@abi-software/mapintegratedvuer 1.7.1 → 1.8.0-beta.1

package/dist/{ContentMixin-BTZsoldP.js → ContentMixin-B9DtqhYT.js}

@@ -1,10 +1,10 @@
 import "vue";
-import { u as d, d as u, E as r, T as p, e as h, f as m } from "./index-DkVmhrWU.js";
+import { u as p, d as u, E as r, T as d, e as h, f as m } from "./index-B_H6BPK_.js";
 import { mapStores as g } from "pinia";
 function y(e) {
   return e[0].toUpperCase() + e.substring(1);
 }
-const w = {
+const I = {
   emits: ["flatmap-provenance-ready", "resource-selected", "species-changed"],
   props: {
     /**
@@ -22,7 +22,7 @@ const w = {
     }
   },
   computed: {
-    ...g(d, u),
+    ...g(p, u),
     idNamePair() {
       return this.splitFlowStore.idNamePair;
     },
@@ -56,7 +56,7 @@ const w = {
       this.settingsStore.updateMapManager(e);
     },
     trackOpenMap: function(e) {
-      p.sendEvent({
+      d.sendEvent({
         event: "interaction_event",
         event_name: "portal_maps_open_map",
         category: e,
@@ -80,12 +80,12 @@ const w = {
      * Callback when the vuers emit a selected event.
      */
     resourceSelected: function(e, t) {
-      var n, o, l, f;
+      var s, o, l, f;
       if (this.resourceHasAction(t)) {
         r.emit("PopoverActionClick", t);
         return;
       }
-      let i, s = !1;
+      let i, n = !1;
       const a = {
         paneIndex: this.entry.id,
         type: e,
@@ -94,7 +94,7 @@ const w = {
         eventType: void 0
       };
       if (e == "MultiFlatmap" || e == "Flatmap")
-        if (a.internalName = (n = t == null ? void 0 : t.feature) != null && n.label ? t.feature.label : this.idNamePair[t.feature.models], t.eventType == "click")
+        if (a.internalName = (s = t == null ? void 0 : t.feature) != null && s.label ? t.feature.label : this.idNamePair[t.feature.models], t.eventType == "click")
           if (a.eventType = "selected", t.feature.type == "marker") {
             let c = a.internalName;
             this.settingsStore.isFeaturedMarkerIdentifier(
@@ -110,16 +110,16 @@ const w = {
               facet: c,
               facetPropPath: "anatomy.organ.category.name",
               term: "Anatomical structure"
-            }, s = !0, e == "MultiFlatmap" && this.$refs.multiflatmap.getCurrentFlatmap().mapImp.clearSearchResults();
-          } else t.feature.type == "feature" && this.syncMode && (s = !0);
-        else t.eventType == "mouseenter" && (a.eventType = "highlighted", s = !0);
+            }, n = !0, e == "MultiFlatmap" && this.$refs.multiflatmap.getCurrentFlatmap().mapImp.clearSearchResults();
+          } else t.feature.type == "feature" && this.syncMode && (n = !0);
+        else t.eventType == "mouseenter" && (a.eventType = "highlighted", n = !0);
       else e == "Scaffold" && (t && t[0] && ((((o = t[0].data) == null ? void 0 : o.id) === void 0 || ((l = t[0].data) == null ? void 0 : l.id) === "") && (t[0].data.id = (f = t[0].data) == null ? void 0 : f.group), a.internalName = t[0].data.id, t[0].data.lastActionOnMarker === !0 && (i = {
         type: "Facet",
         facet: y(t[0].data.id),
         facetPropPath: "anatomy.organ.category.name",
         term: "Anatomical structure"
-      })), a.eventType = "selected", s = !0);
-      i && r.emit("PopoverActionClick", i), s && this.$emit("resource-selected", a);
+      })), a.eventType = "selected", n = !0);
