@abi-software/mapintegratedvuer 1.9.2 → 1.9.3-beta.0

package/dist/{ContentMixin-DO6jlHIh.js → ContentMixin-W2PTyJZz.js}

@@ -1,17 +1,17 @@
-import { markRaw as v } from "vue";
-import { u as b, p as M, q as A, E as f, T as C, r as S, s as F, v as $, x as H } from "./index-BcpVBq1h.js";
-import { mapStores as I } from "pinia";
+import { markRaw as w } from "vue";
+import { u as b, b as F, c as M, E as f, T as C, d as S, e as I, f as A, l as H } from "./index-DMpfPm6s.js";
+import { mapStores as N } from "pinia";
 const d = function(e) {
   return e ? [...new Set(e.map((t) => JSON.stringify(t)))].map(
     (t) => JSON.parse(t)
   ) : [];
-}, g = [], w = async function(e, t) {
-  const n = t.filter(
+}, g = [], v = async function(e, t) {
+  const i = t.filter(
     (s) => g.some((a) => a.taxon === s)
-  ), i = g.filter(
-    (s) => n.includes(s.taxon)
+  ), n = g.filter(
+    (s) => i.includes(s.taxon)
   ), o = t.filter(
-    (s) => !n.includes(s)
+    (s) => !i.includes(s)
   );
   if (o.length) {
     const s = await e.queryLabels(o);
@@ -20,32 +20,32 @@ const d = function(e) {
         let { entity: r, label: l } = a;
         l === "Mammalia" && (l = "Mammalia not otherwise specified");
         const c = { taxon: r, label: l };
-        i.push(c), g.push(c);
-      }), i;
+        n.push(c), g.push(c);
+      }), n;
   } else
-    return i;
+    return n;
 }, y = function(e, t) {
   if (!e || !t) return !1;
-  let n = JSON.stringify(e), i = JSON.stringify(t);
-  return n.indexOf(i) !== -1;
+  let i = JSON.stringify(e), n = JSON.stringify(t);
+  return i.indexOf(n) !== -1;
 }, p = (e, t) => {
-  const n = e.name ?? e, i = t.name ?? t, o = n.toUpperCase(), s = i.toUpperCase();
+  const i = e.name ?? e, n = t.name ?? t, o = i.toUpperCase(), s = n.toUpperCase();
   return o < s ? -1 : o > s ? 1 : 0;
 };
-let N = function() {
+let $ = function() {
   this.initialise = function(e) {
     this.flatmapAPI = e, this.destinations = [], this.origins = [], this.components = [], this.rawURLs = [], this.controller = void 0, this.uberons = [], this.lookUp = [], this.connectivitySource = "sckan";
   }, this.createTooltipData = async function(e, t) {
-    let n = [];
-    t.feature.hyperlinks && t.feature.hyperlinks.length > 0 ? n = t.feature.hyperlinks : n = this.rawURLs;
-    let i;
+    let i = [];
+    t.feature.hyperlinks && t.feature.hyperlinks.length > 0 ? i = t.feature.hyperlinks : i = this.rawURLs;
+    let n;
     if (t.provenanceTaxonomy) {
-      i = [];
+      n = [];
       try {
-        const s = await w(e, t.provenanceTaxonomy);
+        const s = await v(e, t.provenanceTaxonomy);
         s.length && s.forEach((a) => {
           const { label: r } = a;
-          i.push(r);
+          n.push(r);
         });
       } catch (s) {
         console.log(s);
@@ -60,9 +60,9 @@ let N = function() {
       componentsWithDatasets: this.componentsWithDatasets,
       title: t.label,
       featureId: t.resource,
-      hyperlinks: n,
+      hyperlinks: i,
       provenanceTaxonomy: t.provenanceTaxonomy,
-      provenanceTaxonomyLabel: i,
+      provenanceTaxonomyLabel: n,
       connectivitySource: this.connectivitySource
     };
   }, this.updateTooltipData = function(e) {
@@ -77,66 +77,66 @@ let N = function() {
       connectivitySource: this.connectivitySource
     };
   }, this.createComponentsLabelList = function(e, t) {
-    let n = [];
-    return e.forEach((i) => {
-      n.push(this.createLabelFromNeuralNode(i[0]), t), i.length === 2 && n.push(this.createLabelFromNeuralNode(i[1]), t);
-    }), n;
+    let i = [];
+    return e.forEach((n) => {
+      i.push(this.createLabelFromNeuralNode(n[0]), t), n.length === 2 && i.push(this.createLabelFromNeuralNode(n[1]), t);
