@abi-software/flatmapvuer 0.3.3 → 0.3.5

package/src/components/FlatmapVuer.vue

@@ -1,1358 +1,1358 @@
-<template>
-  <div
-    class="flatmap-container"
-    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
-            :content="warningMessage"
-            placement="right"
-            :appendToBody="false"
-            trigger="manual"
-            popper-class="warning-popper flatmap-popper right-popper"
-            v-model="hoverVisibilities[6].value"
-            ref="warningPopover"
-          ></el-popover>
-          <i
-            class="el-icon-warning warning-icon"
-            v-if="displayWarning && warningMessage"
-            @mouseover="showToolitip(6)"
-            @mouseout="hideToolitip(6)"
-            v-popover:warningPopover
-          >
-          <span class="warning-text">Beta</span>
-        </i>
-        </div>
-        <el-popover
-          :content="latestChangesMessage"
-          placement="right"
-          v-if="displayLatestChanges"
-          :appendToBody="false"
-          trigger="manual"
-          popper-class="warning-popper flatmap-popper right-popper"
-          v-model="hoverVisibilities[7].value"
-          ref="latestChangesPopover"
-        ></el-popover>
-        <i
-          class="el-icon-warning latest-changesicon"
-          v-if="displayLatestChanges && latestChangesMessage"
-          @mouseover="showToolitip(7)"
-          @mouseout="hideToolitip(7)"
-          v-popover:latestChangesPopover
-        >
-          <span class="warning-text">What's new?</span>
-        </i>
-      </div>
-
-      <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"
-          v-if="pathways.length > 0 && pathControls"
-          v-popover:checkBoxPopover
-        >
-          <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>
-          <el-row>
-            <el-col :span="12">
-              <div class="pathways-display-text">Pathways</div>
-            </el-col>
-            <el-col :span="12">
-              <el-checkbox
-                class="all-checkbox"
-                :indeterminate="isIndeterminate"
-                v-model="checkAll"
-                @change="handleCheckAllChange"
-              >Display all</el-checkbox>
-            </el-col>
-          </el-row>
-          <el-checkbox-group
-            v-model="checkedItems"
-            size="small"
-            class="checkbox-group"
-            @change="handleCheckedItemsChange"
-          >
-            <div class="checkbox-group-inner">
-              <el-row v-for="item in pathways" :key="item.type" :label="item.type">
-                <div class="checkbox-container">
-                  <el-checkbox
-                    class="my-checkbox"
-                    :label="item.type"
-                    @change="visibilityToggle()"
-                    :checked="true"
-                  >
-                    <div class="path-visual" :class="item.type"></div>
-                    {{item.label}}
-                  </el-checkbox>
-                </div>
-              </el-row>
-            </div>
-          </el-checkbox-group>
-        </div>
-        <div
-          @click="toggleDrawer"
-          class="drawer-button"
-          :class="{ open: drawerOpen, close: !drawerOpen }"
-        >
-          <i class="el-icon-arrow-left"></i>
-        </div>
-      </div>
-      <el-popover
-        ref="backgroundPopover"
-        placement="top-start"
-        width="175"
-        :appendToBody="false"
-        trigger="click"
-        popper-class="background-popper"
-      >
-        <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>
-      <el-popover
-        content="Change background color"
-        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 background-colour"
-          :class="{ open: drawerOpen, close: !drawerOpen }"
-          slot="reference"
-          @mouseover.native="showToolitip(3)"
-          @mouseout.native="hideToolitip(3)"
-        />
-      </el-popover>
-      <Tooltip
-        ref="tooltip"
-        class="tooltip"
-        :content="tooltipContent"
-        @resource-selected="resourceSelected"
-      />
-    </div>
-  </div>
-</template>
-
-<script>
-/* eslint-disable no-alert, no-console */
-import Vue from "vue";
-import Tooltip from "./Tooltip";
-import { MapSvgIcon, MapSvgSpriteColor } from "@abi-software/svg-sprite";
-import {
-  Checkbox,
-  CheckboxGroup,
-  Col,
-  Loading,
-  Radio,
-  RadioGroup,
-  Row
-} 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";
-
-locale.use(lang);
-Vue.use(Checkbox);
-Vue.use(CheckboxGroup);
-Vue.use(Col);
-Vue.use(Loading.directive);
-Vue.use(Radio);
-Vue.use(RadioGroup);
-Vue.use(Row);
-const ResizeSensor = require("css-element-queries/src/ResizeSensor");
-
-const mapResize = map => {
-  return () => {
-    if (map) map.resize();
-  };
-};
-
-export default {
-  name: "FlatmapVuer",
-  components: {
-    MapSvgIcon,
-    MapSvgSpriteColor,
-    Tooltip
-  },
-  beforeCreate: function() {
-    this.mapManager = undefined;
-    this.mapImp = undefined;
-  },
-  methods: {
-    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();
-        this.checkedItems = this.mapImp.pathTypes().map(item => item.type);
-        this.isIndeterminate = false;
-        this.checkAll = true;
-      }
-    },
-    /**
-     * 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();
-      }
-    },
-    visibilityToggle: function() {
-      if (this.mapImp) {
-        this.mapImp.showPaths(this.checkedItems);
-      }
-    },
-    handleCheckedItemsChange: function(value) {
-      let checkedCount = value.length;
-      this.checkAll = checkedCount === this.pathways.length;
-      this.isIndeterminate =
-        checkedCount > 0 && checkedCount < this.pathways.length;
-    },
-    handleCheckAllChange(val) {
-      this.checkedItems = val ? this.pathways.map(a => a.type) : [];
-      this.isIndeterminate = false;
-      if (this.mapImp) {
-        this.mapImp.showPaths(this.checkedItems);
-      }
-    },
-    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 payload = {
-            dataset: data.dataset,
-            taxonomy: taxonomy,
-            resource: resource,
-            label: label,
-            feature: data,
-            userData: args,
-            eventType: eventType
-          };
-          // Disable the nueron pop up for now.
