@abi-software/mapintegratedvuer 1.16.1 → 1.16.3-simulation.0

package/dist/{ContentMixin-C3-OeGQ0.js → ContentMixin-CXBghkG4.js}

@@ -1,278 +1,8 @@
-import { markRaw as y } from "vue";
-import { c as C, u as E, d as O, e as N, E as f, T as b, f as R, h as x, i as w, l as P, j as B, J as X } from "./index-CGSECPAp.js";
-import { mapStores as U } from "pinia";
-const M = function(e) {
-  return e ? [...new Set(e.map((r) => JSON.stringify(r)))].map(
-    (r) => JSON.parse(r)
-  ) : [];
-}, d = [], T = async function(e, r) {
-  const t = r.filter(
-    (i) => d.some((s) => s.taxon === i)
-  ), n = d.filter(
-    (i) => t.includes(i.taxon)
-  ), a = r.filter(
-    (i) => !t.includes(i)
-  );
-  if (a.length) {
-    const i = await e.queryLabels(a);
-    if (i.length)
-      return i.forEach((s) => {
-        let { entity: l, label: o } = s;
-        o === "Mammalia" && (o = "Mammalia not otherwise specified");
-        const c = { taxon: l, label: o };
-        n.push(c), d.push(c);
-      }), n;
-  } else
-    return n;
-}, L = function(e, r) {
-  if (!e || !r) return !1;
-  let t = JSON.stringify(e), n = JSON.stringify(r);
-  return t.indexOf(n) !== -1;
-}, A = (e, r) => {
-  const t = e.name ?? e, n = r.name ?? r, a = t.toUpperCase(), i = n.toUpperCase();
-  return a < i ? -1 : a > i ? 1 : 0;
-};
-let S = 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 = "map", this.noMapConnectivity = !1;
-  }, this.createTooltipData = async function(e, r) {
-    let t = [];
-    r.feature.hyperlinks && r.feature.hyperlinks.length > 0 ? t = r.feature.hyperlinks : t = this.rawURLs;
-    let n;
-    if (r.provenanceTaxonomy) {
-      n = [];
-      try {
-        const i = await T(e, r.provenanceTaxonomy);
-        i.length && i.forEach((s) => {
-          const { label: l } = s;
-          n.push(l);
-        });
-      } catch (i) {
-        console.log(i);
-      }
-    }
-    return {
-      destinations: this.destinations,
-      origins: this.origins,
-      components: this.components,
-      destinationsWithDatasets: this.destinationsWithDatasets,
-      originsWithDatasets: this.originsWithDatasets,
-      componentsWithDatasets: this.componentsWithDatasets,
-      title: r.label,
-      featureId: r.resource,
-      hyperlinks: t,
-      provenanceTaxonomy: r.provenanceTaxonomy,
-      provenanceTaxonomyLabel: n,
-      connectivitySource: this.connectivitySource,
-      noMapConnectivity: this.noMapConnectivity
-    };
-  }, this.updateTooltipData = function(e) {
-    return {
-      ...e,
-      origins: this.origins,
-      originsWithDatasets: this.originsWithDatasets,
-      components: this.components,
-      componentsWithDatasets: this.componentsWithDatasets,
-      destinations: this.destinations,
-      destinationsWithDatasets: this.destinationsWithDatasets,
-      connectivitySource: this.connectivitySource,
-      noMapConnectivity: this.noMapConnectivity
-    };
-  }, this.createComponentsLabelList = function(e, r) {
-    let t = [];
-    return e.forEach((n) => {
-      t.push(this.createLabelFromNeuralNode(n[0]), r), n.length === 2 && t.push(this.createLabelFromNeuralNode(n[1]), r);
-    }), t;
-  }, this.createLabelLookup = function(e, r) {
-    return new Promise(async (t) => {
-      let n = {};
-      this.uberons = [];
-      const a = await T(e, r);
-      a.length && (a.forEach((i) => {
-        const { taxon: s, label: l } = i;
-        n[s] = l, this.uberons.push({
-          id: s,
-          name: l
-        });
-      }), t(n));
-    });
-  }, this.buildConnectivitySqlStatement = function(e) {
-    let r = "select knowledge from knowledge where entity in (";
-    if (e.length === 1)
-      r += `'${e[0]}')`;
-    else if (e.length > 1)
-      for (let t in e)
-        r += `'${e[t]}'${t >= e.length - 1 ? ")" : ","} `;
-    return r;
-  }, this.buildLabelSqlStatement = function(e) {
-    let r = "select entity, label from labels where entity in (";
-    if (e.length === 1)
-      r += `'${e[0]}')`;
-    else if (e.length > 1)
-      for (let t in e)
-        r += `'${e[t]}'${t >= e.length - 1 ? ")" : ","} `;
-    return r;
-  }, this.findAllIdsFromConnectivity = function(e) {
-    let r = e.connectivity.flat(), t = [...new Set(r)], n = [];
-    return t.forEach((a) => {
-      Array.isArray(a) ? n.push(a.flat()) : n.push(a);
-    }), [...new Set(n.flat())];
-  }, this.flattenConnectivity = function(e) {
-    let r = e.flat(), t = [...new Set(r)], n = [];
-    return t.forEach((a) => {
-      Array.isArray(a) ? n.push(a.flat()) : n.push(a);
-    }), n.flat();
-  }, this.findComponents = function(e, r, t, n) {
-    let a = e.connectivity.flat(), i = M(a), s = [], l = !1;
-    return i.forEach((o) => {
-      l = !1, L(r, o) && (l = !0), n && L(n, o) && (l = !0), L(t, o) && (l = !0), l || s.push(o);
-    }), s;
-  }, this.retrieveFlatmapKnowledgeForEvent = async function(e, r) {
-    this.controller && this.controller.abort(), this.controller = new AbortController(), this.controller.signal;
-    const t = r.resource;
-    if (this.destinations = [], this.origins = [], this.components = [], this.rawURLs = [], !t || t.length === 0 || !t[0]) return;
