@abi-software/mapintegratedvuer 1.8.0-beta.1 → 1.8.0-isan.2

package/src/mixins/ContentMixin.js

@@ -9,6 +9,9 @@ import { useSettingsStore } from '../stores/settings';
 import { useSplitFlowStore } from '../stores/splitFlow';
 import Tagging from '../services/tagging.js';
 
+import { FlatmapQueries } from "@abi-software/flatmapvuer/src/services/flatmapQueries.js";
+import { getKnowledgeSource, loadAndStoreKnowledge } from "@abi-software/flatmapvuer/src/services/flatmapKnowledge.js";
+
 function capitalise(text) {
   return text[0].toUpperCase() + text.substring(1)
 }
@@ -73,8 +76,6 @@ export default {
         EventBus.emit("OpenNewMap", type);
         this.trackOpenMap(`open_new_${type}_map`);
       }
-
-      this.onConnectivityInfoClose();
     },
     onMapmanagerLoaded: function (mapManager) {
       this.settingsStore.updateMapManager(mapManager);
@@ -107,42 +108,37 @@ export default {
     /**
      * Callback when the vuers emit a selected event.
      */
-    resourceSelected: function (type, resource) {
+    resourceSelected: function (type, resources) {
+      const resource = resources[0]
       // Skip processing if resources already has actions
-      if (this.resourceHasAction(resource)) {
+      if (resource && this.resourceHasAction(resource)) {
         EventBus.emit("PopoverActionClick", resource);
         return;
       }
-
       let returnedAction = undefined;
       let action = "none";
       let fireResourceSelected = false;
       const result = {
         paneIndex: this.entry.id,
         type: type,
-        resource: resource,
+        resource: resources,
         internalName: undefined,
         eventType: undefined,
       };
-
-
       if (type == "MultiFlatmap" || type == "Flatmap") {
-        result.internalName = resource?.feature?.label ? resource.feature.label : this.idNamePair[resource.feature.models];
+        const flatmapImp = this.getFlatmapImp();
+        result.internalName = resource?.feature?.label ?
+          resource.feature.label : this.idNamePair[resource.feature.models];
         if (resource.eventType == "click") {
           result.eventType = "selected";
           if (resource.feature.type == "marker") {
+
             let label = result.internalName;
-            if (
-              this.settingsStore.isFeaturedMarkerIdentifier(
-                resource.feature.id
-              )
-            ) {
+            if (this.settingsStore.isFeaturedMarkerIdentifier(resource.feature.id)) {
               // It is a featured dataset search for DOI.
               returnedAction = {
                 type: "Search",
-                term: this.settingsStore.featuredMarkerDoi(
-                  resource.feature.id
-                ),
+                term: this.settingsStore.featuredMarkerDoi(resource.feature.id),
                 featuredDataset: true,
               };
             } else {
@@ -151,17 +147,43 @@ export default {
                 type: "Facet",
                 facet: label,
                 facetPropPath: "anatomy.organ.category.name",
+                facetSubPropPath: "anatomy.organ.name",
                 term: "Anatomical structure",
               };
+              let labels = new Set();
+              if (resource?.feature['marker-terms']) {
+                if(resource.feature['marker-terms'].length > 0) {
+                  resource.feature['marker-terms'].forEach((term) => {
+                    labels.add(term.label)
+                  });
+                  labels.add(label)
+                  if (labels.size > 0) {
+                    returnedAction = {
+                      type: "Facets",
+                      labels: [...labels],
+                    };
+                  }
+                } else if (resource?.feature?.models) {
+                  returnedAction = {
+                    type: "PMRSearch",
+                    term: resource.feature.models,
+                  };
+                }
+              }
             }
-
             fireResourceSelected = true;
             if (type == "MultiFlatmap") {
-              const flatmap =
-                this.$refs.multiflatmap.getCurrentFlatmap().mapImp;
-              flatmap.clearSearchResults();
+              flatmapImp.clearSearchResults();
             }
           } else if (resource.feature.type == "feature") {
+            if (flatmapImp.options && flatmapImp.options.style === 'functional') {
+              if (resource.feature?.hyperlinks?.pmr) {
+                returnedAction = {
+                  type: "URL",
+                  resource: resource.feature?.hyperlinks?.pmr,
+                };
+              }
+            }
             // Do no open scaffold in sync map
             if (this.syncMode) {
               fireResourceSelected = true;
@@ -174,16 +196,16 @@ export default {
           fireResourceSelected = true;
         }
       } else if (type == "Scaffold") {
-        if (resource && resource[0]) {
-          if (resource[0].data?.id === undefined || resource[0].data?.id === "") {
-            resource[0].data.id = resource[0].data?.group;
+        if (resource) {
+          if (resource.data?.id === undefined || resource.data?.id === "") {
+            resource.data.id = resource.data?.group;
           }
-          result.internalName = resource[0].data.id;
+          result.internalName = resource.data.id;
           // Facet search if marker is clicked
-          if (resource[0].data.lastActionOnMarker === true) {
+          if (resource.data.lastActionOnMarker === true) {
             returnedAction = {
               type: "Facet",
-              facet: capitalise(resource[0].data.id),
+              facet: capitalise(resource.data.id),
               facetPropPath: "anatomy.organ.category.name",
               term: "Anatomical structure",
             };
@@ -248,7 +270,7 @@ export default {
             return fetch(`${this.apiLocation}get-related-terms/${id}`)
               .then(response => response.json())
               .then(data => {
-                if (data.uberon.array.length > 0) {
+                if (data.uberon?.array.length > 0) {
                   name =
                     data.uberon.array[0].name.charAt(0).toUpperCase() +
                     data.uberon.array[0].name.slice(1);
@@ -458,75 +480,64 @@ export default {
         this.endHelp();
       }
     },
-    getConnectivitiesByDOI: async function (hoverDOI) {
-      const currentFlatmap = this.$refs.multiflatmap.getCurrentFlatmap();
-      const response = await currentFlatmap.searchConnectivitiesByReference(hoverDOI);
-      return response;
-    },
-    highlightAnatomies: async function (mapImp, hoverAnatomies, hoverDOI) {
-      const itemsToHighlight = [...hoverAnatomies];
-      const hoverHighlightOptions = this.settingsStore.hoverHighlightOptions;
+    flatmapHighlight: async function (flatmap, hoverAnatomies, hoverDOI, hoverConnectivity) {
+      let toHighlight = [...hoverAnatomies, ...hoverConnectivity];
+      const globalSettings = this.settingsStore.globalSettings;
+      
 
