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1.11 (#71)
* Remove access to backing gsheet and fix submitter name capture. * update read.me
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‎README.md‎

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Original file line numberDiff line numberDiff line change
@@ -8,11 +8,24 @@ The chrome extension is used by the ClinGen curation workflow (link) ...
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This "main" branch is for the v2.x which split from v1.x after 1.9.6. The latest changes to v1.x can be found in the 1.10 branch.
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## Release Notes
11-
### v1.10 changes (see branch 1.10 for code)
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### v1.11 changes
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* Changed data repository google sheet to prevent user direct access in order to prevent user's from changing data after capture.
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* Fixed bug in capturing submitter name introduced in v1.10.
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### v1.10 changes
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This version required some considerable modifications to deal with the html changes to the ClinVar HTML in handling the new section at the bottom called "Flagged Submissions".
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* Chrome extension broke due to new "Flagged Submission" UI. [#69](https://github.com/clingen-data-model/clinvar-curation-input-tool/issues/69)
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* In the chrome extension change 'non-contributory' to 'flagging candidate' [#68](https://github.com/clingen-data-model/clinvar-curation-input-tool/issues/68)
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20+
### v1.9.8 changes
21+
* Update Non-contributory category headings (missed in 1.9.7) [#57](https://github.com/clingen-data-model/clinvar-scv-curator-ext/issues/57)
22+
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### v1.9.7 changes
24+
* Modify text of several Non-contributory reasons (and update historical data to match modified text) [#58](https://github.com/clingen-data-model/clinvar-scv-curator-ext/issues/58)
25+
* Update Non-contributory action reasons (remove some, modify text of others) [#57](https://github.com/clingen-data-model/clinvar-scv-curator-ext/issues/57)
26+
* Remove Follow Up option [#57](https://github.com/clingen-data-model/clinvar-scv-curator-ext/issues/57)
27+
* Remove ability to annotate a VCV [#57](https://github.com/clingen-data-model/clinvar-scv-curator-ext/issues/57)
28+
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### v2.0.2 changes
1730
* Updated category headings that were missed in the 2.0.1 release [#57](https://github.com/clingen-data-model/clinvar-scv-curator-ext/issues/57)
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‎scvc/background.html‎

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@@ -0,0 +1,8 @@
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<html>
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<head>
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<title></title>
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<script src="background.js"></script>
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</head>
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<body></body>
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<script src="https://apis.google.com/js/client.js?onload=onGAPILoad"></script>
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</html>

‎scvc/background.js‎

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const API_KEY = 'AIzaSyADs3YruA9LTaRjc7hS94SQvKbQXJSpMp0';
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const DISCOVERY_DOCS = ["https://sheets.googleapis.com/$discovery/rest?version=v4"];
3+
4+
// Create a rule that will show the page action when the conditions are met.
5+
const kMatchRule = {
6+
// Declare the rule conditions.
7+
conditions: [new chrome.declarativeContent.PageStateMatcher({
8+
pageUrl: {hostEquals: 'www.ncbi.nlm.nih.gov',
9+
pathContains: 'variation'}})],
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// Shows the page action when the condition is met.
11+
actions: [new chrome.declarativeContent.ShowPageAction()]
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}
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// Register the runtime.onInstalled event listener.
15+
chrome.runtime.onInstalled.addListener(function() {
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// Overrride the rules to replace them with kMatchRule.
17+
chrome.declarativeContent.onPageChanged.removeRules(undefined, function() {
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chrome.declarativeContent.onPageChanged.addRules([kMatchRule]);
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});
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});
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function onGAPILoad() {
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gapi.client.init({
24+
apiKey: API_KEY,
25+
discoveryDocs: DISCOVERY_DOCS,
26+
}).then(function () {
27+
console.log('gapi initialized');
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}, function(error) {
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console.log('error on initialize', error);
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alert('error on initialize...'+error);
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});
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}
33+
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// Listen for messages from popup.js
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chrome.extension.onMessage.addListener(
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function(request, sender, sendResponse) {
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// verify that the request originated from the chrome-extension popup.html form
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if (!sender.url.includes("chrome-extension")) return false;
40+
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// Get the users email
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chrome.identity.getProfileUserInfo(function(userinfo){
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if (!userinfo.email) {
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alert("No email captured. Please set your browser profile to sync with your google account to bypass this message in the future.");
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}
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else {
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request.user_email=userinfo.email;
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}
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});
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// Get the token
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chrome.identity.getAuthToken({interactive: true}, function(token) {
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// Set scvc auth token
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gapi.auth.setToken({
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'access_token': token,
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});
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let body = {};
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let range = "";
61+
62+
if (request.scv) {
63+
range = request.scv_range;
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body = {values: [[
65+
request.vcv,
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request.name,
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request.scv,
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request.submitter,
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request.interp,
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request.action,
71+
request.reason,
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request.notes,
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new Date(), // Timestamp
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request.submitter_id,
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request.variation_id,
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request.user_email
77+
]]};
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}
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80+
// Append values to the spreadsheet
81+
gapi.client.sheets.spreadsheets.values.append({
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spreadsheetId: request.spreadsheet,
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range: range,
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valueInputOption: 'USER_ENTERED',
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resource: body
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}).then((response) => {
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// On success
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console.log(`${response.result.updates.updatedCells} cells appended.`)
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sendResponse({success: true});
90+
}, function(error) {
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// On error
92+
console.log('error appending values', error)
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alert("Error appending values to google sheet...\n"+JSON.stringify(error));
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});
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})
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// Wait for response
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return true;
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}
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);