-          if (data && data.type !== "marker")
-            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: function(data) {
-      if (
-        data.eventType == "click" &&
-        this.hasNeuronTooltip(data)
-      ) {
-        this.createTooltipFromNeuronCuration(data);
-        this.mapImp.showPopup(
-          this.mapImp.modelFeatureIds(data.resource[0])[0],
-          this.$refs.tooltip.$el,
-          { className: "flatmapvuer-popover", positionAtLastClick: true }
-        );
-        this.popUpCssHacks();
-      }
-    },
-    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(".mapboxgl-popup-close-button").style.display =
-        "block";
-      this.$refs.tooltip.$el.style.display = "flex";
-      document.querySelector(".mapboxgl-popup-close-button").onclick = () => {
-        document.querySelector(".flatmap-tooltip-popup").style.display =
-          "block";
-      };
-    },
-    resourceSelected: function(action) {
-      this.$emit("resource-selected", action);
-    },
-    hasNeuronTooltip: function(data) {
-
-      // neural data check
-      if (data.resource[0]){
-        if (data.resource[0].includes('ilxtr:neuron')){
-          return true
-        }
-      }
-      // annotated with datset check
-      if (data.dataset) {
-        return true
-      }
-
-      // if there is no cuff, neural data, or dataset we do not display neuron tooltip
-      return false
-
-    },
-    createTooltipFromNeuronCuration: function(data) {
-      const feature = data.resource[0];
-      let content = {
-        title: undefined,
-        components: undefined,
-        start: undefined,
-        distribution: undefined,
-        actions: []
-      };
-
-      this.tooltipVisible = false;
-
-      // neural data check
-      if (feature){
-        if (feature.includes('ilxtr:neuron')){
-          this.tooltipVisible = true;
-          this.tooltipContent = content;
-          this.tooltipContent.uberon = feature;
-          this.tooltipContent.title = data.label;
-          this.tooltipContent.featureIds = [feature];
-          this.tooltipContent.actions.push({
-            title: "Search for datasets",
-            label: "Neuron Datasets",
-            resource: feature.split(":")[1],
-            type: "Neuron Search",
-            feature: feature,
-            nervePath: true
-          });
-        }
-      }
-      // annotated with datset check
-      if (data.dataset) {
-        this.tooltipVisible = true;
-        this.tooltipContent = content;
-        this.tooltipContent.uberon = feature;
-        this.tooltipContent.title = data.label;
-        this.tooltipContent.actions.push({
-          title: "View dataset",
-          resource: data.dataset,
-          type: "URL",
-          feature: feature,
-          nervePath: false
-        });
-      }
-    },
-    // Keeping this as an API
-    showPopup: function(featureId, node, options) {
-      let myOptions = options;
-      if (this.mapImp) {
-        if (myOptions) {
-          if (!myOptions.className) myOptions.className = "flatmapvuer-popover";
-        } else {
-          myOptions = { className: "flatmapvuer-popover", positionAtLastClick: true };
-        }
-        this.mapImp.showPopup(featureId, node, myOptions);
-      }
-    },
-    showMarkerPopup: function(featureId, node, options) {
-      if (this.mapImp) {
-        this.mapImp.showMarkerPopup(featureId, node, options);
-      }
-    },
-    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) {
-        this.tooltipWait = setTimeout(() => {
-          this.hoverVisibilities[tooltipNumber].value = true;
-        }, 500);
-      }
-    },
-    hideToolitip: function(tooltipNumber) {
-      if (!this.inHelp) {
-        this.hoverVisibilities[tooltipNumber].value = false;
-        clearTimeout(this.tooltipWait);
-      }
-    },
-    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(".mapboxgl-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()
-        };
-        return state;
-      }
-      return undefined;
-    },
-    setState: function(state) {
-      if (state) {
-        if (this.mapImp && state.entry) {
-          if (this.entry == state.entry)
-            if (state.viewport) {
-              this.mapImp.setState(state.viewport);
-            }
-        } else {
-          this.createFlatmap(state);
-        }
-      }
-    },
-    createFlatmap: function(state) {
-      if (!this.mapImp && !this.loading) {
-        this.loading = true;
-        let minimap = false;
-        if (this.displayMinimap) {
-          minimap = { position: "top-right" };
-        }
-        let entry = this.entry;
-        if (state && state.entry) entry = state.entry;
-        let promise1 = this.mapManager.loadMap(
-          entry,
-          this.$refs.display,
-          this.eventCallback(),
-          {
-            //fullscreenControl: false,
-            //annotatable: false,
-            //debug: true,
-            featureInfo: this.featureInfo,
-            "min-zoom": this.minZoom,
-            pathControls: false,
-            searchable: this.searchable,
-            tooltips: this.tooltips,
-            minimap: minimap
-          }
-        );
-        promise1.then(returnedObject => {
-          this.mapImp = returnedObject;
-          this.sensor = new ResizeSensor(
-            this.$refs.display,
-            mapResize(this.mapImp)
-          );
-          this.mapImp.setBackgroundOpacity(1);
-          this.backgroundChangeCallback(this.currentBackground);
-          this.pathways = this.mapImp.pathTypes();
-          this.$emit("ready", this);
-          this.loading = false;
-          if (this._viewportToBeSet)
-            this.mapImp.setState(this._viewportToBeSet);
-          else if (state && state.viewport)
-            this.mapImp.setState(state.viewport);
-        });
-      } else if (state) {
-        if (this.entry == state.entry) this._viewportToBeSet = state.viewport;
-      }
-    },
-    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.