-    let n = this.queryForConnectivityNew(e, t[0]);
-    return await Promise.all([n]);
-  }, this.queryForConnectivityNew = function(e, r, t = "map", n = !0) {
-    return this.connectivitySource = t, new Promise((a) => {
-      (t === "map" ? this.queryMapConnectivity(e.mapMetadata.uuid, r) : e.queryKnowledge(r)).then((s) => {
-        if (this.checkConnectivityExists(s)) {
-          t === "map" && (this.noMapConnectivity = !1);
-          let l = s;
-          n ? this.processConnectivity(e, l).then((o) => {
-            s.references && (this.rawURLs = [...s.references]), a(o);
-          }) : a(l);
-        } else t === "map" ? (this.connectivitySource = "sckan", this.noMapConnectivity = !0, e.queryKnowledge(r).then((l) => {
-          if (this.checkConnectivityExists(l)) {
-            let o = l;
-            n ? this.processConnectivity(e, o).then((c) => {
-              l.references && (this.rawURLs = [...l.references]), a(c);
-            }) : a(o);
-          } else
-            a(!1);
-        }).catch(() => a(!1))) : a(!1);
-      }).catch((s) => {
-        s.name === "AbortError" || console.warn(`Unable to get the knowledge for the entity ${r}.`), a(!1);
-      });
-    });
-  }, this.queryMapConnectivity = async function(e, r) {
-    const t = this.flatmapAPI + `flatmap/${e}/connectivity/${r}`;
-    try {
-      const n = await fetch(t);
-      if (!n.ok)
-        throw new Error(`Response status: ${n.status}`);
-      return await n.json();
-    } catch (n) {
-      throw new Error(n);
-    }
-  }, this.queryForConnectivity = function(e, r, t, n = !0) {
-    const a = { sql: this.buildConnectivitySqlStatement(r) }, i = {
-      method: "POST",
-      headers: {
-        "Content-Type": "application/json"
-      },
-      body: JSON.stringify(a),
-      ...t ? { signal: t } : {}
-      // add signal to header if it exists
-    };
-    return new Promise((s) => {
-      fetch(`${this.flatmapAPI}knowledge/query/`, i).then((l) => l.json()).then((l) => {
-        if (this.connectivityExists(l)) {
-          let o = JSON.parse(l.values[0][0]);
-          n ? this.processConnectivity(e, o).then((c) => {
-            s(c);
-          }) : s(o);
-        } else
-          s(!1);
-      }).catch((l) => {
-        l.name === "AbortError" || console.error("Error:", l), s(!1);
-      });
-    });
-  }, this.checkConnectivityExists = function(e) {
-    var r;
-    return e && ((r = e.connectivity) == null ? void 0 : r.length);
-  }, this.connectivityExists = function(e) {
-    return !!(e.values && e.values.length > 0 && JSON.parse(e.values[0][0]).connectivity && JSON.parse(e.values[0][0]).connectivity.length > 0);
-  }, 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, r) {
-    let t = this.findIfNodeIsSingle(e);
-    if (t)
-      return r[t];
-    let n = r[e[0]];
-    return e.length === 2 && e[1].length > 0 && e[1].forEach((a) => {
-      r[a] == null ? n += `, ${a}` : n += `, ${r[a]}`;
-    }), n;
-  }, this.flattenAndFindDatasets = function(e, r, t) {
-    let n = this.flattenConnectivity(e), a = this.flattenConnectivity(r), i = this.flattenConnectivity(t);
-    this.originsWithDatasets = this.uberons.filter(
-      (s) => n.indexOf(s.id) !== -1
-    ).sort(A), this.componentsWithDatasets = this.uberons.filter(
-      (s) => a.indexOf(s.id) !== -1
-    ).sort(A), this.destinationsWithDatasets = this.uberons.filter(
-      (s) => i.indexOf(s.id) !== -1
-    ).sort(A);
-  }, this.processConnectivity = function(e, r) {
-    return new Promise((t) => {
-      let n = [], a = [], i;
-      if (r && r["node-phenotypes"]) {
-        const o = ["ilxtr:hasSomaLocatedIn"], c = ["ilxtr:hasAxonPresynapticElementIn", "ilxtr:hasAxonSensorySubcellularElementIn"];
-        o.forEach((u) => {
-          u in r["node-phenotypes"] && n.push(...r["node-phenotypes"][u]);
-        }), n = M(n), c.forEach((u) => {
-          u in r["node-phenotypes"] && a.push(...r["node-phenotypes"][u]);
-        }), a = M(a);
-      } else
-        a = M(r.axons), r.somas && r.somas.length > 0 && n.push(...r.somas), r.dendrites && r.dendrites.length > 0 && n.push(...r.dendrites), n = M(n), i = r.somas;
-      const s = this.findComponents(r, a, n, i), l = this.findAllIdsFromConnectivity(r);
-      this.createLabelLookup(e, l).then((o) => {
-        this.origins = n.map(
-          (c) => this.createLabelFromNeuralNode(c, o)
-        ).sort(A), this.components = s.map(
-          (c) => this.createLabelFromNeuralNode(c, o)
-        ).sort(A), this.destinations = a.map(
-          (c) => this.createLabelFromNeuralNode(c, o)
-        ).sort(A), this.flattenAndFindDatasets(n, s, a), t({
-          ids: {
-            dendrites: n,
-            components: s,
-            axons: a
-          },
-          labels: {
-            origins: this.origins,
-            components: this.components,
-            destinations: this.destinations
-          }
-        });
-      });
-    });
-  }, this.buildPubmedSqlStatement = function(e) {
-    let r = "select distinct publication from publications where entity in (";
