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49e516c
stashing
cucinellclark Feb 28, 2026
086489a
Merge branch 'copilot-dev' of github.com:cucinellclark/bvbrc_website …
cucinellclark Feb 28, 2026
57fcc0f
Merge branch 'copilot-dev' of github.com:cucinellclark/bvbrc_website …
cucinellclark Mar 4, 2026
46f39ab
stash archaeopteryx
Mar 13, 2026
291f42d
changing grids to use cursor pagination
Apr 9, 2026
06b560c
Merge branch 'BV-BRC:alpha' into alpha
cucinellclark Apr 9, 2026
af97f6b
Merge branch 'copilot-dev' of github.com:cucinellclark/bvbrc_website …
cucinellclark May 13, 2026
b5f2d01
Merge remote-tracking branch 'origin/alpha' into copilot-dev
cucinellclark May 13, 2026
bc36efd
syncing copilot dev with alpha
cucinellclark May 13, 2026
7b4ff30
updating to handle new agent setup
cucinellclark May 13, 2026
fefade5
removing workflow plan
cucinellclark May 13, 2026
ef62b01
stashing
May 15, 2026
c295279
Merge branch 'alpha' into copilot-dev
May 21, 2026
f982f3a
Merge branch 'copilot-dev' into copilot-dev-agents
May 21, 2026
a1642fc
updating sse events
cucinellclark May 21, 2026
bf1334f
adding auto submission preferences
cucinellclark May 26, 2026
ed72e68
hopefully updating th front end to work with the workflow engine better
cucinellclark May 27, 2026
0eda770
fixing front end workflow response
cucinellclark May 27, 2026
530f6d0
trying to stop conflicting streams
cucinellclark May 27, 2026
d173fe0
adding support for text files in chat
cucinellclark May 27, 2026
eacf191
improvements to support multi-agent setup
Jun 5, 2026
141d9f8
Merge remote-tracking branch 'origin/alpha' into copilot-dev-agents
cucinellclark Jun 12, 2026
d60aef1
Update frontend to use GoWe workflow engine API
cucinellclark Jun 12, 2026
a0790b7
Propagate submission_id for GoWe status tracking
cucinellclark Jun 12, 2026
9e807f2
Merge branch 'copilot-dev-agents' of github.com:cucinellclark/bvbrc_w…
Jun 12, 2026
36f9b02
adding workspace object selection widgets
Jul 17, 2026
0809e12
updates
cucinellclark Jul 17, 2026
50ec5bd
updating
cucinellclark Jul 17, 2026
a52eecd
updating
cucinellclark Jul 17, 2026
8433579
new UI card for answered questions
cucinellclark Jul 18, 2026
3a18811
fixing random undefined message
cucinellclark Jul 18, 2026
0c4ed0c
fixing more undefined messages
cucinellclark Jul 18, 2026
96eed79
get rid of empty message
cucinellclark Jul 18, 2026
efbb25a
some fixes
cucinellclark Jul 18, 2026
9dc4317
omit empty assistsant messages
cucinellclark Jul 18, 2026
952b2d4
more fix attempts
cucinellclark Jul 18, 2026
3ffe80c
another fix
cucinellclark Jul 18, 2026
8a65f1c
attempeting interactive genome groups
cucinellclark Jul 19, 2026
7fe8177
sticker plan tracker
cucinellclark Jul 19, 2026
1747a50
fixes
cucinellclark Jul 19, 2026
2b83aca
bug fixes
cucinellclark Jul 19, 2026
4c9c1d1
updating
cucinellclark Jul 19, 2026
6210218
fixes
cucinellclark Jul 19, 2026
b197462
removing plan when switching chats
cucinellclark Jul 19, 2026
904b70b
updating
cucinellclark Jul 19, 2026
43d8684
updates to genome group chat UI
cucinellclark Jul 19, 2026
18b3d44
more fix attempts
cucinellclark Jul 19, 2026
1f7545f
switching to radio button
cucinellclark Jul 19, 2026
51c426b
fixes
cucinellclark Jul 20, 2026
ea886ac
fixes
cucinellclark Jul 20, 2026
269266a
changes to support waiting for job completion
cucinellclark Jul 20, 2026
f8ef457
plan card polling
cucinellclark Jul 20, 2026
e0bad41
fixing list link in planning card
cucinellclark Jul 22, 2026
32e8cb9
fix double slash bug
cucinellclark Jul 22, 2026
b853abf
fixing url encoding
Jul 22, 2026
c38b0d0
edit and resubmit
cucinellclark Jul 22, 2026
3decc42
link fix
cucinellclark Jul 22, 2026
64cf93f
hopeful fable updates
cucinellclark Jul 22, 2026
a4ab072
fixes for workflows in UI
cucinellclark Aug 11, 2026
a5dfec4
changes to planning agent interaction
cucinellclark Aug 12, 2026
3eb39f1
disabling plan tracker
cucinellclark Aug 12, 2026
a629da6