+    }), i;
   }, this.createLabelLookup = function(e, t) {
-    return new Promise(async (n) => {
-      let i = {};
+    return new Promise(async (i) => {
+      let n = {};
       this.uberons = [];
-      const o = await w(e, t);
+      const o = await v(e, t);
       o.length && (o.forEach((s) => {
         const { taxon: a, label: r } = s;
-        i[a] = r, this.uberons.push({
+        n[a] = r, this.uberons.push({
           id: a,
           name: r
         });
-      }), n(i));
+      }), i(n));
     });
   }, this.buildConnectivitySqlStatement = function(e) {
     let t = "select knowledge from knowledge where entity in (";
     if (e.length === 1)
       t += `'${e[0]}')`;
     else if (e.length > 1)
-      for (let n in e)
-        t += `'${e[n]}'${n >= e.length - 1 ? ")" : ","} `;
+      for (let i in e)
+        t += `'${e[i]}'${i >= e.length - 1 ? ")" : ","} `;
     return t;
   }, this.buildLabelSqlStatement = function(e) {
     let t = "select entity, label from labels where entity in (";
     if (e.length === 1)
       t += `'${e[0]}')`;
     else if (e.length > 1)
-      for (let n in e)
-        t += `'${e[n]}'${n >= e.length - 1 ? ")" : ","} `;
+      for (let i in e)
+        t += `'${e[i]}'${i >= e.length - 1 ? ")" : ","} `;
     return t;
   }, this.findAllIdsFromConnectivity = function(e) {
-    let t = e.connectivity.flat(), n = [...new Set(t)], i = [];
-    return n.forEach((o) => {
-      Array.isArray(o) ? i.push(o.flat()) : i.push(o);
-    }), [...new Set(i.flat())];
+    let t = e.connectivity.flat(), i = [...new Set(t)], n = [];
+    return i.forEach((o) => {
+      Array.isArray(o) ? n.push(o.flat()) : n.push(o);
+    }), [...new Set(n.flat())];
   }, this.flattenConnectivity = function(e) {
-    let t = e.flat(), n = [...new Set(t)], i = [];
-    return n.forEach((o) => {
-      Array.isArray(o) ? i.push(o.flat()) : i.push(o);
-    }), i.flat();
-  }, this.findComponents = function(e, t, n, i) {
+    let t = e.flat(), i = [...new Set(t)], n = [];
+    return i.forEach((o) => {
+      Array.isArray(o) ? n.push(o.flat()) : n.push(o);
+    }), n.flat();
+  }, this.findComponents = function(e, t, i, n) {
     let o = e.connectivity.flat(), s = d(o), a = [], r = !1;
     return s.forEach((l) => {
-      r = !1, y(t, l) && (r = !0), i && y(i, l) && (r = !0), y(n, l) && (r = !0), r || a.push(l);
+      r = !1, y(t, l) && (r = !0), n && y(n, l) && (r = !0), y(i, l) && (r = !0), r || a.push(l);
     }), a;
   }, this.retrieveFlatmapKnowledgeForEvent = async function(e, t) {
     this.controller && this.controller.abort(), this.controller = new AbortController(), this.controller.signal;
-    const n = t.resource;
-    if (this.destinations = [], this.origins = [], this.components = [], this.rawURLs = [], !n || n.length === 0 || !n[0]) return;
-    let i = this.queryForConnectivityNew(e, n[0]);
-    return await Promise.all([i]);
-  }, this.queryForConnectivityNew = function(e, t, n = "sckan", i = !0) {
-    return this.connectivitySource = n, new Promise((o) => {
-      (n === "map" ? this.queryMapConnectivity(e.provenance.uuid, t) : e.queryKnowledge(t)).then((a) => {
+    const i = t.resource;
+    if (this.destinations = [], this.origins = [], this.components = [], this.rawURLs = [], !i || i.length === 0 || !i[0]) return;
+    let n = this.queryForConnectivityNew(e, i[0]);
+    return await Promise.all([n]);
+  }, this.queryForConnectivityNew = function(e, t, i = "sckan", n = !0) {
+    return this.connectivitySource = i, new Promise((o) => {
+      (i === "map" ? this.queryMapConnectivity(e.provenance.uuid, t) : e.queryKnowledge(t)).then((a) => {