-    if (e.length === 1)
-      r += `'${e[0]}')`;
-    else if (e.length > 1)
-      for (let t in e)
-        r += `'${e[t]}'${t >= e.length - 1 ? ")" : ","} `;
-    return r;
-  }, this.buildPubmedSqlStatementForModels = function(e) {
-    return `select distinct publication from publications where entity = '${e}'`;
-  }, this.queryKnowledge = async (e, r) => {
-    const t = `${this.flatmapAPI}/knowledge/query/`, a = await fetch(t, {
-      method: "POST",
-      headers: {
-        Accept: "application/json"
-      },
-      body: JSON.stringify({ sql: e, params: r })
-    });
-    if (!a.ok)
-      throw new Error(`Cannot access ${t}`);
-    const i = await a.json();
-    if ("error" in i)
-      throw new TypeError(i.error);
-    return i.values;
-  };
-};
-const I = [
+import { markRaw as M } from "vue";
+import { c as T, u as w, d as I, e as S, f as _, T as F, E as f, h as b, i as C, J as O } from "./index-Bym6cokq.js";
+import { mapStores as E } from "pinia";
+import { getKnowledgeSource as d, FlatmapQueries as L, loadAndStoreKnowledge as N } from "@abi-software/flatmapvuer";
+const R = [
   {
     id: 0,
     nerve_id: "ILX:0793723",
@@ -1085,50 +815,50 @@ const I = [
     "FMA subclasses (in human nerves)": ["FMA:6892", "FMA:6893"],
     "subclass labels": ["Right T9 grey ramus communicans", "Left T9 grey ramus communicans"]
   }
-], $ = () => {
+], B = () => {
   const e = {};
-  return I.forEach((r) => {
-    const t = r.nerve_id, n = r.label.toLowerCase(), a = r["subclass labels"];
-    if (t && n !== "nerve") {
-      if (!a.length)
+  return R.forEach((r) => {
+    const a = r.nerve_id, n = r.label.toLowerCase(), t = r["subclass labels"];
+    if (a && n !== "nerve") {
+      if (!t.length)
         return;
-      t in e || (e[t] = {});
-      const i = a.map((s) => s.toLowerCase()).sort();
-      e[t] = {
+      a in e || (e[a] = {});
+      const s = t.map((l) => l.toLowerCase()).sort();
+      e[a] = {
         nerve: n,
-        subNerves: i
+        subNerves: s
       };
     }
   }), e;
-}, H = () => {
+}, X = () => {
   let e = [], r = {
     key: "scaffold.connectivity.nerve",
     label: "Nerves",
     children: []
-  }, t = [];
-  for (const n of I) {
+  }, a = [];
+  for (const n of R) {
     if (n.label === "nerve")
       continue;
-    let a = {
+    let t = {
       facetPropPath: "scaffold.connectivity.nerve",
       label: "",
       children: []
-    }, i = [];
-    for (const [s, l] of Object.entries(n))
-      if (s === "label" && (a.label = l), s === "subclass labels")
-        for (const o of l)
-          i.push({
+    }, s = [];
+    for (const [l, i] of Object.entries(n))
+      if (l === "label" && (t.label = i), l === "subclass labels")
+        for (const o of i)
+          s.push({
             facetPropPath: "scaffold.connectivity.subnerve",
             label: o
           });
-    i.length && (a.children = i.sort((s, l) => s.label.localeCompare(l.label)), t.push(a));
+    s.length && (t.children = s.sort((l, i) => l.label.localeCompare(i.label)), a.push(t));
   }
-  return t.length && (r.children = t.sort((n, a) => n.label.localeCompare(a.label)), e.push(r)), e;
+  return a.length && (r.children = a.sort((n, t) => n.label.localeCompare(t.label)), e.push(r)), e;
 };
-function D(e) {
+function x(e) {
   return e[0].toUpperCase() + e.substring(1);
 }
-const J = {
+const $ = {
   emits: ["flatmap-provenance-ready", "resource-selected", "species-changed"],
   props: {
     /**
@@ -1147,7 +877,7 @@ const J = {
   },
   inject: ["showGlobalSettings", "showOpenMapButton"],
   computed: {
-    ...U(C, E, O, N),
+    ...E(T, w, I, S),
     idNamePair() {
       return this.splitFlowStore.idNamePair;
     },
@@ -1173,17 +903,19 @@ const J = {
   },
   methods: {
     toggleMinimap: function(e, r) {
-      var t;
+      var a;
       if (this.multiflatmapRef) {
-        const n = this.multiflatmapRef.getCurrentFlatmap(), a = n == null ? void 0 : n.mapImp;
-        if (a)
+        const n = this.multiflatmapRef.getCurrentFlatmap(), t = n == null ? void 0 : n.mapImp;
+        if (t)
           if (e === !0) {
             if (r === !1) {
-              const i = ((t = a.options) == null ? void 0 : t.minimap) || { position: "top-right" };
-              a.createMinimap(i), n.addResizeButtonToMinimap(), n.minimapSmall = !1;
+              const s = ((a = t.options) == null ? void 0 : a.minimap) || {
+                position: "top-right"
+              };
+              t.createMinimap(s), n.addResizeButtonToMinimap(), n.minimapSmall = !1;
             }
           } else
-            a.closeMinimap();
+            t.closeMinimap();
       }
     },
     onConnectivityItemClose() {
@@ -1204,7 +936,7 @@ const J = {
       this.settingsStore.updateMapManager(e);
     },
     trackOpenMap: function(e) {
-      b.sendEvent({
+      F.sendEvent({
         event: "interaction_event",
         event_name: "portal_maps_open_map",
         category: e,
@@ -1234,14 +966,14 @@ const J = {
      * Callback when the vuers emit a selected event.