‎scvc/content.js‎

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
1-
const SPREADSHEET_ID = '1pzuWR409vSmoFX9inmoU6el6vjG0SniB1KrxWLeVpaA'; // production
2-
// const SPREADSHEET_ID = '1W1rbALtDt9CmhoTsLUYJEYKOeakzWAlZrtIhGSUl5II'; // dev copy
1+
//const SPREADSHEET_ID = '1pzuWR409vSmoFX9inmoU6el6vjG0SniB1KrxWLeVpaA';
2+
const SPREADSHEET_ID = '1dUnmBZSnz3aeB948b7pIq0iT7_FuCDvtv6FXaVsNcOo';
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const SCV_RANGE = 'SCVs';
44
const VCV_RANGE = 'VCVs';
55

@@ -13,30 +13,30 @@ chrome.runtime.sendMessage({
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// Listen for messages from the popup.
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chrome.runtime.onMessage.addListener((msg, sender, response) => {
1515

16-
// console.log('===== CONTENT.js event recieved: msg:', msg, new Date().getTime())
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// First, validate the message's structure.
18-
if ((msg.from === 'popup') && (msg.subject === 'DOMInfo')) {
19-
function getMatch(text, re, grp) {
20-
var result;
21-
result = text.match(re);
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if (result === null) {
23-
return "";
24-
}
25-
return result[grp];
26-
}
27-
// Collect the necessary data.
28-
var cond_origin_re = /(.*)\nAllele origin: (.*)/i;
29-
var review_method_re = /(.*)\n.*\n*Method: (.*)/i;
30-
var subm_scv_re = /(.*)(\n.*)*\nAccession: (.*)\nFirst in ClinVar: (.*)\nLast updated: (.*)/i;
31-
var interp_re = /(.*)\n\((.*)\)/i;
32-
var subm_id_re = /\/clinvar\/submitters\/([0-9]*)\//i;
16+
// First, validate the message's structure.
17+
if ((msg.from === 'popup') && (msg.subject === 'DOMInfo')) {
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34-
var vcv_interp_re = /<dt>Interpretation:<\/dt>\s*<dd.*>\s*(.*)[\x200B]*\s*<p>/i
35-
var vcv_revstat_re = /<dt>Review status:<\/dt>\s*<dd>.*(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).*\<\/dd>\s*/is
36-
var vcv_most_recent_re = /<dt>Most recent Submission:<\/dt>\s*<dd>\s*(\w{3} \d+\, \d{4})\s*<\/dd>/i
37-
var vcv_last_eval_re = /<dt>Last evaluated:<\/dt>\s*<dd>\s*(\w{3} \d+\,\d{4})\s*<\/dd>\s*/i
38-
var vcv_accession_re = /<dt>Accession:<\/dt>\s*<dd>\s*(VCV[0-9]*\.[0-9]*)\s*<\/dd>\s*/i
39-
var vcv_variation_id_re = /<dt>Variation ID:<\/dt>\s*<dd>\s*(\d+)\s*<\/dd>\s*/i
19+
function getMatch(text, re, grp) {
20+
var result;
21+
result = text.match(re);
22+
if (result === null) {
23+
return "";
24+
}
25+
return result[grp];
26+
}
27+
28+
// Collect the necessary data.
29+
var cond_origin_re = /\W*Allele origin:.*?(\w+([\,\s]+\w+)*)/is;
30+
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|Flagged submission)\s(Method:\s([\w\,\s]+))*/is;
31+
var subm_scv_re = /\W*"https:\/\/www\.ncbi\.nlm\.nih\.gov\/\/clinvar\/submitters\/(\d+)\/">(.+)<\/a>.*?Accession:.*?(SCV\d+\.\d+).*?First in ClinVar:\W(\w+\s\d+\,\s\d+).*?Last updated:.*?(\w+\s\d+\,\s\d+)/is;
32+
var interp_re = /\W*(\w+([\s\/\-\,]*\w+)*).*?\(([\w\s\,\-]+)\)/is;
33+
34+
var vcv_interp_re = /Interpretation:.*?<dd.*?>.*?(\w+([\s\/\-\,]*\w+)*)/is;
35+
var vcv_revstat_re = /Review status:.*?(<[^>]+>[^<]*?)*?(\w+([\,\s]+\w+)*)/is;
36+
var vcv_most_recent_re = /Most recent Submission:.*?(\w+\s\d+\,\s\d+)/is;
37+
var vcv_last_eval_re = /Last evaluated:.*?(\w+\s\d+\,\s\d+)/is;
38+
var vcv_accession_re = /Accession:.*?(VCV\d+\.\d+)/is;
39+
var vcv_variation_id_re = /Variation ID:.*?(\d+)/is;
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4141
var domInfo = {
4242
spreadsheet: SPREADSHEET_ID,
@@ -52,44 +52,41 @@ chrome.runtime.onMessage.addListener((msg, sender, response) => {
5252
row: []
5353
};
5454

