip
+          this.createTooltipFromNeuronCuration(data)
+        }
+      }
+    },
+    popUpCssHacks: function () {
+      // Below is a hack to remove flatmap tooltips while popup is open
+      let ftooltip = document.querySelector('.flatmap-tooltip-popup')
+      if (ftooltip) ftooltip.style.display = 'none'
+      document.querySelector('.maplibregl-popup-close-button').style.display =
+        'block'
+      this.$refs.tooltip.$el.style.display = 'flex'
+      document.querySelector('.maplibregl-popup-close-button').onclick = () => {
+        document.querySelector('.flatmap-tooltip-popup').style.display = 'block'
+      }
+    },
+    closeTooltip: function () {
+      this.$refs.tooltip.$el.style.display = 'none'
+      document.querySelectorAll('.maplibregl-popup').forEach((item) => {
+        item.style.display = 'none'
+      })
+    },
+    createTooltipFromNeuronCuration: async function (data) {
+      this.tooltipEntry = await this.flatmapQueries.createTooltipData(data)
+      this.displayTooltip(data.resource[0])
+    },
+    // Keeping this as an API
+    showPopup: function (featureId, node, options) {
+      let myOptions = options
+      if (this.mapImp) {
+        if (myOptions) {
+          if (!myOptions.className) myOptions.className = 'custom-popup'
+        } else {
+          myOptions = { className: 'custom-popup', positionAtLastClick: true }
+        }
+        this.mapImp.showPopup(featureId, node, myOptions)
+      }
+    },
+    showMarkerPopup: function (featureId, node, options) {
+      if (this.mapImp) {
+        this.mapImp.showMarkerPopup(featureId, node, options)
+      }
+    },
+    closeMinimap: function () {
+      let minimapEl = this.$refs.flatmapContainer.querySelector(
+        '.maplibregl-ctrl-minimap'
+      ) // find minimap
+      if (this.minimapSmall) {
+        //switch the classes on the minimap
+        minimapEl.classList.add('enlarge')
+        minimapEl.classList.remove('shrink')
+      } else {
+        minimapEl.classList.add('shrink')
+        minimapEl.classList.remove('enlarge')
+      }
+      this.minimapSmall = !this.minimapSmall
+    },
+    addResizeButtonToMinimap: function () {
+      let minimapEl = this.$refs.flatmapContainer.querySelector(
+        '.maplibregl-ctrl-minimap'
+      )
+      if (minimapEl) {
+        if (this.$refs.minimapResize &&
+        this.$refs.minimapResize.$el.parentNode) {
+          this.$refs.minimapResize.$el.parentNode.removeChild(
+            this.$refs.minimapResize.$el)
+        }
+        minimapEl.appendChild(this.$refs.minimapResize.$el)
+        this.minimapResizeShow = true
+      }
+    },
+    setHelpMode: function (helpMode) {
+      if (helpMode) {
+        this.inHelp = true
+        this.hoverVisibilities.forEach((item) => {
+          item.value = true
+        })
+        this.openFlatmapHelpPopup()
+      } else {
+        this.inHelp = false
+        this.hoverVisibilities.forEach((item) => {
+          item.value = false
+        })
+        this.closeFlatmapHelpPopup()
+      }
+    },
+    showToolitip: function (tooltipNumber) {
+      if (!this.inHelp) {
+        clearTimeout(this.tooltipWait[tooltipNumber])
+        this.tooltipWait[tooltipNumber] = setTimeout(() => {
+          this.hoverVisibilities[tooltipNumber].value = true
+        }, 500)
+      }
+    },
+    hideToolitip: function (tooltipNumber) {
+      if (!this.inHelp) {
+        clearTimeout(this.tooltipWait[tooltipNumber])
+        this.tooltipWait[tooltipNumber] = setTimeout(() => {
+          this.hoverVisibilities[tooltipNumber].value = false
+        }, 500)
+      }
+    },
+    displayTooltip: function (feature) {
