@abi-software/flatmapvuer 1.19.1-demo.0 → 1.20.0

package/src/App.vue

@@ -247,6 +247,9 @@ export default {
           taxo: 'UBERON:0001759',
           uuid: '0ea568ec-538d-52f3-a8e7-0437d844e1cf',
         },
+        FC: {
+          uuid: '0525bdec-ce68-5230-b10e-bdde3269e55f',
+        },
         Sample: { taxo: 'NCBITaxon:1', displayWarning: true },
         'Functional Connectivity': {
           taxo: 'FunctionalConnectivity',
@@ -273,8 +276,8 @@ export default {
       mapSettings: [],
       //flatmapAPI: "https://mapcore-demo.org/current/flatmap/v2/"
       //flatmapAPI: "https://mapcore-demo.org/devel/flatmap/v3/"
-      //flatmapAPI: "https://mapcore-demo.org/current/flatmap/v3/",
-      flatmapAPI: 'https://mapcore-demo.org/devel/flatmap/v4/',
+      flatmapAPI: "https://mapcore-demo.org/current/flatmap/v3/",
+      //flatmapAPI: 'https://mapcore-demo.org/devel/flatmap/v4/',
       //flatmapAPI: 'https://mapcore-demo.org/curation/flatmap/',
       //flatmapAPI: "https://mapcore-demo.org/fccb/flatmap/"
       //flatmapAPI: "https://mapcore-demo.org/staging/flatmap/v1/"

package/src/components/FlatmapVuer.vue

@@ -557,7 +557,6 @@ import { capitalise, normaliseAlertToStringArray } from './utilities.js';
 import yellowstar from '../icons/yellowstar';
 import ResizeSensor from 'css-element-queries/src/ResizeSensor';
 import flatmap from '../services/flatmapLoader.js';
-import { attachSomaLocationMarkerMethods } from '../services/somaLocationMarkers.js';
 import { AnnotationService } from '@abi-software/sparc-annotation';
 import { mapState } from 'pinia';
 import { useMainStore } from '@/store/index';
@@ -2787,7 +2786,7 @@ export default {
         });
         promise1
           .then((returnedObject) => {
-            this.mapImp = attachSomaLocationMarkerMethods(returnedObject);
+            this.mapImp = returnedObject;
             this.serverURL = this.mapImp.makeServerUrl('').slice(0, -1);
             let mapVersion = this.mapImp.details.version;
             this.setFlightPathInfo(mapVersion);

package/src/services/flatmapQueries.js

@@ -123,6 +123,7 @@ let FlatmapQueries = function () {
     this.singleConnectivityList = [];
     this.hasSingleConnectivityList = false;
     this.rawURLs = [];
+    this.expertConsultants = [];
     this.controller = undefined;
     this.uberons = [];
     this.lookUp = [];
@@ -167,6 +168,7 @@ let FlatmapQueries = function () {
       title: eventData.label,
       featureId: eventData.resource,
       hyperlinks: hyperlinks,
+      'expert-consultants': this.expertConsultants,
       provenanceTaxonomy: eventData.provenanceTaxonomy,
       provenanceTaxonomyLabel: taxonomyLabel,
       connectivitySource: this.connectivitySource,
@@ -317,6 +319,7 @@ let FlatmapQueries = function () {
     this.componentsCombinations = [];
     this.singleConnectivityList = [];
     this.rawURLs = [];
+    this.expertConsultants = [];
     if (!keastIds || keastIds.length === 0 || !keastIds[0]) return;
 
     let prom1 = await this.queryForConnectivityNew(mapImp, keastIds[0]); // This on returns a promise so dont need 'await'
@@ -362,6 +365,9 @@ let FlatmapQueries = function () {
                   // with publications from both PubMed and Others
                   this.rawURLs = [...response.references];
                 }
+                if (response['expert-consultants']) {
+                  this.expertConsultants = [...response['expert-consultants']];
+                }
                 resolve(processedConnectivity);
               });
             } else resolve(connectivity);
@@ -383,6 +389,9 @@ let FlatmapQueries = function () {
                         // with publications from both PubMed and Others
                         this.rawURLs = [...fallbackResponse.references];
                       }
+                      if (fallbackResponse['expert-consultants']) {
+                        this.expertConsultants = [...fallbackResponse['expert-consultants']];
+                      }
                       resolve(processedConnectivity);
                     });
                   } else resolve(connectivity);