         if (this.checkConnectivityExists(a)) {
           let r = a;
-          i ? this.processConnectivity(e, r).then((l) => {
+          n ? this.processConnectivity(e, r).then((l) => {
             a.references && (this.rawURLs = [...a.references]), o(l);
           }) : o(r);
         } else
@@ -146,40 +146,30 @@ let N = function() {
       });
     });
   }, this.queryMapConnectivity = async function(e, t) {
-    const n = this.flatmapAPI + `flatmap/${e}/connectivity/${t}`;
+    const i = this.flatmapAPI + `flatmap/${e}/connectivity/${t}`;
     try {
-      const i = await fetch(n);
-      if (!i.ok)
-        throw new Error(`Response status: ${i.status}`);
-      return await i.json();
-    } catch (i) {
-      throw new Error(i);
-    }
-  }, this.queryMapPaths = async function(e) {
-    const t = this.flatmapAPI + `flatmap/${e}/pathways`;
-    try {
-      const n = await fetch(t);
+      const n = await fetch(i);
       if (!n.ok)
         throw new Error(`Response status: ${n.status}`);
       return await n.json();
     } catch (n) {
       throw new Error(n);
     }
-  }, this.queryForConnectivity = function(e, t, n, i = !0) {
+  }, this.queryForConnectivity = function(e, t, i, n = !0) {
     const o = { sql: this.buildConnectivitySqlStatement(t) }, s = {
       method: "POST",
       headers: {
         "Content-Type": "application/json"
       },
       body: JSON.stringify(o),
-      ...n ? { signal: n } : {}
+      ...i ? { signal: i } : {}
       // add signal to header if it exists
     };
     return new Promise((a) => {
       fetch(`${this.flatmapAPI}knowledge/query/`, s).then((r) => r.json()).then((r) => {
         if (this.connectivityExists(r)) {
           let l = JSON.parse(r.values[0][0]);
-          i ? this.processConnectivity(e, l).then((c) => {
+          n ? this.processConnectivity(e, l).then((c) => {
             a(c);
           }) : a(l);
         } else
@@ -196,45 +186,45 @@ let N = function() {
   }, this.findIfNodeIsSingle = function(e) {
     return e.length === 1 ? (console.error("Server returns a single node", e), e[0]) : e.length === 2 && e[1].length === 0 ? e[0] : !1;
   }, this.createLabelFromNeuralNode = function(e, t) {
-    let n = this.findIfNodeIsSingle(e);
-    if (n)
-      return t[n];
-    let i = t[e[0]];
+    let i = this.findIfNodeIsSingle(e);
+    if (i)
+      return t[i];
+    let n = t[e[0]];
     return e.length === 2 && e[1].length > 0 && e[1].forEach((o) => {
-      t[o] == null ? i += `, ${o}` : i += `, ${t[o]}`;
-    }), i;
-  }, this.flattenAndFindDatasets = function(e, t, n) {
-    let i = this.flattenConnectivity(e), o = this.flattenConnectivity(t), s = this.flattenConnectivity(n);
+      t[o] == null ? n += `, ${o}` : n += `, ${t[o]}`;
+    }), n;
+  }, this.flattenAndFindDatasets = function(e, t, i) {
+    let n = this.flattenConnectivity(e), o = this.flattenConnectivity(t), s = this.flattenConnectivity(i);
     this.originsWithDatasets = this.uberons.filter(
-      (a) => i.indexOf(a.id) !== -1
+      (a) => n.indexOf(a.id) !== -1
     ).sort(p), this.componentsWithDatasets = this.uberons.filter(
       (a) => o.indexOf(a.id) !== -1
     ).sort(p), this.destinationsWithDatasets = this.uberons.filter(
       (a) => s.indexOf(a.id) !== -1
     ).sort(p);
   }, this.processConnectivity = function(e, t) {
-    return new Promise((n) => {
-      let i = [], o = [], s;
+    return new Promise((i) => {
+      let n = [], o = [], s;
       if (t && t["node-phenotypes"]) {
         const l = ["ilxtr:hasSomaLocatedIn"], c = ["ilxtr:hasAxonPresynapticElementIn", "ilxtr:hasAxonSensorySubcellularElementIn"];
         l.forEach((h) => {
-          i.push(...t["node-phenotypes"][h]);