removing messages and grids chat window tabs
cucinellclark Aug 12, 2026
efbdff3
turn of edit mode if on and press edit button
cucinellclark Aug 12, 2026
c3d8b26
adding go to session folder button
cucinellclark Aug 14, 2026
deb12b3
creating chats folder
cucinellclark Aug 14, 2026
154ad2d
removing dead coce
cucinellclark Aug 18, 2026
c7f91ce
figuring out screenshot issue
Aug 19, 2026
adba8ae
removing lots of unneeded code
cucinellclark Aug 19, 2026
49ea72b
fixing screenshot
cucinellclark Aug 19, 2026
41a08f1
stll some issues
cucinellclark Aug 19, 2026
3dd7913
save to downloads folder for debugging
cucinellclark Aug 19, 2026
cd13cfb
removing save to downloads
cucinellclark Aug 19, 2026
401d4f4
added an attachments button and have them appear in the chips below t…
Aug 19, 2026
02f20ad
trying to rework chat cards
cucinellclark Aug 20, 2026
ae1664f
reworking how links and such are generated, downloads
cucinellclark Aug 20, 2026
16e1bda
attempting workflow info rework
cucinellclark Aug 21, 2026
c76dfea
fixing planning bug
cucinellclark Aug 21, 2026
9576f77
fixing plan card
cucinellclark Aug 21, 2026
8759478
removing plan card genome group creation
cucinellclark Aug 21, 2026
0c9ae5f
fixing job service name in scroll card job status
cucinellclark Aug 21, 2026
adf75a7
trying to get better job updates
cucinellclark Aug 21, 2026
43eeac0
removing rectangle button, creating solo chat view
cucinellclark Aug 24, 2026
8fdc427
consolidating chat scroll card buttons
cucinellclark Aug 24, 2026
bd6a7cc
moving report an issue button and disabling chat button in the chat view
cucinellclark Aug 24, 2026
9151a35
adding resend button and moving copy button below user message
cucinellclark Aug 25, 2026
16a9f1c
fixing button layout
cucinellclark Aug 25, 2026
8c98025
fixing
cucinellclark Aug 25, 2026
84bdb6c
fixing couple more things
cucinellclark Aug 25, 2026
658a915
making refresh arrow lighter
cucinellclark Aug 25, 2026
447ba99
changing opacity
cucinellclark Aug 25, 2026
34f5e8d
reworking text input area
cucinellclark Aug 25, 2026
644ee5f
putting spacing on the input widget
cucinellclark Aug 25, 2026
4a9d79f
increasing padding
cucinellclark Aug 25, 2026
aad0a79
remove top header report an issue
cucinellclark Aug 25, 2026
9e6a9d5
moving edit session button
cucinellclark Aug 25, 2026
a58104a
increasing padding for input widget
cucinellclark Aug 25, 2026
b6b36b7
putting border around input area
cucinellclark Aug 25, 2026
67db731
adding shadow to composer
cucinellclark Aug 25, 2026
784f677
slightly stronger shadow
cucinellclark Aug 25, 2026
205c5b3
fixing ui plan bug
cucinellclark Aug 25, 2026
264f695
fixing bugs due to two chat isntances
cucinellclark Aug 25, 2026
cb02cd6
dealing with needs input during plans
cucinellclark Aug 25, 2026
a288ca8
fixing chat session title but
cucinellclark Aug 26, 2026
a10c46b
attempting to fix fasta in text display issue
cucinellclark Aug 27, 2026
b24438b
trying to enable reconnecting
cucinellclark Aug 31, 2026
f73c405
trhing to make a fix
cucinellclark Aug 31, 2026
47a654e
trying to fix update issue
cucinellclark Aug 31, 2026
22f71d6
debugging
cucinellclark Aug 31, 2026
19fdd92
moving rating stars to options, running chip
cucinellclark Aug 31, 2026
19ad230
trying to fix running polling
cucinellclark Aug 31, 2026
356c998
removing running chip color flux
cucinellclark Aug 31, 2026
25fa9a9
fixing some scroll bar and chat title bugs
cucinellclark Sep 2, 2026
ec83d49
fixing pdf attachment bug
cucinellclark Sep 2, 2026
1adfa6e
extending workspace upload to a couple other things
cucinellclark Sep 2, 2026
dc1c8e6
feat: update queued SSE copy to use gateway message
cucinellclark Sep 14, 2026
6e087c2
fixing chat session title bug
cucinellclark Sep 14, 2026
6eb97d1
fixing username bug
cucinellclark Sep 14, 2026
c728fe6
Revert "fixing username bug"
cucinellclark Sep 14, 2026
39cc0f2
Revert "fixing chat session title bug"
cucinellclark Sep 14, 2026
29c8d07
