@abi-software/flatmapvuer 0.3.5 → 0.3.6

package/package-lock.json

@@ -1,19 +1,18 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "0.3.2",
+  "version": "0.3.3",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
     "@abi-software/flatmap-viewer": {
-      "version": "2.2.1-beta.8",
-      "resolved": "https://registry.npmjs.org/@abi-software/flatmap-viewer/-/flatmap-viewer-2.2.1-beta.8.tgz",
-      "integrity": "sha512-oMGQW2V7JvuA84HtO8EyQZcimMD5g+8WA3Myvq636q6dQw4v7QdMRu9jdj9WdcwuIViVvOpOEGuqowSn8GzZzw==",
+      "version": "2.2.0-beta.16",
+      "resolved": "https://registry.npmjs.org/@abi-software/flatmap-viewer/-/flatmap-viewer-2.2.0-beta.16.tgz",
+      "integrity": "sha512-1Eu4IRJFcQANNBuNK/kRVyzP8kRz+FXulPZKoWS62Mvf2B9D1YjmqQ1+ldO5bbCxZiwH5xhH4AGOFi2KJ54lkQ==",
       "requires": {
         "@babel/runtime": "^7.10.4",
         "@turf/area": "^6.0.1",
         "@turf/bbox": "^6.0.1",
         "@turf/helpers": "^6.1.4",
-        "bezier-js": "^6.1.0",
         "maplibre-gl": ">=1.15.3",
         "minisearch": "^2.2.1",
         "polylabel": "^1.1.0"
@@ -3081,11 +3080,6 @@
         "tweetnacl": "^0.14.3"
       }
     },
-    "bezier-js": {
-      "version": "6.1.0",
-      "resolved": "https://registry.npmjs.org/bezier-js/-/bezier-js-6.1.0.tgz",
-      "integrity": "sha512-oc8fkHqG0R+dQuNiXVbPMB0cc8iDqkLAjbA2gq26QmV8tZqW9GGI7iNEX1ioRWlZperQS7v5BX03+9FLVWZbSw=="
-    },
     "bfj": {
       "version": "6.1.2",
       "resolved": "https://registry.npmjs.org/bfj/-/bfj-6.1.2.tgz",
@@ -6581,16 +6575,6 @@
       "integrity": "sha1-jFoUlNIGbFcMw7/kSWF1rMTVAqs=",
       "dev": true
     },
-    "global-prefix": {
-      "version": "3.0.0",
-      "resolved": "https://registry.npmjs.org/global-prefix/-/global-prefix-3.0.0.tgz",
-      "integrity": "sha512-awConJSVCHVGND6x3tmMaKcQvwXLhjdkmomy2W+Goaui8YPgYgXJZewhg3fWC+DlfqqQuWg8AwqjGTD2nAPVWg==",
-      "requires": {
-        "ini": "^1.3.5",
-        "kind-of": "^6.0.2",
-        "which": "^1.3.1"
-      }
-    },
     "globals": {
       "version": "11.12.0",
       "resolved": "https://registry.npmjs.org/globals/-/globals-11.12.0.tgz",
@@ -7264,11 +7248,6 @@
       "integrity": "sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ==",
       "dev": true
     },
-    "ini": {
-      "version": "1.3.8",
-      "resolved": "https://registry.npmjs.org/ini/-/ini-1.3.8.tgz",
-      "integrity": "sha512-JV/yugV2uzW5iMRSiZAyDtQd+nxtUnjeLt0acNdw98kKLrvuRVyB80tsREOE7yvGVgalhZ6RNXCmEHkUKBKxew=="
-    },
     "inquirer": {
       "version": "7.3.3",
       "resolved": "https://registry.npmjs.org/inquirer/-/inquirer-7.3.3.tgz",
@@ -7762,7 +7741,8 @@
     "isexe": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/isexe/-/isexe-2.0.0.tgz",
-      "integrity": "sha1-6PvzdNxVb/iUehDcsFctYz8s+hA="
+      "integrity": "sha1-6PvzdNxVb/iUehDcsFctYz8s+hA=",
+      "dev": true
     },
     "isobject": {
       "version": "3.0.1",
@@ -7915,7 +7895,8 @@
     "kind-of": {
       "version": "6.0.3",
       "resolved": "https://registry.npmjs.org/kind-of/-/kind-of-6.0.3.tgz",
-      "integrity": "sha512-dcS1ul+9tmeD95T+x28/ehLgd9mENa3LsvDTtzm3vyBEO7RPptvAD+t44WVXaUjTBRcrpFeFlC8WCruUR456hw=="
+      "integrity": "sha512-dcS1ul+9tmeD95T+x28/ehLgd9mENa3LsvDTtzm3vyBEO7RPptvAD+t44WVXaUjTBRcrpFeFlC8WCruUR456hw==",
+      "dev": true
     },
     "launch-editor": {
       "version": "2.2.1",
@@ -8193,32 +8174,31 @@
       }
     },
     "maplibre-gl": {
-      "version": "2.4.0",
-      "resolved": "https://registry.npmjs.org/maplibre-gl/-/maplibre-gl-2.4.0.tgz",
-      "integrity": "sha512-csNFylzntPmHWidczfgCZpvbTSmhaWvLRj9e1ezUDBEPizGgshgm3ea1T5TCNEEBq0roauu7BPuRZjA3wO4KqA==",
+      "version": "2.1.9",
+      "resolved": "https://registry.npmjs.org/maplibre-gl/-/maplibre-gl-2.1.9.tgz",
+      "integrity": "sha512-pnWJmILeZpgA5QSI7K7xFK3yrkyYTd9srw3fCi2Ca52Phm78hsznPwUErEQcZLfxXKn/1h9t8IPdj0TH0NBNbg==",
       "requires": {
-        "@mapbox/geojson-rewind": "^0.5.2",
+        "@mapbox/geojson-rewind": "^0.5.1",
         "@mapbox/jsonlint-lines-primitives": "^2.0.2",
         "@mapbox/mapbox-gl-supported": "^2.0.1",
         "@mapbox/point-geometry": "^0.1.0",
-        "@mapbox/tiny-sdf": "^2.0.5",
+        "@mapbox/tiny-sdf": "^2.0.4",
         "@mapbox/unitbezier": "^0.0.1",
         "@mapbox/vector-tile": "^1.3.1",
         "@mapbox/whoots-js": "^3.1.0",
-        "@types/geojson": "^7946.0.10",
+        "@types/geojson": "^7946.0.8",
         "@types/mapbox__point-geometry": "^0.1.2",
         "@types/mapbox__vector-tile": "^1.3.0",
         "@types/pbf": "^3.0.2",
         "csscolorparser": "~1.0.3",
-        "earcut": "^2.2.4",
+        "earcut": "^2.2.3",
         "geojson-vt": "^3.2.1",
         "gl-matrix": "^3.4.3",
-        "global-prefix": "^3.0.0",
         "murmurhash-js": "^1.0.0",
         "pbf": "^3.2.1",
         "potpack": "^1.0.2",
         "quickselect": "^2.0.0",
-        "supercluster": "^7.1.5",
+        "supercluster": "^7.1.4",
         "tinyqueue": "^2.0.3",
         "vt-pbf": "^3.1.3"
       }
@@ -13679,6 +13659,7 @@
       "version": "1.3.1",
       "resolved": "https://registry.npmjs.org/which/-/which-1.3.1.tgz",
       "integrity": "sha512-HxJdYWq1MTIQbJ3nw0cqssHoTNU267KlrDuGZ1WYlxDStUtKUhOaJmh112/TZmHxxUfuJqPXSOm7tDyas0OSIQ==",
+      "dev": true,
       "requires": {
         "isexe": "^2.0.0"
       }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmapvuer",
-  "version": "0.3.5",
+  "version": "0.3.6",
   "main": "./dist/flatmapvuer.common.js",
   "files": [
     "dist/*",
@@ -10,14 +10,13 @@
     "*.js"
   ],
   "scripts": {
-    "start": "vue-cli-service serve",
     "serve": "vue-cli-service serve --port 8082",
     "build": "vue-cli-service build --dest test_html --mode staging",
     "build-bundle": "vue-cli-service build --target lib --name flatmapvuer ./src/components/index.js",
     "lint": "vue-cli-service lint"
   },
   "dependencies": {
-    "@abi-software/flatmap-viewer": "^2.2.1-beta.8",
+    "@abi-software/flatmap-viewer": "^2.2.0-beta.16",
     "@abi-software/svg-sprite": "^0.1.14",
     "core-js": "^3.3.2",
     "css-element-queries": "^1.2.2",

