@abi-software/flatmapvuer 1.8.2-beta.0 → 1.8.3-beta.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "1.8.2-beta.0",
+  "version": "1.8.3-beta.0",
   "license": "Apache-2.0",
   "files": [
     "dist/*",
@@ -44,7 +44,7 @@
   },
   "dependencies": {
     "@abi-software/flatmap-viewer": "3.2.13",
-    "@abi-software/map-utilities": "^1.4.0",
+    "@abi-software/map-utilities": "^1.4.3-beta.0",
     "@abi-software/sparc-annotation": "0.3.2",
     "@abi-software/svg-sprite": "^1.0.1",
     "@element-plus/icons-vue": "^2.3.1",

package/src/App.vue

@@ -283,6 +283,10 @@ export default {
           taxo: 'FunctionalConnectivity',
           displayWarning: true,
         },
+        Test: {
+          "taxo": "NCBITaxon:1",
+          "displayWarning": true
+        },
       },
       tooltipContent: undefined,
       tStyle: {

package/src/components/FlatmapVuer.vue

@@ -589,6 +589,7 @@ Please use `const` to assign meaningful names to them...
         :tooltipEntry="tooltipEntry"
         :annotationDisplay="viewingMode === 'Annotation'"
         @annotation="commitAnnotationEvent"
+        @onActionClick="onActionClick"
       />
     </div>
   </div>
@@ -638,6 +639,7 @@ import { mapState } from 'pinia'
 import { useMainStore } from '@/store/index'
 import { DrawToolbar, Tooltip, TreeControls } from '@abi-software/map-utilities'
 import '@abi-software/map-utilities/dist/style.css'
+import EventBus from './EventBus.js'
 
 const ERROR_MESSAGE = 'cannot be found on the map.';
 
@@ -1882,6 +1884,14 @@ export default {
         }
       });
     },
+    changeConnectivitySource: function (payload) {
+      const { featureId, connectivitySource } = payload;
+      const newwPromise = this.flatmapQueries.queryForConnectivityNew(this.mapImp, featureId, null, connectivitySource);
+      Promise.resolve(newwPromise).then((result) => {
+        this.tooltipEntry = this.flatmapQueries.updateTooltipData(this.tooltipEntry);
+        this.$emit('connectivity-info-open', this.tooltipEntry);
+      })
+    },
     /**
      * @public
      * Function to create/display tooltips from the provided ``data``.
@@ -2203,6 +2213,10 @@ export default {
         // Get connectivity knowledge source | SCKAN release
         if (this.mapImp.provenance?.connectivity) {
           this.tooltipEntry['knowledge-source'] = getKnowledgeSource(this.mapImp);
+
+          // Map id and uuid to load connectivity information from the map
+          this.tooltipEntry['mapId'] = this.mapImp.provenance.id;
+          this.tooltipEntry['mapuuid'] = this.mapImp.provenance.uuid;
         }
         this.$emit('connectivity-info-open', this.tooltipEntry);
       }
@@ -2688,6 +2702,7 @@ export default {
                   provenanceTaxonomy: feature.taxons,
                 }
                 if (this.viewingMode === "Exploration" || this.viewingMode === "Annotation") {
+                  this.featuresAlert = feature.alert
                   this.checkAndCreatePopups(data)
                 } else if (this.viewingMode === 'Neuron Connection') {
                   setTimeout(() => {
@@ -2717,6 +2732,9 @@ export default {
       if (this.mapImp) return this.mapImp.search(term)
       return []
     },
+    onActionClick: function (data) {
+      EventBus.emit('onActionClick', data)
+    },
   },
   props: {
     /**

package/src/services/flatmapKnowledge.js

@@ -46,12 +46,14 @@ function loadAndStoreKnowledge(mapImp, flatmapQueries) {
     where source="${knowledgeSource}"
     order by source desc`;
   const flatmapKnowledge = sessionStorage.getItem('flatmap-knowledge');
+  const flatmapKnowledgeSource = sessionStorage.getItem('flatmap-knowledge-source');
 
-  if (!flatmapKnowledge) {
+  if (!flatmapKnowledge || flatmapKnowledgeSource !== knowledgeSource) {
     flatmapQueries.flatmapQuery(sql).then((response) => {
       const mappedData = response.values.map(x => x[0]);
       const parsedData = mappedData.map(x => JSON.parse(x));
       sessionStorage.setItem('flatmap-knowledge', JSON.stringify(parsedData));
+      sessionStorage.setItem('flatmap-knowledge-source', knowledgeSource);
       updateFlatmapKnowledgeCache();
     });
   }
@@ -69,6 +71,7 @@ function removeFlatmapKnowledgeCache() {
   const keys = [
     'flatmap-knowledge',
     'flatmap-knowledge-expiry',
+    'flatmap-knowledge-source',
   ];
   keys.forEach((key) => {
     sessionStorage.removeItem(key);

package/src/services/flatmapQueries.js

@@ -125,6 +125,18 @@ let FlatmapQueries = function () {
     return tooltipData
   }
 
