@abi-software/mapintegratedvuer 1.21.1 → 1.22.0

package/src/mixins/DynamicMarkerMixin.js

@@ -1,16 +1,12 @@
-
 import { mapStores } from 'pinia';
 import { useSettingsStore } from '../stores/settings';
 
 // remove duplicates by stringifying the objects
 const removeDuplicates = function (arrayOfAnything) {
-  if (!arrayOfAnything) return []
-  return [...new Set(arrayOfAnything.map((e) => JSON.stringify(e)))].map((e) =>
-    JSON.parse(e)
-  )
-}
+  if (!arrayOfAnything) return [];
+  return [...new Set(arrayOfAnything.map((e) => JSON.stringify(e)))].map((e) => JSON.parse(e));
+};
 
-/* eslint-disable no-alert, no-console */
 export default {
   computed: {
     ...mapStores(useSettingsStore),
@@ -20,11 +16,11 @@ export default {
       if (this.mouseHovered) {
         const result = {
           paneIndex: this.entry.id,
-          eventType: "panZoom",
+          eventType: 'panZoom',
           payload: payload,
           type: this.entry.type,
         };
-        this.$emit("resource-selected", result);
+        this.$emit('resource-selected', result);
       }
     },
     /**
@@ -35,34 +31,34 @@ export default {
       if (!this.flatmapReady) return;
 
       let flatmapImp = flatmap;
-      if (!flatmapImp)
-        flatmapImp = this.getFlatmapImp();
+      if (!flatmapImp) flatmapImp = this.getFlatmapImp();
 
       if (flatmapImp) {
         // Set the dataset markers
-        let markers = this.settingsStore.globalSettings.displayMarkers ? this.settingsStore.markers : [];
+        let markers = this.settingsStore.globalSettings.displayMarkers
+          ? this.settingsStore.markers
+          : [];
         markers = removeDuplicates(markers);
         flatmapImp.clearMarkers();
         flatmapImp.clearClusteredAnatomicalMarkers();
         flatmapImp.addClusteredAnatomicalMarkers(markers);
 
         // Set the featured markers
-        if (this.entry.type === "MultiFlatmap") {
+        if (this.entry.type === 'MultiFlatmap') {
           this.restoreFeaturedMarkers(flatmapImp);
         }
       }
     },
     // removeMarkersNotOnFlatmap: rewrites the dataset marker list to only include markers that are on the flatmap
     removeMarkersNotOnFlatmap(flatmapImp, datasets) {
-
       // dataset markers are in the form [{id: "discoverId", terms: ["term1", "term2"]}, {id:....}]
       let fma = flatmapImp.anatomicalIdentifiers;
-      let markersOnFlatmap = []
+      let markersOnFlatmap = [];
 
       // the block below steps through each dataset and checks each term to see if it is in the flatmap
       for (let i = 0; i < datasets.length; i++) {
         let dataset = datasets[i];
-        let datasetAdjusted = {id: dataset.id, terms: []};
+        let datasetAdjusted = { id: dataset.id, terms: [] };
         for (let j = 0; j < dataset.terms.length; j++) {
           if (fma.includes(dataset.terms[j])) {
             datasetAdjusted.terms.push(dataset.terms[j]);
@@ -80,5 +76,5 @@ export default {
         this.flatmapMarkerUpdate(flatmapImp);
       }
     },
-  }
-}
+  },
+};

package/src/mixins/RetrieveContextCardMixin.js

@@ -1,5 +1,3 @@
-
-/* eslint-disable no-alert, no-console */
 export default {
   // Note that the setting store is included in MapContent.vue
   methods: {
@@ -9,8 +7,8 @@ export default {
 
       // get the context file from scicrunch
       const sciResults = await this.getContextFileFromScicrunch(datasetId, scaffoldPath);
-      if (!sciResults.success){
-        return {} // return empty object if no context file is found (the empty object will be added to the entry)
+      if (!sciResults.success) {
+        return {}; // return empty object if no context file is found (the empty object will be added to the entry)
       }
 