+      i && r.emit("PopoverActionClick", i), n && this.$emit("resource-selected", a);
     },
     resourceHasAction: function(e) {
       return e.type === "URL" || e.type === "Search" || e.type === "Neuron Search" || e.type == "Facet" || e.type == "Facets";
@@ -144,24 +144,24 @@ const w = {
       if (e.resource && e.resource.resource && (i = e.resource.resource[0]), this.entry.type === "Scaffold") {
         if (this.$refs.scaffold.findObjectsWithGroupName(t).length === 0) {
           if (e.resource && e.resource.feature) {
-            const n = h(e.resource.feature.models);
-            if (n.length > 0) return n;
+            const s = h(e.resource.feature.models);
+            if (s.length > 0) return s;
           }
           let a = m(t);
           if (a)
             return a;
           if (i && e.eventType === "selected")
-            return fetch(`${this.apiLocation}get-related-terms/${i}`).then((n) => n.json()).then((n) => {
-              if (n.uberon.array.length > 0)
-                return t = n.uberon.array[0].name.charAt(0).toUpperCase() + n.uberon.array[0].name.slice(1), i = n.uberon.array[0].id.toUpperCase(), { id: i, name: t };
+            return fetch(`${this.apiLocation}get-related-terms/${i}`).then((s) => s.json()).then((s) => {
+              if (s.uberon.array.length > 0)
+                return t = s.uberon.array[0].name.charAt(0).toUpperCase() + s.uberon.array[0].name.slice(1), i = s.uberon.array[0].id.toUpperCase(), { id: i, name: t };
             });
         }
       } else if (this.entry.type === "MultiFlatmap")
         if (t === "Bladder")
           t = "Urinary Bladder";
         else {
-          const s = h(t);
-          s.length > 0 && (t = s[0]);
+          const n = h(t);
+          n.length > 0 && (t = n[0]);
         }
       return { id: i, name: t };
     },
@@ -169,11 +169,11 @@ const w = {
     getDatasetAnatomyInfo: function(e) {
       fetch(`${this.apiLocation}dataset_info/anatomy?identifier=${e}`).then((t) => t.json()).then((t) => {
         const i = t.result[0];
-        let s;
+        let n;
         try {
-          s = i.anatomy.organ[0].curie;
+          n = i.anatomy.organ[0].curie;
         } catch {
-          s = void 0;
+          n = void 0;
         }
         let a;
         try {
@@ -181,21 +181,21 @@ const w = {
         } catch {
           a = void 0;
         }
-        let n;
+        let s;
         try {
           let o = 0, l = !1;
           for (; !l && o < i.organisms.subject.length; ) {
             const f = i.organisms.subject[o];
-            f.species && (n = f.species.name, l = !0), o += 1;
+            f.species && (s = f.species.name, l = !0), o += 1;
           }
         } catch {
-          n = void 0;
+          s = void 0;
         }
         this.settingsStore.updateFeaturedMarker({
           identifier: e,
-          marker: s,
+          marker: n,
           doi: a,
-          species: n
+          species: s
         });
       });
     },
@@ -279,11 +279,29 @@ const w = {
     checkEndHelpMouseDown: function(e) {
       e.target.closest(".help-mode-dialog") || this.endHelp();
     },
-    mapHoverHighlight: function(e) {
+    getConnectivitiesByDOI: async function(e) {
+      return await this.$refs.multiflatmap.getCurrentFlatmap().searchConnectivitiesByReference(e);
+    },
+    highlightAnatomies: async function(e, t, i) {
