Replace Prototype.js with jQuery #412

Copilot · 2026-01-27T16:07:44Z

Replaces Prototype.js patterns with jQuery to avoid Array.prototype pollution that was interfering with phylotree.js.

Changes Made

jQuery Integration

Added jQuery 3.7.1 locally to /scripts/jquery-3.7.1.min.js
Updated mainTemplate.jsp and defaultTemplate.jsp to load local jQuery

JavaScript File Updates

common.js:

new Ajax.Request() → $.ajax() with dataType: 'text'
$$('.class') → $('.class')
$('id') → $('#id')
new Element() → $('<tag>')
.observe() → .on()
.hasClassName() → .hasClass()
.firstDescendant() → .children().first()

submissionSummary.js:

.addClassName() → .addClass()
.select() → .find()
.update() → .html()
.invoke('setStyle', ...) → .css()
.size() → .length
AJAX call uses dataType: 'text' to prevent auto script execution

analysisEditor.js:

Same pattern replacements as above

DWR Autocomplete Error Handling

Added proper error handlers to all DWR autocomplete callbacks in defaultTemplate.jsp
Configured global DWR error handler to log errors to console instead of showing alert dialogs
Prevents "undefined" error alerts when database returns empty results

Code Review Fixes

Use jQuery's .prop() method for checkbox/radio checked property
Use attribute selectors for IDs containing dots

Removed

native-compat.js (no longer needed with jQuery)

Security

Security scanning completed with no alerts found
jQuery 3.7.1 has no known vulnerabilities

Notes

The eval() usage in submissionSummary.js is pre-existing code that parses the server response. This should be addressed separately with proper JSON parsing.

Original prompt

The JS code base was quite reliant on prototype.js, an old JavaScript library that interfered with the phylogenetic tree drawer widget, and more generally, was doing too much with the JavaScript API. We are phasing this out, but this is raising some challenges that need to be addressed. In particular, we need less-intrusive alternatives to enable the following:

DOM Selection/Manipulation - $('id'), $$('.class'), .select(), .update() - this occurs mostly in common.js and we simply need replacement calls to get elements
by ID, class name, and so on. EIther this is done within common.js or by using a modern drop-in replacement (possibly jQuery?)

AJAX Requests - new Ajax.Request() in common.js (openHelp function),
submissionSummary.js. Here, too, we need a modern drop-in replacement.

Event Handling - .observe('click', ...), especially for check/uncheck all buttons in
common.js. Same: what do we do here. Implement our own solution or migrate to a modern library?

Element Creation - new Element('input', {...}). Here too: how to work around this?

Class/Style Methods - .addClassName(), .hasClassName(), .setStyle(), .invoke(). How to work around this?

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

Co-authored-by: rvosa <[email protected]>

rvosa · 2026-01-27T16:16:23Z

@copilot 1. Pivot to jQuery

Co-authored-by: rvosa <[email protected]>

Copilot · 2026-01-27T16:25:31Z

@copilot 1. Pivot to jQuery

Done. Pivoted to jQuery 3.7.1 (loaded via CDN with SRI hash). All Prototype.js patterns in common.js, submissionSummary.js, and analysisEditor.js have been converted to jQuery equivalents. The native-compat.js shim has been removed. See commit 6a20de3.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

cdnjs.cloudflare.com
- Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)
code.jquery.com
- Triggering command: /usr/bin/curl curl -sL REDACTED -o jquery.min.js (dns block)
- Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)
- Triggering command: /usr/bin/wget wget -q REDACTED -O jquery.min.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

Configure Actions setup steps to set up my environment, which run before the firewall is enabled
Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Update image paths in styles.css

rvosa · 2026-01-27T20:13:43Z

@copilot can we just have jQuery locally in the same place as the other scripts? There's really no need for complicated CDN trickery and it feels more fragile to me. Call me oldschool.

Co-authored-by: rvosa <[email protected]>

Copilot · 2026-01-27T20:19:37Z

@copilot can we just have jQuery locally in the same place as the other scripts? There's really no need for complicated CDN trickery and it feels more fragile to me. Call me oldschool.

Added jQuery 3.7.1 locally to /scripts/jquery-3.7.1.min.js and updated both templates to reference it. See commit a2edee3.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

code.jquery.com
- Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)
- Triggering command: /usr/bin/curl curl -sL REDACTED -o jquery-3.7.1.min.js (dns block)
- Triggering command: /usr/bin/wget wget -q REDACTED -O jquery-3.7.1.min.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

Configure Actions setup steps to set up my environment, which run before the firewall is enabled
Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

rvosa · 2026-01-27T20:27:05Z

@copilot not quite there yet:

VM993:26 Uncaught SyntaxError: Failed to execute 'appendChild' on 'Node': Unexpected token ':'
    at m (jquery-3.7.1.min.js:2:880)
    at ce.globalEval (jquery-3.7.1.min.js:2:3031)
    at text script (jquery-3.7.1.min.js:2:80994)
    at jquery-3.7.1.min.js:2:77349
    at l (jquery-3.7.1.min.js:2:77466)
    at XMLHttpRequest.<anonymous> (jquery-3.7.1.min.js:2:80265)
m @ jquery-3.7.1.min.js:2
globalEval @ jquery-3.7.1.min.js:2
text script @ jquery-3.7.1.min.js:2
(anonymous) @ jquery-3.7.1.min.js:2
l @ jquery-3.7.1.min.js:2
(anonymous) @ jquery-3.7.1.min.js:2
XMLHttpRequest.send
send @ jquery-3.7.1.min.js:2
ajax @ jquery-3.7.1.min.js:2
(anonymous) @ submissionSummary.js:500
initialize @ common.js:57
onload @ analyses.html:96

Co-authored-by: rvosa <[email protected]>

Copilot · 2026-01-27T20:29:31Z

@copilot not quite there yet:

...