-     */
-    searchAndShowResult: function(term) {
-      if (this.mapImp) {
-        if (term === undefined || term === "") {
-          this.mapImp.clearSearchResults();
-          return true;
-        } else {
-          let searchResults = this.mapImp.search(term);
-          if (searchResults && searchResults.__featureIds.length > 0) {
-            this.mapImp.showSearchResults(searchResults);
-            return true;
-          }
-          else
-            this.mapImp.clearSearchResults();
-        }
-      }
-      return false;
-    }
-  },
-  props: {
-    entry: String,
-    featureInfo: {
-      type: Boolean,
-      default: false
-    },
-    minZoom: {
-      type: Number,
-      default: 4
-    },
-    pathControls: {
-      type: Boolean,
-      default: true
-    },
-    searchable: {
-      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
-    },
-    warningMessage: {
-      type: String,
-      default: "Beta feature - This map is based on the connectivity of a rat. New connectivity and species specificity will be added as the SPARC program progress."
-    },
-    displayLatestChanges: {
-      type: Boolean,
-      default: false,
-    },
-    latestChangesMessage: {
-      type: String,
-      default: "Bladder connectivity can now be explored and searched on when selected! To see it, click on any of the paths coming from the bladder. Other pathways will be searchable soon.",
-    },
-    /**
-     * 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/flatmaps/"
-    },
-    sparcAPI: {
-      type: String,
-      default: "https://api.sparc.science/"
-    },
-  },
-  provide() {
-    return {
-      sparcAPI: this.sparcAPI,
-      flatmapAPI: this.flatmapAPI
-    }
-  },
-  data: function() {
-    return {
-      checkedItems: [],
-      pathways: [],
-      isIndeterminate: false,
-      checkAll: true,
-      hoverVisibilities: [
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false },
-        { value: false }
-      ],
-      inHelp: false,
-      currentBackground: "white",
-      availableBackground: ["white", "lightskyblue", "black"],
-      loading: false,
-      flatmapMarker: flatmapMarker,
-      drawerOpen: true,
-      tooltipContent: { featureIds: []},
-      colourRadio: true,
-      outlinesRadio: true
-    };
-  },
-  watch: {
-    entry: function() {
-      if (!this.state) this.createFlatmap();
-    },
-    helpMode: function(val) {
-      this.setHelpMode(val);
-    },
-    state: {
-      handler: function(state) {
-        this.setState(state);
-      },
-      immediate: true,
-      deep: true
-    }
-  },
-  mounted: function() {
-    const flatmap = require("@abi-software/flatmap-viewer");
-    this.mapManager = new flatmap.MapManager(this.flatmapAPI);
-    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/checkbox";
-@import "~element-ui/packages/theme-chalk/src/checkbox-group";
-@import "~element-ui/packages/theme-chalk/src/loading";
-@import "~element-ui/packages/theme-chalk/src/row";
-
-.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-changesicon {
-  color: $success;
-
-  &:hover {
-    cursor: pointer;
-  }
-}
-
-.latest-changestext {
-  font-family: Asap, sans-serif;
-  font-size: 15px;
-  vertical-align: 5px;
-}
-
-.path-visual {
-  margin: 3px 0;
-  height: 3px;
-  width: 25px;
-  margin-right: 5px;
-  display: inline-block;
-  &.cns {
-    background: #9b1fc1;
-  }
-  &.lcn {
-    background: #f19e38;
-  }
-  &.para-pre {
-    background: #3f8f4a;
-  }
-  &.para-post {
-    background: repeating-linear-gradient(
-      90deg,
-      #3f8f4a,
-      #3f8f4a 6px,
-      transparent 0,
-      transparent 9px
-    );
-  }
-  &.sensory {
-    background: #2a62f6;
-  }
-  &.somatic {
-    background: #98561d;
-  }
-  &.symp-pre {
-    background: #ea3423;
-  }
-  &.symp-post {
-    background: repeating-linear-gradient(
-      90deg,
-      #ea3423,
-      #ea3423 6px,
-      transparent 0,
-      transparent 9px
-    );
-  }
-}
-
-.flatmap-container {
-  height: 100%;
-  width: 100%;
-}
-
-.pathway-location {
-  position: absolute;
-  bottom: 0px;
-  transition: all 1s ease;
-  &.open {
-    left: 0px;
-  }
-  &.close {
-    left: -298px;
-  }
-}
-
-.pathway-container {
-  float: left;
-  padding-left: 16px;
-  padding-right: 18px;
-  max-height: calc(100% - 184px);
-  text-align: left;
-  overflow: auto;
-  border: 1px solid rgb(220, 223, 230);
-  padding-top: 7px;
-  padding-bottom: 16px;
-  background: #ffffff;
-}
-
-.pathways-display-text {
-  width: 59px;
-  height: 20px;
-  color: rgb(48, 49, 51);
-  font-size: 14px;
-  font-weight: normal;
-  line-height: 20px;
-  margin-left: 8px;
-}
-
-.all-checkbox {
-  float: right;
-}
-
-.checkbox-container {
-  display: flex;
-  cursor: pointer;
-}
-
-.checkbox-group {
-  width: 260px;
-  border: 1px solid rgb(144, 147, 153);
-  border-radius: 4px;
-  background: #ffffff;
-}
-
-.my-checkbox {
-  background-color: #fff;
-  width: 100%;
-}