package/src/services/somaLocationMarkers.js

@@ -1,129 +0,0 @@
-const SOMA_MARKER_COLOUR = '#1b7f6b';
-const SOMA_MARKER_SECONDARY_COLOUR = '#f4f1de';
-const SOMA_MARKER_TEXT_COLOUR = '#12312b';
-const SOMA_MARKER_MAX_COUNT_LABEL = '99+';
-
-const normalizeSomaLocations = function (somaLocations) {
-  return (Array.isArray(somaLocations) ? somaLocations : [])
-    .map((item) => ({
-      label: String(item?.label || '').trim(),
-      curie: String(item?.curie || '').trim(),
-      count: Number(item?.count || 0),
-    }))
-    .filter((item) => item.curie && item.count > 0);
-};
-
-const formatCount = function (count) {
-  if (count > 99) return SOMA_MARKER_MAX_COUNT_LABEL;
-  return String(count);
-};
-
-const createSomaLocationMarkerElement = function (somaLocation) {
-  const wrapper = document.createElement('div');
-  wrapper.className = 'flatmapvuer-soma-location-marker';
-  wrapper.title = somaLocation.label || somaLocation.curie;
-  wrapper.style.width = '34px';
-  wrapper.style.height = '48px';
-  wrapper.style.display = 'flex';
-  wrapper.style.alignItems = 'center';
-  wrapper.style.justifyContent = 'center';
-  wrapper.style.transform = 'translate(-50%, -100%)';
-
-  const countLabel = formatCount(somaLocation.count);
-  wrapper.innerHTML = `<svg xmlns="http://www.w3.org/2000/svg" viewBox="-1 -1 27 42" width="34" height="48" aria-hidden="true">
-    <ellipse style="fill: rgb(0, 0, 0); fill-opacity: 0.18;" cx="12" cy="36" rx="8" ry="4"/>
-    <path d="M12.25.25a12.254 12.254 0 0 0-12 12.494
-             c0 6.444 6.488 12.109 11.059 22.564.549 1.256 1.333 1.256 1.882 0
-             C17.762 24.853 24.25 19.186 24.25 12.744A12.254 12.254 0 0 0 12.25.25Z"
-          style="fill:${SOMA_MARKER_COLOUR};stroke:${SOMA_MARKER_SECONDARY_COLOUR};stroke-width:1.1"/>
-    <circle cx="12.5" cy="12.5" r="8" fill="${SOMA_MARKER_SECONDARY_COLOUR}"/>
-    <text x="12.5" y="16.1" text-anchor="middle" style="font-size:7.5px;font-weight:700;fill:${SOMA_MARKER_TEXT_COLOUR};font-family:Arial, sans-serif">${countLabel}</text>
-  </svg>`;
-
-  return wrapper;
-};
-
-const resolveMarkerPlacement = function (mapImp, curie) {
-  const featureIds = Array.isArray(mapImp?.modelFeatureIds?.(curie))
-    ? mapImp.modelFeatureIds(curie)
-    : [];
-  const placements = [];
-  const seenFeatureUris = new Set();
-
-  for (const featureId of featureIds) {
-    const annotation = mapImp.annotation(featureId);
-    const featureUri = String(annotation?.uri || '').trim();
-    if (featureUri && !seenFeatureUris.has(featureUri)) {
-      seenFeatureUris.add(featureUri);
-      placements.push({
-        type: 'feature-uri',
-        value: featureUri,
-      });
-    }
-  }
-
-  // Fall back to model placement only when no feature URI can be resolved.
-  if (!placements.length && featureIds.length) {
-    placements.push({
-      type: 'model',
-      value: curie,
-    });
-  }
-
-  return placements;
-};
-
-export const attachSomaLocationMarkerMethods = function (mapImp) {
-  if (!mapImp || mapImp.addSomaLocationMarkers) {
-    return mapImp;
-  }
-
-  let markerIds = [];
-
-  mapImp.clearSomaLocationMarkers = function () {
-    markerIds.forEach((markerId) => {
-      mapImp.removeMarker(markerId);
-    });
-    markerIds = [];
-  };
-
-  mapImp.addSomaLocationMarkers = function (somaLocations) {
-    const normalizedSomaLocations = normalizeSomaLocations(somaLocations);
-    const placedSomaLocations = [];
-
-    mapImp.clearSomaLocationMarkers();
-
-    normalizedSomaLocations.forEach((somaLocation) => {
-      const placements = resolveMarkerPlacement(mapImp, somaLocation.curie);
-      if (!placements.length) return;
-
-      let somaLocationPlaced = false;
-      placements.forEach((placement) => {
-        const markerElement = createSomaLocationMarkerElement(somaLocation);
-        let addedMarkerIds = [];
-
-        if (placement.type === 'feature-uri') {
-          addedMarkerIds = mapImp.addMarkerByFeatureUri(placement.value, {
-            element: markerElement,
-          });
-        } else if (placement.type === 'model') {
-          const markerId = mapImp.addMarker(placement.value, { element: markerElement });
-          addedMarkerIds = markerId > -1 ? [markerId] : [];
-        }
-
-        if (!addedMarkerIds.length) return;
-
-        markerIds.push(...addedMarkerIds);
-        somaLocationPlaced = true;
-      });
-
-      if (somaLocationPlaced) {
-        placedSomaLocations.push(somaLocation);
-      }
-    });
-
-    return placedSomaLocations;
-  };
-
-  return mapImp;
-};