@abi-software/flatmapvuer 1.8.1-beta.3 → 1.8.2-beta.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "1.8.1-beta.3",
+  "version": "1.8.2-beta.0",
   "license": "Apache-2.0",
   "files": [
     "dist/*",
@@ -44,7 +44,7 @@
   },
   "dependencies": {
     "@abi-software/flatmap-viewer": "3.2.13",
-    "@abi-software/map-utilities": "^1.4.1-beta.1",
+    "@abi-software/map-utilities": "^1.4.0",
     "@abi-software/sparc-annotation": "0.3.2",
     "@abi-software/svg-sprite": "^1.0.1",
     "@element-plus/icons-vue": "^2.3.1",

package/src/components/FlatmapVuer.vue

@@ -2203,10 +2203,6 @@ 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);
       }

package/src/services/flatmapQueries.js

@@ -193,7 +193,7 @@ let FlatmapQueries = function () {
     return [...new Set(found.flat())]
   }
 
-  this.flattenConntectivity = function (connectivity) {
+  this.flattenConnectivity = function (connectivity) {
     let dnodes = connectivity.flat() // get nodes from edgelist
     let nodes = [...new Set(dnodes)] // remove duplicates
     let found = []
@@ -207,7 +207,7 @@ let FlatmapQueries = function () {
     return found.flat()
   }
 
-  this.findComponents = function (connectivity) {
+  this.findComponents = function (connectivity, axons, dendrites) {
     let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
     let nodes = removeDuplicates(dnodes)
 
@@ -216,13 +216,10 @@ let FlatmapQueries = function () {
     nodes.forEach((node) => {
       terminal = false
       // Check if the node is an destination or origin (note that they are labelled dendrite and axon as opposed to origin and destination)
-      if (inArray(connectivity.axons, node)) {
+      if (inArray(axons, node)) {
         terminal = true
       }
-      if (connectivity.somas && inArray(connectivity.somas, node)) {
-        terminal = true
-      }
-      if (inArray(connectivity.dendrites, node)) {
+      if (inArray(dendrites, node)) {
         terminal = true
       }
       if (!terminal) {
@@ -383,86 +380,72 @@ let FlatmapQueries = function () {
     return label
   }
 
-  this.flattenAndFindDatasets = function (components, axons, dendrites) {
+  this.flattenAndFindDatasets = function (dendrites, components, axons) {
     // process the nodes for finding datasets (Note this is not critical to the tooltip, only for the 'search on components' button)
-    let componentsFlat = this.flattenConntectivity(components)
-    let axonsFlat = this.flattenConntectivity(axons)
-    let dendritesFlat = this.flattenConntectivity(dendrites)
+    let dendritesFlat = this.flattenConnectivity(dendrites)
+    let componentsFlat = this.flattenConnectivity(components)
+    let axonsFlat = this.flattenConnectivity(axons)
 
     // Filter for the anatomy which is annotated on datasets
-    this.destinationsWithDatasets = this.uberons.filter(
-      (ub) => axonsFlat.indexOf(ub.id) !== -1
-    )
     this.originsWithDatasets = this.uberons.filter(
       (ub) => dendritesFlat.indexOf(ub.id) !== -1
     )
     this.componentsWithDatasets = this.uberons.filter(
       (ub) => componentsFlat.indexOf(ub.id) !== -1
     )
+    this.destinationsWithDatasets = this.uberons.filter(
+      (ub) => axonsFlat.indexOf(ub.id) !== -1
+    )
   }
 
   this.processConnectivity = function (mapImp, connectivity) {
-    return new Promise((resolve) => {
-      // Filter the origin and destinations from components
-      let components = this.findComponents(connectivity)
+    const sourceKey = ["ilxtr:hasSomaLocatedIn"]
+    const destinationKey = ["ilxtr:hasAxonPresynapticElementIn", "ilxtr:hasAxonSensorySubcellularElementIn"]
 
-      // Remove duplicates
-      let axons = removeDuplicates(connectivity.axons)
-      //Somas will become part of origins, support this for future proof
+    return new Promise((resolve) => {
       let dendrites = []
-      if (connectivity.somas && connectivity.somas.length > 0) {
-        dendrites.push(...connectivity.somas)
-      }
-      if (connectivity.dendrites && connectivity.dendrites.length > 0) {
-        dendrites.push(...connectivity.dendrites)
-      }
+      let axons = []
+
+      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)
 
       // Create list of ids to get labels for
-      let conIds = this.findAllIdsFromConnectivity(connectivity)
-
+      const conIds = this.findAllIdsFromConnectivity(connectivity)
       // Create readable labels from the nodes. Setting this to 'this.origins' updates the display
       this.createLabelLookup(mapImp, conIds).then((lookUp) => {
-        this.destinations = axons.map((a) =>
-          this.createLabelFromNeuralNode(a, lookUp)
-        )
         this.origins = dendrites.map((d) =>
           this.createLabelFromNeuralNode(d, lookUp)
         )
         this.components = components.map((c) =>
           this.createLabelFromNeuralNode(c, lookUp)
         )
-        this.flattenAndFindDatasets(components, axons, dendrites)
+        this.destinations = axons.map((a) =>
+          this.createLabelFromNeuralNode(a, lookUp)
+        )
+        this.flattenAndFindDatasets(dendrites, components, axons)
         resolve({
           ids: {
-            axons: axons,
             dendrites: dendrites,
             components: components,
+            axons: axons,
           },
           labels: {
-            destinations: this.destinations,
             origins: this.origins,
             components: this.components,
+            destinations: this.destinations,
           }
         })
       })
     })
   }
 
-  this.flattenConntectivity = function (connectivity) {
-    let dnodes = connectivity.flat() // get nodes from edgelist
-    let nodes = [...new Set(dnodes)] // remove duplicates
-    let found = []
-    nodes.forEach((n) => {
-      if (Array.isArray(n)) {
-        found.push(n.flat())
-      } else {
-        found.push(n)
-      }
-    })
-    return found.flat()
-  }
-
   this.buildPubmedSqlStatement = function (keastIds) {
     let sql = 'select distinct publication from publications where entity in ('
     if (keastIds.length === 1) {