-
-.checkbox-group-inner {
-  padding: 18px;
-}
-
-.flatmap-marker-help {
-  display: inline-block;
-}
-
-::v-deep .popper-bump-right {
-  left: 30px;
-}
-
-::v-deep .el-checkbox__label {
-  padding-left: 5px;
-  color: $app-primary-color;
-  font-size: 12px;
-  font-weight: 500;
-  letter-spacing: 0px;
-  line-height: 14px;
-}
-
-::v-deep .el-checkbox__input {
-  &.is-indeterminate,
-  &.is-checked {
-    .el-checkbox__inner {
-      background-color: $app-primary-color;
-      border-color: $app-primary-color;
-    }
-  }
-}
-
-::v-deep .el-checkbox__label {
-  color: $app-primary-color !important;
-}
-
-.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 .mapboxgl-popup {
-  max-width: 300px !important;
-}
-
-::v-deep .flatmap-tooltip-popup {
-  &.mapboxgl-popup-anchor-bottom {
-    .mapboxgl-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;
-      }
-    }
-  }
-  &.mapboxgl-popup-anchor-top {
-    .mapboxgl-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;
-      }
-    }
-  }
-  .mapboxgl-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;
-    }
-  }
-  .mapboxgl-popup-tip {
-    display: none;
-  }
-}
-
-::v-deep .mapboxgl-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 {
-  .mapboxgl-popup-content::after {
-    top: 99.9%;
-  }
-}
-
-::v-deep .flatmap-tooltip-dialog {
-  .mapboxgl-popup-tip {
-    display: none;
-  }
-}
-
-::v-deep .flatmap-marker-popup {
-  .mapboxgl-popup-content {
-    padding: 0px;
-  }
-}
-
-::v-deep .flatmapvuer-popover {
-  .mapboxgl-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;
-}
-
-.background-colour {
-  bottom: 16px;
-  position: absolute;
-  transition: all 1s ease;
-}
-.background-colour.open {
-  left: 322px;
-}
-.background-colour.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: 200px;
-  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;
-      }
-    }
-  }
-}
-
-.backgroundText {
-  color: rgb(48, 49, 51);
-  font-size: 14px;
-  font-weight: normal;
-  line-height: 20px;
-}
-
-.backgroundControl {
-  display: flex;
-  margin-top: 16px;
-}
-
-.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: white;
-  }
-}
-
-.togglePaths {
-  top: 201px;
-  right: 20px;
-  position: absolute;
-}
-
-.icon-button {
-  height: 24px !important;
-  width: 24px !important;
-  color: $app-primary-color;
-  &:hover {
-    cursor: pointer;
-  }
-}
-
-::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 {
-  .mapboxgl-popup-tip {
-    border-bottom-color: $app-primary-color;
-  }
-  .mapboxgl-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;
-    .mapboxgl-popup-close-button {
-      display: none;
-    }
-  }
-}
-
-::v-deep .flatmap-popper {
-  
-}
-
-::v-deep .popper-zoomout {
-  padding-right: 13px !important;
-  left: -21px !important;
-}
-
-::v-deep .popper-zoomout {
-  .popper__arrow {
-    left: 53px !important;
-  }
-}
-
-::v-deep .mapboxgl-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 #e4e7ed;
-  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);
-  border-left: 0;
-  background-color: #ffffff;
-  i {
-    margin-top: 12px;
-    color: $app-primary-color;
-    transition-delay: 0.9s;
-  }
-  &.open {
-    i {
-      transform: rotate(0deg) scaleY(2.5);
-    }
-  }
-  &.close {
-    i {
-      transform: rotate(180deg) scaleY(2.5);
-    }
-  }
-}
-
-::v-deep .mapboxgl-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;
-    }
-  }
-  .el-radio__input {
-    &.is-checked {
-      & + .el-radio__label {
-        color: $app-primary-color;
-      }
-      .el-radio__inner {
-        border-color: $app-primary-color;
-        background: $app-primary-color;
-      }
-    }
-  }
-}
-</style>
-
+<template>
+  <div
+    class="flatmap-container"
+    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
+            :content="warningMessage"
+            placement="right"
+            :appendToBody="false"
+            trigger="manual"
+            popper-class="warning-popper flatmap-popper right-popper"
+            v-model="hoverVisibilities[6].value"
+            ref="warningPopover"
+          ></el-popover>
+          <i
+            class="el-icon-warning warning-icon"
+            v-if="displayWarning && warningMessage"
+            @mouseover="showToolitip(6)"
+            @mouseout="hideToolitip(6)"
+            v-popover:warningPopover
+          >
+          <span class="warning-text">Beta</span>
+        </i>
+        </div>
+        <el-popover
+          :content="latestChangesMessage"
+          placement="right"
+          v-if="displayLatestChanges"
+          :appendToBody="false"
+          trigger="manual"
+          popper-class="warning-popper flatmap-popper right-popper"
+          v-model="hoverVisibilities[7].value"
+          ref="latestChangesPopover"
+        ></el-popover>
+        <i
+          class="el-icon-warning latest-changesicon"
+          v-if="displayLatestChanges && latestChangesMessage"
+          @mouseover="showToolitip(7)"