       // return the context file
@@ -18,15 +16,15 @@ export default {
       return {
         s3uri: sciResults.s3uri,
         contextCardUrl: fullPath,
-      }
+      };
     },
     splitInfoFromUrl: function (url) {
       // example url: "https://mapcore-demo.org/current/sparc-api-v2/s3-resource/221/3/files/derivative/Scaffolds/mouse_colon_metadata.json",
-      // find the part after 's3-resource' 
+      // find the part after 's3-resource'
       let s3path = url.split('s3-resource')[1];
-      let basePath = url.split('files/')[0] + 'files/' // This gives us the base path for our relative path we will get from scicrunch
-      let scaffoldPath = url.split('files/')[1].split('?')[0] // This gives us the relative path to the file we want to get from scicrunch
-      let s3uri = '?' + url.split('?')[1] // This gives us the uri needed to get the file from s3
+      let basePath = url.split('files/')[0] + 'files/'; // This gives us the base path for our relative path we will get from scicrunch
+      let scaffoldPath = url.split('files/')[1].split('?')[0]; // This gives us the relative path to the file we want to get from scicrunch
+      let s3uri = '?' + url.split('?')[1]; // This gives us the uri needed to get the file from s3
 
       // split the url by '/'
       const parts = s3path.split('/');
@@ -39,45 +37,52 @@ export default {
     },
     getContextFileFromScicrunch: async function (datasetId, scaffoldPath) {
       // get the context file from scicrunch
-      let results = await fetch(`${this.settingsStore.sparcApi}/dataset_info/using_multiple_discoverIds/?discoverIds=${datasetId}`)
-        .then(response => response.json())
-        .then(data => {
+      let results = await fetch(
+        `${this.settingsStore.sparcApi}/dataset_info/using_multiple_discoverIds/?discoverIds=${datasetId}`,
+      )
+        .then((response) => response.json())
+        .then((data) => {
           // get the context info from the response
-          if (data.numberOfHits === 1) { // check if there is only one hit (We don't want to use the data if there are multiple hits)
-            const contextFile = data.results[0]['abi-contextual-information']
+          if (data.numberOfHits === 1) {
+            // check if there is only one hit (We don't want to use the data if there are multiple hits)
+            const contextFile = data.results[0]['abi-contextual-information'];
 
             // check if there is only one context file and if so return it
-            if ( contextFile && contextFile.length === 1) {
+            if (contextFile && contextFile.length === 1) {
               return {
                 success: true,
-                contextFile: contextFile[0], 
-                s3uri: data.results[0]['s3uri']
-              }
+                contextFile: contextFile[0],
+                s3uri: data.results[0]['s3uri'],
+              };
             }
 
             // If there are multiple context files, find the one that matches the scaffold path
             else if (contextFile && contextFile.length > 1) {
-              let search = this.findContextInforForFilePath(data.results[0]['abi-context-file'], scaffoldPath);
+              let search = this.findContextInforForFilePath(
+                data.results[0]['abi-context-file'],
+                scaffoldPath,
+              );
               if (search) {
                 return {
                   success: true,
-                  contextFile: search, 
-                  s3uri: data.results[0]['s3uri']
-                }
+                  contextFile: search,
+                  s3uri: data.results[0]['s3uri'],
+                };
               }
             }
           }
-          return {success: false};
-        }).catch(error => {
+          return { success: false };
+        })
+        .catch((error) => {
           console.error('Error:', error);
-          return {success: false};
+          return { success: false };
         });
       return results;
     },
     findContextInforForFilePath: function (dataciteInfo, filePath) {
       // find the context file that matches the scaffold path
-      let result = dataciteInfo.find((info) => info.datacite.isDerivedFrom.path.includes(filePath))
-      return result?.dataset?.path
-    }
-  }
-}
+      let result = dataciteInfo.find((info) => info.datacite.isDerivedFrom.path.includes(filePath));
+      return result?.dataset?.path;
+    },
+  },
+};

