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Merged
InfinityBowman merged 4 commits into from
Dec 19, 2025
Merged

74 amstar2 user notes #90

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0d451a0
added notes in the amstar checklist
InfinityBowman Dec 18, 2025
56816f2
Apply Prettier formatting
actions-user Dec 18, 2025
f76ef18
add notes to reconcile tab
InfinityBowman Dec 19, 2025
d5ab9f0
fix reactivity from external users
InfinityBowman Dec 19, 2025
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2 changes: 1 addition & 1 deletion .github/copilot-instructions.md
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ Do not worry about migrations either client side or backend unless specifically

## Libraries

Use Zod for schema and input validation.
Use Zod for schema and input validation (backend).
Use Drizzle ORM for database interactions and migrations.
Use Better-Auth for authentication and user management.
Use Zag.js for UI components and design system.
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8 changes: 4 additions & 4 deletions .vscode/mcp.json
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Expand Up @@ -4,10 +4,10 @@
"type": "stdio",
"command": "node",
"args": ["${workspaceFolder}/packages/mcp/server.js"]
},
"stripe": {
"type": "http",
"url": "https://mcp.stripe.com"
}
// "stripe": {
// "type": "http",
// "url": "https://mcp.stripe.com"
// }
}
}
2 changes: 1 addition & 1 deletion packages/mcp/server.js
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Expand Up @@ -42,7 +42,7 @@ registerCodeReviewTools(server, repoRoot);
async function main() {
const transport = new StdioServerTransport();
await server.connect(transport);
console.error('Corates MCP Server started');
console.log('Corates MCP Server started');
}

main().catch(err => {
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2 changes: 1 addition & 1 deletion packages/mcp/tools/lint.js
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Expand Up @@ -12,7 +12,7 @@ export function registerLintTools(server, repoRoot) {
fix: z.boolean().optional().default(false).describe('Whether to run lint with --fix'),
},
async ({ fix = false }) => {
const command = `pnpm run lint${fix ? ' -- --fix' : ''}`;
const command = `pnpm run lint${fix ? ' --fix' : ''}`;

try {
const { stdout, stderr } = await exec(command, {
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28 changes: 11 additions & 17 deletions packages/ui/src/zag/Collapsible.jsx
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Expand Up @@ -13,17 +13,15 @@ import { createMemo, createUniqueId } from 'solid-js';
* @param {JSX.Element} props.children - The content to show/hide
*/
export default function Collapsible(props) {
const open = () => props.open;
const defaultOpen = () => props.defaultOpen;
const disabled = () => props.disabled;
const trigger = () => props.trigger;
const children = () => props.children;

const service = useMachine(collapsible.machine, () => ({
id: createUniqueId(),
open: open(),
defaultOpen: defaultOpen(),
disabled: disabled(),
get open() {
return props.open;
},
defaultOpen: props.defaultOpen,
get disabled() {
return props.disabled;
},
onOpenChange(details) {
props.onOpenChange?.(details.open);
},
Expand All @@ -33,34 +31,30 @@ export default function Collapsible(props) {

return (
<div {...api().getRootProps()}>
{trigger()?.(api())}
{props.trigger?.(api())}
<div {...api().getContentProps()} class='collapsible-content overflow-hidden'>
{children()}
{props.children}
</div>
<style>{`
.collapsible-content[data-state="open"] {
animation: collapsible-slideDown 200ms ease-out;
animation: collapsible-slideDown 150ms ease-out;
}
.collapsible-content[data-state="closed"] {
animation: collapsible-slideUp 200ms ease-out;
animation: collapsible-slideUp 150ms ease-out;
}
@keyframes collapsible-slideDown {
from {
opacity: 0;
height: 0;
}
to {
opacity: 1;
height: var(--height);
}
}
@keyframes collapsible-slideUp {
from {
opacity: 1;
height: var(--height);
}
to {
opacity: 0;
height: 0;
}
}
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70 changes: 69 additions & 1 deletion packages/web/src/components/checklist-ui/AMSTAR2Checklist.jsx
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Expand Up @@ -3,6 +3,7 @@ import { AMSTAR_CHECKLIST } from '@/AMSTAR2/checklist-map.js';
import { createChecklist as createAMSTAR2Checklist } from '@/AMSTAR2/checklist.js';
import { FaSolidCircleInfo } from 'solid-icons/fa';
import { Tooltip, FloatingPanel } from '@corates/ui';
import NoteEditor from '@checklist-ui/common/NoteEditor.jsx';

export function Question1(props) {
const state = () => props.checklistState().q1;
Expand Down Expand Up @@ -329,6 +330,12 @@ export function Question9(props) {
}, 10);
}

