Changes to add other species links to the working icons

Author: bdls-jamal

Eplant/views/NavigatorViewer/NavigatorView.tsx

@@ -11,7 +11,6 @@ import CellEFPIcon from './Icons/CellEFPIcon';
 import GeneInfoViewIcon from './Icons/GeneInfoViewerIcon'; /** Placeholder icon for those that are not yet implemented in ePlant3 */
 import PlantEFPIcon from './Icons/PlantEFPIcon'
 import * as constants from './constants';
-//import { NavigatorContext, useViewSwitch, ViewSwitchProvider} from './index';
 import { NavigatorContext, ViewSwitchProvider} from './index';
 
 
@@ -52,6 +51,21 @@ const grameneLinks: { [key: string]: string } = {
   "default": "https://ensembl.gramene.org/Arabidopsis_thaliana/Gene/Summary?g={geneName}"
 };
 
+/**
+ * Static declaration of other ePlant site links for non-Arabidopsis species
+ */
+const ePlantLinks:{ [key: string]: string } = {
+  "POPLAR": "https://bar.utoronto.ca/eplant_poplar/",
+  "SOYBEAN": "https://bar.utoronto.ca/eplant_soybean/",
+  "M. TRUNCATULA": "https://bar.utoronto.ca/eplant_medicago/",
+  "TOMATO": "https://bar.utoronto.ca/eplant_tomato/",
+  "POTATO": "https://bar.utoronto.ca/eplant_potato/",
+  "GRAPE": "",
+  "RICE": "https://bar.utoronto.ca/eplant_rice/",
+  "MAIZE": "https://bar.utoronto.ca/eplant_maize/",
+  "BARLEY": "https://bar.utoronto.ca/eplant_barley/",
+};
+
 /** 
  * Generate Gramene link based on species and gene name
  * @param species - The species name
@@ -916,8 +930,19 @@ useEffect(() => {
               onClick={(event) => {
                 /** Extract the geneName */
                 const geneName = displayName;
-                /** Call switch view function to swap the view using designated view id and gene name */
+                /** Get species from node data or props - default to Arabidopsis */
+                const species = node.data.metadata?.genome;
+                
                 switchViewAndGene('plant', geneName);
+
+               /** Call switch view function with species information */
+                if (!species || !(species in ePlantLinks)) {
+                  /** Call switch view function to swap the view using designated view id and gene name */
+                  switchViewAndGene('plant', geneName);
+                } else {
+                  /** Handle external species navigation */
+                  switchViewAndGene('plant', geneName, ePlantLinks[species]);
+                }
               }}
             >
               <rect
@@ -945,8 +970,19 @@ useEffect(() => {
               onClick={(event) => {
                 /** Extract the geneName */
                 const geneName = displayName;
-                /** Call switch view function to swap the view using designated view id and gene name */
+                /** Get species from node data or props - default to Arabidopsis */
+                const species = node.data.metadata?.genome;
+                
                 switchViewAndGene('Cell eFP', geneName);
+
+               /** Call switch view function with species information */
+                if (!species || !(species in ePlantLinks)) {
+                  /** Call switch view function to swap the view using designated view id and gene name */
+                  switchViewAndGene('Cell eFP', geneName);
+                } else {
+                  /** Handle external species navigation */
+                  switchViewAndGene('Cell eFP', geneName, ePlantLinks[species]);
+                }
               }}
             >
               <rect

Eplant/views/ViewGeneSwitching.tsx

@@ -19,7 +19,7 @@ interface ViewSwitchContextType {
   /** Function to switch gene only */
   switchGeneOnly: (geneName: string) => Promise<void>;
   /** Function to switch both view and gene */
-  switchViewAndGene: (viewId: string, geneName: string) => Promise<void>;
+  switchViewAndGene: (viewId: string, geneName: string, species?: string) => Promise<void>;
 }
 
 /** Default context value */
@@ -111,12 +111,25 @@ export const createViewSwitchProvider = () => {
       }
     };
 
+    /**
+     * Handles navigation to external species links
+     * @param speciesUrl - The URL to navigate to
+     * @param geneName - The gene identifier
+     */
+        const handleExternalSpecies = (speciesUrl: string, geneName: string): void => {
+          /** const fullUrl = `${speciesUrl}${geneName}`; */ 
+          const fullUrl = `${speciesUrl}`;
+          window.open(fullUrl, '_blank');
+        };
+
     /**
      * Switches only the view, keeping the current gene
      * @param viewId - ID of the view to switch to
      */
     const switchViewOnly = async (viewId: string): Promise<void> => {
+      
       const targetView = validateView(viewId);
+      
       if (targetView) {
         setActiveViewId(targetView.id);
         setActiveView(targetView);
@@ -127,8 +140,15 @@ export const createViewSwitchProvider = () => {
      * Switches only the gene, keeping the current view
      * @param geneName - Name of the gene to switch to
      */
-    const switchGeneOnly = async (geneName: string): Promise<void> => {
+    const switchGeneOnly = async (geneName: string, speciesUrl?: string): Promise<void> => {
+      
+      if (speciesUrl) {
+        handleExternalSpecies(speciesUrl, geneName);
+        return;
+      }
+      
       const geneticElement = await loadGene(geneName);
+      
       if (geneticElement) {
         addGeneticElements([geneticElement]);
         setActiveGeneId(geneticElement.id);
@@ -141,7 +161,13 @@ export const createViewSwitchProvider = () => {
      * @param viewId - ID of the view to switch to
      * @param geneName - Name of the gene to switch to
      */
-    const switchViewAndGene = async (viewId: string, geneName: string): Promise<void> => {
+    const switchViewAndGene = async (viewId: string, geneName: string, speciesUrl?: string): Promise<void> => {
+      
+      if (speciesUrl) {
+        handleExternalSpecies(speciesUrl, geneName);
+        return;
+      }
+
       const targetView = validateView(viewId);
       const geneticElement = await loadGene(geneName);
 
@@ -161,7 +187,7 @@ export const createViewSwitchProvider = () => {
           activeGene, 
           switchViewOnly,
           switchGeneOnly,
-          switchViewAndGene 
+          switchViewAndGene
         }}
       >
         {children}