Fix PubMed URL issue

src/services/flatmapQueries.js

@@ -222,7 +222,7 @@ let FlatmapQueries = function () {
     this.origins = []
     this.components = []
     if (!keastIds || keastIds.length == 0) return
-    
+
     let prom1 = this.queryForConnectivity(keastIds, signal) // This on returns a promise so dont need 'await'
     let prom2 = await this.pubmedQueryOnIds(eventData)
     let results = await Promise.all([prom1, prom2])
@@ -281,10 +281,10 @@ let FlatmapQueries = function () {
     if (node.length === 1) { // If the node is in the form [id]
       console.error("Server returns a single node", node)
       return node[0]
-    } else {  
+    } else {
       if (node.length === 2 && node[1].length === 0) { // If the node is in the form [id, []]
         return node[0]
-      } else {  
+      } else {
         return false // If the node is in the form [id, [id1, id2]]
       }
     }
@@ -294,7 +294,7 @@ let FlatmapQueries = function () {
 
     // Check if the node is a single node or a node with multiple children
     let nodeIsSingle = this.findIfNodeIsSingle(node)
-   
+
     // Case where node is in the form [id]
     if (nodeIsSingle) {
       return lookUp[nodeIsSingle]
@@ -390,6 +390,31 @@ let FlatmapQueries = function () {
     return pubmedId.split(':')[1]
   }
 
+  this.extractTermFromURLString = function (urlStr) {
+    if (!urlStr) return;
+
+    const str = decodeURIComponent(urlStr);
+
+    let term = '';
+    const names = [
+      'doi.org/',
+      'nih.gov/pubmed/',
+      'pubmed.ncbi.nlm.nih.gov/'
+    ];
+    names.forEach((name) => {
+      const lastIndex = str.lastIndexOf(name);
+      if (lastIndex !== -1) {
+        term = str.slice(lastIndex + name.length);
+      }
+    });
+
+    if (term.endsWith('/')) {
+      term = term.slice(0, -1);
+    }
+
+    return term;
+  }
+
   this.buildPubmedSqlStatement = function (keastIds) {
     let sql = 'select distinct publication from publications where entity in ('
     if (keastIds.length === 1) {
@@ -430,11 +455,7 @@ let FlatmapQueries = function () {
       this.flatmapQuery(sql).then((data) => {
         // Create pubmed url on paths if we have them
         if (data.values.length > 0) {
-          this.urls = [
-            this.pubmedSearchUrl(
-              data.values.map((id) => this.stripPMIDPrefix(id[0]))
-            ),
-          ]
+          this.urls = this.getURLsForPubMed(data);
           resolve(true)
         } else {
           // Create pubmed url on models
@@ -451,11 +472,7 @@ let FlatmapQueries = function () {
       this.buildPubmedSqlStatementForModels(source)
     ).then((data) => {
       if (Array.isArray(data.values) && data.values.length > 0) {
-        this.urls = [
-          this.pubmedSearchUrl(
-            data.values.map((id) => this.stripPMIDPrefix(id[0]))
-          ),
-        ]
+        this.urls = this.getURLsForPubMed(data);
         return true
       } else {
         this.urls = [] // Clears the pubmed search button
@@ -464,6 +481,19 @@ let FlatmapQueries = function () {
     })
   }
 
+  this.getURLsForPubMed = function (data) {
+    const ids = data.values.map((id) => this.extractTermFromURLString(id[0]));
+    const transformedIDs = this.transformPubMedSearchTerms(ids);
+    return [
+      this.pubmedSearchUrl(transformedIDs)
+    ];
+  };
+
+  this.transformPubMedSearchTerms = function (ids) {
+    // to search multiple terms on PubMed
+    return ids.join(' OR ');
+  };
+
   this.pubmedSearchUrl = function (ids) {
     let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
     let params = new URLSearchParams()