-        }), i = d(i), c.forEach((h) => {
-          o.push(...t["node-phenotypes"][h]);
+          h in t["node-phenotypes"] && n.push(...t["node-phenotypes"][h]);
+        }), n = d(n), c.forEach((h) => {
+          h in t["node-phenotypes"] && o.push(...t["node-phenotypes"][h]);
         }), o = d(o);
       } else
-        o = d(t.axons), t.somas && t.somas.length > 0 && i.push(...t.somas), t.dendrites && t.dendrites.length > 0 && i.push(...t.dendrites), i = d(i), s = t.somas;
-      const a = this.findComponents(t, o, i, s), r = this.findAllIdsFromConnectivity(t);
+        o = d(t.axons), t.somas && t.somas.length > 0 && n.push(...t.somas), t.dendrites && t.dendrites.length > 0 && n.push(...t.dendrites), n = d(n), s = t.somas;
+      const a = this.findComponents(t, o, n, s), r = this.findAllIdsFromConnectivity(t);
       this.createLabelLookup(e, r).then((l) => {
-        this.origins = i.map(
+        this.origins = n.map(
           (c) => this.createLabelFromNeuralNode(c, l)
         ).sort(p), this.components = a.map(
           (c) => this.createLabelFromNeuralNode(c, l)
         ).sort(p), this.destinations = o.map(
           (c) => this.createLabelFromNeuralNode(c, l)
-        ).sort(p), this.flattenAndFindDatasets(i, a, o), n({
+        ).sort(p), this.flattenAndFindDatasets(n, a, o), i({
           ids: {
-            dendrites: i,
+            dendrites: n,
             components: a,
             axons: o
           },
@@ -251,8 +241,8 @@ let N = function() {
     if (e.length === 1)
       t += `'${e[0]}')`;
     else if (e.length > 1)
-      for (let n in e)
-        t += `'${e[n]}'${n >= e.length - 1 ? ")" : ","} `;
+      for (let i in e)
+        t += `'${e[i]}'${i >= e.length - 1 ? ")" : ","} `;
     return t;
   }, this.buildPubmedSqlStatementForModels = function(e) {
     return `select distinct publication from publications where entity = '${e}'`;
@@ -264,12 +254,12 @@ let N = function() {
         "Content-Type": "application/json"
       },
       body: JSON.stringify(t)
-    }).then((n) => n.json()).catch((n) => {
-      console.error("Error:", n);
+    }).then((i) => i.json()).catch((i) => {
+      console.error("Error:", i);
     });
   };
 };
-function P(e) {
+function T(e) {
   return e[0].toUpperCase() + e.substring(1);
 }
 const D = {
@@ -289,8 +279,9 @@ const D = {
       default: !1
     }
   },
+  inject: ["showGlobalSettings", "showOpenMapButton"],
   computed: {
-    ...I(b, M, A),
+    ...N(b, F, M),
     idNamePair() {
       return this.splitFlowStore.idNamePair;
     },
@@ -305,12 +296,22 @@ const D = {
     },
     annotationSidebar() {
       return this.settingsStore.annotationSidebar;
+    },
+    // Hide local settings if global settings are shown
+    showLocalSettings() {
+      return !this.showGlobalSettings;
     }
   },
   mounted: function() {
     f.on("startHelp", () => {
       this.startHelp();
-    }), this.multiflatmapRef = this.$refs.multiflatmap, this.flatmapRef = this.$refs.flatmap, this.scaffoldRef = this.$refs.scaffold, this.connectivityKnowledge = this.connectivitiesStore.globalConnectivities;
+    }), f.on("connectivity-item-close", () => {
+      if (this.multiflatmapRef) {
+        const e = this.multiflatmapRef.getCurrentFlatmap();
+        e && e.closeTooltip();
+      }
+      this.flatmapRef && this.flatmapRef.closeTooltip();
+    }), this.multiflatmapRef = this.$refs.multiflatmap, this.flatmapRef = this.$refs.flatmap, this.scaffoldRef = this.$refs.scaffold, this.connectivityKnowledge = this.connectivitiesStore.globalConnectivities, this.connectivityFilterOptions = this.connectivitiesStore.filterOptions, this.connectivityFilterSources = this.connectivitiesStore.filterSources;