      */
     resourceSelected: function(e, r) {
-      var s, l, o, c;
-      const t = r[0];
-      if (this.resourceHasAction(t)) {
-        f.emit("PopoverActionClick", t);
+      var l, i, o, u;
+      const a = r[0];
+      if (this.resourceHasAction(a)) {
+        f.emit("PopoverActionClick", a);
         return;
       }
-      let n, a = !1;
-      const i = {
+      let n, t = !1;
+      const s = {
         paneIndex: this.entry.id,
         type: e,
         resource: r,
@@ -1249,44 +981,41 @@ const J = {
         eventType: void 0
       };
       if (e == "MultiFlatmap" || e == "Flatmap")
-        if (i.internalName = (s = t == null ? void 0 : t.feature) != null && s.label ? t.feature.label : this.idNamePair[t.feature.models], t.eventType == "click") {
-          if (i.eventType = "selected", t.feature.type == "marker") {
-            let u = i.internalName;
-            if (this.settingsStore.isFeaturedMarkerIdentifier(t.feature.id))
+        if (s.internalName = (l = a == null ? void 0 : a.feature) != null && l.label ? a.feature.label : this.idNamePair[a.feature.models], a.eventType == "click") {
+          if (s.eventType = "selected", a.feature.type == "marker") {
+            let h = s.internalName;
+            if (this.settingsStore.isFeaturedMarkerIdentifier(a.feature.id))
               n = {
                 type: "Search",
-                term: this.settingsStore.featuredMarkerDoi(t.feature.id),
+                term: this.settingsStore.featuredMarkerDoi(a.feature.id),
                 featuredDataset: !0
               };
             else {
               n = {
                 type: "Facet",
-                facets: [u]
+                facets: [h]
               };
-              let h = /* @__PURE__ */ new Set();
-              if (t.feature["dataset-terms"].forEach((m) => {
-                h.add(m.label ? m.label : m.term);
-              }), h.size === 0 && h.add(u), n.facets = [...h], this.settingsStore.hasAppliedFacets(h) && this.settingsStore.appliedFacets.length <= h.size)
+              let c = /* @__PURE__ */ new Set();
+              if (a.feature["dataset-terms"].forEach((m) => {
+                c.add(m.label ? m.label : m.term);
+              }), c.size === 0 && c.add(h), n.facets = [...c], this.settingsStore.hasAppliedFacets(c) && this.settingsStore.appliedFacets.length <= c.size)
                 return;
               if (this.settingsStore.appliedFacets.length) {
-                if (!this.settingsStore.hasAppliedFacets(h)) {
-                  const m = [.../* @__PURE__ */ new Set([
-                    ...this.settingsStore.appliedFacets,
-                    ...h
-                  ])];
+                if (!this.settingsStore.hasAppliedFacets(c)) {
+                  const m = [.../* @__PURE__ */ new Set([...this.settingsStore.appliedFacets, ...c])];
                   this.settingsStore.updateAppliedFacets(m);
                 }
               } else
-                h.size > 1 && (n.type = "Facets"), this.settingsStore.updateAppliedFacets(n.facets);
+                c.size > 1 && (n.type = "Facets"), this.settingsStore.updateAppliedFacets(n.facets);
             }
-            a = !0, e == "MultiFlatmap" && this.$refs.multiflatmap.getCurrentFlatmap().mapImp.clearSearchResults();
+            t = !0, e == "MultiFlatmap" && this.$refs.multiflatmap.getCurrentFlatmap().mapImp.clearSearchResults();
           }
-        } else t.eventType == "mouseenter" && (i.eventType = "highlighted", a = !0);
-      else e == "Scaffold" && (t && ((((l = t.data) == null ? void 0 : l.id) === void 0 || ((o = t.data) == null ? void 0 : o.id) === "") && (t.data.id = (c = t.data) == null ? void 0 : c.group), i.internalName = t.data.id, t.data.lastActionOnMarker === !0 && (n = {
+        } else a.eventType == "mouseenter" && (s.eventType = "highlighted", t = !0);
+      else e == "Scaffold" && (a && ((((i = a.data) == null ? void 0 : i.id) === void 0 || ((o = a.data) == null ? void 0 : o.id) === "") && (a.data.id = (u = a.data) == null ? void 0 : u.group), s.internalName = a.data.id, a.data.lastActionOnMarker === !0 && (n = {
         type: "Facet",
-        facets: [D(t.data.id)]
-      })), i.eventType = "selected", a = !0);
-      n && f.emit("PopoverActionClick", n), a && this.$emit("resource-selected", i);
+        facets: [x(a.data.id)]
+      })), s.eventType = "selected", t = !0);
+      n && f.emit("PopoverActionClick", n), t && this.$emit("resource-selected", s);
     },
     resourceHasAction: function(e) {
       return e && (e.type === "URL" || e.type === "Search" || e.type === "Neuron Search" || e.type == "Facet" || e.type == "Facets");
@@ -1299,63 +1028,63 @@ const J = {
     getNameAndIdFromSyncData: async function(e) {
       let r = e.internalName;
       r === void 0 && e.resource && (r = e.resource.label);
-      let t;
-      if (e.resource && e.resource.resource && (t = e.resource.resource[0]), this.entry.type === "Scaffold") {
+      let a;
+      if (e.resource && e.resource.resource && (a = e.resource.resource[0]), this.entry.type === "Scaffold") {
         if (this.$refs.scaffold.findObjectsWithGroupName(r).length === 0) {