fix: rename .chats to chats in session workspace paths
cucinellclark Sep 17, 2026
ee08ea6
planning and execution mode
cucinellclark Sep 18, 2026
0fe072a
improvements
cucinellclark Sep 18, 2026
ed4949f
fix(copilot): render markdown images in chat replies as links, not <img>
cucinellclark Oct 8, 2026
3161062
fix(copilot): register a new user's first chat (page-load session)
cucinellclark Oct 8, 2026
ab332b8
fix(copilot): sidebar entry for a restored, never-saved session
cucinellclark Oct 8, 2026
9a062e3
feat(copilot): "Submit this job" sends the card's blocked_actions for…
cucinellclark Oct 12, 2026
364e15e
feat(copilot): TURN_IN_FLIGHT returns the message to the input box
cucinellclark Oct 12, 2026
b4475a5
fix(copilot): a finished turn in another chat no longer shows up in t…
cucinellclark Oct 12, 2026
661acbd
copilot: prepared-jobs card asks one Yes / No / Other question (D4 Ph…
cucinellclark Oct 14, 2026
fc6ae10
copilot: plans run in Plan mode; a step pauses on its question (D4 Ph…
cucinellclark Oct 14, 2026
72e1507
copilot: a question card keeps its answer when the chat re-renders
cucinellclark Oct 14, 2026
31b7c25
copilot: Stop before the first event stops the turn by session
cucinellclark Oct 15, 2026
bb2278b
Merge BV-BRC/BV-BRC-Web alpha (v3.60.5) into alpha-hardening
cucinellclark Oct 15, 2026
3008c72
copilot: chat titles come from the first user message only
cucinellclark Oct 15, 2026
670bd9c
copilot: plan actions show "Running" in the sidebar
cucinellclark Oct 15, 2026
e63748d
copilot: jump-to-latest button; "New response" when a reply finishes …
cucinellclark Oct 15, 2026
468a0bb
Copilot UI fixes: delete confirm, cog menu acts on its chat, clarifyi…
cucinellclark Oct 15, 2026
221ae03
copilot: download links in answers fetch every row (cursor paging)
cucinellclark Oct 20, 2026
afc8fc2
copilot: questions card for every agent; answers go back to who asked
cucinellclark Oct 20, 2026
3639cb6
copilot: big downloads write to disk as they arrive (Chrome/Edge); di…
cucinellclark Oct 20, 2026
2b35102
copilot: download dialog says when the browser holds the file in memory
cucinellclark Oct 20, 2026
c2b7b2f
copilot: center the jump-to-latest arrow
cucinellclark Oct 20, 2026
6de089b
copilot: show the Copilot button when logged out, with a log-in prompt
cucinellclark Oct 20, 2026
939e87f
copilot: job-completed messages appear without a reload
cucinellclark Oct 20, 2026
3faf650
copilot: execution card knows edit_group ("Update this group?")
cucinellclark Oct 20, 2026
2628741
copilot: a job-completed message found by the poll lights "New response"
cucinellclark Oct 20, 2026
a9cb523
copilot: live progress as structured steps, four switchable views
cucinellclark Oct 22, 2026
21b680f
copilot: progress card is collapsed for everyone; no view toggle
cucinellclark Oct 22, 2026
f0cf2b0
Merge upstream/alpha (v3.60.7) into alpha-hardening
cucinellclark Oct 26, 2026
300a120
copilot: follow the progress card while a turn runs
cucinellclark Oct 26, 2026
f06120c
copilot: remove dead tool_call code and the retired CopilotToolHandler
cucinellclark Oct 26, 2026
f191262
copilot: workspace path chips keep spaces; chip links encoded
cucinellclark Oct 27, 2026
c1b9e29
copilot: remove WorkflowEngine, uncalled methods, source_tool (cleanu…
cucinellclark Oct 27, 2026
f53466c
copilot: remove the hidden Files/Workflows/Images panels and the sele…
cucinellclark Oct 27, 2026
9cf2767
config.js: back to the upstream defaults
cucinellclark Oct 28, 2026
4a1fbf7
Grids: back to upstream offset paging (drop cursor pagination from th…
cucinellclark Oct 28, 2026
f8de966
Merge upstream/alpha (v3.60.8) into alpha-hardening
cucinellclark Oct 29, 2026
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67 changes: 10 additions & 57 deletions public/js/p3/app/p3app.js
Original file line number Diff line number Diff line change
Expand Up @@ -63,49 +63,18 @@ define([
}).placeAt(document.body);
this.chatButton = chatButton;