+      this.mapImp.showPopup(
+        this.mapImp.modelFeatureIds(feature)[0],
+        this.$refs.tooltip.$el,
+        { className: 'flatmapvuer-popover', positionAtLastClick: true }
+      )
+      this.popUpCssHacks()
+    },
+    openFlatmapHelpPopup: function () {
+      if (this.mapImp) {
+        let heartId = this.mapImp.modelFeatureIds('UBERON:0000948')
+        if (heartId && heartId.length > 0) {
+          const elm = 'Click for more information'
+          this.mapImp.showPopup(heartId[0], elm, {
+            anchor: 'top',
+            className: 'flatmap-popup-popper',
+          })
+        }
+      }
+    },
+    closeFlatmapHelpPopup: function () {
+      this.$el
+        .querySelectorAll('.maplibregl-popup-close-button')
+        .forEach((item) => {
+          item.click()
+        })
+    },
+    getLabels: function () {
+      let labels = []
+      if (this.mapImp) {
+        let annotations = this.mapImp.annotations
+        for (let value of annotations.values()) {
+          if (value.label) labels.push(value.label)
+        }
+        return Array.from(new Set(labels))
+      }
+    },
+    getState: function () {
+      if (this.mapImp) {
+        let state = {
+          entry: this.entry,
+          viewport: this.mapImp.getState(),
+        }
+        const identifier = this.mapImp.getIdentifier()
+        if (this.biologicalSex) state['biologicalSex'] = this.biologicalSex
+        else if (identifier && identifier.biologicalSex)
+          state['biologicalSex'] = identifier.biologicalSex
+        if (identifier && identifier.uuid) state['uuid'] = identifier.uuid
+        return state
+      }
+      return undefined
+    },
+    setState: function (state) {
+      if (state) {
+        if (
+          this.mapImp &&
+          state.entry &&
+          this.entry == state.entry &&
+          (!state.biologicalSex || state.biologicalSex === this.biologicalSex)
+        ) {
+          if (state.viewport) {
+            this.mapImp.setState(state.viewport)
+          }
+        } else {
+          this.createFlatmap(state)
+        }
+        this.setStateRequired = false
+      }
+    },
+    restoreMapState: function (state) {
+      if (state) {
+        if (state.viewport) this.mapImp.setState(state.viewport)
+        if (state.searchTerm) this.searchAndShowResult(state.searchTerm, true)
+      }
+    },
+    createFlatmap: function (state) {
+      if (!this.mapImp && !this.loading) {
+        this.loading = true
+        let minimap = false
+        if (this.displayMinimap) {
+          minimap = { position: 'top-right' }
+        }
+
+        //As for flatmap-viewer@2.2.7, see below for the documentation
+        //for the identifier:
+
+        //@arg identifier {string|Object}
+        // A string or object identifying the map to load. If a string its
+        // value can be either the map's ``uuid``, assigned at generation time,
+        // or taxon and biological sex identifiers of the species that the map
+        // represents. The latest version of a map is loaded unless it has been
+        // identified using a ``uuid`` (see below).
+        // @arg identifier.taxon {string} The taxon identifier of the species
+        //  represented by the map. This is specified as metadata in the map's source file.
+        // @arg identifier.biologicalSex {string} The biological sex of the species
+        // represented by the map. This is specified as metadatain the map's source file.
+        // @arg identifier.uuid {string} The unique uuid the flatmap. If given then this exact map will
+        //  be loaded, overriding ``taxon`` and ``biologicalSex``.