+      const n = [...t], a = this.settingsStore.hoverHighlightOptions;
+      if (a.highlightConnectedPaths) {
+        const s = await e.queryPathsForFeatures(t);
+        s && n.push(...s);
+      }
+      if (a.highlightDOIPaths) {
+        const s = await this.getConnectivitiesByDOI(i);
+        s && n.push(...s);
+      }
+      return n;
+    },
+    mapHoverHighlight: function() {
       if (this.visible) {
-        const t = this.settingsStore.hoverAnatomies, i = this.settingsStore.hoverOrgans;
-        t.length || i.length ? (clearTimeout(this.hoverDelay), this.multiflatmapRef || this.flatmapRef ? e == null || e.zoomToFeatures(t, { noZoomIn: !0 }) : this.scaffoldRef && (e == null || e.changeHighlightedByName(i, "", !1))) : this.hoverDelay = setTimeout(() => {
-          this.multiflatmapRef || this.flatmapRef ? e == null || e.clearSearchResults() : this.scaffoldRef && (e == null || e.changeHighlightedByName(i, "", !1));
+        const e = this.settingsStore.hoverAnatomies, t = this.settingsStore.hoverOrgans, i = this.settingsStore.hoverDOI;
+        let n = null, a = null;
+        this.flatmapRef && (n = this.$refs.flatmap.mapImp), this.multiflatmapRef && (n = this.$refs.multiflatmap.getCurrentFlatmap().mapImp), this.scaffoldRef && (a = this.$refs.scaffold), n && n.clearSearchResults(), e.length || t.length ? (clearTimeout(this.hoverDelay), this.multiflatmapRef || this.flatmapRef ? this.highlightAnatomies(n, e, i).then((s) => {
+          n.selectFeatures(s);
+        }) : this.scaffoldRef && (a == null || a.changeHighlightedByName(t, "", !1))) : this.hoverDelay = setTimeout(() => {
+          this.multiflatmapRef || this.flatmapRef ? n == null || n.clearSearchResults() : this.scaffoldRef && (a == null || a.changeHighlightedByName(t, "", !1));
         }, 500);
       }
     },
@@ -335,5 +353,5 @@ const w = {
   }
 };
 export {
-  w as C
+  I as C
 };

package/dist/{Flatmap-TK-35whY.js → Flatmap-BMowLXfS.js}

@@ -1,8 +1,8 @@
-import { _ as c, i as h, t as u, T as l, E as r } from "./index-DkVmhrWU.js";
-import { C as I } from "./ContentMixin-BTZsoldP.js";
-import { D as g, y as M } from "./style-CDBCHm5P.js";
-import { resolveComponent as s, openBlock as p, createElementBlock as y, createVNode as v, createBlock as S, createCommentVNode as C } from "vue";
-const F = {
+import { _ as d, b as h, t as u, T as s, E as r } from "./index-B_H6BPK_.js";
+import { C as I } from "./ContentMixin-B9DtqhYT.js";
+import { D as g, a as M } from "./style-Bt2YbWCx.js";
+import { resolveComponent as l, openBlock as p, createElementBlock as v, createVNode as y, createBlock as C, createCommentVNode as S } from "vue";
+const w = {
   name: "Flatmap",
   mixins: [I, g],
   components: {
@@ -23,69 +23,69 @@ const F = {
       var e;
       return (e = this.$refs.flatmap) == null ? void 0 : e.mapImp;
     },
-    flatmaprResourceSelected: function(e, a) {
-      if (this.resourceSelected(e, a), a.eventType === "click" && a.feature.type === "feature") {
-        const n = {
-          label: a.label || "",
-          id: a.feature.id || "",
-          featureId: a.feature.featureId || "",
-          taxonomy: a.taxonomy || "",
-          resources: a.resource.join(", ")
-        }, t = u(n);
-        l.sendEvent({
+    flatmaprResourceSelected: function(e, t) {
+      if (this.resourceSelected(e, t), t.eventType === "click" && t.feature.type === "feature") {
