@abi-software/flatmap-viewer 2.4.1-b.4 → 2.4.2-b.1

package/README.rst

@@ -38,7 +38,7 @@ The map server endpoint is specified as ``MAP_ENDPOINT`` in ``src/main.js``. It
 Package Installation
 ====================
 
-* ``npm install @abi-software/flatmap-viewer@2.4.1-b.4``
+* ``npm install @abi-software/flatmap-viewer@2.4.2-b.1``
 
 Documentation
 -------------

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmap-viewer",
-  "version": "2.4.1-b.4",
+  "version": "2.4.2-b.1",
   "description": "Flatmap viewer using Maplibre GL",
   "repository": "https://github.com/AnatomicMaps/flatmap-viewer.git",
   "main": "src/main.js",

package/src/flatmap-viewer.js

@@ -545,11 +545,12 @@ class FlatMap
     __updateFeatureIdMapEntry(propertyId, featureIdMap, featureId)
     //============================================================
     {
-        const featureIds = featureIdMap.get(propertyId);
+        const id = utils.normaliseId(propertyId)
+        const featureIds = featureIdMap.get(id);
         if (featureIds) {
             featureIds.push(featureId);
         } else {
-            featureIdMap.set(propertyId, [featureId]);
+            featureIdMap.set(id, [featureId]);
         }
     }
 

package/src/interactions.js

@@ -1202,7 +1202,7 @@ export class UserInteractions
 
         for (const featureId of featureIds) {
             const annotation = this._flatmap.annotation(featureId);
-            if (!annotation.geometry.includes('Polygon')) {
+            if (!('markerPosition' in annotation) && !annotation.geometry.includes('Polygon')) {
                 continue;
             }
             if (!('marker' in annotation)) {
@@ -1216,17 +1216,16 @@ export class UserInteractions
                 // inside the marker container <div>.
                 const colour = options.colour || '#005974';
                 const markerHTML = options.element ? new maplibregl.Marker({element: options.element})
-                                                   : new maplibregl.Marker({color: colour});
+                                                   : new maplibregl.Marker({color: colour, scale: 0.5});
 
                 const markerElement = document.createElement('div');
                 const markerIcon = document.createElement('div');
                 markerIcon.innerHTML = markerHTML.getElement().innerHTML;
-                markerIcon.className = 'flatmap-marker';
                 markerElement.id = `marker-${markerId}`;
                 markerElement.appendChild(markerIcon);
 
                 const markerPosition = this.__markerPosition(featureId, annotation);
-                const marker = new maplibregl.Marker({marker: markerElement})
+                const marker = new maplibregl.Marker({element: markerElement})
                                              .setLngLat(markerPosition)
                                              .addTo(this._map);
                 markerElement.addEventListener('mouseenter',

package/src/main.js

@@ -62,6 +62,7 @@ export async function standaloneViewer(map_endpoint=null, options={})
         showId: true,
         showPosition: false,
         standalone: true,
+        annotator: true,
     }, options);
 
     function loadMap(id, taxon, sex)

package/src/utils.js

@@ -22,7 +22,11 @@ limitations under the License.
 
 //==============================================================================
 
-const NO_NORMALISATION = ['http', 'https', 'urn', 'NCBITaxon'];
+// A PMID is a "1- to 8-digit accession number with no leading zeros"
+const ZERO_PAD_PREFIXES = {
+    'ILX':    7,
+    'UBERON': 7
+};
 
 //==============================================================================
 
@@ -105,11 +109,11 @@ export function normaliseId(id)
     }
     const parts = id.split(':')
     const lastPart = parts[parts.length - 1]
-    if (NO_NORMALISATION.includes(parts[0]) || !'0123456789'.includes(lastPart[0])) {
-        return id;
+    if (parts[0].toUpperCase() in ZERO_PAD_PREFIXES && '0123456789'.includes(lastPart[0])) {
+        parts[parts.length - 1] = lastPart.padStart(ZERO_PAD_PREFIXES[parts[0].toUpperCase()], '0');
+        return parts.join(':');
     }
-    parts[parts.length - 1] = lastPart.padStart(8, '0');
-    return parts.join(':');
+    return id;
 }
 
 //==============================================================================

package/static/css/flatmap-viewer.css

@@ -230,12 +230,6 @@ label[for=layer-all-layers] {
     font-weight: bold;
 }
 
-/* Markers */
-
-.flatmap-marker {
-    transform: scale(0.5);
-}
-
 /* Annotator */
 .flex-auto {
     flex: 1 1 auto;