+
+        let identifier = { taxon: this.entry }
+        if (this.uuid) {
+          identifier.uuid = this.uuid
+        }
+        //This now handle the uses of uuid when resuming states
+        if (state) {
+          if (state.uuid) {
+            identifier = { uuid: state.uuid }
+          } else if (state.entry) {
+            identifier.taxon = state.entry
+            if (state.biologicalSex) {
+              identifier['biologicalSex'] = state.biologicalSex
+            } else if (identifier.taxon === 'NCBITaxon:9606') {
+              //For backward compatibility
+              identifier['biologicalSex'] = 'PATO:0000384'
+            }
+          }
+        } else {
+          // Set the bioloicalSex now if map is not resumed from
+          // a saved state
+          if (this.biologicalSex) {
+            identifier['biologicalSex'] = this.biologicalSex
+          }
+        }
+
+        let promise1 = this.mapManager.loadMap(
+          identifier,
+          this.$refs.display,
+          this.eventCallback(),
+          {
+            //fullscreenControl: false,
+            //annotatable: false,
+            //debug: true,
+            featureInfo: this.featureInfo,
+            'min-zoom': this.minZoom,
+            layerControl: true,
+            pathControls: true,
+            searchable: this.searchable,
+            tooltips: this.tooltips,
+            minimap: minimap,
+          }
+        )
+        promise1.then((returnedObject) => {
+          this.mapImp = returnedObject
+          this.serverUUID = this.mapImp.getIdentifier().uuid
+          this.onFlatmapReady()
+          if (this._stateToBeSet) this.restoreMapState(this._stateToBeSet)
+          else {
+            this.restoreMapState(state)
+          }
+        })
+      } else if (state) {
+        this._stateToBeSet = {
+          viewport: state.viewport,
+          searchTerm: state.searchTerm,
+        }
+        if (this.mapImp && !this.loading)
+          this.restoreMapState(this._stateToBeSet)
+      }
+    },
+    computePathControlsMaximumHeight() {
+      const elem = this.$refs.display
+      if (elem) {
+        const computed = getComputedStyle(elem)
+        const padding =
+          parseInt(computed.paddingTop) + parseInt(computed.paddingBottom)
+        const height = elem.clientHeight - padding
+        this.pathwaysMaxHeight = height - 170
+      }
+    },
+    mapResize: function () {
+      try {
+        this.computePathControlsMaximumHeight()
+        if (this.mapImp) {
+          this.mapImp.resize()
+          this.showMinimap(this.displayMinimap)
+          if (this.mapImp._minimap) {
+            this.mapImp._minimap._miniMap.resize()
+          }
+        }
+      } catch {
+        console.error('Map resize error')
+      }
+    },
+    onFlatmapReady: function () {
+      // onFlatmapReady is used for functions that need to run immediately after the flatmap is loaded
+      this.sensor = new ResizeSensor(this.$refs.display, this.mapResize)
+      if (this.mapImp.options && this.mapImp.options.style === 'functional') {
+        this.isFC = true
+      }
+      this.mapImp.setBackgroundOpacity(1)
+      this.backgroundChangeCallback(this.currentBackground)
+      this.pathways = this.mapImp.pathTypes()
+      this.mapImp.enableCentrelines(false)
+      //Disable layers for now
+      //this.layers = this.mapImp.getLayers();
+      this.processSystems(this.mapImp.getSystems())
+      this.processTaxon(this.flatmapAPI, this.mapImp.taxonIdentifiers)
+      this.addResizeButtonToMinimap()
+      this.loading = false
+      this.computePathControlsMaximumHeight()
+      this.drawerOpen = true
+      this.mapResize()
+      this.$emit('ready', this)
+    },
+    showMinimap: function (flag) {
+      if (this.mapImp) this.mapImp.showMinimap(flag)
+    },
+    showPathwaysDrawer: function (flag) {
+      this.drawerOpen = flag
+    },
+    /**
+     * Function to display features with annotation matching the provided term,
+     * with the option to display the label using displayLabel flag.
+     */
+    searchAndShowResult: function (term, displayLabel) {
+      if (this.mapImp) {
+        if (term === undefined || term === '') {
+          this.mapImp.clearSearchResults()
+          return true
+        } else {
+          const searchResults = this.mapImp.search(term)
+          if (
+            searchResults &&
+            searchResults.results &&
+            searchResults.results.length > 0
+          ) {
+            this.mapImp.showSearchResults(searchResults)
+            if (
+              displayLabel &&
+              searchResults.results[0].featureId &&
+              searchResults.results[0].text
+            ) {
+              const annotation = this.mapImp.annotation(
+                searchResults.results[0].featureId
+              )
+              this.mapImp.showPopup(
+                searchResults.results[0].featureId,
+                annotation.label,
+                {
+                  className: 'custom-popup',
+                  positionAtLastClick: false,
+                  preserveSelection: true,
+                }
+              )
+            }
+            return true
+          } else this.mapImp.clearSearchResults()
+        }
+      }
+      return false
+    },
+    /**
+     * Get the list of suggested terms
+     */
+    searchSuggestions: function (term) {
+      if (this.mapImp) return this.mapImp.search(term)
+      return []
+    },
+  },
+  props: {
+    entry: String,
+    uuid: String,
+    biologicalSex: {
+      type: String,
+      default: '',
+    },
+    featureInfo: {
+      type: Boolean,
+      default: false,
+    },
+    minZoom: {
+      type: Number,
+      default: 4,
+    },
+    pathControls: {
+      type: Boolean,
+      default: false,
+    },
+    searchable: {
+      type: Boolean,
+      default: false,
+    },
+    layerControl: {
+      type: Boolean,
+      default: false,
+    },
+    tooltips: {
+      type: Boolean,
+      default: true,
+    },
+    helpMode: {
+      type: Boolean,
+      default: false,
+    },
+    renderAtMounted: {
+      type: Boolean,
+      default: true,
+    },
+    displayMinimap: {
+      type: Boolean,
+      default: false,
+    },
+    displayWarning: {
+      type: Boolean,
+      default: false,
+    },
+    /**
+     * Flag to determine rather open map UI should be
+     * presented or not.