package/src/App.vue

@@ -91,8 +91,8 @@ export default {
       displayCloseButton: false,
       initial: "Rat",
       helpMode: false,
-      //flatmapAPI: "https://mapcore-demo.org/current/flatmap/v2/"
-      flatmapAPI: "https://mapcore-demo.org/devel/flatmap/v3/"
+      flatmapAPI: "https://mapcore-demo.org/current/flatmap/v2/"
+      // flatmapAPI: "https://mapcore-demo.org/devel/flatmap/v3/"
       // flatmapAPI: "https://mapcore-demo.org/fccb/flatmap/"
       // flatmapAPI: "https://mapcore-demo.org/devel/flatmap/v1/"
     }

package/src/components/Tooltip.vue

@@ -28,7 +28,6 @@
           </div>
           <div v-for="origin in origins" class="attribute-content"  :key="origin">
             {{ capitalise(origin) }}
-            <div class="seperator"></div>
           </div>
           <el-button v-show="originsWithDatasets.length > 0" class="button" @click="openDendrites">
             Explore origin data
@@ -38,7 +37,6 @@
           <div class="attribute-title">Components</div>
           <div v-for="component in components" class="attribute-content"  :key="component">
             {{ capitalise(component) }}
-            <div class="seperator"></div>
           </div>
         </div>
         <div v-if="this.destinations" class="block">
@@ -58,7 +56,6 @@
           </div>
           <div v-for="destination in destinations" class="attribute-content"  :key="destination">
             {{ capitalise(destination) }}
-            <div class="seperator"></div>
           </div>
           <el-button v-show="destinationsWithDatasets.length > 0" class="button" @click="openAxons">
             Explore destination data
@@ -112,12 +109,6 @@ const titleCase = (str) => {
   return str.replace(/\w\S*/g, (t) => { return t.charAt(0).toUpperCase() + t.substr(1).toLowerCase() });
 }
 
