@abi-software/flatmap-viewer 2.4.1-b.1 → 2.4.1-b.3

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.1``
+* ``npm install @abi-software/flatmap-viewer@2.4.1-b.3``
 
 Documentation
 -------------

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/flatmap-viewer",
-  "version": "2.4.1-b.1",
+  "version": "2.4.1-b.3",
   "description": "Flatmap viewer using Maplibre GL",
   "repository": "https://github.com/AnatomicMaps/flatmap-viewer.git",
   "main": "src/main.js",

package/src/controls/taxons.js

@@ -0,0 +1,73 @@
+/******************************************************************************
+
+Flatmap viewer and annotation tool
+
+Copyright (c) 2019 - 2023  David Brooks
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+**/
+//==============================================================================
+
+import { Control } from './controls';
+
+//==============================================================================
+
+export class TaxonsControl extends Control
+{
+    constructor(flatmap)
+    {
+        super(flatmap, 'taxon', 'taxons');
+        this.__taxonIds = flatmap.taxonIdentifiers.sort();
+    }
+
+    _addControlDetails()
+    //==================
+    {
+        let lines = 0;
+        let enabled = 0;
+        for (const taxonId of this.__taxonIds) {
+            const input = this._addControlLine(`${this.__prefix}${taxonId}`, taxonId);
+            input.checked = true;
+            enabled += 1;
+            lines += 1;
+        }
+        return {
+            enabled: enabled,
+            total: lines
+        };
+    }
+
+    _enableAll(enable)
+    //================
+    {
+        for (const taxonId of this.__taxonIds) {
+            const checkbox = document.getElementById(`${this.__prefix}${taxonId}`);
+            if (checkbox) {
+                checkbox.checked = enable;
+                this.__flatmap.enableConnectivityByTaxonIds(taxonId, enable);
+            }
+        }
+    }
+
+    __enableControl(id, enable)
+    //=========================
+    {
+        for (const taxonId of this.__taxonIds) {
+            if (id === taxonId) {
+                this.__flatmap.enableConnectivityByTaxonIds(taxonId, enable);
+            }
+        }
+    }
+
+}

package/src/flatmap-viewer.js

@@ -39,6 +39,7 @@ import {UserInteractions} from './interactions.js';
 
 import {MinimapControl} from './controls/minimap.js';
 import {NavigationControl} from './controls/controls.js';
+import {APINATOMY_PATH_PREFIX} from './pathways';
 
 import * as images from './images.js';
 import * as utils from './utils.js';
@@ -49,6 +50,15 @@ const MAP_MAKER_SEPARATE_LAYERS_VERSION = 1.4;
 
 //==============================================================================
 
+/**
+ * The taxon identifier used when none has been given.
+ *
+ * @type       {string}
+ */
+export const UNCLASSIFIED_TAXON_ID = 'NCBITaxon:2787823';   // unclassified entries
+
+//==============================================================================
+
 /**
 * Maps are not created directly but instead are created and loaded by
 * :meth:`LoadMap` of :class:`MapManager`.
@@ -533,7 +543,7 @@ class FlatMap
     }
 
     __updateFeatureIdMapEntry(propertyId, featureIdMap, featureId)
-    //======================================================
+    //============================================================
     {
         const featureIds = featureIdMap.get(propertyId);
         if (featureIds) {
@@ -543,18 +553,22 @@ class FlatMap
         }
     }
 
-    __updateFeatureIdMap(property, featureIdMap, annotation)
-    //======================================================
+    __updateFeatureIdMap(property, featureIdMap, annotation, missingId=null)
+    //======================================================================
     {
-        if (property in annotation) {
+        if (property in annotation && annotation[property].length) {
             const propertyId = annotation[property];
             if (Array.isArray(propertyId)) {
                 for (const id of propertyId) {
                     this.__updateFeatureIdMapEntry(id, featureIdMap, annotation.featureId);
                 }
             } else {
-                this.__updateFeatureIdMapEntry(propertyId, featureIdMap, annotation.featureId)
+                this.__updateFeatureIdMapEntry(propertyId, featureIdMap, annotation.featureId);
             }
+        } else if (missingId !== null
+               && 'models' in annotation
+               && annotation.models.startsWith(APINATOMY_PATH_PREFIX)) {
+            this.__updateFeatureIdMapEntry(missingId, featureIdMap, annotation.featureId);
         }
     }
 