+          @mouseout="hideToolitip(7)"
+          v-popover:latestChangesPopover
+        >
+          <span class="warning-text">What's new?</span>
+        </i>
+      </div>
+
+      <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"
+          v-if="pathways.length > 0 && pathControls"
+          v-popover:checkBoxPopover
+        >
+          <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>
+          <el-row>
+            <el-col :span="12">
+              <div class="pathways-display-text">Pathways</div>
+            </el-col>
+            <el-col :span="12">
+              <el-checkbox
+                class="all-checkbox"
+                :indeterminate="isIndeterminate"
+                v-model="checkAll"
+                @change="handleCheckAllChange"
+              >Display all</el-checkbox>
+            </el-col>
+          </el-row>
+          <el-checkbox-group
+            v-model="checkedItems"
+            size="small"
+            class="checkbox-group"
+            @change="handleCheckedItemsChange"
+          >
+            <div class="checkbox-group-inner">
+              <el-row v-for="item in pathways" :key="item.type" :label="item.type">
+                <div class="checkbox-container">
+                  <el-checkbox
+                    class="my-checkbox"
+                    :label="item.type"
+                    @change="visibilityToggle()"
+                    :checked="true"
+                  >
+                    <div class="path-visual" :class="item.type"></div>
+                    {{item.label}}
+                  </el-checkbox>
+                </div>
+              </el-row>
+            </div>
+          </el-checkbox-group>
+        </div>
+        <div
+          @click="toggleDrawer"
+          class="drawer-button"
+          :class="{ open: drawerOpen, close: !drawerOpen }"
+        >
+          <i class="el-icon-arrow-left"></i>
+        </div>
+      </div>
+      <el-popover
+        ref="backgroundPopover"
+        placement="top-start"
+        width="175"
+        :appendToBody="false"
+        trigger="click"
+        popper-class="background-popper"
+      >
+        <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>
+      <el-popover
+        content="Change background color"
+        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 background-colour"
+          :class="{ open: drawerOpen, close: !drawerOpen }"
+          slot="reference"
+          @mouseover.native="showToolitip(3)"
+          @mouseout.native="hideToolitip(3)"
+        />
+      </el-popover>
+      <Tooltip
+        ref="tooltip"
+        class="tooltip"
+        :content="tooltipContent"
+        @resource-selected="resourceSelected"
+      />
+    </div>
+  </div>
+</template>
+
+<script>
+/* eslint-disable no-alert, no-console */
+import Vue from "vue";
+import Tooltip from "./Tooltip";
+import { MapSvgIcon, MapSvgSpriteColor } from "@abi-software/svg-sprite";
+import {
+  Checkbox,
+  CheckboxGroup,
+  Col,
+  Loading,
+  Radio,
+  RadioGroup,
+  Row
+} 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";
+
+locale.use(lang);
+Vue.use(Checkbox);
+Vue.use(CheckboxGroup);
+Vue.use(Col);
+Vue.use(Loading.directive);
+Vue.use(Radio);
+Vue.use(RadioGroup);
+Vue.use(Row);
+const ResizeSensor = require("css-element-queries/src/ResizeSensor");
+
+const mapResize = map => {
+  return () => {
+    if (map) map.resize();
+  };
+};
+
+export default {
+  name: "FlatmapVuer",
+  components: {
+    MapSvgIcon,
+    MapSvgSpriteColor,
+    Tooltip
+  },
+  beforeCreate: function() {
+    this.mapManager = undefined;
+    this.mapImp = undefined;
+  },
+  methods: {
+    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();
+        this.checkedItems = this.mapImp.pathTypes().map(item => item.type);
+        this.isIndeterminate = false;
+        this.checkAll = true;
+      }
+    },
+    /**
+     * 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();
+      }
+    },
+    visibilityToggle: function() {
+      if (this.mapImp) {
+        this.mapImp.showPaths(this.checkedItems);
+      }
+    },
+    handleCheckedItemsChange: function(value) {
+      let checkedCount = value.length;
+      this.checkAll = checkedCount === this.pathways.length;
+      this.isIndeterminate =
+        checkedCount > 0 && checkedCount < this.pathways.length;
+    },
+    handleCheckAllChange(val) {
+      this.checkedItems = val ? this.pathways.map(a => a.type) : [];
+      this.isIndeterminate = false;
+      if (this.mapImp) {
+        this.mapImp.showPaths(this.checkedItems);
+      }
+    },
+    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 payload = {
+            dataset: data.dataset,
+            taxonomy: taxonomy,
+            resource: resource,
+            label: label,
+            feature: data,
+            userData: args,
+            eventType: eventType
+          };
+          // Disable the nueron pop up for now.