-const inArray = function(ar1, ar2){
-    let as1 = JSON.stringify(ar1)
-    let as2 = JSON.stringify(ar2)
-    return as1.indexOf(as2) !== -1
-}
-
 const capitalise = function(str){
   if (str)
     return str.charAt(0).toUpperCase() + str.slice(1)
@@ -204,32 +195,6 @@ export default {
     pubmedSearchUrlUpdate: function (val){
       this.pubmedSearchUrl = val
     },
-    findAllIdsFromConnectivity(connectivity){
-      let dnodes = connectivity.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 [... new Set(found.flat())]
-    },
-    flattenConntectivity(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()
-    },
     findComponents: function(connectivity){
       let dnodes = connectivity.connectivity.flat() // get nodes from edgelist
       let nodes = [...new Set(dnodes)] // remove duplicates
@@ -237,20 +202,26 @@ export default {
       let found = []
       let terminal = false
       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)){
-          terminal = true
-        }
-        if(inArray(connectivity.dendrites, node)){
-          terminal = true
-        }
-        if (!terminal){
-          found.push(node)
-        }
+          let n = node.flat() // Find all terms on the 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)
+          n.forEach(s=>{
+              if(connectivity.axons.includes(s)){
+                  terminal = true
+              }
+              if(connectivity.dendrites.includes(s)){
+                  terminal = true
+              }
+          })
+          if (!terminal){
+            found.push(node)
+          }
       })
 
-      return found
+      // remove duplicates
+      let foundUnique = [...new Set(found.map(n=>n[0]))]
+      return foundUnique
     },
     getOrganCuries: function(){
       fetch(`${this.sparcAPI}get-organ-curies/`)
@@ -305,29 +276,6 @@ export default {
           })
       })
     },
-    createComponentsLabelList: function(components, lookUp){
-      let labelList = []
-      components.forEach(n=>{
-        labelList.push(this.createLabelFromNeuralNode(n[0]), lookUp)
-        if (n.length === 2){
-          labelList.push(this.createLabelFromNeuralNode(n[1]), lookUp)
-        }
-      })
-      return labelList
-    },
-    createLabelFromNeuralNode: function(node, lookUp){
-      let label = lookUp[node[0]]
-      if (node.length === 2 && node[1].length > 0){
-        node[1].forEach(n=>{
-          if (lookUp[n] == undefined){
-            label += `, ${n}` 
-          } else {
-            label += `, ${lookUp[n]}`
-          }
-        })
-      }
-      return label
-    },
     pathwayQuery: function(keastIds){
       this.destinations = []
       this.origins = []
@@ -345,30 +293,20 @@ export default {
       .then(response => response.json())
       .then(data => {
         let connectivity = JSON.parse(data.values[0][0])
-        
-        // Filter the origin and destinations from components
         let components = this.findComponents(connectivity)
 
-        // process the nodes for finding datasets
-        let componentsFlat = this.flattenConntectivity(components)
-        let axons = connectivity.axons
-        let dendrites = connectivity.dendrites
-        let axonsFlat = this.flattenConntectivity(axons)
-        let dendritesFlat = this.flattenConntectivity(dendrites)
-
-        let conIds = this.findAllIdsFromConnectivity(connectivity)  // Create list of ids to get labels for
-
-        // Create readable labels from the nodes. Setting this to 'this.origins' updates the display
+        // Create list of ids to get labels for
+        let conIds = connectivity.axons.concat(connectivity.dendrites.concat(components))
         this.createLabelLookup(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.destinations = connectivity.axons.map(a=>lookUp[a])
+          this.origins = connectivity.dendrites.map(d=>lookUp[d])
+          this.components = components.map(c=>lookUp[c])
         })
 
         // 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 => connectivity.axons.indexOf(ub.id) !== -1)
+        this.originsWithDatasets = this.uberons.filter(ub => connectivity.dendrites.indexOf(ub.id) !== -1)
+        this.componentsWithDatasets = this.uberons.filter(ub => connectivity.dendrites.indexOf(ub.id) !== -1)
         this.loading = false
       })
       .catch((error) => {
@@ -441,12 +379,6 @@ export default {
   margin-left: 8px;
 }
 
-.seperator {
-  width:90%;
-  height:0.5px;
-  background-color:#bfbec2;
-}
-
 .main {
   font-size: 14px;
   text-align: left;