+     */
+    enableOpenMapUI: {
+      type: Boolean,
+      default: false,
+    },
+    openMapOptions: {
+      type: Array,
+      default: function () {
+        return [
+          {
+            display: 'Open AC Map',
+            key: 'AC',
+          },
+          {
+            display: 'Open FC Map',
+            key: 'FC',
+          },
+          {
+            display: 'Open 3D Human Map',
+            key: '3D',
+          },
+        ]
+      },
+    },
+    showStarInLegend: {
+      type: Boolean,
+      default: false,
+    },
+    isLegacy: {
+      type: Boolean,
+      default: false,
+    },
+    displayLatestChanges: {
+      type: Boolean,
+      default: false,
+    },
+    /**
+     * State containing state of the flatmap.
+     */
+    state: {
+      type: Object,
+      default: undefined,
+    },
+    /**
+     * Specify the endpoint of the flatmap server.
+     */
+    flatmapAPI: {
+      type: String,
+      default: 'https://mapcore-demo.org/current/flatmap/v3/',
+    },
+    sparcAPI: {
+      type: String,
+      default: 'https://api.sparc.science/',
+    },
+  },
+  provide() {
+    return {
+      flatmapAPI: this.flatmapAPI,
+      sparcAPI: this.sparcAPI,
+    }
+  },
+  data: function () {
+    return {
+      annotationEntry: {},
+      serverUUID: undefined,
+      layers: [],
+      pathways: [],
+      sckanDisplay: [
+        {
+          label: 'Display Path with SCKAN',
+          key: 'VALID',
+        },
+      ],
+      centreLines: [
+        {
+          label: 'Display Nerves',
+          key: 'centrelines',
+          enabled: false,
+        },
+      ],
+      systems: [],
+      taxonConnectivity: [],
+      pathwaysMaxHeight: 1000,
+      hoverVisibilities: [
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+      ],
+      yellowstar: yellowstar,
+      isFC: false,
+      inHelp: false,
+      currentBackground: 'white',
+      availableBackground: ['white', 'lightskyblue', 'black'],
+      loading: false,
+      flatmapMarker: flatmapMarker,
+      tooltipEntry: createUnfilledTooltipData(),
+      connectivityTooltipVisible: false,
+      drawerOpen: false,
+      annotationRadio: false,
+      colourRadio: true,
+      outlinesRadio: true,
+      minimapResizeShow: false,
+      minimapSmall: false,
+      currentActive: '',
+      currentHover: '',
+      viewingMode: 'Exploration',
+      viewingModes: ['Annotation', 'Exploration', 'Network Discovery'],
+      openMapRef: undefined,
+      backgroundIconRef: undefined,
+    }
+  },
+  watch: {
+    entry: function () {
+      if (!this.state) this.createFlatmap()
+    },
+    helpMode: function (val) {
+      this.setHelpMode(val)
+    },
+    state: {
+      handler: function (state) {
+        if (this.mapManager) {
+          this.setState(state)
+        } else {
+          //this component has not been mounted yet
+          this.setStateRequired = true
+        }
+      },
+      immediate: true,
+      deep: true,
+    },
+  },
+  mounted: function () {
+    this.openMapRef = ref(this.$refs.openMapRef)
+    this.backgroundIconRef = ref(this.$refs.backgroundIconRef)
+    this.tooltipWait = []
+    this.tooltipWait.length = this.hoverVisibilities.length
+    this.mapManager = new flatmap.MapManager(this.flatmapAPI)
+    this.flatmapQueries = new FlatmapQueries()
+    this.flatmapQueries.initialise(this.flatmapAPI)
+    if (this.state) {