           if (e.resource && e.resource.feature) {
-            const i = R(e.resource.feature.models);
-            if (i.length > 0) return i;
+            const s = b(e.resource.feature.models);
+            if (s.length > 0) return s;
           }
-          let a = x(r);
-          if (a)
-            return a;
-          if (t && e.eventType === "selected")
-            return fetch(`${this.apiLocation}get-related-terms/${t}`).then((i) => i.json()).then((i) => {
-              var s;
-              if (((s = i.uberon) == null ? void 0 : s.array.length) > 0)
-                return r = i.uberon.array[0].name.charAt(0).toUpperCase() + i.uberon.array[0].name.slice(1), t = i.uberon.array[0].id.toUpperCase(), { id: t, name: r };
+          let t = C(r);
+          if (t)
+            return t;
+          if (a && e.eventType === "selected")
+            return fetch(`${this.apiLocation}get-related-terms/${a}`).then((s) => s.json()).then((s) => {
+              var l;
+              if (((l = s.uberon) == null ? void 0 : l.array.length) > 0)
+                return r = s.uberon.array[0].name.charAt(0).toUpperCase() + s.uberon.array[0].name.slice(1), a = s.uberon.array[0].id.toUpperCase(), { id: a, name: r };
             });
         }
       } else if (this.entry.type === "MultiFlatmap")
         if (r === "Bladder")
           r = "Urinary Bladder";
         else {
-          const n = R(r);
+          const n = b(r);
           n.length > 0 && (r = n[0]);
         }
-      return { id: t, name: r };
+      return { id: a, name: r };
     },
     // Get the species and andaotmy info for the featured datasets
     getDatasetAnatomyInfo: function(e) {
       fetch(`${this.apiLocation}dataset_info/anatomy?identifier=${e}`).then((r) => r.json()).then((r) => {
-        const t = r.result[0];
+        const a = r.result[0];
         let n;
         try {
-          n = t.anatomy.organ[0].curie;
+          n = a.anatomy.organ[0].curie;
         } catch {
           n = void 0;
         }
-        let a;
+        let t;
         try {
-          a = t.item.curie;
+          t = a.item.curie;
         } catch {
-          a = void 0;
+          t = void 0;
         }
-        let i;
+        let s;
         try {
-          let s = 0, l = !1;
-          for (; !l && s < t.organisms.subject.length; ) {
-            const o = t.organisms.subject[s];
-            o.species && (i = o.species.name, l = !0), s += 1;
+          let l = 0, i = !1;
+          for (; !i && l < a.organisms.subject.length; ) {
+            const o = a.organisms.subject[l];
+            o.species && (s = o.species.name, i = !0), l += 1;
           }
         } catch {
-          i = void 0;
+          s = void 0;
         }
         this.settingsStore.updateFeaturedMarker({
           identifier: e,
           marker: n,
-          doi: a,
-          species: i
+          doi: t,
+          species: s
         });
       });
     },
@@ -1367,24 +1096,41 @@ const J = {
     // Check if the new featured dataset api has any info
     newFeaturedDatasetApiHasInfo: async function() {
       let r = await (await fetch(`${this.apiLocation}get_featured_dataset`)).json();
-      return !r.datasets || r.datasets.length == 0 ? !1 : r.datasets.map((t) => t.id);
+      return !r.datasets || r.datasets.length == 0 ? !1 : r.datasets.map((a) => a.id);
     },
     flatmapResourceSelected: function(e, r) {
-      var s;
+      var l;
       this.resourceSelected(e, r);
-      const t = r[0], { eventType: n, feature: a } = t, { viewingMode: i } = this.settingsStore.globalSettings;
-      if (n === "click" && a.type === "feature" && ((s = a.models) != null && s.startsWith("ilxtr:"))) {
-        const l = [];
+      const a = r[0], { eventType: n, feature: t } = a, { viewingMode: s } = this.settingsStore.globalSettings;
+      if (n === "click" && t.type === "feature" && ((l = t.models) != null && l.startsWith("ilxtr:"))) {
+        const i = [];
         r.forEach((o) => {
-          const { models: c } = o.feature;
-          l.push(c);
-        }), b.sendEvent({
+          const { models: u } = o.feature;
+          i.push(u);
+        }), F.sendEvent({
           event: "interaction_event",
           event_name: "portal_maps_connectivity",
-          category: l.join(", "),
-          location: e + " " + i
+          category: i.join(", "),
+          location: e + " " + s
         });
       }
+      if (n === "click" && t.type === "feature" && e === "Flatmap") {
+        const { component: i, variable: o } = this.mappingStore.mapToCellMLIdentifiers(t.mapUUID, t.id);
+        if (!i || !o)
+          return;
+        const u = {
+          component: i,
+          featureId: t.id,
+          mapId: t.mapUUID,
+          offset: { left: 15, top: 15 },
+          ownerId: this.entry.id,
+          position: { x: this.elementX + this.left, y: this.elementY + this.top },
+          protocol: a.protocol,
+          variable: o,
+          windowId: `simulation-window-${this.entry.id}-${i}-${o}`
+        };
+        this.simulationPlotStore.requestSimulation(u);
+      }
     },
     /**
      * Get a list of featured datasets to display.