+  this.updateTooltipData = function (tooltipEntry) {
+    return {
+      ...tooltipEntry,
+      origins: this.origins,
+      originsWithDatasets: this.originsWithDatasets,
+      components: this.components,
+      componentsWithDatasets: this.componentsWithDatasets,
+      destinations: this.destinations,
+      destinationsWithDatasets: this.destinationsWithDatasets,
+    };
+  }
+
   this.createComponentsLabelList = function (components, lookUp) {
     let labelList = []
     components.forEach((n) => {
@@ -207,7 +219,7 @@ let FlatmapQueries = function () {
     return found.flat()
   }
 
-  this.findComponents = function (connectivity, axons, dendrites) {
+  this.findComponents = function (connectivity, axons, dendrites, somas) {
     let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
     let nodes = removeDuplicates(dnodes)
 
@@ -219,6 +231,9 @@ let FlatmapQueries = function () {
       if (inArray(axons, node)) {
         terminal = true
       }
+      if (somas && inArray(somas, node)) {
+        terminal = true
+      }
       if (inArray(dendrites, node)) {
         terminal = true
       }
@@ -245,14 +260,22 @@ let FlatmapQueries = function () {
     this.rawURLs = []
     if (!keastIds || keastIds.length == 0 || !keastIds[0]) return
 
-    let prom1 = this.queryForConnectivityNew(mapImp, keastIds, signal) // This on returns a promise so dont need 'await'
+    // set connectivity source if available
+    const connectivitySource = localStorage.getItem('connectivity-source');
+
+    let prom1 = this.queryForConnectivityNew(mapImp, keastIds, signal, connectivitySource) // This on returns a promise so dont need 'await'
     let results = await Promise.all([prom1])
     return results
   }
 
-  this.queryForConnectivityNew = function (mapImp, keastIds, signal, processConnectivity=true) {
+  this.queryForConnectivityNew = function (mapImp, keastIds, signal, connectivitySource, processConnectivity=true) {
     return new Promise((resolve) => {
-      mapImp.queryKnowledge(keastIds[0])
+      const mapuuid = mapImp.provenance.uuid;
+      const queryAPI = connectivitySource === 'map'
+                        ? this.queryMapConnectivity(mapuuid, keastIds[0])
+                        : mapImp.queryKnowledge(keastIds[0]);
+
+      queryAPI
         .then((response) => {
           if (this.checkConnectivityExists(response)) {
             let connectivity = response;
@@ -287,6 +310,21 @@ let FlatmapQueries = function () {
     })
   }
 
+  this.queryMapConnectivity = async function (mapuuid, pathId) {
+    const url = this.flatmapApi + `flatmap/${mapuuid}/connectivity/${pathId}`;
+
+    try {
+      const response = await fetch(url);
+      if (!response.ok) {
+        throw new Error(`Response status: ${response.status}`);
+      }
+
+      return await response.json();
+    } catch (error) {
+      throw new Error(error);
+    }
+  },
+
   this.queryForConnectivity = function (mapImp, keastIds, signal, processConnectivity=true) {
     const data = { sql: this.buildConnectivitySqlStatement(keastIds) }
     const headers = {
@@ -399,23 +437,35 @@ let FlatmapQueries = function () {
   }
 
   this.processConnectivity = function (mapImp, connectivity) {
-    const sourceKey = ["ilxtr:hasSomaLocatedIn"]
-    const destinationKey = ["ilxtr:hasAxonPresynapticElementIn", "ilxtr:hasAxonSensorySubcellularElementIn"]
-
     return new Promise((resolve) => {
       let dendrites = []
       let axons = []
+      let somas = undefined
+      if (connectivity && connectivity["node-phenotypes"]) {
+        const sourceKey = ["ilxtr:hasSomaLocatedIn"]
+        const destinationKey = ["ilxtr:hasAxonPresynapticElementIn", "ilxtr:hasAxonSensorySubcellularElementIn"]
+        sourceKey.forEach((key)=>{
+          dendrites.push(...connectivity["node-phenotypes"][key])
+        })
+        dendrites = removeDuplicates(dendrites)
+        destinationKey.forEach((key)=>{
+          axons.push(...connectivity["node-phenotypes"][key])
+        })
+        axons = removeDuplicates(axons)
+      } else {
+        // Remove duplicates
+        axons = removeDuplicates(connectivity.axons)
+        //Somas will become part of origins, support this for future proof
+        if (connectivity.somas && connectivity.somas.length > 0) {
+          dendrites.push(...connectivity.somas)
+        }
+        if (connectivity.dendrites && connectivity.dendrites.length > 0) {
+          dendrites.push(...connectivity.dendrites)
+        }
+        somas = connectivity.somas
+      }
 
-      sourceKey.forEach((key)=>{
-        dendrites.push(...connectivity["node-phenotypes"][key])
-      })
-      dendrites = removeDuplicates(dendrites)
-      destinationKey.forEach((key)=>{
-        axons.push(...connectivity["node-phenotypes"][key])
-      })
-      axons = removeDuplicates(axons)
-      const components = this.findComponents(connectivity, axons, dendrites)
-
+      const components = this.findComponents(connectivity, axons, dendrites, somas)
       // Create list of ids to get labels for
       const conIds = this.findAllIdsFromConnectivity(connectivity)
       // Create readable labels from the nodes. Setting this to 'this.origins' updates the display