+        const a = {
+          label: t.label || "",
+          id: t.feature.id || "",
+          featureId: t.feature.featureId || "",
+          taxonomy: t.taxonomy || "",
+          resources: t.resource.join(", ")
+        }, n = u(a);
+        s.sendEvent({
           event: "interaction_event",
           event_name: "portal_maps_connectivity",
-          category: t,
+          category: n,
           location: e + " " + this.$refs.flatmap.viewingMode
         });
       }
     },
     flatmapReadyCall: function(e) {
-      let a = { id: this.entry.id, prov: this.getFlatmapImp().provenance };
-      r.emit("mapImpProv", a), this.$emit("flatmap-provenance-ready", a), this.flatmapReadyForMarkerUpdates(e), r.emit("mapLoaded", e);
+      let t = { id: this.entry.id, prov: this.getFlatmapImp().provenance };
+      r.emit("mapImpProv", t), this.$emit("flatmap-provenance-ready", t), this.flatmapReadyForMarkerUpdates(e), r.emit("mapLoaded", e);
     },
     onPathwaySelectionChanged: function(e) {
-      const { label: a, property: n, checked: t, selectionsTitle: i } = e;
-      l.sendEvent({
+      const { label: t, property: a, checked: n, selectionsTitle: i } = e;
+      s.sendEvent({
         event: "interaction_event",
         event_name: "portal_maps_pathway_change",
-        category: a + " [" + n + "] " + t,
+        category: t + " [" + a + "] " + n,
         location: i
       });
     },
     highlightFeatures: function(e) {
-      let a = e.name;
-      const n = this.$refs.flatmap.mapImp;
-      if (a) {
-        const t = n.search(a);
-        t.featureIds[0] && n.highlightFeatures([
-          n.modelForFeature(t.featureIds[0])
+      let t = e.name;
+      const a = this.$refs.flatmap.mapImp;
+      if (t) {
+        const n = a.search(t);
+        n.featureIds[0] && a.highlightFeatures([
+          a.modelForFeature(n.featureIds[0])
         ]);
       }
     },
     /**
      * Append the list of suggested terms to suggestions
      */
-    searchSuggestions: function(e, a) {
+    searchSuggestions: function(e, t) {
       if (e && this.$refs.flatmap.mapImp) {
-        const n = this.$refs.flatmap.mapImp.search(e);
-        (n.__featureIds || n.featureIds).forEach((i) => {
+        const a = this.$refs.flatmap.mapImp.search(e);
+        (a.__featureIds || a.featureIds).forEach((i) => {
           const o = this.$refs.flatmap.mapImp.annotation(i);
-          o && o.label && a.push(o.label);
+          o && o.label && t.push(o.label);
         });
       }
     },
-    zoomToFeatures: function(e, a) {
-      let n = e.name;
-      const t = this.$refs.flatmap.mapImp;
-      if (n) {
-        const i = t.search(n);
+    zoomToFeatures: function(e, t) {
+      let a = e.name;
+      const n = this.$refs.flatmap.mapImp;
+      if (a) {
+        const i = n.search(a);
         if (i.featureIds.length) {
-          let o = t.modelForFeature(i.featureIds[0]);
-          o ? (a && t.selectFeatures(o), t.zoomToFeatures(o)) : t.clearSearchResults();
+          let o = n.modelForFeature(i.featureIds[0]);
+          o ? (t && n.selectFeatures(o), n.zoomToFeatures(o)) : n.clearSearchResults();
         }
       } else
-        t.clearSearchResults();
+        n.clearSearchResults();
     },
     changeViewingMode: function(e) {
       this.$refs.flatmap.changeViewingMode(e);