// Create blue rectangle button for showing chat button when hidden
var showChatRectButton = domConstruct.create('div', {
className: 'ShowChatRectButton',
innerHTML: '<span class="show-chat-plus">+</span>',
title: 'show copilot button',
style: {
display: 'none'
}
});
domConstruct.place(showChatRectButton, document.body);

// Function to get chat button visibility from localStorage
function getChatButtonVisibility() {
try {
if (window && window.localStorage) {
var stored = localStorage.getItem('copilot-chat-button-visible');
return stored !== null ? (stored === 'true') : true; // default to visible
}
} catch (e) {
console.warn('Unable to read chat button visibility from localStorage', e);
}
return true; // default to visible
}

// Initialize showChatRectButton visibility based on localStorage
var initialChatButtonVisible = getChatButtonVisibility();
if (!initialChatButtonVisible) {
domStyle.set(showChatRectButton, 'display', 'block');
}

// Add click handler for the rectangle button
on(showChatRectButton, 'click', function(evt) {
Topic.publish('showChatButton', true);
});

Topic.subscribe('hideChatButton', lang.hitch(this, function(checked) {
domStyle.set(showChatRectButton, 'display', 'block');
}));

Topic.subscribe('showChatButton', lang.hitch(this, function(checked) {
domStyle.set(showChatRectButton, 'display', 'none');
}));
})
} else {
// Logged out: the button is shown too; a click asks the visitor to
// log in (ChatButton.onClick) instead of opening the chat.
this.chatButton = new ChatButton({
region: 'center',
width: '60px',
height: '60px',
backgroundColor: '#007bff',
borderRadius: '50%'
}).placeAt(document.body);
}

on(document, 'keydown', function (evt) {
Expand Down Expand Up @@ -692,7 +661,6 @@ define([
}, false)
// show the upload and jobs widget
window.App.uploadJobsWidget('show');
window.App.chatButtonWidget('show');
window.App.checkSU();
window.App.alreadyLoggedIn = true;
} else {
Expand Down Expand Up @@ -874,21 +842,6 @@ define([
console.log('I should not see the upload and jobs widget');
}
},
chatButtonWidget: function (action) {
if (action === 'show') {
var chatButton = new ChatButton({
region: 'center',
width: '60px',
height: '60px',
backgroundColor: '#007bff',
borderRadius: '50%',
display: 'flex',
alignItems: 'center',
});
} else {
console.log('I should not see the chat button');
}
},
_showQueryLogIndicator: function () {
var el = dom.byId('querylog-indicator');
if (el) { domClass.remove(el, 'dijitHidden'); }
Expand Down
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