55-
var variantBox = document.evaluate(".//div[contains(concat(' ', @class, ' '),' variant-box ')]/dl", document, null, XPathResult.ANY_TYPE, null);
56-
var variantBoxHTML = variantBox.iterateNext().innerHTML;
57-
domInfo.vcv = getMatch(variantBoxHTML, vcv_accession_re, 1);
58-
domInfo.vcv_review = getMatch(variantBoxHTML, vcv_revstat_re, 1);
59-
domInfo.vcv_most_recent = getMatch(variantBoxHTML, vcv_most_recent_re, 1);
60-
domInfo.vcv_eval_date = getMatch(variantBoxHTML, vcv_last_eval_re, 1);
61-
domInfo.variation_id = getMatch(variantBoxHTML, vcv_variation_id_re, 1);
62-
domInfo.vcv_interp = getMatch(variantBoxHTML, vcv_interp_re, 1);
55+
var variantBox = document.evaluate(".//div[contains(concat(' ', @class, ' '),' variant-box ')]/dl", document, null, XPathResult.ANY_TYPE, null );
56+
var variantBoxHTML = variantBox.iterateNext().innerHTML;
6357

64-
domInfo.name = document.querySelectorAll('#id_first h4')[0].innerText;
65-
var scvarray = document.querySelectorAll('#assertion-list tbody tr');
66-
scvarray.forEach(myFunction);
58+
domInfo.vcv = getMatch(variantBoxHTML, vcv_accession_re, 1);
59+
domInfo.vcv_review = getMatch(variantBoxHTML, vcv_revstat_re, 2);
60+
domInfo.vcv_most_recent = getMatch(variantBoxHTML, vcv_most_recent_re, 1);
61+
domInfo.vcv_eval_date = getMatch(variantBoxHTML, vcv_last_eval_re, 1);
62+
domInfo.variation_id = getMatch(variantBoxHTML, vcv_variation_id_re, 1);
63+
domInfo.vcv_interp = getMatch(variantBoxHTML, vcv_interp_re, 1);
6764

68-
function myFunction(value, index, array) {
69-
var interp_match = value.cells[0].innerText.match(interp_re);
70-
var review_method_match = value.cells[1].innerText.match(review_method_re);
71-
var cond_origin_match = value.cells[2].innerText.match(cond_origin_re);
72-
var subm_scv_match = value.cells[3].innerText.match(subm_scv_re);
73-
var subm_id = value.cells[3].innerHTML.match(subm_id_re)[1];
65+
domInfo.name = document.querySelectorAll('#id_first h4')[0].innerText;
66+
var scvarray = document.querySelectorAll('#assertion-list tbody tr');
67+
68+
scvarray.forEach(myFunction);
7469