+          if (data && data.type !== "marker")
+            this.checkAndCreatePopups(payload);
+          this.$emit("resource-selected", payload);
+        } else {
+          this.$emit("pan-zoom-callback", data);
+        }
+      };
+    },
+    // checkNeuronClicked shows a neuron path pop up if a path was recently clicked
+    checkAndCreatePopups: function(data) {
+      if (
+        data.eventType == "click" &&
+        this.hasNeuronTooltip(data)
+      ) {
+        this.createTooltipFromNeuronCuration(data);
+        this.mapImp.showPopup(
+          this.mapImp.modelFeatureIds(data.resource[0])[0],
+          this.$refs.tooltip.$el,
+          { className: "flatmapvuer-popover", positionAtLastClick: true }
+        );
+        this.popUpCssHacks();
+      }
+    },
+    popUpCssHacks: function() {
+      // Below is a hack to remove flatmap tooltips while popup is open
+      let ftooltip = document.querySelector(".flatmap-tooltip-popup");
+      if (ftooltip) ftooltip.style.display = "none";
+      document.querySelector(".mapboxgl-popup-close-button").style.display =
+        "block";
+      this.$refs.tooltip.$el.style.display = "flex";
+      document.querySelector(".mapboxgl-popup-close-button").onclick = () => {
+        document.querySelector(".flatmap-tooltip-popup").style.display =
+          "block";
+      };
+    },
+    resourceSelected: function(action) {
+      this.$emit("resource-selected", action);
+    },
+    hasNeuronTooltip: function(data) {
+
+      // neural data check
+      if (data.resource[0]){
+        if (data.resource[0].includes('ilxtr:neuron')){
+          return true
+        }
+      }
+      // annotated with datset check
+      if (data.dataset) {
+        return true
+      }
+
+      // if there is no cuff, neural data, or dataset we do not display neuron tooltip
+      return false
+
+    },
+    createTooltipFromNeuronCuration: function(data) {
+      const feature = data.resource[0];
+      let content = {
+        title: undefined,
+        components: undefined,
+        start: undefined,
+        distribution: undefined,
+        actions: []
+      };
+
+      this.tooltipVisible = false;
+
+      // neural data check
+      if (feature){
+        if (feature.includes('ilxtr:neuron')){
+          this.tooltipVisible = true;
+          this.tooltipContent = content;
+          this.tooltipContent.uberon = feature;
+          this.tooltipContent.title = data.label;
+          this.tooltipContent.featureIds = [feature];
+          this.tooltipContent.actions.push({
+            title: "Search for datasets",
+            label: "Neuron Datasets",
+            resource: feature.split(":")[1],
+            type: "Neuron Search",
+            feature: feature,
+            nervePath: true
+          });
+        }
+      }
+      // annotated with datset check
+      if (data.dataset) {
+        this.tooltipVisible = true;
+        this.tooltipContent = content;
+        this.tooltipContent.uberon = feature;
+        this.tooltipContent.title = data.label;
+        this.tooltipContent.actions.push({
+          title: "View dataset",
+          resource: data.dataset,
+          type: "URL",
+          feature: feature,
+          nervePath: false
+        });
+      }
+    },
+    // Keeping this as an API
+    showPopup: function(featureId, node, options) {
+      let myOptions = options;
+      if (this.mapImp) {
+        if (myOptions) {
+          if (!myOptions.className) myOptions.className = "flatmapvuer-popover";
+        } else {
+          myOptions = { className: "flatmapvuer-popover", positionAtLastClick: true };
+        }
+        this.mapImp.showPopup(featureId, node, myOptions);
+      }
+    },
+    showMarkerPopup: function(featureId, node, options) {
+      if (this.mapImp) {
+        this.mapImp.showMarkerPopup(featureId, node, options);
+      }
+    },
+    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) {
+        this.tooltipWait = setTimeout(() => {
+          this.hoverVisibilities[tooltipNumber].value = true;
+        }, 500);
+      }
+    },
+    hideToolitip: function(tooltipNumber) {
+      if (!this.inHelp) {
+        this.hoverVisibilities[tooltipNumber].value = false;
+        clearTimeout(this.tooltipWait);
+      }
+    },
+    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.$el
+        .querySelectorAll(".mapboxgl-popup-close-button")
+        .forEach(item => {
+          item.click();
+        });
+    },
+    getLabels: function() {
+      let labels = [];
+      if (this.mapImp) {
+        let annotations = this.mapImp.annotations;
+        for (let value of annotations.values()) {
+          if (value.label) labels.push(value.label);
+        }
+        return Array.from(new Set(labels));
+      }
+    },
+    getState: function() {
+      if (this.mapImp) {
+        let state = {
+          entry: this.entry,
+          viewport: this.mapImp.getState()
+        };
+        return state;
+      }
+      return undefined;
+    },
+    setState: function(state) {
+      if (state) {
+        if (this.mapImp && state.entry) {
+          if (this.entry == state.entry)
+            if (state.viewport) {
+              this.mapImp.setState(state.viewport);
+            }
+        } else {
+          this.createFlatmap(state);
+        }
+      }
+    },
+    createFlatmap: function(state) {
+      if (!this.mapImp && !this.loading) {
+        this.loading = true;
+        let minimap = false;
+        if (this.displayMinimap) {
+          minimap = { position: "top-right" };
+        }
+        let entry = this.entry;
+        if (state && state.entry) entry = state.entry;
+        let promise1 = this.mapManager.loadMap(
+          entry,
+          this.$refs.display,
+          this.eventCallback(),
+          {
+            //fullscreenControl: false,
+            //annotatable: false,
+            //debug: true,
+            featureInfo: this.featureInfo,
+            "min-zoom": this.minZoom,
+            pathControls: false,
+            searchable: this.searchable,
+            tooltips: this.tooltips,
+            minimap: minimap
+          }
+        );
+        promise1.then(returnedObject => {
+          this.mapImp = returnedObject;
+          this.sensor = new ResizeSensor(
+            this.$refs.display,
+            mapResize(this.mapImp)
+          );
+          this.mapImp.setBackgroundOpacity(1);
+          this.backgroundChangeCallback(this.currentBackground);
+          this.pathways = this.mapImp.pathTypes();
+          this.$emit("ready", this);
+          this.loading = false;
+          if (this._viewportToBeSet)
+            this.mapImp.setState(this._viewportToBeSet);
+          else if (state && state.viewport)
+            this.mapImp.setState(state.viewport);
+        });
+      } else if (state) {
+        if (this.entry == state.entry) this._viewportToBeSet = state.viewport;
+      }
+    },
+    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.
