Merge pull request #202 from apriltuesday/EVA-3462

EVA-3462: Support DOIs in study view
EBIvariation · Jan 11, 2024 · 3a7ffd0 · 3a7ffd0
2 parents ec2be8f + b003580
commit 3a7ffd0
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Showing 6 changed files with 31 additions and 17 deletions.
diff --git a/Gruntfile.js b/Gruntfile.js
@@ -15,7 +15,7 @@ module.exports = function (grunt) {
         // Metadata.
         meta: {
             version: {
-                eva: '4.4.12'
+                eva: '4.4.13'
             },
             submissionTemplate: {
                 version: 'V1.1.5'

diff --git a/bower.json b/bower.json
@@ -1,6 +1,6 @@
 {
   "name": "eva-web",
-  "version": "4.4.12",
+  "version": "4.4.13",
   "homepage": "https://github.com/EBIvariation/eva-web",
   "authors": [
     "EVA development team <[email protected]>"

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "commons",
-  "version": "4.4.12",
+  "version": "4.4.13",
   "description": "javascript commons",
   "repository": {
     "type": "git",

diff --git a/src/js/eva.js b/src/js/eva.js
@@ -414,12 +414,24 @@ Eva.prototype = {
         });
     },
     _getPublications: function() {
-        $('.pubmed-id').each(function(i, obj) {
+        $('.publication-id').each(function(i, obj) {
             obj = $(obj);
-            var pubmedId = obj.html();
-            obj.html('<p>Attempting to retrieve publication information for PubMed ID <a class="external publication" href="http://europepmc.org/abstract/MED/' + pubmedId + '">' + pubmedId + '...</p>');
-            if(pubmedId && pubmedId != '-') {
-                var url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=ext_id:' + pubmedId + ' src:med&format=json';
+            var curie = obj.html();
+            if (curie && curie != '-') {
+                obj.html('<p>Attempting to retrieve publication information for ' + curie + '...</p>');
+                var splitCurie = curie.split(":");
+                if (splitCurie.length < 2) {
+                    var datasource = "PUBMED";
+                    var identifier = splitCurie[0];
+                } else {
+                    var datasource = splitCurie[0].toUpperCase();
+                    var identifier = splitCurie[1];
+                }
+                // Assume this is a PubMed ID or DOI
+                var url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=ext_id:' + identifier + ' src:med&format=json';
+                if (datasource === "DOI") {
+                    url = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DOI:' + identifier + '&format=json';
+                }
                 // Make the actual AJAX call...
                 $.ajax({
                     type: 'GET',
@@ -429,28 +441,30 @@ Eva.prototype = {
                     success: function (response) {
                         var data = response.resultList.result[0];
                         if (data) {
+                            var id = data.id;
+                            var source = data.source;
                             var title = data.title;
                             var authors = data.authorString;
                             var journal = data.journalTitle;
                             var volume = data.journalVolume;
                             var year = data.pubYear;
                             var pages = data.pageInfo;
-                            var pmid = data.pmid;
 
-                            var paper_output = '<p class="publications"><a class="external publication" href="http://europepmc.org/abstract/MED/' + pmid + '">' + title + '</a><br />';
+                            var paper_output = '<p class="publications"><a class="external publication" href="http://europepmc.org/abstract/' + source + '/' + id + '">' + title + '</a><br />';
                             paper_output += authors + '<br />';
                             paper_output += '<em>' + journal + '</em> <strong>' + volume + '</strong>:' + year + ' ' + pages + '</p>';
                             obj.html(paper_output);
                         }
                     },
                     error: function (x, y, z) {
-                        obj.html('PubMed:<a class="external publication" href="http://www.ncbi.nlm.nih.gov/pubmed/?term=' + pubmedId + '" target="_blank">' + pubmedId + '</a><br />');
+                        // Don't necessarily know where this CURIE comes from, so just output it without link
+                        obj.html(curie+'<br />');
                         // x.responseText should have what's wrong
                     }
                 });
 
-            }else{
-                obj.html(pubmedId);
+            } else {
+                obj.html(curie);
             }
         });
         return;

diff --git a/src/js/views/eva-study-view.js b/src/js/views/eva-study-view.js
@@ -143,10 +143,10 @@ EvaStudyView.prototype = {
         var pubLinks = '';
         if(!_.isEmpty(publications) && publications != '-') {
             for (i = 0; i < publications.length; i++) {
-                pubLinks += '<a class="pubmed-id" href="http://www.ncbi.nlm.nih.gov/pubmed/?term=' + publications[i] + '" target="_blank">' + publications[i]  + '</a><br />'
+                pubLinks += '<span class="publication-id">' + publications[i]  + '</span><br />'
             }
         } else {
-            pubLinks = '<span class="pubmed-id">-</span>';
+            pubLinks = '<span class="publication-id">-</span>';
         }
 
         // Links to taxonomies

diff --git a/tests/acceptance/study_view.js b/tests/acceptance/study_view.js
@@ -183,8 +183,8 @@ function dgvaCheckSummaryTable(driver){
 }
 
 function checkPublications(driver){
-    driver.wait(until.elementLocated(By.className("pubmed-id")), config.wait()).then(function(text) {
-       driver.findElement(By.className('pubmed-id')).getText().then(function(text){
+    driver.wait(until.elementLocated(By.className("publication-id")), config.wait()).then(function(text) {
+       driver.findElement(By.className('publication-id')).getText().then(function(text){
            var regExp = /^-$|^\w+/;
            if(text != '-'){
                text = text.split("\n");