@abi-software/map-utilities 1.4.1-beta.0 → 1.4.2-beta.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-utilities",
-  "version": "1.4.1-beta.0",
+  "version": "1.4.2-beta.0",
   "files": [
     "dist/*",
     "src/*",

package/src/components/ConnectivityGraph/graph.js

@@ -25,6 +25,43 @@ import cytoscape from 'cytoscape'
 
 //==============================================================================
 
+const inArray = function (ar1, ar2) {
+    if (!ar1 || !ar2) return false
+    let as1 = JSON.stringify(ar1)
+    let as2 = JSON.stringify(ar2)
+    return as1.indexOf(as2) !== -1
+}
+
+const removeDuplicates = function (arrayOfAnything) {
+    if (!arrayOfAnything) return []
+    return [...new Set(arrayOfAnything.map((e) => JSON.stringify(e)))].map((e) =>
+      JSON.parse(e)
+    )
+}
+
+const findComponents = function (knowledge, axons, dendrites) {
+    let dnodes = knowledge.connectivity.flat() // get nodes from edgelist
+    let nodes = removeDuplicates(dnodes)
+
+    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(axons, node)) {
+        terminal = true
+      }
+      if (inArray(dendrites, node)) {
+        terminal = true
+      }
+      if (!terminal) {
+        found.push(node)
+      }
+    })
+
+    return found
+  }
+
 export class ConnectivityGraph extends EventTarget
 {
     cyg = null
@@ -46,10 +83,23 @@ export class ConnectivityGraph extends EventTarget
     async addConnectivity(knowledge)
     //=====================================================
     {
-        this.axons = knowledge.axons.map(node => JSON.stringify(node))
-        this.dendrites = knowledge.dendrites.map(node => JSON.stringify(node))
-        if (knowledge.somas?.length) {
-            this.somas = knowledge.somas.map(node => JSON.stringify(node))
+        const sourceKey = ["ilxtr:hasSomaLocatedIn"]
+        const destinationKey = ["ilxtr:hasAxonPresynapticElementIn", "ilxtr:hasAxonSensorySubcellularElementIn"]
+
+        const source = []
+        const destination = []
+        sourceKey.forEach((key)=>{
+          source.push(...knowledge["node-phenotypes"][key])
+        })
+        destinationKey.forEach((key)=>{
+          destination.push(...knowledge["node-phenotypes"][key])
+        })
+        const via = findComponents(knowledge, source, destination)
+
+        this.dendrites = source.map(node => JSON.stringify(node))
+        this.axons = destination.map(node => JSON.stringify(node))
+        if (via?.length) {
+            this.somas = via.map(node => JSON.stringify(node))
         }
         if (knowledge.connectivity.length) {
             for (const edge of knowledge.connectivity) {
@@ -160,7 +210,6 @@ export class ConnectivityGraph extends EventTarget
     {
         return [
             ...this.dendrites,
-            ...this.somas
         ]
     }
 
@@ -181,14 +230,11 @@ export class ConnectivityGraph extends EventTarget
             label: label.join('\n')
         }
         if (this.axons.includes(id)) {
-            if (this.dendrites.includes(id) || this.somas.includes(id)) {
-                result['both-a-d'] = true
-            } else {
-                result['axon'] = true
-            }
-        } else if (this.dendrites.includes(id) || this.somas.includes(id)) {
+            result['axon'] = true
+        } else if (this.dendrites.includes(id)) {
             result['dendrite'] = true
-
+        } else {
+            result['somas'] = true
         }
         return result
     }
@@ -241,7 +287,7 @@ const GRAPH_STYLE = [
         }
     },
     {
-        'selector': 'node[both-a-d]',
+        'selector': 'node[somas]',
         'style': {
             // 'background-color': 'gray',
             'shape': 'round-rectangle',

package/src/components/Tooltip/AnnotationPopup.vue

@@ -41,7 +41,7 @@
               <strong class="sub-title">Previous submissions:</strong>
             </el-row>
             <div class="entry" v-for="(sub, index) in prevSubs" :key="index">
-              <el-row class="dialog-text" v-if="sub.creator">
+              <el-row class="dialog-text">
                 <strong>{{ formatTime(sub.created) }}</strong>
                 {{ sub.creator.name }}
               </el-row>
@@ -65,7 +65,7 @@
             </div>
           </template>
         </template>
-        <template v-if="authenticated || offlineAnnotate">
+        <template v-if="authenticated">
           <template v-if="isEditable">
             <el-row class="dialog-spacer"></el-row>
             <el-row v-if="!editing">
@@ -217,9 +217,6 @@ export default {
     updatedCopyContent: function () {
       return this.getUpdateCopyContent();
     },
-    offlineAnnotate: function () {
-      return this.annotationEntry["offline"];
-    },
   },
   methods: {
     processEvidences: function(sub) {
@@ -265,15 +262,7 @@ export default {
       return new Date(dateString).toLocaleDateString(undefined, options);
     },
     updatePrevSubmissions: function () {
-      if (this.offlineAnnotate) {
-        const offlineAnnotation = JSON.parse(sessionStorage.getItem('offline-annotation')) || [];
-        this.prevSubs = offlineAnnotation.filter((offline) => {
-          return (
-            offline.resource === this.annotationEntry.resourceId &&
-            offline.item.id === this.annotationEntry.featureId
-          )
-        });
-      } else if (this.$annotator && this.authenticated) {
+      if (this.$annotator && this.authenticated) {
         if (
           this.annotationEntry["resourceId"] &&
           this.annotationEntry["featureId"]
@@ -353,6 +342,7 @@ export default {
           this.$annotator
             ?.addAnnotation(this.userApiKey, userAnnotation)
             .then(() => {
+              this.$emit("annotation", userAnnotation);
               this.errorMessage = "";
               this.resetSubmission();
               this.updatePrevSubmissions();
@@ -361,7 +351,6 @@ export default {
               this.errorMessage =
                 "There is a problem with the submission, please try again later";
             });
-          this.$emit("annotation", userAnnotation);
         }
       }
     },
@@ -407,11 +396,9 @@ export default {
       if (this.prevSubs.length) {
         let annotationContent = '<div><strong>Annotations:</strong></div>\n<br>';
         this.prevSubs.map((sub, index) => {
-          if (sub.creator) {
-            annotationContent += `<div><strong>Created:</strong>${this.formatTime(sub.created)}</div>\n<br>`;
-            annotationContent += `<div><strong>Creator:</strong>${sub.creator.name}</div>\n<br>`;
-            annotationContent += `<div><strong>Email:</strong>${sub.creator.email}</div>\n<br>`;
-          }
+          annotationContent += `<div><strong>Created:</strong>${this.formatTime(sub.created)}</div>\n<br>`;
+          annotationContent += `<div><strong>Creator:</strong>${sub.creator.name}</div>\n<br>`;
+          annotationContent += `<div><strong>Email:</strong>${sub.creator.email}</div>\n<br>`;
           if (sub.body.evidence.length) {
             let evidenceContent = '';
             sub.body.evidence.forEach((evi, index) => {
@@ -446,10 +433,10 @@ export default {
         this.creator = userData;
         if (!userData.orcid) this.creator.orcid = "0000-0000-0000-0000";
         this.authenticated = true;
+        this.updatePrevSubmissions();
       } else {
         this.errorMessage = "";
       }
-      this.updatePrevSubmissions();
     });
   },
 };