Merge pull request #201 from tcezard/fix/link_ENA_Assembly

Replace the ENA base URL of the link to point to correct location
EBIvariation · Jan 5, 2024 · ec2be8f · ec2be8f
2 parents c4a4891 + 350f418
commit ec2be8f
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/src/js/eva-config.js b/src/js/eva-config.js
@@ -126,7 +126,9 @@ VARIANT_TYPE_SO_MAP = {"SNV": "SO:0001483",
                        "NO_SEQUENCE_ALTERATION" : "SO:0002073",
                        "MNV": "SO:0002007"};
 SO_SERVICE = "http://www.sequenceontology.org/browser/current_release/term";
-ENA_ASSEMBLY_LOOKUP_SERVICE = "https://www.ebi.ac.uk/ena/browser/api/xml";
+ENA_XML_API_SERVICE = "https://www.ebi.ac.uk/ena/browser/api/xml";
+ENA_TEXT_API_SERVICE = "https://www.ebi.ac.uk/ena/browser/api/text";
+ENA_VIEW_LINK_SERVICE = "https://www.ebi.ac.uk/ena/browser/view";
 NCBI_ASSEMBLY_LOOKUP_SERVICE = "https://www.ncbi.nlm.nih.gov/assembly";
 ASSEMBLY_GCA_TO_GCF_SYNONYMS = {"GCA_000409795.2" : "GCF_000409795.2" /*Vervet Monkey*/,
                                 "GCA_001625215.1" : "GCF_001625215.1" /*Carrot*/,

diff --git a/src/js/views/eva-variant-view.js b/src/js/views/eva-variant-view.js
@@ -45,7 +45,7 @@ EvaVariantView.prototype = {
     },
 
     getChromosomeNumberForAccession: function(chromosomeAccession, lineLimit) {
-          var ENA_TEXT_API_URL = "https://www.ebi.ac.uk/ena/browser/api/text/" + chromosomeAccession + "?lineLimit=" + lineLimit + "&annotationOnly=true";
+          var ENA_TEXT_API_URL = ENA_TEXT_API_SERVICE + "/" + chromosomeAccession + "?lineLimit=" + lineLimit + "&annotationOnly=true";
           var response = EvaManager.getAPICallResult(ENA_TEXT_API_URL, 'text', this.contigAccessionNotResolvedHandler.bind(this));
           var responseLines = response.split("\n");
           var numLines = responseLines.length;
@@ -129,7 +129,7 @@ EvaVariantView.prototype = {
         // Default to assembly accession alone
         this.assemblyNameMap[assemblyAccession] = assemblyAccession;
 
-        var assemblyENAXmlUrl = ENA_ASSEMBLY_LOOKUP_SERVICE + "/" + assemblyAccession + "?display=xml"
+        var assemblyENAXmlUrl = ENA_XML_API_SERVICE + "/" + assemblyAccession + "?display=xml"
         var xmlResult = EvaManager.getAPICallResult(assemblyENAXmlUrl, 'xml', this.assemblyAccessionNotResolvedHandler.bind(this));
 
         if (xmlResult) {
@@ -146,7 +146,7 @@ EvaVariantView.prototype = {
             assembly = assembly.toUpperCase();
             var assemblyLookupService = "";
             if (assembly.startsWith("GCA")) {
-                assemblyLookupService = ENA_ASSEMBLY_LOOKUP_SERVICE;
+                assemblyLookupService = ENA_VIEW_LINK_SERVICE;
             } else if (assembly.startsWith("GCF")) {
                 assemblyLookupService = NCBI_ASSEMBLY_LOOKUP_SERVICE;
             }