@@ -98,29 +98,32 @@ const F = {
   },
   mounted: function() {
     r.on("annotation-close", (e) => {
-      const a = this.$refs.flatmap;
-      e != null && e.tabClose && a && this.$refs.flatmap.annotationEventCallback({}, { type: "aborted" });
+      const t = this.$refs.flatmap;
+      e != null && e.tabClose && t && this.$refs.flatmap.annotationEventCallback({}, { type: "aborted" });
     }), r.on("markerUpdate", () => {
       this.flatmapMarkerUpdate(void 0);
     }), r.on("hoverUpdate", () => {
-      this.mapHoverHighlight(this.$refs.flatmap.mapImp);
+      this.mapHoverHighlight();
     }), r.on("show-connectivity", (e) => {
-      const { featureIds: a, offset: n } = e, t = this.$refs.flatmap;
-      t && t.moveMap(a, {
-        offsetX: n ? -150 : 0,
+      const { featureIds: t, offset: a } = e, n = this.$refs.flatmap;
+      n && n.moveMap(t, {
+        offsetX: a ? -150 : 0,
         zoom: 4
       });
+    }), r.on("show-reference-connectivities", (e) => {
+      const t = this.$refs.flatmap;
+      t && t.showConnectivitiesByReference(e);
     });
   }
-}, w = { class: "viewer-container" };
-function b(e, a, n, t, i, o) {
-  const m = s("FlatmapVuer"), f = s("HelpModeDialog");
-  return p(), y("div", w, [
-    v(m, {
+}, F = { class: "viewer-container" };
+function b(e, t, a, n, i, o) {
+  const m = l("FlatmapVuer"), f = l("HelpModeDialog");
+  return p(), v("div", F, [
+    y(m, {
       state: e.entry.state,
       entry: e.entry.resource,
       mapManager: e.mapManager,
-      onResourceSelected: a[0] || (a[0] = (d) => o.flatmaprResourceSelected(e.entry.type, d)),
+      onResourceSelected: t[0] || (t[0] = (c) => o.flatmaprResourceSelected(e.entry.type, c)),
       onPanZoomCallback: e.flatmapPanZoomCallback,
       name: e.entry.resource,
       style: { height: "100%", width: "100%" },
@@ -151,17 +154,17 @@ function b(e, a, n, t, i, o) {
       onPathwaySelectionChanged: o.onPathwaySelectionChanged,
       onMapmanagerLoaded: e.onMapmanagerLoaded
     }, null, 8, ["state", "entry", "mapManager", "onPanZoomCallback", "name", "minZoom", "helpMode", "helpModeActiveItem", "helpModeDialog", "onHelpModeLastItem", "onShownTooltip", "onShownMapTooltip", "onAnnotationOpen", "onAnnotationClose", "annotationSidebar", "onConnectivityInfoOpen", "onConnectivityInfoClose", "onConnectivityGraphError", "connectivityInfoSidebar", "onReady", "flatmapAPI", "sparcAPI", "onOpenMap", "onPathwaySelectionChanged", "onMapmanagerLoaded"]),
-    e.helpMode && e.useHelpModeDialog ? (p(), S(f, {
+    e.helpMode && e.useHelpModeDialog ? (p(), C(f, {
       key: 0,
       ref: "flatmapHelp",
       flatmapRef: e.flatmapRef,
       lastItem: e.helpModeLastItem,
       onShowNext: e.onHelpModeShowNext,
       onFinishHelpMode: e.onFinishHelpMode
-    }, null, 8, ["flatmapRef", "lastItem", "onShowNext", "onFinishHelpMode"])) : C("", !0)
+    }, null, 8, ["flatmapRef", "lastItem", "onShowNext", "onFinishHelpMode"])) : S("", !0)
   ]);
 }
-const R = /* @__PURE__ */ c(F, [["render", b], ["__scopeId", "data-v-9e155ca8"]]);
+const k = /* @__PURE__ */ d(w, [["render", b], ["__scopeId", "data-v-e3d04e7c"]]);
 export {
-  R as default
+  k as default
 };

package/dist/{Iframe-rZ__11EG.js → Iframe-fNcVYbXe.js}

@@ -1,6 +1,6 @@
-import { C as r } from "./ContentMixin-BTZsoldP.js";
+import { C as r } from "./ContentMixin-B9DtqhYT.js";