       // to highlight connected paths
-      if (hoverHighlightOptions.highlightConnectedPaths) {
-        const connectionsFromFeatures = await mapImp.queryPathsForFeatures(hoverAnatomies);
-        if (connectionsFromFeatures) {
-          itemsToHighlight.push(...connectionsFromFeatures);
+      if (globalSettings.highlightConnectedPaths) {
+        const hoverEntry = hoverAnatomies.length ? hoverAnatomies :
+          hoverConnectivity.length ? hoverConnectivity :
+            []
+        const connectedPaths = await flatmap.retrieveConnectedPaths(hoverEntry);
+        if (connectedPaths) {
+          toHighlight.push(...connectedPaths);
         }
       }
 
       // to highlight related paths from reference DOI
-      if (hoverHighlightOptions.highlightDOIPaths) {
-        const connectionsFromDOI = await this.getConnectivitiesByDOI(hoverDOI);
+      if (globalSettings.highlightDOIPaths) {
+        const connectionsFromDOI = await flatmap.searchConnectivitiesByReference(hoverDOI);
         if (connectionsFromDOI) {
-          itemsToHighlight.push(...connectionsFromDOI);
+          toHighlight.push(...connectionsFromDOI);
         }
       }
-
-      return itemsToHighlight;
+      toHighlight = [...new Set(toHighlight)];
+      return toHighlight;
     },
-    mapHoverHighlight: function () {
+    cardHoverHighlight: function () {
       if (this.visible) {
         const hoverAnatomies = this.settingsStore.hoverAnatomies;
         const hoverOrgans = this.settingsStore.hoverOrgans;
         const hoverDOI = this.settingsStore.hoverDOI;
-        let mapImp = null;
-        let scaffold = null;
-
-        if (this.flatmapRef) {
-          mapImp = this.$refs.flatmap.mapImp;
-        }
+        const hoverConnectivity = this.settingsStore.hoverConnectivity;
 
-        if (this.multiflatmapRef) {
-          mapImp = this.$refs.multiflatmap.getCurrentFlatmap().mapImp;
-        }
-
-        if (this.scaffoldRef) {
-          scaffold = this.$refs.scaffold;
-        }
+        let flatmap = null;
+        let scaffold = null;
+        if (this.flatmapRef) flatmap = this.$flatmapRef;
+        if (this.multiflatmapRef) flatmap = this.$multiflatmapRef;
+        if (this.scaffoldRef) scaffold = this.$scaffoldRef;
 