75-
domInfo.row.push({
76-
submitter: subm_scv_match[1],
77-
scv: subm_scv_match[3],
78-
submitter_id: subm_id,
79-
subm_date: subm_scv_match[5],
80-
condition: cond_origin_match[1],
81-
origin: cond_origin_match[2],
82-
review: review_method_match[1],
83-
method: review_method_match[2],
84-
interp: interp_match[1],
85-
eval_date: interp_match[2]
86-
});
87-
}
88-
// Directly respond to the sender (popup),
89-
// through the specified callback.
90-
response(domInfo);
91-
}
92-
93-
return true;
70+
function myFunction(value, index, array) {
71+
var interp_match = value.cells[0].innerHTML.match(interp_re);
72+
var review_method_match = value.cells[1].innerText.match(review_method_re);
73+
var cond_origin_match = value.cells[2].innerHTML.match(cond_origin_re);
74+
var subm_scv_match = value.cells[3].innerHTML.match(subm_scv_re);
9475

76+
domInfo.row.push({
77+
submitter_id: subm_scv_match[1],
78+
submitter: subm_scv_match[2],
79+
scv: subm_scv_match[3],
80+
subm_date: subm_scv_match[5],
81+
origin: cond_origin_match[1],
82+
review: review_method_match[1],
83+
method: review_method_match[3] == undefined ? "" : review_method_match[3],
84+
interp: interp_match[1],
85+
eval_date: interp_match[3]
86+
});
87+
}
88+
// Directly respond to the sender (popup),
89+
// through the specified callback.
90+
response(domInfo);
91+
}
9592
});

‎scvc/manifest.json‎

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@@ -1,32 +1,29 @@
11
{
2-
"name": "ClinVar Curator",
3-
"version": "2.0.2",
4-
"description": "Capture SCV notes from ClinVar variant screen in a google sheet.",
5-
"manifest_version": 3,
6-
"key": "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAwC5g4vkDlMPFTsByPnG9WI9lY+IPWddES8SK3cxCuBQE5qSdgEgtDhrRLhXSvcIdUUCDwD7JzEPdQ0IhC3APwsKQJPQlDRweZvyFaTJOm6r5Blp3HvLphDuKZQwUoEzMuXK7IAby05kXPZTMSHas+0m00hHoR8ls//tqKoYt7N/lVj6Mry6nSpr5wFU17HPO8MksyxFlNDhu5OYcgOdTNjUiWthjZ8Xxd0ajdaR1QRoqVCQduUTSAzeptQ1+zYZtEX7+HF8jfZqc5BQDa5GoCuDyTvFvQAHl3Phz3zMWpvcGWR3jCMHD5zthiO8NKX+h2fXbGGrYhuwtQmHLWmTAsQIDAQAB",
7-
"oauth2": {
8-
"client_id": "974091131481-ffhgjpl8vh91e5qber2486eikrhf42ec.apps.googleusercontent.com",
9-
"scopes": ["https://www.googleapis.com/auth/spreadsheets"]
10-
},
11-
"content_security_policy": {
12-
"extension_pages": "script-src 'self'; object-src 'self'"
13-
},
14-
"action": {
15-
"default_title": "Clinvar Curator",
16-
"default_popup": "popup.html"
17-
},
18-
"background": {
19-
"service_worker": "service-worker.js",
20-
"type": "module"
21-
},
22-
"permissions": [
23-
"identity", "identity.email", "storage", "declarativeContent", "tabs"
24-
],
25-
"host_permissions": ["https://www.ncbi.nlm.nih.gov/clinvar/variation/*"],
26-
"content_scripts": [{
27-
"matches": ["https://www.ncbi.nlm.nih.gov/clinvar/variation/*"],
28-
"js": ["content.js"],
29-
"run_at": "document_end",
30-
"all_frames": false
31-
}]
2+
"name": "ClinVar Curator",
3+
"version": "1.11",
4+
"description": "Capture SCV notes from ClinVar variant screen in a google sheet.",
5+
"manifest_version": 2,
6+
"key" : "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAwC5g4vkDlMPFTsByPnG9WI9lY+IPWddES8SK3cxCuBQE5qSdgEgtDhrRLhXSvcIdUUCDwD7JzEPdQ0IhC3APwsKQJPQlDRweZvyFaTJOm6r5Blp3HvLphDuKZQwUoEzMuXK7IAby05kXPZTMSHas+0m00hHoR8ls//tqKoYt7N/lVj6Mry6nSpr5wFU17HPO8MksyxFlNDhu5OYcgOdTNjUiWthjZ8Xxd0ajdaR1QRoqVCQduUTSAzeptQ1+zYZtEX7+HF8jfZqc5BQDa5GoCuDyTvFvQAHl3Phz3zMWpvcGWR3jCMHD5zthiO8NKX+h2fXbGGrYhuwtQmHLWmTAsQIDAQAB",
7+
"oauth2": {
8+
"client_id": "974091131481-ffhgjpl8vh91e5qber2486eikrhf42ec.apps.googleusercontent.com",
9+
"scopes":["https://www.googleapis.com/auth/spreadsheets"]
10+
},
11+
"content_security_policy": "script-src 'self' https://apis.google.com/; object-src 'self'",
12+
"page_action": {
13+
"default_title": "Clinvar Curator",
14+
"default_popup": "popup.html"
15+
},
16+
"background": {
17+
"page": "background.html",
18+
"persistent": true
19+
},
20+
"permissions": [
21+
"https://www.ncbi.nlm.nih.gov/clinvar/variation/*","identity", "identity.email", "storage", "declarativeContent"
22+
],
23+
"content_scripts": [{
24+
"matches": ["https://www.ncbi.nlm.nih.gov/clinvar/variation/*"],
25+
"js": ["content.js"],
26+
"run_at": "document_end",
27+
"all_frames": false
28+
}]
3229
}