+      //State is set and require to set the state
+      if (this.setStateRequired) {
+        this.setState(this.state)
+      }
+    } else if (this.renderAtMounted) {
+      this.createFlatmap()
+    }
+  },
+}
+</script>
+
+<style lang="scss" scoped>
+@use 'element-plus/theme-chalk/src/button';
+@use 'element-plus/theme-chalk/src/loading';
+@use 'element-plus/theme-chalk/src/row';
+@use 'element-plus/theme-chalk/src/select';
+
+.beta-popovers {
+  position: absolute;
+  top: 90px;
+  left: 16px;
+  text-align: left;
+  font-size: 25px;
+}
+
+.warning-icon {
+  color: $warning;
+
+  &:hover {
+    cursor: pointer;
+  }
+}
+
+.warning-text {
+  font-family: Asap, sans-serif;
+  font-size: 15px;
+  vertical-align: 5px;
+}
+
+.latest-map-text {
+  color: $app-primary-color;
+  font-family: Asap, sans-serif;
+  font-size: 12px;
+  margin-top: 5px;
+  vertical-align: 10px;
+  cursor: pointer;
+}
+
+.latest-changesicon {
+  color: $success;
+
+  &:hover {
+    cursor: pointer;
+  }
+}
+
+.latest-changestext {
+  font-family: Asap, sans-serif;
+  font-size: 15px;
+  vertical-align: 5px;
+}
+
+.flatmap-container {
+  height: 100%;
+  width: 100%;
+}
+
+.pathway-location {
+  position: absolute;
+  bottom: 0px;
+  transition: all 1s ease;
+  &.open {
+    left: 0px;
+  }
+  &.close {
+    left: -298px;
+  }
+}
+
+.svg-legends-container {
+  width: 70%;
+  height: auto;
+  position: relative;
+  max-height: 140px;
+}
+
+.pathway-container {
+  float: left;
+  padding-left: 16px;
+  padding-right: 18px;
+  text-align: left;
+  overflow: auto;
+  border: 1px solid rgb(220, 223, 230);
+  padding-bottom: 16px;
+  background: #ffffff;
+  overflow-x: hidden;
+  scrollbar-width: thin;
+
+  transition: all 1s ease;
+  &.open {
+    opacity: 1;
+  }
+  &.close {
+    opacity: 0;
+  }
+
+  &::-webkit-scrollbar {
+    width: 4px;
+  }
+
+  &::-webkit-scrollbar-thumb {
+    border-radius: 10px;
+    box-shadow: inset 0 0 6px #c0c4cc;
+  }
+}
+
+.flatmap-marker-help {
+  display: inline-block;
+}
+
+:deep(.popper-bump-right) {
+  left: 30px;
+}
+
+.el-dropdown-link {
+  cursor: pointer;
+  color: #409eff;
+}
+.el-icon-arrow-down {
+  font-size: 12px;
+}
+.demonstration {
+  display: block;
+  color: #8492a6;
+  font-size: 14px;
+  margin-bottom: 20px;
+}
+
+.tooltip {
+  display: none;
+}
+
+:deep(.maplibregl-popup) {
+  max-width: 300px !important;
+}
+
+:deep(.flatmap-tooltip-popup) {
+  &.maplibregl-popup-anchor-bottom {
+    .maplibregl-popup-content {
+      margin-bottom: 12px;
+      &::after,
+      &::before {
+        top: 100%;
+        border-width: 12px;
+      }
+      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
+      &::after {
+        margin-top: -1px;
+        border-color: rgb(255, 255, 255) transparent transparent transparent;
+      }
+      /* this border color controlls the outside, thin border */
+      &::before {
+        margin: 0 auto;
+        border-color: $app-primary-color transparent transparent transparent;
+      }
+    }
+  }
+  &.maplibregl-popup-anchor-top {
+    .maplibregl-popup-content {
+      margin-top: 18px;
+      &::after,
+      &::before {
+        top: calc(-100% + 6px);
+        border-width: 12px;
+      }
+      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
+      &::after {
+        margin-top: 1px;
+        border-color: transparent transparent rgb(255, 255, 255) transparent;
+      }