   },
   methods: {
     toggleSyncMode: function() {
@@ -349,12 +350,12 @@ const D = {
      */
     resourceSelected: function(e, t) {
       var a, r, l, c;
-      const n = t[0];
-      if (this.resourceHasAction(n)) {
-        f.emit("PopoverActionClick", n);
+      const i = t[0];
+      if (this.resourceHasAction(i)) {
+        f.emit("PopoverActionClick", i);
         return;
       }
-      let i, o = !1;
+      let n, o = !1;
       const s = {
         paneIndex: this.entry.id,
         type: e,
@@ -363,17 +364,17 @@ const D = {
         eventType: void 0
       };
       if (e == "MultiFlatmap" || e == "Flatmap")
-        if (s.internalName = (a = n == null ? void 0 : n.feature) != null && a.label ? n.feature.label : this.idNamePair[n.feature.models], n.eventType == "click")
-          if (s.eventType = "selected", n.feature.type == "marker") {
+        if (s.internalName = (a = i == null ? void 0 : i.feature) != null && a.label ? i.feature.label : this.idNamePair[i.feature.models], i.eventType == "click")
+          if (s.eventType = "selected", i.feature.type == "marker") {
             let h = s.internalName;
-            if (this.settingsStore.isFeaturedMarkerIdentifier(n.feature.id))
-              i = {
+            if (this.settingsStore.isFeaturedMarkerIdentifier(i.feature.id))
+              n = {
                 type: "Search",
-                term: this.settingsStore.featuredMarkerDoi(n.feature.id),
+                term: this.settingsStore.featuredMarkerDoi(i.feature.id),
                 featuredDataset: !0
               };
             else {
-              i = {
+              n = {
                 type: "Facet",
                 facet: h,
                 facetPropPath: "anatomy.organ.category.name",
@@ -381,23 +382,23 @@ const D = {
                 term: "Anatomical structure"
               };
               let u = /* @__PURE__ */ new Set();
-              n.feature["marker-terms"].forEach((m) => {
+              i.feature["marker-terms"].forEach((m) => {
                 u.add(m.label);
-              }), u.add(h), u.size > 0 && (i = {
+              }), u.add(h), u.size > 0 && (n = {
                 type: "Facets",
                 labels: [...u]
               });
             }
             o = !0, e == "MultiFlatmap" && this.$refs.multiflatmap.getCurrentFlatmap().mapImp.clearSearchResults();
-          } else n.feature.type == "feature" && this.syncMode && (o = !0);
-        else n.eventType == "mouseenter" && (s.eventType = "highlighted", o = !0);
-      else e == "Scaffold" && (n && ((((r = n.data) == null ? void 0 : r.id) === void 0 || ((l = n.data) == null ? void 0 : l.id) === "") && (n.data.id = (c = n.data) == null ? void 0 : c.group), s.internalName = n.data.id, n.data.lastActionOnMarker === !0 && (i = {
+          } else i.feature.type == "feature" && this.syncMode && (o = !0);
+        else i.eventType == "mouseenter" && (s.eventType = "highlighted", o = !0);
+      else e == "Scaffold" && (i && ((((r = i.data) == null ? void 0 : r.id) === void 0 || ((l = i.data) == null ? void 0 : l.id) === "") && (i.data.id = (c = i.data) == null ? void 0 : c.group), s.internalName = i.data.id, i.data.lastActionOnMarker === !0 && (n = {
         type: "Facet",
-        facet: P(n.data.id),
+        facet: T(i.data.id),
         facetPropPath: "anatomy.organ.category.name",
         term: "Anatomical structure"
       })), s.eventType = "selected", o = !0);
-      i && f.emit("PopoverActionClick", i), o && this.$emit("resource-selected", s);
+      n && f.emit("PopoverActionClick", n), o && this.$emit("resource-selected", s);
     },
     resourceHasAction: function(e) {