@@ -1393,11 +1139,11 @@ const J = {
       let e = [], r = await this.oldFeaturedDatasetApiHasInfo();
       if (r) e = r;
       else {
-        let t = await this.newFeaturedDatasetApiHasInfo();
-        t && (e = t);
+        let a = await this.newFeaturedDatasetApiHasInfo();
+        a && (e = a);
       }
-      this.settingsStore.updateFeatured(e), e.forEach((t) => {
-        this.getDatasetAnatomyInfo(t);
+      this.settingsStore.updateFeatured(e), e.forEach((a) => {
+        this.getDatasetAnatomyInfo(a);
       });
     },
     flatmapMarkerUpdate() {
@@ -1435,42 +1181,40 @@ const J = {
     checkEndHelpMouseDown: function(e) {
       e.target.closest(".help-mode-dialog") || this.endHelp();
     },
-    flatmapHighlight: async function(e, r, t, n) {
-      let a = [...r, ...n];
-      const i = this.settingsStore.globalSettings;
-      if (i.highlightConnectedPaths) {
-        const s = r.length ? r : n.length ? n : [], l = await e.retrieveConnectedPaths(s);
-        l && a.push(...l);
+    flatmapHighlight: async function(e, r, a, n) {
+      let t = [...r, ...n];
+      const s = this.settingsStore.globalSettings;
+      if (s.highlightConnectedPaths) {
+        const l = r.length ? r : n.length ? n : [], i = await e.retrieveConnectedPaths(l);
+        i && t.push(...i);
       }
-      if (i.highlightDOIPaths) {
-        const s = await e.searchConnectivitiesByReference(t);
-        s && a.push(...s);
+      if (s.highlightDOIPaths) {
+        const l = await e.searchConnectivitiesByReference(a);
+        l && t.push(...l);
       }
-      return a = [...new Set(a)], a;
+      return t = [...new Set(t)], t;
     },
     sidebarHoverHighlight: function(e) {
-      var r, t;
+      var r, a;
       if (this.visible && ((this.flatmapRef || this.multiflatmapRef) && this.flatmapReady || this.scaffoldRef && this.scaffoldLoaded)) {
-        const n = this.settingsStore.hoverAnatomies, a = this.settingsStore.hoverOrgans, i = this.settingsStore.hoverDOI, s = this.settingsStore.hoverConnectivity;
-        let l = null, o = null;
-        this.flatmapRef && (l = this.flatmapRef), this.multiflatmapRef && (l = this.multiflatmapRef.getCurrentFlatmap()), this.scaffoldRef && (o = this.scaffoldRef), clearTimeout(this.highlightDelay), !n.length && !a.length && !i && !s.length && ((this.multiflatmapRef || this.flatmapRef) && l ? l.mapImp && !l.mapImp.contextLost && ((r = l.mapImp) == null || r.clearSearchResults(), e.connectivityProcessed && ((t = l.mapImp) == null || t.setPaint({ dimmed: !0 }))) : this.scaffoldRef && o && o.changeHighlightedByName(a, "", !1)), this.highlightDelay = setTimeout(() => {
-          (n.length || a.length || i || s.length) && ((this.multiflatmapRef || this.flatmapRef) && l ? this.flatmapHighlight(l, n, i, s).then((c) => {
+        const n = this.settingsStore.hoverAnatomies, t = this.settingsStore.hoverOrgans, s = this.settingsStore.hoverDOI, l = this.settingsStore.hoverConnectivity;
+        let i = null, o = null;
+        this.flatmapRef && (i = this.flatmapRef), this.multiflatmapRef && (i = this.multiflatmapRef.getCurrentFlatmap()), this.scaffoldRef && (o = this.scaffoldRef), clearTimeout(this.highlightDelay), !n.length && !t.length && !s && !l.length && ((this.multiflatmapRef || this.flatmapRef) && i ? i.mapImp && !i.mapImp.contextLost && ((r = i.mapImp) == null || r.clearSearchResults(), e.connectivityProcessed && ((a = i.mapImp) == null || a.setPaint({ dimmed: !0 }))) : this.scaffoldRef && o && o.changeHighlightedByName(t, "", !1)), this.highlightDelay = setTimeout(() => {
+          (n.length || t.length || s || l.length) && ((this.multiflatmapRef || this.flatmapRef) && i ? this.flatmapHighlight(i, n, s, l).then((u) => {
             try {
-              l.showConnectivityTooltips({
-                connectivityInfo: { featureId: c },
+              i.showConnectivityTooltips({
+                connectivityInfo: { featureId: u },
                 data: []
               });
-            } catch (u) {
-              if (console.log(u), s.length && l.mapImp) {
-                const h = l.mapImp.uuid;
-                c.every(
-                  (v) => this.connectivityKnowledge[h].some(
-                    (p) => p.id === v
-                  )
-                ) || l.mapImp && !l.mapImp.contextLost && l.mapImp.clearSearchResults();
+            } catch {
+              if (l.length && i.mapImp) {
+                const c = i.mapImp.uuid;
+                u.every(
+                  (v) => this.connectivityKnowledge[c].some((p) => p.id === v)
+                ) || i.mapImp && !i.mapImp.contextLost && i.mapImp.clearSearchResults();
               }
             }
-          }) : this.scaffoldRef && o && o.changeHighlightedByName(a, "", !1));
+          }) : this.scaffoldRef && o && o.changeHighlightedByName(t, "", !1));
         }, 100);
       }
     },
@@ -1507,80 +1251,95 @@ const J = {
       this.flatmapService = await this.mockUpFlatmapService(), this.loadConnectivityExplorerConfig(this.flatmapService);
     },
     mockUpFlatmapService: async function() {