         // reset
-        if (mapImp) {
-          mapImp.clearSearchResults();
+        if ((this.multiflatmapRef || this.flatmapRef) && flatmap) {
+          flatmap.mapImp.clearSearchResults();
+        } else if (this.scaffoldRef && scaffold) {
+          scaffold.changeHighlightedByName(hoverOrgans, "", false);
         }
 
-        if (hoverAnatomies.length || hoverOrgans.length) {
-          clearTimeout(this.hoverDelay);
-          if (this.multiflatmapRef || this.flatmapRef) {
-            this.highlightAnatomies(mapImp, hoverAnatomies, hoverDOI).then((itemsToHighlight) => {
-              mapImp.selectFeatures(itemsToHighlight);
+        if (hoverAnatomies.length || hoverOrgans.length || hoverDOI || hoverConnectivity.length) {
+          if ((this.multiflatmapRef || this.flatmapRef) && flatmap) {
+            this.flatmapHighlight(flatmap, hoverAnatomies, hoverDOI, hoverConnectivity).then((paths) => {
+              try {
+                flatmap.zoomToFeatures(paths);
+              } catch (error) {
+                console.log(error)
+              }
             });
-          } else if (this.scaffoldRef) {
-            scaffold?.changeHighlightedByName(hoverOrgans, "", false);
+          } else if (this.scaffoldRef && scaffold) {
+            scaffold.changeHighlightedByName(hoverOrgans, "", false);
           }
-        } else {
-          this.hoverDelay = setTimeout(() => {
-            if (this.multiflatmapRef || this.flatmapRef) {
-              mapImp?.clearSearchResults();
-            } else if (this.scaffoldRef) {
-              scaffold?.changeHighlightedByName(hoverOrgans, "", false);
-            }
-          }, 500);
         }
       }
     },
@@ -539,12 +550,58 @@ export default {
     onConnectivityInfoOpen: function (connectivityInfoData) {
       EventBus.emit('connectivity-info-open', connectivityInfoData);
     },
-    onConnectivityInfoClose: function () {
-      EventBus.emit('connectivity-info-close');
-    },
     onConnectivityGraphError: function (errorInfo) {
       EventBus.emit('connectivity-graph-error', errorInfo);
     },
+    loadConnectivityKnowledge: async function (flatmap) {
+      const sckanVersion = getKnowledgeSource(flatmap);
+      const flatmapQueries = markRaw(new FlatmapQueries());
+      flatmapQueries.initialise(this.flatmapAPI);
+      const knowledge = await loadAndStoreKnowledge(flatmap, flatmapQueries);
+      this.connectivityKnowledge = knowledge.filter((item) => {
+        if (item.source === sckanVersion && item.connectivity?.length) return true;
+        return false;
+      });
+      EventBus.emit("connectivity-knowledge", this.connectivityKnowledge);
+    },
+    connectivityQueryFilter: async function (flatmap, payload) {
+      let results = this.connectivityKnowledge;
+      if (payload.type === "query-update") {
+        if (this.query !== payload.value) this.target = [];
+        this.query = payload.value;
+      } else if (payload.type === "filter-update") {
+        this.filter = payload.value;
+        this.target = [];
+      } else if (payload.type === "query-filter-update") {
+        this.query = payload.query;
+        this.filter = payload.filter;
+        this.target = payload.data;
+        // restore connectivity explorer content
+        if (!this.query) {
+          EventBus.emit("connectivity-knowledge", [...results]);
+        }
+        return;
+      }
+      if (this.query) {
+        let flag = "", order = [], suggestions = [], paths = [];
+        this.searchSuggestions(this.query, suggestions);
+        const labels = [...new Set(suggestions)];
+        flag = 'label';
+        order = labels;
+        if (labels.length === 1) {
+          const options = {
+            type: this.filter.map(f => f.facet.toLowerCase()),
+            target: this.target.map(d => d.id),
+          };
+          paths = await flatmap.retrieveConnectedPaths([this.query], options);
+          flag = 'id';
+          order = [this.query, ...paths.filter(item => item !== this.query)];
+        }
+        results = results.filter(item => paths.includes(item.id) || labels.includes(item.label));
+        results.sort((a, b) => order.indexOf(a[flag]) - order.indexOf(b[flag]));
+      }
+      EventBus.emit("connectivity-knowledge", results);
+    }
   },
   data: function () {
     return {
@@ -564,8 +621,11 @@ export default {
       scaffoldRef: null,
       scaffoldLoaded: false,
       isInHelp: false,
-      hoverDelay: undefined,
       mapManager: undefined,
+      connectivityKnowledge: [],
+      query: "",
+      filter: [],
+      target: [], // Support origins/components/destinations term search
     };
   },
   created: function () {