       return e.type === "URL" || e.type === "Search" || e.type === "Neuron Search" || e.type == "Facet" || e.type == "Facets";
@@ -418,53 +419,53 @@ const D = {
     getNameAndIdFromSyncData: async function(e) {
       let t = e.internalName;
       t === void 0 && e.resource && (t = e.resource.label);
-      let n;
-      if (e.resource && e.resource.resource && (n = e.resource.resource[0]), this.entry.type === "Scaffold") {
+      let i;
+      if (e.resource && e.resource.resource && (i = e.resource.resource[0]), this.entry.type === "Scaffold") {
         if (this.$refs.scaffold.findObjectsWithGroupName(t).length === 0) {
           if (e.resource && e.resource.feature) {
             const s = S(e.resource.feature.models);
             if (s.length > 0) return s;
           }
-          let o = F(t);
+          let o = I(t);
           if (o)
             return o;
-          if (n && e.eventType === "selected")
-            return fetch(`${this.apiLocation}get-related-terms/${n}`).then((s) => s.json()).then((s) => {
+          if (i && e.eventType === "selected")
+            return fetch(`${this.apiLocation}get-related-terms/${i}`).then((s) => s.json()).then((s) => {
               var a;
               if (((a = s.uberon) == null ? void 0 : a.array.length) > 0)
-                return t = s.uberon.array[0].name.charAt(0).toUpperCase() + s.uberon.array[0].name.slice(1), n = s.uberon.array[0].id.toUpperCase(), { id: n, name: t };
+                return t = s.uberon.array[0].name.charAt(0).toUpperCase() + s.uberon.array[0].name.slice(1), i = s.uberon.array[0].id.toUpperCase(), { id: i, name: t };
             });
         }
       } else if (this.entry.type === "MultiFlatmap")
         if (t === "Bladder")
           t = "Urinary Bladder";
         else {
-          const i = S(t);
-          i.length > 0 && (t = i[0]);
+          const n = S(t);
+          n.length > 0 && (t = n[0]);
         }
-      return { id: n, name: t };
+      return { id: i, name: t };
     },
     // Get the species and andaotmy info for the featured datasets
     getDatasetAnatomyInfo: function(e) {
       fetch(`${this.apiLocation}dataset_info/anatomy?identifier=${e}`).then((t) => t.json()).then((t) => {
-        const n = t.result[0];
-        let i;
+        const i = t.result[0];
+        let n;
         try {
-          i = n.anatomy.organ[0].curie;
+          n = i.anatomy.organ[0].curie;
         } catch {
-          i = void 0;
+          n = void 0;
         }
         let o;
         try {
-          o = n.item.curie;
+          o = i.item.curie;
         } catch {
           o = void 0;
         }
         let s;
         try {
           let a = 0, r = !1;
-          for (; !r && a < n.organisms.subject.length; ) {
-            const l = n.organisms.subject[a];
+          for (; !r && a < i.organisms.subject.length; ) {
+            const l = i.organisms.subject[a];
             l.species && (s = l.species.name, r = !0), a += 1;
           }
         } catch {
@@ -472,7 +473,7 @@ const D = {
         }
         this.settingsStore.updateFeaturedMarker({
           identifier: e,
-          marker: i,
+          marker: n,
           doi: o,
           species: s
         });
@@ -486,7 +487,7 @@ const D = {
     // Check if the new featured dataset api has any info
     newFeaturedDatasetApiHasInfo: async function() {
       let t = await (await fetch(`${this.apiLocation}get_featured_dataset`)).json();
-      return !t.datasets || t.datasets.length == 0 ? !1 : t.datasets.map((n) => n.id);
+      return !t.datasets || t.datasets.length == 0 ? !1 : t.datasets.map((i) => i.id);
     },
     /**
      * Get a list of featured datasets to display.
