issue-96 (#97)

closes issue #96

Author: larrybabb

README.md

@@ -6,6 +6,8 @@ The chrome extension is used by the ClinGen curation workflow (link) ...
 - The google sheet containing these curations is then utilized by the downstream systems to generate QC reports, statitistics and submissions of these curations to be regularly submitted to NCBI clinvar to support the eventual integration into the actual ClinVar dataset.
 
 ## Release Notes
+### v3.2
+* ClinVar UI changes on Jun.09.2025 introduced issues with the germline SCV table information scraping from the html. This has been resolved.
 
 ### v3.1
 * ClinVar UI changes on Feb.24.2025 introduced issues with the top-level VCV information scraping from the html. This has been resolved.

scvc/content.js

@@ -4,8 +4,8 @@ const SCV_RANGE = 'SCVs';
 // Inform the background page that
 // this tab should have a page-action.
 chrome.runtime.sendMessage({
-  from: 'content',
-  subject: 'showPageAction',
+    from: 'content',
+    subject: 'showPageAction',
 });
 
 function getMatch(text, re, grp) {
@@ -18,7 +18,7 @@ function getMatch(text, re, grp) {
 }
 
 function extractClinVarData() {
-   
+
     // Collect the necessary data.
     var cond_origin_re = /\W*Allele origin:.*?(\w+([\,\s]+\w+)*)/is;
     var review_method_re = /(practice guideline|reviewed by expert panel|no assertion provided|no interpretation for the single variant|criteria provided, multiple submitters, no conflicts|criteria provided, single submitter|criteria provided, conflicting interpretations|no assertion criteria provided|no classification provided|Flagged submission).*?Method:.*?([\w\,\s]+)*/is;
@@ -47,20 +47,21 @@ function extractClinVarData() {
 
     var variantBox = document.evaluate("//div[@id='new-variant-details']//dl", document, null, XPathResult.ANY_TYPE, null );
     var variantBoxHTML = variantBox.iterateNext().innerHTML;
-  
+
     clinvarData.name            = document.querySelectorAll('#variant-details-table div div dl dd p')[0].innerText;
     clinvarData.vcv             = getMatch(variantBoxHTML, vcv_accession_re, 1);
     clinvarData.variation_id    = getMatch(variantBoxHTML, vcv_variation_id_re, 1);
     clinvarData.vcv_review      = vcvReviewStatus;
     clinvarData.vcv_interp      = vcvClassificationText;
-  
+
     var timelineArray = document.querySelectorAll('table.timeline-table tbody tr td');
     clinvarData.vcv_most_recent = timelineArray[2].innerHTML;
     clinvarData.vcv_eval_date   = timelineArray[3].innerHTML;
-      
-    var scvarray = document.querySelectorAll('#new-submission-germline table tbody tr');
+    
+
+    var scvarray = document.querySelectorAll('.submissions-germline-list tbody tr.germline-sub-col');
     scvarray.forEach(myFunction);
-  
+
     function myFunction(value, index, array) {
         var interp_match = value.cells[0].innerHTML.match(interp_re);
         var review_method_match = value.cells[1].innerHTML.match(review_method_re);

scvc/manifest.json

@@ -1,7 +1,7 @@
 {
   "manifest_version": 3,
   "name": "ClinVar Curator (v3)",
-  "version": "3.1",
+  "version": "3.2",
   "description": "Extract SCVs for annotation based on the ClinGen ClinVar Curation prolicies.",
 
   "key": "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAwC5g4vkDlMPFTsByPnG9WI9lY+IPWddES8SK3cxCuBQE5qSdgEgtDhrRLhXSvcIdUUCDwD7JzEPdQ0IhC3APwsKQJPQlDRweZvyFaTJOm6r5Blp3HvLphDuKZQwUoEzMuXK7IAby05kXPZTMSHas+0m00hHoR8ls//tqKoYt7N/lVj6Mry6nSpr5wFU17HPO8MksyxFlNDhu5OYcgOdTNjUiWthjZ8Xxd0ajdaR1QRoqVCQduUTSAzeptQ1+zYZtEX7+HF8jfZqc5BQDa5GoCuDyTvFvQAHl3Phz3zMWpvcGWR3jCMHD5zthiO8NKX+h2fXbGGrYhuwtQmHLWmTAsQIDAQAB",