+      &::before {
+        margin: 0 auto;
+        border-color: transparent transparent $app-primary-color transparent;
+      }
+    }
+  }
+  .maplibregl-popup-content {
+    border-radius: 4px;
+    box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);
+    pointer-events: none;
+    display: none;
+    background: #fff;
+    border: 1px solid $app-primary-color;
+    padding-left: 6px;
+    padding-right: 6px;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    &::after,
+    &::before {
+      content: '';
+      display: block;
+      position: absolute;
+      width: 0;
+      height: 0;
+      border-style: solid;
+      flex-shrink: 0;
+    }
+  }
+  .maplibregl-popup-tip {
+    display: none;
+  }
+}
+
+:deep(.maplibregl-popup) {
+  &.flatmap-marker-popup {
+    box-shadow: 1px 1px 2px rgba(0, 0, 0, 0.1);
+    pointer-events: auto;
+    background: #fff;
+  }
+}
+
+/* Fix for chrome bug where under triangle pops up above one on top of it  */
+.selector:not(*:root),
+:deep(.flatmap-tooltip-popup) {
+  .maplibregl-popup-content::after {
+    top: 99.9%;
+  }
+}
+
+:deep(.flatmap-tooltip-dialog) {
+  .maplibregl-popup-tip {
+    display: none;
+  }
+}
+
+:deep(.flatmap-marker-popup){
+  .maplibregl-popup-content {
+    padding: 0px;
+  }
+}
+
+:deep(.flatmapvuer-popover) {
+  .maplibregl-popup-close-button {
+    position: absolute;
+    right: 0.5em;
+    top: 0;
+    border: 0;
+    border-radius: 0 3px 0 0;
+    cursor: pointer;
+    background-color: transparent;
+    font-size: 2.5em;
+    color: grey;
+    top: 0.95em;
+  }
+}
+
+.zoomOut {
+  padding-left: 8px;
+}
+
+.fitWindow {
+  padding-left: 8px;
+}
+
+.yellow-star-legend {
+  width: 130px;
+  cursor: pointer;
+}
+
+.settings-group {
+  bottom: 16px;
+  position: absolute;
+  transition: all 1s ease;
+  &.open {
+    left: 322px;
+  }
+  &.close {
+    left: 24px;
+  }
+}
+
+:deep(.background-popper.el-popover.el-popper) {
+  padding: 5px 12px;
+  background-color: #ffffff;
+  border: 1px solid $app-primary-color;
+  box-shadow: 0px 2px 12px 0px rgba(0, 0, 0, 0.06);
+  height: 290px;
+  min-width: 200px;
+  .el-popper__arrow {
+    &:before {
+      border-color: $app-primary-color;
+    }
+  }
+}
+
+:deep(.open-map-popper.el-popover.el-popper) {
+  padding-top: 5px;
+  padding-bottom: 5px;
+  background-color: #ffffff;
+  border: 1px solid $app-primary-color;
+  box-shadow: 0px 2px 12px 0px rgba(0, 0, 0, 0.06);
+  min-width: 188px;
+
+  .el-row ~ .el-row {
+    margin-top: 8px;
+  }
+
+  .el-button {
+    padding-top: 5px;
+    padding-bottom: 5px;
+    background: #f3e6f9;
+    border-color: $app-primary-color;
+    color: $app-primary-color;
+  }
+
+  .el-popper__arrow {
+    &:before {
+      border-color: $app-primary-color;
+    }
+  }
+}
+
+.backgroundText {
+  color: rgb(48, 49, 51);
+  font-size: 14px;
+  font-weight: normal;
+  line-height: 20px;
+}
+
+.backgroundControl {
+  display: flex;
+}
+
+.backgroundChoice {
+  width: 20px;
+  height: 20px;
+  border: 1px solid rgb(144, 147, 153);
+  margin-left: 20px;
+  &.active {
+    border: 2px solid $app-primary-color;
+  }
+  &:hover {
+    cursor: pointer;
+  }
+  &.white {
+    background-color: white;
+    margin-left: 10px;
+  }
+  &.black {
+    background-color: black;
+  }
+  &.lightskyblue {
+    background-color: lightskyblue;
+  }
+}
+
+.icon-button {
+  height: 24px !important;
+  width: 24px !important;