‎scvc/popup.html‎

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Original file line numberDiff line numberDiff line change
@@ -12,10 +12,10 @@
1212
<body class="p-2" style="width:600px;">
1313

1414
<div class="container">
15-
<div class="row bg-primary text-white">
15+
<!-- <div class="row bg-primary text-white">
1616
<div class="col"><a href="#" id="gsheetlink" class="text-white">Google Sheet</a></div>
1717
<div class="col small text-right text-white">(right click to open in a new window)</div>
18-
</div>
18+
</div> -->
1919
<div class="row bg-primary text-white px-2">
2020
<h4 id="vcvid">VCV ID</h4>
2121
</div>
@@ -25,6 +25,7 @@ <h6 id="name">Variant Name</h6>
2525

2626
<div class="row p-2 border border-primary border-bottom-0">
2727
<div class="form-group">
28+
<label for="scvselect">Select an SCV</label>
2829
<label for="scvselect">Select an SCV</label>
2930
<select id="scvselect" name="scvselect" class="form-control" >
3031
<option selected value="">Choose...</option>
@@ -71,7 +72,6 @@ <h6 id="name">Variant Name</h6>
7172
<input type="hidden" id="submitter" name="submitter"/>
7273
<input type="hidden" id="submitter_id" name="submitter_id"/>
7374
<input type="hidden" id="subm_date" name="subm_date"/>
74-
<input type="hidden" id="condition" name="condition"/>
7575
<input type="hidden" id="origin" name="origin"/>
7676
<input type="hidden" id="review" name="review"/>
7777
<input type="hidden" id="method" name="method"/>
@@ -95,33 +95,9 @@ <h6 id="name">Variant Name</h6>
9595
<select id="action" name="action" class="form-control" disabled>
9696
<option selected value="">Choose...</option>
9797
<option id="no-chg-opt" value="No Change">No Change</option>
98-
<!-- <option id="follow-up-opt" value="Follow Up">Follow Up</option> -->
99-
<option id="non-contrib-opt" value="Non-contributory">Non-contributory</option>
100-
<!-- <option id="override-opt" value="Override">Override</option> -->
98+
<option id="non-contrib-opt" value="Flagging Candidate">Flagging Candidate</option>
10199
</select>
102100
</div>
103-
104-
<!-- NOTE: commenting out the Override option since rel 1.9.6
105-
<div id="override" class="col-sm">
106-
<div class="row">
107-
<label for="override-field">Override Field</label>
108-
<select id="override-field" name="override-field" class="form-control" disabled>
109-
<option selected value="">Choose...</option>
110-
<option value="Allele Origin">Allele Origin</option>
111-
<option value="Collection Method">Collection Method</option>
112-
<option value="Condition">Condition</option>
113-
<option value="Inheritance">Inheritance</option>
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<option value="Review Status">Review Status</option>
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<option value="Significance">Significance</option>
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<option value="Other">Other (see notes)...</option>
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</select>
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</div>
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<div class="row">
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<label for="override-value">New Value</label>
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<input id="override-value" name="override-value" class="form-control" disabled>
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</div>
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</div>
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-->
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</div>
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</div>
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