// Get Y.Text for the note (q9 is parent key for q9a/q9b)
const noteYText = () => {
if (!props.getQuestionNote) return null;
return props.getQuestionNote('q9');
};

let containerRef;

return (
Expand All @@ -352,6 +359,9 @@ export function Question9(props) {
columns={question.columns2}
handleChange={handleChangeB}
/>
<Show when={props.getQuestionNote}>
<NoteEditor yText={noteYText()} readOnly={props.readOnly} collapsed={true} />
</Show>
</div>
);
}
Expand Down Expand Up @@ -447,6 +457,12 @@ export function Question11(props) {
}, 10);
}

// Get Y.Text for the note (q11 is parent key for q11a/q11b)
const noteYText = () => {
if (!props.getQuestionNote) return null;
return props.getQuestionNote('q11');
};

let containerRef;

return (
Expand All @@ -473,6 +489,9 @@ export function Question11(props) {
handleChange={handleChangeB}
width='w-48'
/>
<Show when={props.getQuestionNote}>
<NoteEditor yText={noteYText()} readOnly={props.readOnly} collapsed={true} />
</Show>
</div>
);
}
Expand Down Expand Up @@ -646,14 +665,31 @@ export function Question16(props) {
function StandardQuestion(props) {
let containerRef;

// Get the question key from the question text (e.g., "1. Did..." -> "q1")
const questionKey = () => {
const text = props.question?.text || '';
const match = text.match(/^(\d+[a-z]?)\./);
return match ? `q${match[1]}` : null;
};
Comment on lines +668 to +673
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@coderabbitai coderabbitai Bot Dec 19, 2025

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🛠️ Refactor suggestion | 🟠 Major

Regex-based questionKey extraction may be fragile.

The regex pattern /^(\d+[a-z]?)\./ extracts the question key from the question text (e.g., "1. Did..." → "q1"). This creates a tight coupling between UI text and data keys. If question text formatting changes, note retrieval will break silently.

Consider:

  1. Passing an explicit questionKey prop to StandardQuestion instead of deriving it
  2. Maintaining a constant mapping of question objects to their keys
  3. Adding validation that the extracted key matches expected AMSTAR2 question keys (q1-q16)


// Get Y.Text for the note if getQuestionNote is available
const noteYText = () => {
const key = questionKey();
if (!key || !props.getQuestionNote) return null;
return props.getQuestionNote(key);
};