@@ -495,11 +496,11 @@ const D = {
       let e = [], t = await this.oldFeaturedDatasetApiHasInfo();
       if (t) e = t;
       else {
-        let n = await this.newFeaturedDatasetApiHasInfo();
-        n && (e = n);
+        let i = await this.newFeaturedDatasetApiHasInfo();
+        i && (e = i);
       }
-      this.settingsStore.updateFeatured(e), e.forEach((n) => {
-        this.getDatasetAnatomyInfo(n);
+      this.settingsStore.updateFeatured(e), e.forEach((i) => {
+        this.getDatasetAnatomyInfo(i);
       });
     },
     zoomToFeatures: function() {
@@ -558,15 +559,15 @@ const D = {
     checkEndHelpMouseDown: function(e) {
       e.target.closest(".help-mode-dialog") || this.endHelp();
     },
-    flatmapHighlight: async function(e, t, n, i) {
-      let o = [...t, ...i];
+    flatmapHighlight: async function(e, t, i, n) {
+      let o = [...t, ...n];
       const s = this.settingsStore.globalSettings;
       if (s.highlightConnectedPaths) {
-        const a = t.length ? t : i.length ? i : [], r = await e.retrieveConnectedPaths(a);
+        const a = t.length ? t : n.length ? n : [], r = await e.retrieveConnectedPaths(a);
         r && o.push(...r);
       }
       if (s.highlightDOIPaths) {
-        const a = await e.searchConnectivitiesByReference(n);
+        const a = await e.searchConnectivitiesByReference(i);
         a && o.push(...a);
       }
       return o = [...new Set(o)], o;
@@ -574,12 +575,15 @@ const D = {
     cardHoverHighlight: function() {
       var e;
       if (this.visible) {
-        const t = this.settingsStore.hoverAnatomies, n = this.settingsStore.hoverOrgans, i = this.settingsStore.hoverDOI, o = this.settingsStore.hoverConnectivity;
+        const t = this.settingsStore.hoverAnatomies, i = this.settingsStore.hoverOrgans, n = this.settingsStore.hoverDOI, o = this.settingsStore.hoverConnectivity;
         let s = null, a = null;
-        this.flatmapRef && (s = this.flatmapRef), this.multiflatmapRef && (s = this.multiflatmapRef.getCurrentFlatmap()), this.scaffoldRef && (a = this.scaffoldRef), clearTimeout(this.highlightDelay), !t.length && !n.length && !i && !o.length && ((this.multiflatmapRef || this.flatmapRef) && s ? (e = s.mapImp) == null || e.clearSearchResults() : this.scaffoldRef && a && a.changeHighlightedByName(n, "", !1)), this.highlightDelay = setTimeout(() => {
-          (t.length || n.length || i || o.length) && ((this.multiflatmapRef || this.flatmapRef) && s ? this.flatmapHighlight(s, t, i, o).then((r) => {
+        this.flatmapRef && (s = this.flatmapRef), this.multiflatmapRef && (s = this.multiflatmapRef.getCurrentFlatmap()), this.scaffoldRef && (a = this.scaffoldRef), clearTimeout(this.highlightDelay), !t.length && !i.length && !n && !o.length && ((this.multiflatmapRef || this.flatmapRef) && s ? (e = s.mapImp) == null || e.clearSearchResults() : this.scaffoldRef && a && a.changeHighlightedByName(i, "", !1)), this.highlightDelay = setTimeout(() => {
+          (t.length || i.length || n || o.length) && ((this.multiflatmapRef || this.flatmapRef) && s ? this.flatmapHighlight(s, t, n, o).then((r) => {
             try {
-              s.zoomToFeatures(r);
+              s.showConnectivityTooltips({
+                connectivityInfo: { featureId: r },