+     */
+    searchAndShowResult: function(term) {
+      if (this.mapImp) {
+        if (term === undefined || term === "") {
+          this.mapImp.clearSearchResults();
+          return true;
+        } else {
+          let searchResults = this.mapImp.search(term);
+          if (searchResults && searchResults.__featureIds.length > 0) {
+            this.mapImp.showSearchResults(searchResults);
+            return true;
+          }
+          else
+            this.mapImp.clearSearchResults();
+        }
+      }
+      return false;
+    }
+  },
+  props: {
+    entry: String,
+    featureInfo: {
+      type: Boolean,
+      default: false
+    },
+    minZoom: {
+      type: Number,
+      default: 4
+    },
+    pathControls: {
+      type: Boolean,
+      default: true
+    },
+    searchable: {
+      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
+    },
+    warningMessage: {
+      type: String,
+      default: "Beta feature - This map is based on the connectivity of a rat. New connectivity and species specificity will be added as the SPARC program progress."
+    },
+    displayLatestChanges: {
+      type: Boolean,
+      default: false,
+    },
+    latestChangesMessage: {
+      type: String,
+      default: "Bladder connectivity can now be explored and searched on when selected! To see it, click on any of the paths coming from the bladder. Other pathways will be searchable soon.",
+    },
+    /**
+     * 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/flatmaps/"
+    },
+    sparcAPI: {
+      type: String,
+      default: "https://api.sparc.science/"
+    },
+  },
+  provide() {
+    return {
+      sparcAPI: this.sparcAPI,
+      flatmapAPI: this.flatmapAPI
+    }
+  },
+  data: function() {
+    return {
+      checkedItems: [],
+      pathways: [],
+      isIndeterminate: false,
+      checkAll: true,
+      hoverVisibilities: [
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false },
+        { value: false }
+      ],
+      inHelp: false,
+      currentBackground: "white",
+      availableBackground: ["white", "lightskyblue", "black"],
+      loading: false,
+      flatmapMarker: flatmapMarker,
+      drawerOpen: true,
+      tooltipContent: { featureIds: []},
+      colourRadio: true,
+      outlinesRadio: true
+    };
+  },
+  watch: {
+    entry: function() {
+      if (!this.state) this.createFlatmap();
+    },
+    helpMode: function(val) {
+      this.setHelpMode(val);
+    },
+    state: {
+      handler: function(state) {
+        this.setState(state);
+      },
+      immediate: true,
+      deep: true
+    }
+  },
+  mounted: function() {
+    const flatmap = require("@abi-software/flatmap-viewer");
+    this.mapManager = new flatmap.MapManager(this.flatmapAPI);
+    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/checkbox";
+@import "~element-ui/packages/theme-chalk/src/checkbox-group";
+@import "~element-ui/packages/theme-chalk/src/loading";
+@import "~element-ui/packages/theme-chalk/src/row";
+
+.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-changesicon {
+  color: $success;
+
+  &:hover {
+    cursor: pointer;
+  }
+}
+
+.latest-changestext {
+  font-family: Asap, sans-serif;
+  font-size: 15px;
+  vertical-align: 5px;
+}
+
+.path-visual {
+  margin: 3px 0;
+  height: 3px;
+  width: 25px;
+  margin-right: 5px;
+  display: inline-block;
+  &.cns {
+    background: #9b1fc1;
+  }
+  &.lcn {
+    background: #f19e38;
+  }
+  &.para-pre {
+    background: #3f8f4a;
+  }
+  &.para-post {
+    background: repeating-linear-gradient(
+      90deg,
+      #3f8f4a,
+      #3f8f4a 6px,
+      transparent 0,
+      transparent 9px
+    );
+  }
+  &.sensory {
+    background: #2a62f6;
+  }
+  &.somatic {
+    background: #98561d;
+  }
+  &.symp-pre {
+    background: #ea3423;
+  }
+  &.symp-post {
+    background: repeating-linear-gradient(
+      90deg,
+      #ea3423,
+      #ea3423 6px,
+      transparent 0,
+      transparent 9px
+    );
+  }
+}
+
+.flatmap-container {
+  height: 100%;
+  width: 100%;
+}
+
+.pathway-location {
+  position: absolute;
+  bottom: 0px;
+  transition: all 1s ease;
+  &.open {
+    left: 0px;
+  }
+  &.close {
+    left: -298px;
+  }
+}
+
+.pathway-container {
+  float: left;
+  padding-left: 16px;
+  padding-right: 18px;