-      const t = (await (await fetch(this.flatmapAPI)).json()).filter((u) => u.id === "human-flatmap_male").sort((u, h) => h.created.localeCompare(u.created))[0], n = t.uuid, a = t.sckan["knowledge-source"], s = await (await fetch(`${this.flatmapAPI}/flatmap/${n}/pathways`)).json();
-      this.flatmapQueries = y(new S()), this.flatmapQueries.initialise(this.flatmapAPI);
-      const l = {
+      const a = (await (await fetch(this.flatmapAPI)).json()).filter((h) => h.id === "human-flatmap_male").sort((h, c) => c.created.localeCompare(h.created))[0], n = a.uuid, t = a.sckan["knowledge-source"], l = await (await fetch(`${this.flatmapAPI}/flatmap/${n}/pathways`)).json();
+      this.flatmapQueries = M(new L()), this.flatmapQueries.initialise(this.flatmapAPI);
+      const i = {
         mapMetadata: {
           uuid: n,
           connectivity: {
-            ...t.sckan
+            ...a.sckan
           }
         },
-        pathways: s,
+        pathways: l,
         resource: this.entry.resource,
-        knowledgeSource: a,
-        queryKnowledge: async (u) => {
-          const h = "select knowledge from knowledge where (source=? or source is null) and entity=? order by source desc", m = [a, u], v = await this.flatmapQueries.queryKnowledge(h, m);
+        knowledgeSource: t,
+        queryKnowledge: async (h) => {
+          const c = "select knowledge from knowledge where (source=? or source is null) and entity=? order by source desc", m = [t, h], v = await this.flatmapQueries.queryKnowledge(c, m);
           return JSON.parse(v);
         },
-        queryLabels: async (u) => {
-          const h = `select source, entity, knowledge from knowledge where (source=? or source is null) and entity in (?${", ?".repeat(u.length - 1)}) order by entity, source desc`, m = [a, ...u], v = await this.flatmapQueries.queryKnowledge(h, m), p = [];
+        queryLabels: async (h) => {
+          const c = `select source, entity, knowledge from knowledge where (source=? or source is null) and entity in (?${", ?".repeat(
+            h.length - 1
+          )}) order by entity, source desc`, m = [t, ...h], v = await this.flatmapQueries.queryKnowledge(c, m), p = [];
           let g;
-          for (const F of v)
-            if (F[1] !== g) {
-              const _ = JSON.parse(F[2]);
+          for (const A of v)
+            if (A[1] !== g) {
+              const y = JSON.parse(A[2]);
               p.push({
-                entity: F[1],
-                label: _.label || F[1]
-              }), g = F[1];
+                entity: A[1],
+                label: y.label || A[1]
+              }), g = A[1];
             }
           return p;
         }
-      }, o = H();
+      }, o = X();
       return {
         mockup: !0,
-        getFilterOptions: async (u, h) => {
-          const v = await X(this.flatmapAPI, u, h, void 0);
+        getFilterOptions: async (h, c) => {
+          const v = await O(
+            this.flatmapAPI,
+            h,
+            c,
+            void 0
+          );
           return [...o, ...v];
         },
-        getTermNerveMaps: $,
-        mapImp: l
+        getTermNerveMaps: B,
+        mapImp: i
       };
     },
     loadConnectivityExplorerConfig: async function(e) {
-      var i;
-      const r = e.mapImp, t = w(r), n = e.mockup ? r.resource : r.uuid;
-      let a = [];
-      if (!this.connectivityKnowledge[t]) {
-        this.flatmapQueries = y(new S()), this.flatmapQueries.initialise(this.flatmapAPI);
-        const s = await P(r, this.flatmapQueries);
-        this.connectivityKnowledge[t] = s.filter((l) => {
+      var s;
+      const r = e.mapImp, a = d(r), n = e.mockup ? r.resource : r.uuid;
+      let t = [];
+      if (!this.connectivityKnowledge[a]) {
+        this.flatmapQueries = M(new L()), this.flatmapQueries.initialise(this.flatmapAPI);
+        const l = await N(r, this.flatmapQueries);
+        this.connectivityKnowledge[a] = l.filter((i) => {
           var o;
-          return (o = l.connectivity) == null ? void 0 : o.length;
-        }).sort((l, o) => l.label.localeCompare(o.label));
+          return (o = i.connectivity) == null ? void 0 : o.length;
+        }).sort((i, o) => i.label.localeCompare(o.label));
       }
       if (!this.connectivityKnowledge[n]) {
-        const s = ((i = r.pathways) == null ? void 0 : i.paths) || {};
-        this.connectivityKnowledge[n] = this.connectivityKnowledge[t].filter((l) => l.id in s);
+        const l = ((s = r.pathways) == null ? void 0 : s.paths) || {};
+        this.connectivityKnowledge[n] = this.connectivityKnowledge[a].filter(
+          (i) => i.id in l
+        );
       }
-      if (!this.connectivityFilterOptions[n] && !e.mockup && (this.connectivityFilterOptions[n] = await e.getFilterOptions(r, this.connectivityKnowledge[n])), e.mockup) {
-        const s = e.getTermNerveMaps() || {}, l = JSON.parse(JSON.stringify(this.connectivityKnowledge[n]));
-        this.connectivityKnowledge[n] = l.map((c) => {
-          var h;
-          let u = c;
-          if ((h = c.nerves) != null && h.length) {