package/src/mixins/DynamicMarkerMixin.js

@@ -40,8 +40,9 @@ export default {
 
       if (flatmapImp) {
         // Set the dataset markers
-        let markers = this.settingsStore.globalSettings.displayMarker ? this.settingsStore.markers : [];
+        let markers = this.settingsStore.globalSettings.displayMarkers ? this.settingsStore.markers : [];
         markers = removeDuplicates(markers);
+        let multiMarkers = this.settingsStore.globalSettings.displayMarkers ? this.settingsStore.multiScaleMarkers : [];
         let fmMarkers = this.removeMarkersNotOnFlatmap(flatmapImp, markers);
         flatmapImp.clearMarkers();
         flatmapImp.clearDatasetMarkers();
@@ -54,6 +55,7 @@ export default {
         } else {
           flatmapImp.addDatasetMarkers(fmMarkers);
         }
+        flatmapImp.addMarkers(multiMarkers,{ className: "standard-marker" } );
 
         // Set the featured markers
         if (this.entry.type === "MultiFlatmap") {

package/src/stores/settings.js

@@ -11,6 +11,7 @@ export const useSettingsStore = defineStore('settings', {
       algoliaKey: undefined,
       algoliaId: undefined,
       pennsieveApi: undefined,
+      pmrHost: "https://models.physiomeproject.org/",
       flatmapAPI: undefined,
       nlLinkPrefix: undefined,
       mapManager: undefined,
@@ -18,9 +19,11 @@ export const useSettingsStore = defineStore('settings', {
       facets: { species: [], gender: [], organ: [] },
       numberOfDatasetsForFacets: [],
       markers: [],
+      multiScaleMarkers: ["cvs:functional.whole-body", "cvs:functional.tissue", "cvs:functional.cell"],
       hoverAnatomies: [],
       hoverOrgans: [],
       hoverDOI: '',
+      hoverConnectivity: [],
       featuredMarkers: [],
       featuredMarkerIdentifiers: [],
       featuredMarkerDois: [],
@@ -30,12 +33,11 @@ export const useSettingsStore = defineStore('settings', {
       useHelpModeDialog: false,
       connectivityInfoSidebar: true,
       annotationSidebar: true,
-      hoverHighlightOptions: {
-        highlightConnectedPaths: false,
-        highlightDOIPaths: false,
-      },
       globalSettings: {
-        displayMarker: true,
+        displayMarkers: true,
+        highlightConnectedPaths: false,
+        highlightDOIPaths: false, // comment out to hide in settings
+        interactiveMode: 'dataset', // dataset, connectivity, multiscale
       },
     }
   },
@@ -53,7 +55,7 @@ export const useSettingsStore = defineStore('settings', {
       let updatedSettings = [];
       for (const [key, value] of Object.entries(settings)) {
         const attribute = state.globalSettings[key];
-        if (!attribute || (attribute !== value)) {
+        if (attribute === undefined || (attribute !== value)) {
           updatedSettings.push(key);
         }
       }
@@ -91,13 +93,17 @@ export const useSettingsStore = defineStore('settings', {
     updateRootUrl(rootUrl) {
       this.rootUrl = rootUrl;
     },
+    updatePmrHost(pmrHost) {
+      this.pmrHost = pmrHost ? pmrHost : "https://models.physiomeproject.org/";
+    },
     updateMarkers(markers) {
       this.markers = markers;
     },
-    updateHoverFeatures(anatomies, organs, doi) {
+    updateHoverFeatures(anatomies, organs, doi, connectivity) {
       this.hoverAnatomies = anatomies;
       this.hoverOrgans = organs;
       this.hoverDOI = doi;
+      this.hoverConnectivity = connectivity;
     },
     updateFeatured(datasetIdentifiers) {
       this.featuredMarkerIdentifiers = new Array(datasetIdentifiers.length);
@@ -181,9 +187,6 @@ export const useSettingsStore = defineStore('settings', {
     updateAnnotationSidebar(annotationSidebar) {
       this.annotationSidebar = annotationSidebar;
     },
-    updateHoverHighlightOptions(hoverHighlightOptions) {
-      this.hoverHighlightOptions = hoverHighlightOptions;
-    },
     updateGlobalSettings(globalSettings) {
       for (const [key, value] of Object.entries(globalSettings)) {
         this.globalSettings[key] = value;