 import { openBlock as o, createElementBlock as t, createElementVNode as s } from "vue";
-import { _ as n } from "./index-DkVmhrWU.js";
+import { _ as n } from "./index-B_H6BPK_.js";
 const a = {
   name: "Iframe",
   mixins: [r]

package/dist/{MultiFlatmap-CCvlF-pw.js → MultiFlatmap-DuKi1y2A.js}

@@ -1,6 +1,6 @@
-import { _ as u, i as h, a as y, g, E as r, t as M, T as p } from "./index-DkVmhrWU.js";
-import { C as v } from "./ContentMixin-BTZsoldP.js";
-import { D as I, F as C } from "./style-CDBCHm5P.js";
+import { _ as u, b as h, a as y, g, E as r, t as M, T as p } from "./index-B_H6BPK_.js";
+import { C as v } from "./ContentMixin-B9DtqhYT.js";
+import { D as I, T as C } from "./style-Bt2YbWCx.js";
 import { resolveComponent as f, openBlock as c, createElementBlock as S, createVNode as F, createBlock as k, createCommentVNode as w } from "vue";
 const b = '<svg width="72px" height="72px" viewBox="0 0 24 24" fill="yellow"><path d="M11.0748 3.25583C11.4141 2.42845 12.5859 2.42845 12.9252 3.25583L14.6493 7.45955C14.793 7.80979 15.1221 8.04889 15.4995 8.07727L20.0303 8.41798C20.922 8.48504 21.2841 9.59942 20.6021 10.1778L17.1369 13.1166C16.8482 13.3614 16.7225 13.7483 16.8122 14.1161L17.8882 18.5304C18.1 19.3992 17.152 20.0879 16.3912 19.618L12.5255 17.2305C12.2034 17.0316 11.7966 17.0316 11.4745 17.2305L7.60881 19.618C6.84796 20.0879 5.90001 19.3992 6.1118 18.5304L7.18785 14.1161C7.2775 13.7483 7.1518 13.3614 6.86309 13.1166L3.3979 10.1778C2.71588 9.59942 3.07796 8.48504 3.96971 8.41798L8.50046 8.07727C8.87794 8.04889 9.20704 7.80979 9.35068 7.45955L11.0748 3.25583Z" stroke="#000000" stroke-width="2"/></svg>', d = (e) => {
   const t = [
@@ -283,12 +283,17 @@ const b = '<svg width="72px" height="72px" viewBox="0 0 24 24" fill="yellow"><pa
           zoom: 4
         });
       }
+    }), r.on("show-reference-connectivities", (e) => {
+      if (this.flatmapReady && this.$refs.multiflatmap) {
+        const t = this.$refs.multiflatmap.getCurrentFlatmap();
+        t && t.showConnectivitiesByReference(e);
+      }
     }), r.on("connectivity-component-click", (e) => {
       this.showConnectivityTooltips(e);
     }), r.on("markerUpdate", () => {
       this.flatmapReady && this.flatmapMarkerUpdate(this.$refs.multiflatmap.getCurrentFlatmap().mapImp);
     }), r.on("hoverUpdate", () => {
-      this.flatmapReady && this.mapHoverHighlight(this.$refs.multiflatmap.getCurrentFlatmap().mapImp);
+      this.flatmapReady && this.mapHoverHighlight();
     });
   }
 }, H = { class: "viewer-container" };
@@ -341,7 +346,7 @@ function L(e, t, a, n, o, i) {
     }, null, 8, ["multiflatmapRef", "lastItem", "onShowNext", "onFinishHelpMode"])) : w("", !0)
   ]);
 }
-const T = /* @__PURE__ */ u(R, [["render", L], ["__scopeId", "data-v-f3105a40"]]);
+const A = /* @__PURE__ */ u(R, [["render", L], ["__scopeId", "data-v-4f713fcd"]]);
 export {
-  T as default
+  A as default
 };

package/dist/{Plot-DcgcIWVY.js → Plot-3jlnqIiS.js}

@@ -1,7 +1,7 @@
 import { PlotVuer as o } from "@abi-software/plotvuer";
-import { C as r } from "./ContentMixin-BTZsoldP.js";
+import { C as r } from "./ContentMixin-B9DtqhYT.js";
 import { resolveComponent as a, openBlock as n, createBlock as s } from "vue";
-import { _ as m } from "./index-DkVmhrWU.js";
+import { _ as m } from "./index-B_H6BPK_.js";
 const p = {
   name: "Plot",
   mixins: [r],