-            const v = c.nerves.flat(1 / 0).reduce((p, g) => (g in s && p.push(s[g]), p), []);
-            v != null && v.length && (a.push(...v), u["nerve-label"] = v.sort((p, g) => p.nerve.localeCompare(g.nerve)));
+      if (!this.connectivityFilterOptions[n] && !e.mockup && (this.connectivityFilterOptions[n] = await e.getFilterOptions(
+        r,
+        this.connectivityKnowledge[n]
+      )), e.mockup) {
+        const l = e.getTermNerveMaps() || {}, i = JSON.parse(JSON.stringify(this.connectivityKnowledge[n]));
+        this.connectivityKnowledge[n] = i.map((u) => {
+          var c;
+          let h = u;
+          if ((c = u.nerves) != null && c.length) {
+            const v = u.nerves.flat(1 / 0).reduce((p, g) => (g in l && p.push(l[g]), p), []);
+            v != null && v.length && (t.push(...v), h["nerve-label"] = v.sort((p, g) => p.nerve.localeCompare(g.nerve)));
           }
-          return u;
-        }).filter((c) => c["nerve-label"]), this.connectivityFilterOptions[n] || (this.connectivityFilterOptions[n] = await e.getFilterOptions(r, this.connectivityKnowledge[n])), a = a.map((c) => c.nerve.toLowerCase());
+          return h;
+        }).filter((u) => u["nerve-label"]), this.connectivityFilterOptions[n] || (this.connectivityFilterOptions[n] = await e.getFilterOptions(
+          r,
+          this.connectivityKnowledge[n]
+        )), t = t.map((u) => u.nerve.toLowerCase());
         const o = JSON.parse(JSON.stringify(this.connectivityFilterOptions[n]));
-        this.connectivityFilterOptions[n] = o.map((c) => {
-          if (c.key === "scaffold.connectivity.nerve") {
-            const u = c.children.filter((h) => a.includes(h.label.toLowerCase()));
-            return { ...c, children: u };
+        this.connectivityFilterOptions[n] = o.map((u) => {
+          if (u.key === "scaffold.connectivity.nerve") {
+            const h = u.children.filter((c) => t.includes(c.label.toLowerCase()));
+            return { ...u, children: h };
           } else
-            return c;
+            return u;
         });
       } else
         this.connectivityFilterSources[n] || (this.connectivityFilterSources[n] = e.getFilterSources()), this.connectivitiesStore.updateFilterSources(this.connectivityFilterSources);
@@ -1594,28 +1353,38 @@ const J = {
         provenanceTaxonomy: e.taxons,
         feature: []
       });
-      return r.knowledgeSource = w(this.flatmapService.mapImp), r.mapId = this.flatmapService.mapImp.mapMetadata.id, r.mapuuid = this.flatmapService.mapImp.mapMetadata.uuid, r["nerve-label"] = e["nerve-label"], r.ready = !0, r;
+      return r.knowledgeSource = d(this.flatmapService.mapImp), r.mapId = this.flatmapService.mapImp.mapMetadata.id, r.mapuuid = this.flatmapService.mapImp.mapMetadata.uuid, r["nerve-label"] = e["nerve-label"], r.ready = !0, r;
     },
     getKnowledgeTooltip: async function(e) {
-      this.tooltipEntry = [], e.data.forEach((n) => this.tooltipEntry.push({ title: n.label, featureId: [n.id], ready: !1 })), f.emit("connectivity-info-open", this.tooltipEntry);
+      this.tooltipEntry = [], e.data.forEach(
+        (n) => this.tooltipEntry.push({
+          title: n.label,
+          featureId: [n.id],
+          ready: !1
+        })
+      ), f.emit("connectivity-info-open", this.tooltipEntry);
       let r = [];
       for (let n = 0; n < e.data.length; n++)
         r.push(await this.knowledgeTooltipQuery(e.data[n]));
       this.tooltipEntry = await Promise.all(r), this.tooltipEntry.map((n) => n.featureId[0]).length > 0 && f.emit("connectivity-info-open", this.tooltipEntry);
     },
     changeConnectivitySource: async function(e, r) {
-      var i, s;
-      const { entry: t, connectivitySource: n } = e, a = (s = (i = this == null ? void 0 : this.flatmapService) == null ? void 0 : i.mapImp) == null ? void 0 : s.mapMetadata.uuid;
-      r.includes(a) || (r.push(a), await this.flatmapQueries.queryForConnectivityNew(this.flatmapService.mapImp, t.featureId[0], n), this.tooltipEntry = this.tooltipEntry.map((l) => l.featureId[0] === t.featureId[0] ? this.flatmapQueries.updateTooltipData(l) : l), f.emit("connectivity-info-open", this.tooltipEntry));
+      var s, l;
+      const { entry: a, connectivitySource: n } = e, t = (l = (s = this == null ? void 0 : this.flatmapService) == null ? void 0 : s.mapImp) == null ? void 0 : l.mapMetadata.uuid;
+      r.includes(t) || (r.push(t), await this.flatmapQueries.queryForConnectivityNew(
+        this.flatmapService.mapImp,
+        a.featureId[0],
+        n
+      ), this.tooltipEntry = this.tooltipEntry.map((i) => i.featureId[0] === a.featureId[0] ? this.flatmapQueries.updateTooltipData(i) : i), f.emit("connectivity-info-open", this.tooltipEntry));
     },
     trackEvent: function(e) {
-      b.sendEvent(e);
+      F.sendEvent(e);
     }
   },
   data: function() {
     return {
       apiLocation: void 0,
-      activeSpecies: B,
+      activeSpecies: _,
       scaffoldCamera: void 0,
       mainStyle: {
         height: this.entry.datasetTitle ? "calc(100% - 30px)" : "100%",
@@ -1651,5 +1420,5 @@ const J = {
   }
 };
 export {
-  J as C
+  $ as C
 };