+  color: $app-primary-color;
+  &:hover {
+    cursor: pointer;
+  }
+}
+
+:deep(.maplibregl-ctrl-minimap) {
+  transform-origin: top right;
+  @media (max-width: 1250px) {
+    height: 125px !important; // important is needed here as we are over-riding the style set by the flatmap
+    width: 180px !important;
+    :deep(.maplibregl-canvas .maplibregl-canvas) {
+      height: 125px !important;
+      width: 180px !important;
+    }
+  }
+  @media (min-width: 1251px) {
+    height: 190px !important;
+    width: 300px !important;
+    :deep(.maplibregl-canvas .maplibregl-canvas) {
+      height: 190px !important;
+      width: 300px !important;
+    }
+  }
+  transition: all 1s ease;
+  &.shrink {
+    transform: scale(0.5);
+    transform: scale(0.5);
+  }
+}
+
+.minimap-resize {
+  position: absolute;
+  pointer-events: all;
+  cursor: pointer;
+  top: 0;
+  right: 0;
+  padding-top: 3px; // needed as icon is offset
+  width: 20px;
+  height: 14px;
+  z-index: 9;
+  transition: all 1s ease;
+  &.shrink {
+    transform: rotate(0deg);
+  }
+  &.enlarge {
+    transform: rotate(180deg) scale(2);
+    padding-bottom: 5px; // note padding is added to the opposite side since it is rotated
+    padding-left: 5px;
+  }
+}
+
+:deep(.flatmap-popper.el-popper.el-popper) {
+  padding: 6px 4px;
+  font-size: 12px;
+  color: rgb(48, 49, 51);
+  background-color: #f3ecf6;
+  border: 1px solid $app-primary-color;
+  white-space: nowrap;
+  min-width: unset;
+  &.warning-popper {
+    min-width: 150px;
+    max-width: 400px;
+    word-break: keep-all;
+    white-space: unset;
+  }
+  .el-popper__arrow {
+    &:before {
+      border-color: $app-primary-color;
+      background-color: #f3ecf6;
+    }
+  }
+}
+
+:deep(.el-loading-spinner) {
+  .path {
+    stroke: $app-primary-color;
+  }
+  .el-loading-text {
+    color: $app-primary-color;
+  }
+}
+
+:deep(.flatmap-popup-popper) {
+  .maplibregl-popup-tip {
+    border-bottom-color: $app-primary-color;
+  }
+  .maplibregl-popup-content {
+    padding: 6px 4px;
+    font-size: 12px;
+    color: rgb(48, 49, 51);
+    background-color: #f3ecf6;
+    border: 1px solid $app-primary-color;
+    white-space: nowrap;
+    min-width: unset;
+    .maplibregl-popup-close-button {
+      display: none;
+    }
+  }
+}
+
+:deep(.popper-zoomout) {
+  padding-right: 13px !important;
+  left: -21px !important;
+}
+
+:deep(.popper-zoomout) {
+  .popper__arrow {
+    left: 53px !important;
+  }
+}
+
+:deep(.maplibregl-popup-content) {
+  padding: 0px;
+}
+
+.bottom-right-control {
+  position: absolute;
+  right: 16px;
+  bottom: 16px;
+}
+
+:deep(.my-drawer) {
+  background: rgba(0, 0, 0, 0);
+  box-shadow: none;
+}
+
+.drawer {
+  :deep(.el-drawer:focus) {
+    outline: none;
+  }
+}
+
+.open-drawer,
+.drawer-button {
+  z-index: 8;
+  width: 20px;
+  height: 40px;
+  border: solid 1px $app-primary-color;
+  text-align: center;
+  vertical-align: middle;
+  cursor: pointer;
+  pointer-events: auto;
+}
+
+.open-drawer {
+  position: absolute;
+  left: 0px;
+  background-color: #f7faff;
+  box-shadow: 0 2px 12px 0 rgba(0, 0, 0, 0.06);
+}
+
+.drawer-button {
+  float: left;
+  margin-top: calc(50% - 36px);
+  background-color: #f9f2fc;
+
+  i {
+    font-weight: 600;
+    margin-top: 12px;
+    color: $app-primary-color;
+    transition-delay: 0.9s;
+  }
+  &.open {
+    i {
+      transform: rotate(0deg) scaleY(2);
+    }
+  }
+  &.close {