+                data: []
+              });
             } catch (l) {
               if (console.log(l), o.length && s.mapImp) {
                 const c = s.mapImp.uuid;
@@ -590,7 +594,7 @@ const D = {
                 ) || s.mapImp.clearSearchResults();
               }
             }
-          }) : this.scaffoldRef && a && a.changeHighlightedByName(n, "", !1));
+          }) : this.scaffoldRef && a && a.changeHighlightedByName(i, "", !1));
         }, 100);
       }
     },
@@ -600,6 +604,9 @@ const D = {
     onAnnotationClose: function() {
       f.emit("annotation-close");
     },
+    updateOfflineAnnotationEnabled: function(e) {
+      f.emit("update-offline-annotation-enabled", e);
+    },
     onConnectivityInfoOpen: function(e) {
       f.emit("connectivity-info-open", e);
     },
@@ -609,21 +616,18 @@ const D = {
     onConnectivityInfoClose: function() {
       f.emit("connectivity-info-close");
     },
-    loadConnectivityKnowledge: async function(e) {
-      const t = $(e), n = v(new N());
+    loadConnectivityExplorerConfig: async function(e) {
+      const t = e.mapImp, i = A(t), n = w(new $());
       n.initialise(this.flatmapAPI);
-      const i = await H(e, n), o = e.uuid;
-      if (this.connectivityKnowledge[t] || (this.connectivityKnowledge[t] = i.filter((s) => {
-        var a;
-        return s.source === t && ((a = s.connectivity) == null ? void 0 : a.length);
-      }).sort((s, a) => s.label.localeCompare(a.label))), !this.connectivitiesStore.globalConnectivities[o]) {
-        const s = await n.queryMapPaths(o), a = s ? s.paths : {};
-        this.connectivityKnowledge[o] = i.filter((r) => {
-          var l;
-          return r.source === t && ((l = r.connectivity) == null ? void 0 : l.length) && r.id in a;
-        }).sort((r, l) => r.label.localeCompare(l.label));
+      const o = await H(t, n), s = t.uuid, a = t.pathways;
+      if (this.connectivityKnowledge[i] || (this.connectivityKnowledge[i] = o.filter((r) => {
+        var l;
+        return r.source === i && ((l = r.connectivity) == null ? void 0 : l.length);
+      }).sort((r, l) => r.label.localeCompare(l.label))), !this.connectivityKnowledge[s]) {
+        const r = a ? a.paths : {};
+        this.connectivityKnowledge[s] = this.connectivityKnowledge[i].filter((l) => l.id in r);
       }
-      this.connectivitiesStore.updateGlobalConnectivities(this.connectivityKnowledge), f.emit("species-layout-connectivity-update");
+      this.connectivitiesStore.updateGlobalConnectivities(this.connectivityKnowledge), this.connectivityFilterOptions[s] || (this.connectivityFilterOptions[s] = await e.getFilterOptions()), this.connectivitiesStore.updateFilterOptions(this.connectivityFilterOptions), this.connectivityFilterSources[s] || (this.connectivityFilterSources[s] = e.getFilterSources()), this.connectivitiesStore.updateFilterSources(this.connectivityFilterSources), f.emit("species-layout-connectivity-update");
     }
   },
   data: function() {
@@ -646,6 +650,8 @@ const D = {
       isInHelp: !1,
       mapManager: void 0,
       connectivityKnowledge: {},
+      connectivityFilterOptions: {},
+      connectivityFilterSources: {},
       highlightDelay: void 0
     };
   },