Fixed. The error was caused by jQuery attempting to auto-execute the server response as a script. Added dataType: 'text' to both AJAX calls in common.js and submissionSummary.js to prevent this behavior. See commit 2a3384d.

rvosa · 2026-01-27T20:50:18Z

@copilot in /treebase-web/user/citationForm.html, when I attempt to enter a Journal Name, there is a problem. What is supposed to happen is that an autocomplete pops up from which I can select a journal name. Note, however, that the database is empty, so there should be no options to autocomplete. But something else happens: an error box pops up with 'undefined. The console shows the following:

engine.js:984 console.trace
dwr.engine._debug @ engine.js:984
dwr.engine.defaultErrorHandler @ engine.js:215
(anonymous) @ engine.js:1121
logHandlerEx @ engine.js:2553
handleException @ engine.js:1107
eval @ VM273:10
eval @ VM273:11
dwr.engine._executeScript @ engine.js:720
stateChange @ engine.js:1791
batch.req.onreadystatechange @ engine.js:1664
XMLHttpRequest.send
send @ engine.js:1691
send2 @ engine.js:1561
send @ engine.js:1525
dwr.engine.endBatch @ engine.js:279
dwr.engine._execute @ engine.js:694
p.findCompleteJournalName @ RemoteJournalNameService.js:14
updateJournalNameList @ citationForm.html:83
getUpdatedChoices @ autocomplete.js:158
(anonymous) @ autocomplete.js:259
setTimeout
onKeyUp @ autocomplete.js:258
(anonymous) @ autocomplete.js:127
engine.js:985 Error: undefined, Error

Co-authored-by: rvosa <[email protected]>

Copilot · 2026-01-27T20:52:48Z

@copilot in /treebase-web/user/citationForm.html, when I attempt to enter a Journal Name, there is a problem. What is supposed to happen is that an autocomplete pops up from which I can select a jou...

Fixed. The "undefined" error was caused by DWR's default error handler being triggered when the database returns no results. Added proper error handlers to all DWR autocomplete callbacks and configured a global DWR error handler to suppress alerts for autocomplete errors. The error will now log to console instead of showing an alert. See commit 73aaf9b.

Initial plan

550bd0b

Copilot AI assigned Copilot and rvosa Jan 27, 2026

Copilot started work on behalf of rvosa January 27, 2026 16:08 View session

Replace Prototype.js with native DOM APIs

3b9d4a2

Co-authored-by: rvosa <[email protected]>

Copilot AI changed the title ~~[WIP] Refactor JS codebase to phase out prototype.js usage~~ Replace Prototype.js with native DOM APIs Jan 27, 2026

Copilot AI requested a review from rvosa January 27, 2026 16:14

Copilot finished work on behalf of rvosa January 27, 2026 16:14

Copilot started work on behalf of rvosa January 27, 2026 16:16 View session

Copilot AI and others added 3 commits January 27, 2026 16:22

Replace Prototype.js with jQuery

6517a08

Co-authored-by: rvosa <[email protected]>

Remove empty jquery.min.js (using CDN instead)

184ee75

Co-authored-by: rvosa <[email protected]>

Address code review feedback: use jQuery prop() and attribute selectors

6a20de3

Co-authored-by: rvosa <[email protected]>

Copilot finished work on behalf of rvosa January 27, 2026 16:26

Merge pull request #413 from TreeBASE/master

16c5a6c

Update image paths in styles.css

Copilot started work on behalf of rvosa January 27, 2026 20:14 View session

Use local jQuery file instead of CDN

a2edee3

Co-authored-by: rvosa <[email protected]>

Copilot finished work on behalf of rvosa January 27, 2026 20:20

Copilot started work on behalf of rvosa January 27, 2026 20:27 View session

Fix jQuery AJAX dataType to prevent auto script execution

2a3384d

Co-authored-by: rvosa <[email protected]>

Copilot finished work on behalf of rvosa January 27, 2026 20:30

Copilot started work on behalf of rvosa January 27, 2026 20:50 View session

Add DWR error handlers to prevent autocomplete alerts on empty database

73aaf9b

Co-authored-by: rvosa <[email protected]>

Copilot AI changed the title ~~Replace Prototype.js with native DOM APIs~~ Replace Prototype.js with jQuery Jan 27, 2026

Copilot finished work on behalf of rvosa January 27, 2026 20:53

rvosa marked this pull request as ready for review January 27, 2026 21:08

rvosa merged commit f38c89d into master Jan 27, 2026
3 checks passed

rvosa deleted the copilot/refactor-js-codebase-replace-prototypejs branch January 27, 2026 21:08

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Replace Prototype.js with jQuery #412

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rvosa commented Jan 27, 2026

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rvosa commented Jan 27, 2026

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rvosa commented Jan 27, 2026

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Replace Prototype.js with jQuery #412

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Changes Made

jQuery Integration

JavaScript File Updates

DWR Autocomplete Error Handling

Code Review Fixes

Removed

Security

Notes

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rvosa commented Jan 27, 2026

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rvosa commented Jan 27, 2026

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Copilot AI commented Jan 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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rvosa commented Jan 27, 2026

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