+  max-height: calc(100% - 184px);
+  text-align: left;
+  overflow: auto;
+  border: 1px solid rgb(220, 223, 230);
+  padding-top: 7px;
+  padding-bottom: 16px;
+  background: #ffffff;
+}
+
+.pathways-display-text {
+  width: 59px;
+  height: 20px;
+  color: rgb(48, 49, 51);
+  font-size: 14px;
+  font-weight: normal;
+  line-height: 20px;
+  margin-left: 8px;
+}
+
+.all-checkbox {
+  float: right;
+}
+
+.checkbox-container {
+  display: flex;
+  cursor: pointer;
+}
+
+.checkbox-group {
+  width: 260px;
+  border: 1px solid rgb(144, 147, 153);
+  border-radius: 4px;
+  background: #ffffff;
+}
+
+.my-checkbox {
+  background-color: #fff;
+  width: 100%;
+}
+
+.checkbox-group-inner {
+  padding: 18px;
+}
+
+.flatmap-marker-help {
+  display: inline-block;
+}
+
+::v-deep .popper-bump-right {
+  left: 30px;
+}
+
+::v-deep .el-checkbox__label {
+  padding-left: 5px;
+  color: $app-primary-color;
+  font-size: 12px;
+  font-weight: 500;
+  letter-spacing: 0px;
+  line-height: 14px;
+}
+
+::v-deep .el-checkbox__input {
+  &.is-indeterminate,
+  &.is-checked {
+    .el-checkbox__inner {
+      background-color: $app-primary-color;
+      border-color: $app-primary-color;
+    }
+  }
+}
+
+::v-deep .el-checkbox__label {
+  color: $app-primary-color !important;
+}
+
+.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 .mapboxgl-popup {
+  max-width: 300px !important;
+}
+
+::v-deep .flatmap-tooltip-popup {
+  &.mapboxgl-popup-anchor-bottom {
+    .mapboxgl-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;
+      }
+    }
+  }
+  &.mapboxgl-popup-anchor-top {
+    .mapboxgl-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;
+      }
+    }
+  }
+  .mapboxgl-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;
+    }
+  }
+  .mapboxgl-popup-tip {
+    display: none;
+  }
+}
+
+::v-deep .mapboxgl-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 {
+  .mapboxgl-popup-content::after {
+    top: 99.9%;
+  }
+}
+
+::v-deep .flatmap-tooltip-dialog {
+  .mapboxgl-popup-tip {
+    display: none;
+  }
+}
+
+::v-deep .flatmap-marker-popup {
+  .mapboxgl-popup-content {
+    padding: 0px;
+  }
+}
+
+::v-deep .flatmapvuer-popover {
+  .mapboxgl-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;
+}
+
+.background-colour {
+  bottom: 16px;
+  position: absolute;
+  transition: all 1s ease;
+}
+.background-colour.open {
+  left: 322px;
+}
+.background-colour.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: 200px;
+  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;
+      }
+    }
+  }
+}
+
+.backgroundText {
+  color: rgb(48, 49, 51);
+  font-size: 14px;
+  font-weight: normal;
+  line-height: 20px;
+}
+
+.backgroundControl {
+  display: flex;
+  margin-top: 16px;
+}
+
+.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: white;
+  }
+}
+
+.togglePaths {
+  top: 201px;
+  right: 20px;
+  position: absolute;
+}
+
+.icon-button {
+  height: 24px !important;
+  width: 24px !important;
+  color: $app-primary-color;
+  &:hover {
+    cursor: pointer;
+  }
+}
+
+::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 {
+  .mapboxgl-popup-tip {
+    border-bottom-color: $app-primary-color;
+  }
+  .mapboxgl-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;
+    .mapboxgl-popup-close-button {
+      display: none;
+    }
+  }
+}
+
+::v-deep .flatmap-popper {
+  
+}
+
+::v-deep .popper-zoomout {
+  padding-right: 13px !important;
+  left: -21px !important;
+}
+
+::v-deep .popper-zoomout {
+  .popper__arrow {
+    left: 53px !important;
+  }
+}
+
+::v-deep .mapboxgl-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 #e4e7ed;
+  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);
+  border-left: 0;
+  background-color: #ffffff;
+  i {
+    margin-top: 12px;
+    color: $app-primary-color;
+    transition-delay: 0.9s;
+  }
+  &.open {
+    i {
+      transform: rotate(0deg) scaleY(2.5);
+    }
+  }
+  &.close {
+    i {
+      transform: rotate(180deg) scaleY(2.5);
+    }
+  }
+}
+
+::v-deep .mapboxgl-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;
+    }
+  }
+  .el-radio__input {
+    &.is-checked {
+      & + .el-radio__label {
+        color: $app-primary-color;
+      }
+      .el-radio__inner {
+        border-color: $app-primary-color;
+        background: $app-primary-color;
+      }
+    }
+  }
+}
+</style>
+