package/src/mixins/S3Bucket.vue

@@ -1,37 +1,34 @@
 <script>
 export default {
-  name: "S3Bucket",
+  name: 'S3Bucket',
   data() {
     return {
       s3Bucket: undefined,
-      s3Prefix: "",
+      s3Prefix: '',
     };
   },
   methods: {
-    updateS3Bucket: function(s3uri) {
+    updateS3Bucket: function (s3uri) {
       this.s3Bucket = undefined;
       if (s3uri) {
-        const substring = s3uri.split("//")[1];
+        const substring = s3uri.split('//')[1];
         if (substring) {
-          this.s3Bucket = substring.split("/")[0];
+          this.s3Bucket = substring.split('/')[0];
           const n = substring.indexOf('/');
           this.s3Prefix = substring.substring(n + 1);
           return;
         }
       }
     },
-    getS3Args: function() {
+    getS3Args: function () {
       if (this.s3Bucket) {
-        return `?s3BucketName=${this.s3Bucket}`
+        return `?s3BucketName=${this.s3Bucket}`;
       }
-      return "";
+      return '';
     },
-    getS3Prefix: function() {
+    getS3Prefix: function () {
       return this.s3Prefix;
-    }
+    },
   },
-
 };
 </script>
-
-

package/src/services/knowledgeMapping.js

@@ -1,77 +1,77 @@
 const knowledgeMap = {
-  "classes": {
-    "cardio_28": {
-      "models": "UBERON:0002165",
-      "name": "Endocardium"
+  classes: {
+    cardio_28: {
+      models: 'UBERON:0002165',
+      name: 'Endocardium',
+    },
+    cardio_29: {
+      models: 'UBERON:0002349',
+      name: 'Myocardium',
     },
-    "cardio_29": {
-      "models": "UBERON:0002349",
-      "name": "Myocardium"
-    }
   },
-  "features": {
-    "v_GLUT2_basal": {
-      "name": "Flow through GLUT2 transporter",
-      "variable": "main/v_GLUT2base"
+  features: {
+    v_GLUT2_basal: {
+      name: 'Flow through GLUT2 transporter',
+      variable: 'main/v_GLUT2base',
     },
-    "v_SGLT1_apical": {
-      "name": "SGLT1 transporter",
-      "variable": "main/v_SGLT1"
+    v_SGLT1_apical: {
+      name: 'SGLT1 transporter',
+      variable: 'main/v_SGLT1',
     },
-    "v_Kir_basal": {
-      "name": "Kir channel",
-      "models": "UBERON:0001536",
-      "variable": "main/v_Kir"
+    v_Kir_basal: {
+      name: 'Kir channel',
+      models: 'UBERON:0001536',
+      variable: 'main/v_Kir',
     },
-    "v_NKA_basal": {
-      "name": "Na/K ATPase",
-      "variable": "main/v_NKA"
+    v_NKA_basal: {
+      name: 'Na/K ATPase',
+      variable: 'main/v_NKA',
     },
-    "v_GLUT2_apical": {
-      "name": "GLUT2 transporter",
-      "variable": "main/v_GLUT2apex"
+    v_GLUT2_apical: {
+      name: 'GLUT2 transporter',
+      variable: 'main/v_GLUT2apex',
     },
-    "q_Na_lumen": {
-      "name": "[Na+] in lumen",
-      "variable": "main/c_Na_gut"
+    q_Na_lumen: {
+      name: '[Na+] in lumen',
+      variable: 'main/c_Na_gut',
     },
-    "q_Na_i": {
-      "name": "[Na+] in intracellular space",
-      "variable": "main/c_Na_int"
+    q_Na_i: {
+      name: '[Na+] in intracellular space',
+      variable: 'main/c_Na_int',
     },
-    "q_Na_blood": {
-      "name": "[Na+] in blood",
-      "variable": "main/c_Na_cap"
+    q_Na_blood: {
+      name: '[Na+] in blood',
+      variable: 'main/c_Na_cap',
     },
-    "q_K_blood": {
-      "name": "[K+] in blood",
-      "variable": "main/c_K_cap"
+    q_K_blood: {
+      name: '[K+] in blood',
+      variable: 'main/c_K_cap',
     },
-    "q_K_i": {
-      "name": "[K+] in intracellular space",
-      "variable": "main/c_K_int"
+    q_K_i: {
+      name: '[K+] in intracellular space',
+      variable: 'main/c_K_int',
     },
-    "q_Glc_lumen": {
-      "name": "[Glucose] in lumen",
-      "variable": "main/c_Glc_gut"
+    q_Glc_lumen: {
+      name: '[Glucose] in lumen',
+      variable: 'main/c_Glc_gut',
     },
-    "q_Glc_i": {
-      "name": "[Glucose] in intracellular space",
-      "variable": "main/c_Glc_int"
+    q_Glc_i: {
+      name: '[Glucose] in intracellular space',
+      variable: 'main/c_Glc_int',
     },
-    "q_Glc_blood": {
-      "name": "[Glucose] in blood",
-      "variable": "main/c_Glc_cap"
-    }
-  }
+    q_Glc_blood: {
+      name: '[Glucose] in blood',
+      variable: 'main/c_Glc_cap',
+    },
+  },
 };
 