@@ -566,7 +580,7 @@ class FlatMap
         this.__updateFeatureIdMap('dataset', this.__datasetToFeatureIds, ann);
         this.__updateFeatureIdMap('models', this.__modelToFeatureIds, ann);
         this.__updateFeatureIdMap('source', this.__mapSourceToFeatureIds, ann);
-        this.__updateFeatureIdMap('taxons', this.__taxonToFeatureIds, ann);
+        this.__updateFeatureIdMap('taxons', this.__taxonToFeatureIds, ann, UNCLASSIFIED_TAXON_ID);
         this.__annIdToFeatureId.set(ann.id, featureId);
     }
 

package/src/interactions.js

@@ -45,6 +45,7 @@ import {AnnotatedControl, BackgroundControl, LayerControl, NerveControl,
 import {PathControl} from './controls/paths';
 import {SearchControl} from './controls/search';
 import {SystemsControl} from './controls/systems';
+import {TaxonsControl} from './controls/taxons';
 
 import * as utils from './utils';
 
@@ -159,11 +160,12 @@ export class UserInteractions
         }
 
         // Note features that are FC systems
-
         this.__systemsManager = new SystemsManager(this._flatmap, this, featuresEnabled);
 
-        // Add various controls when running standalone
+        // All taxons of connectivity paths are enabled by default
+        this.__enabledConnectivityTaxons = new Set(this._flatmap.taxonIdentifiers);
 
+        // Add various controls when running standalone
         if (flatmap.options.standalone) {
             // Add a control to search annotations if option set
             this._map.addControl(new SearchControl(flatmap));
@@ -186,11 +188,14 @@ export class UserInteractions
                 this._map.addControl(new NerveControl(flatmap, this._layerManager, {showCentrelines: false}));
             }
 
-            // SCKAN path and SYSTEMS controls for FC maps
             if (flatmap.options.style === 'functional') {
+                // SCKAN path and SYSTEMS controls for FC maps
                 this._map.addControl(new SystemsControl(flatmap, this.__systemsManager.systems));
                 this._map.addControl(new SCKANControl(flatmap, flatmap.options.layerOptions));
                 this._map.addControl(new AnnotatedControl(this, flatmap.options.layerOptions));
+            } else {
+                // Connectivity taxon control for AC maps
+                this._map.addControl(new TaxonsControl(flatmap));
             }
         }
 
@@ -1136,10 +1141,15 @@ export class UserInteractions
     //=================================================
     {
         if (enable) {
-            this._layerManager.setFilter({taxons: taxonIds});
+            for (const taxonId of taxonIds) {
+               this.__enabledConnectivityTaxons.add(taxonId);
+            }
         } else {
-            this._layerManager.setFilter({taxons: []});
+            for (const taxonId of taxonIds) {
+               this.__enabledConnectivityTaxons.delete(taxonId);
+            }
         }
+        this._layerManager.setFilter({taxons: [...this.__enabledConnectivityTaxons.values()]});
     }
 
     excludeAnnotated(exclude=false)

package/src/pathways.js

@@ -28,6 +28,10 @@ export const PATHWAYS_LAYER = 'pathways';
 
 //==============================================================================
 
+export const APINATOMY_PATH_PREFIX = 'ilxtr:';
+
+//==============================================================================
+
 const PATH_TYPES = [
     { type: "cns", label: "CNS", colour: "#9B1FC1"},
     { type: "intracardiac", label: "Local circuit neuron", colour: "#F19E38"},

package/src/styling.js

@@ -26,7 +26,8 @@ export const VECTOR_TILES_SOURCE = 'vector-tiles';
 
 //==============================================================================
 
-import {PATH_STYLE_RULES} from './pathways.js';
+import {UNCLASSIFIED_TAXON_ID} from './flatmap-viewer';
+import {PATH_STYLE_RULES} from './pathways';
 
 //==============================================================================
 
@@ -482,14 +483,19 @@ export class PathLineLayer extends VectorStyleLayer
         const sckan_filter = sckanFilter(options);
         let taxonFilter = [];
         if ('taxons' in options) {
-            taxonFilter.push('all');
-            taxonFilter.push(['has', 'taxons']);
-            const filterList = ['any'];
-            for (const taxon of options.taxons) {
-                filterList.push(['in', taxon, ['get', 'taxons']]);
+            if (options.taxons.length) {
+                taxonFilter.push('any');
+                for (const taxon of options.taxons) {
+                    if (taxon !== UNCLASSIFIED_TAXON_ID) {
+                        taxonFilter.push(['in', taxon, ['get', 'taxons']]);
+                    } else {
+                        taxonFilter.push(['case', ['has', 'taxons'], false, true]);
+                    }
+                }
+                taxonFilter = [taxonFilter];
+            } else {
+                taxonFilter.push(false);
             }
-            taxonFilter.push(filterList);
-            taxonFilter = [taxonFilter];
         }
 
         return this.__dashed ? [