return (
<div class='bg-white rounded-lg shadow-md p-7 relative' ref={el => (containerRef = el)}>
<div class='bg-white rounded-lg shadow-md p-7 pb-3 relative' ref={el => (containerRef = el)}>
<QuestionInfo question={props.question} containerRef={containerRef} />
<div class='flex'>
<h3 class='font-semibold text-sm text-gray-900 mb-1'>{props.question.text}</h3>
<CriticalButton state={props.state} onUpdate={props.onUpdate} />
</div>
<StandardQuestionInternal columns={props.question.columns} {...props} />
<Show when={props.getQuestionNote}>
<NoteEditor yText={noteYText()} readOnly={props.readOnly} collapsed={true} />
</Show>
</div>
);
}
Expand Down Expand Up @@ -828,68 +864,100 @@ export default function AMSTAR2Checklist(props = {}) {
<Question1
onUpdate={newQ1 => handleChecklistChange({ q1: newQ1 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question2
onUpdate={newQ2 => handleChecklistChange({ q2: newQ2 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question3
onUpdate={newQ3 => handleChecklistChange({ q3: newQ3 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question4
onUpdate={newQ4 => handleChecklistChange({ q4: newQ4 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question5
onUpdate={newQ5 => handleChecklistChange({ q5: newQ5 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question6
onUpdate={newQ6 => handleChecklistChange({ q6: newQ6 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question7
onUpdate={newQ7 => handleChecklistChange({ q7: newQ7 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question8
onUpdate={newQ8 => handleChecklistChange({ q8: newQ8 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question9
onUpdatea={newQ9a => handleChecklistChange({ q9a: newQ9a })}
onUpdateb={newQ9b => handleChecklistChange({ q9b: newQ9b })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question10
onUpdate={newQ10 => handleChecklistChange({ q10: newQ10 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question11
onUpdatea={newQ11a => handleChecklistChange({ q11a: newQ11a })}
onUpdateb={newQ11b => handleChecklistChange({ q11b: newQ11b })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question12
onUpdate={newQ12 => handleChecklistChange({ q12: newQ12 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question13
onUpdate={newQ13 => handleChecklistChange({ q13: newQ13 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question14
onUpdate={newQ14 => handleChecklistChange({ q14: newQ14 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question15
onUpdate={newQ15 => handleChecklistChange({ q15: newQ15 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
<Question16
onUpdate={newQ16 => handleChecklistChange({ q16: newQ16 })}
checklistState={currentChecklist}
getQuestionNote={props.getQuestionNote}
readOnly={props.readOnly}
/>
</div>
</fieldset>
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2 changes: 2 additions & 0 deletions packages/web/src/components/checklist-ui/ChecklistWithPdf.jsx
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Expand Up @@ -23,6 +23,7 @@ export default function ChecklistWithPdf(props) {
// props.pdfs - array of PDFs for multi-PDF selection
// props.selectedPdfId - currently selected PDF ID
// props.onPdfSelect - handler for PDF selection change
// props.getQuestionNote - function to get Y.Text for a question note

return (
<div class='h-full flex flex-col bg-blue-50'>
Expand All @@ -39,6 +40,7 @@ export default function ChecklistWithPdf(props) {
checklist={props.checklist}
onUpdate={props.onUpdate}
readOnly={props.readOnly}
getQuestionNote={props.getQuestionNote}
/>

{/* Second panel: PDF Viewer */}
Expand Down
13 changes: 10 additions & 3 deletions packages/web/src/components/checklist-ui/ChecklistYjsWrapper.jsx
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Expand Up @@ -23,9 +23,13 @@ export default function ChecklistYjsWrapper() {
const [selectedPdfId, setSelectedPdfId] = createSignal(null);

// Use full hook for write operations
const { updateChecklistAnswer, updateChecklist, getChecklistData, addPdfToStudy } = useProject(
params.projectId,
);
const {
updateChecklistAnswer,
updateChecklist,
getChecklistData,
addPdfToStudy,
getQuestionNote,
} = useProject(params.projectId);

// Read data directly from store for faster reactivity
const connectionState = () => projectStore.getConnectionState(params.projectId);
Expand Down Expand Up @@ -362,6 +366,9 @@ export default function ChecklistYjsWrapper() {
pdfs={studyPdfs()}
selectedPdfId={selectedPdfId()}
onPdfSelect={handlePdfSelect}
getQuestionNote={questionKey =>
getQuestionNote(params.studyId, params.checklistId, questionKey)
}
/>
</Show>
</>
Expand Down
2 changes: 2 additions & 0 deletions packages/web/src/components/checklist-ui/GenericChecklist.jsx
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Expand Up @@ -24,6 +24,7 @@ import { ROBINSIChecklist } from '@checklist-ui/ROBINSIChecklist/index.js';
* @param {Object} props.checklist - The checklist state data
* @param {Function} props.onUpdate - Callback for checklist updates
* @param {boolean} [props.readOnly] - Whether the checklist is read-only
* @param {Function} [props.getQuestionNote] - Function to get Y.Text for a question note
*/
export default function GenericChecklist(props) {
// Determine the checklist type from props or state
Expand All @@ -44,6 +45,7 @@ export default function GenericChecklist(props) {
externalChecklist={props.checklist}
onExternalUpdate={props.onUpdate}
readOnly={props.readOnly}
getQuestionNote={props.getQuestionNote}
/>
</Show>
<Show when={checklistType() === CHECKLIST_TYPES.ROBINS_I}>
Expand Down
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