 const getVariableName = (name) => {
   if (Object.hasOwn(knowledgeMap.features, name)) {
-    console.log("pass")
+    console.log('pass');
     const data = knowledgeMap.features[name];
     return data;
   }
 };
 
-export { getVariableName }
+export { getVariableName };

package/src/services/tagging.js

@@ -1,6 +1,6 @@
 import EventBus from '../components/EventBus';
 export default {
-  sendEvent: function(data) {
+  sendEvent: function (data) {
     const taggingData = {
       event: data.event || '',
       event_name: data.event_name || '',
@@ -13,7 +13,7 @@ export default {
       version_id: data.version_id || '',
       doi: data.doi || '',
       citation_type: data.citation_type || '',
-      location: data.location || ''
+      location: data.location || '',
     };
 
     // set debugging mode
@@ -23,5 +23,5 @@ export default {
 
     // Emit data for GTM
     EventBus.emit('trackEvent', taggingData);
-  }
-}
+  },
+};

package/src/stores/connectivities.js

@@ -1,5 +1,31 @@
 import { defineStore } from 'pinia';
-import { listsAreEqual } from "../components/scripts/utilities";
+import { listsAreEqual } from '../components/scripts/utilities';
+
+function mergeConnectivityEntries(existingEntries = [], incomingEntries = []) {
+  const merged = new Map();
+
+  [...existingEntries, ...incomingEntries].forEach((entry) => {
+    if (!entry || entry.id === undefined) {
+      return;
+    }
+
+    const existing = merged.get(entry.id);
+    merged.set(
+      entry.id,
+      existing
+        ? {
+            ...existing,
+            ...entry,
+            'nerve-label': entry['nerve-label'] || existing['nerve-label'],
+            'long-label': entry['long-label'] || existing['long-label'],
+            'expert-consultants': entry['expert-consultants'] || existing['expert-consultants'],
+          }
+        : { ...entry },
+    );
+  });
+
+  return Array.from(merged.values());
+}
 
 export const useConnectivitiesStore = defineStore('connectivities', {
   state: () => {
@@ -20,9 +46,7 @@ export const useConnectivitiesStore = defineStore('connectivities', {
         for (const connectivity of connectivities) {
           const key = connectivity.id;
 
-          acc[key] = acc[key] ?
-            { ...acc[key], ...connectivity } :
-            { ...connectivity };
+          acc[key] = acc[key] ? { ...acc[key], ...connectivity } : { ...connectivity };
         }
 