+    i {
+      transform: rotate(180deg) scaleY(2);
+    }
+  }
+}
+
+:deep(.maplibregl-canvas-container) {
+  canvas {
+    outline: none;
+  }
+}
+
+.backgroundSpacer {
+  border-bottom: 1px solid #e4e7ed;
+  margin-bottom: 10px;
+}
+
+.flatmap-radio {
+  :deep(label) {
+    margin-right: 20px;
+    &:last-child {
+      margin-right: 0px;
+    }
+  }
+  :deep(.el-radio__input) {
+    &.is-checked {
+      & + .el-radio__label {
+        color: $app-primary-color;
+      }
+      .el-radio__inner {
+        border-color: $app-primary-color;
+        background: $app-primary-color;
+      }
+    }
+    .el-radio__inner:hover {
+      border-color: $app-primary-color;
+    }
+  }
+}
+
+:deep(.custom-popup) {
+  .maplibregl-popup-tip {
+    display: none;
+  }
+  .maplibregl-popup-content {
+    border-radius: 4px;
+    box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);
+    pointer-events: none;
+    display: none;
+    background: #fff;
+    font-family: 'Asap', sans-serif;
+    font-size: 12pt;
+    color: $app-primary-color;
+    border: 1px solid $app-primary-color;
+    padding-left: 6px;
+    padding-right: 6px;
+    padding-top: 6px;
+    padding-bottom: 6px;
+    display: flex;
+    justify-content: center;
+    align-items: center;
+    &::after,
+    &::before {
+      content: '';
+      display: block;
+      position: absolute;
+      width: 0;
+      height: 0;
+      border-style: solid;
+      flex-shrink: 0;
+    }
+    .maplibregl-popup-close-button {
+      display: none;
+    }
+  }
+  &.maplibregl-popup-anchor-bottom {
+    .maplibregl-popup-content {
+      margin-bottom: 12px;
+      &::after,
+      &::before {
+        top: 100%;
+        border-width: 12px;
+      }
+      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
+      &::after {
+        margin-top: -1px;
+        border-color: rgb(255, 255, 255) transparent transparent transparent;
+      }
+      /* this border color controlls the outside, thin border */
+      &::before {
+        margin: 0 auto;
+        border-color: $app-primary-color transparent transparent transparent;
+      }
+    }
+  }
+  &.maplibregl-popup-anchor-top {
+    .maplibregl-popup-content {
+      margin-top: 18px;
+      &::after,
+      &::before {
+        top: calc(-100% + 6px);
+        border-width: 12px;
+      }
+      /* this border color controlls the color of the triangle (what looks like the fill of the triangle) */
+      &::after {
+        margin-top: 1px;
+        border-color: transparent transparent rgb(255, 255, 255) transparent;
+      }
+      &::before {
+        margin: 0 auto;
+        border-color: transparent transparent $app-primary-color transparent;
+      }
+    }
+  }
+}
+
+.select-box {
+  border-radius: 4px;
+  border: 1px solid rgb(144, 147, 153);
+  background-color: var(--white);
+  font-weight: 500;
+  color: rgb(48, 49, 51);
+  :deep(.el-input__inner) {
+    height: 30px;
+    color: rgb(48, 49, 51);
+  }
+  :deep() {
+    .el-input__inner {
+      &is-focus,
+      &:focus {
+        border: 1px solid $app-primary-color;
+      }
+    }
+  }
+  :deep(.el-input__icon) {
+    line-height: 30px;
+  }
+}
+
+:deep(.flatmap_dropdown) {
+  min-width: 160px !important;
+  .el-select-dropdown__item {
+    white-space: nowrap;
+    text-align: left;
+    &.selected {
+      color: $app-primary-color;
+      font-weight: normal;
+    }
+  }
+}
+</style>