         return acc;
@@ -38,7 +62,7 @@ export const useConnectivitiesStore = defineStore('connectivities', {
           if (acc[filter.key]) {
             const mergedChildren = [...acc[filter.key].children, ...filter.children];
             const uniqueChildren = Array.from(
-              new Map(mergedChildren.map(child => [child.key, child])).values()
+              new Map(mergedChildren.map((child) => [child.key, child])).values(),
             );
             acc[filter.key].children = uniqueChildren;
           } else {
@@ -76,15 +100,29 @@ export const useConnectivitiesStore = defineStore('connectivities', {
         this.activeConnectivityKeys = activeConnectivityKeys;
         return true;
       } else if (this.connectivitiesUpdated) {
-        this.connectivitiesUpdated = !activeConnectivityKeys.every(ele => ele in this.globalConnectivities);
+        this.connectivitiesUpdated = !activeConnectivityKeys.every(
+          (ele) => ele in this.globalConnectivities,
+        );
         return true;
       }
       return false;
     },
     updateGlobalConnectivities(globalConnectivities) {
       if (globalConnectivities) {
-        if (JSON.stringify(globalConnectivities) !== JSON.stringify(this.globalConnectivities)) {
-          this.globalConnectivities = globalConnectivities;
+        // Each viewer (MultiFlatmap/Flatmap/Scaffold) only knows about its own
+        // uuid/sckanVersion key(s) when it calls this action, and its local
+        // snapshot may be stale for the same entry set. Merge by key and by id
+        // so a later flatmap update does not wipe richer scaffold metadata such
+        // as nerve-label.
+        const merged = { ...this.globalConnectivities };
+
+        Object.entries(globalConnectivities).forEach(([uuid, entries]) => {
+          const existingEntries = merged[uuid] || [];
+          merged[uuid] = mergeConnectivityEntries(existingEntries, entries || []);
+        });
+
+        if (JSON.stringify(merged) !== JSON.stringify(this.globalConnectivities)) {
+          this.globalConnectivities = merged;
           this.connectivitiesUpdated = true;
         }
       }

package/src/stores/entries.js

@@ -1,15 +1,13 @@
 import { defineStore } from 'pinia';
-import { initialDefaultState } from "../components/scripts/utilities";
+import { initialDefaultState } from '../components/scripts/utilities';
 import { getKnowledgeSourceFromProvenance } from '@abi-software/flatmapvuer/src/services/flatmapKnowledge.js';
 
-/* eslint-disable no-alert, no-console */
-
 export const useEntriesStore = defineStore('entries', {
   state: () => {
     return initialDefaultState();
   },
   getters: {
-    findIndexOfId: (state) => id => {
+    findIndexOfId: (state) => (id) => {
       for (let i = 0; i < state.entries.length; i++) {
         if (state.entries[i].id == id) {
           return i;
@@ -31,9 +29,9 @@ export const useEntriesStore = defineStore('entries', {
       this.entries = [];
       Object.assign(this.entries, newEntries);
     },
-    updateViewForEntry( {id, viewUrl}) {
+    updateViewForEntry({ id, viewUrl }) {
       // Update the scaffold with a view url
-      const entry = this.entries.find(entry => entry.id === id);
+      const entry = this.entries.find((entry) => entry.id === id);
       entry.viewUrl = viewUrl;
     },
     updateMapForEntry(entry, prov) {
@@ -44,16 +42,16 @@ export const useEntriesStore = defineStore('entries', {
       }
     },
     updateLabelForEntry(targetEntry, label) {
-      const entryToAssign = this.entries.find(entry => entry.id === targetEntry.id);
+      const entryToAssign = this.entries.find((entry) => entry.id === targetEntry.id);
       if (entryToAssign) {
         entryToAssign['label'] = label;
       }
     },
     updateTitleForEntry(targetEntry, title) {
-      const entryToAssign = this.entries.find(entry => entry.id === targetEntry.id);
+      const entryToAssign = this.entries.find((entry) => entry.id === targetEntry.id);
       if (entryToAssign) {
         entryToAssign['title'] = title;
       }
     },
-  }
+  },
 });

package/src/stores/index.js

@@ -1,24 +1,24 @@
-import { defineStore } from 'pinia'
+import { defineStore } from 'pinia';
 
 /**
  * Activate the store when run the application individually.
- * If the store exist in parent application, 
+ * If the store exist in parent application,
  * instead of creating a new store it will access the parent main store.
  */
 export const useMainStore = defineStore('main', {
   state: () => ({
     userProfile: {
-      token: ''
+      token: '',
     },
   }),
   getters: {
     userToken(state) {
-      return state.userProfile.token
+      return state.userProfile.token;
     },
   },
   actions: {
     setUserToken(value) {
-      this.userProfile.token = value
+      this.userProfile.token = value;
     },
-  }
-})
+  },
+});