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Merge branch 'feat-generate-citations' into development
2 parents fd5db28 + 2b4b684 commit 5400fa7

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Lines changed: 155 additions & 14 deletions

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‎helm-chart/values.yaml‎

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@@ -14,7 +14,7 @@ paperdebuggerMcpServer:
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image: ghcr.io/paperdebugger/paperdebugger-mcp-server:main-14409c5
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paperdebuggerXtraMcpServer:
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image: ghcr.io/paperdebugger/xtragpt-mcp-server:sha-2f1404c
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image: ghcr.io/paperdebugger/xtragpt-mcp-server:sha-16c3861
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mongo:
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in_cluster: true

‎internal/api/user/list_prompts.go‎

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@@ -13,44 +13,60 @@ import (
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)
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var defaultPrompts = []*userv1.Prompt{
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{
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Id: "1",
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CreatedAt: timestamppb.New(time.Time{}),
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UpdatedAt: timestamppb.New(time.Time{}),
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Title: "Tool List",
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Content: "List available MCP tools with a brief description for each tool.",
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IsUserPrompt: false,
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},
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{
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Id: "2",
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CreatedAt: timestamppb.New(time.Time{}),
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UpdatedAt: timestamppb.New(time.Time{}),
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Title: "Search Relevant Papers (Powered by XtraMCP)",
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Content: "First, understand my paper and extract the key ideas into an optimized query to find papers that are relevant to my work. Then search for relevant papers to read.\n\nOptional Args:\ntop_k: 10\nStart Date: None (e.g. 2018-12-31)\nEnd Date: None (e.g. 2025-12-31)",
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Title: "Search Relevant Papers (XtraMCP's Researcher)",
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Content: "You are a research assistant helping to retrieve related academic papers.\n\nStep 1 — Query synthesis:\nCarefully read the provided paper content.\nExtract the core technical ideas, methods, problem setting, and application domain.\nProduce ONE concise, high-signal search query optimized for academic paper retrieval.\n- Prefer technical keywords and established terminology\n- Include model names, task names, or methodological frameworks when applicable\n- Avoid unnecessary elaboration, prose, or citations\n\nStep 2 — Tool invocation:\nCall `search_relevant_papers` using the synthesized query.\n\nTool parameters:\n- query: <your synthesized query>\n- top_k: 10\n- start_date: 2018-12-31\n- end_date: 2025-12-31",
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IsUserPrompt: false,
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},
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{
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Id: "3",
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CreatedAt: timestamppb.New(time.Time{}),
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UpdatedAt: timestamppb.New(time.Time{}),
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Title: "Paper Review (Powered by XtraMCP)",
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Content: "Call review_paper and evaluate my paper.\n\nOptional Args:\nTarget Venue: None (e.g. ICML, NeurIPS, CVPR)\nSeverity Level (blocker | major | minor | nit): Major\nSpecific Sections (default: entire paper): None (e.g. Abstract, Results, <section name in paper>)",
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Title: "Paper Review (XtraMCP's Reviewer)",
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Content: "Call `review_paper` and evaluate my paper.\n\nTool parameters:\nTarget Venue: None (e.g. ICML, NeurIPS, CVPR)\nSeverity Level (blocker | major | minor | nit): Major\nSpecific Sections (default: entire paper): None (e.g. Abstract, Results, <section name in paper>)",
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IsUserPrompt: false,
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},
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{
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Id: "4",
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CreatedAt: timestamppb.New(time.Time{}),
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UpdatedAt: timestamppb.New(time.Time{}),
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Title: "Verify Citations (Powered by XtraMCP)",
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Content: "Call verify_citations to check the validity of all citations in my paper and identify any potential issues such as incorrect formatting, missing information, or inaccurate references.",
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Title: "Verify Citations (XtraMCP's Reviewer)",
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Content: "Call `verify_citations` to check the validity of all citations in my paper and identify any potential issues such as incorrect formatting, missing information, or inaccurate references.",
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IsUserPrompt: false,
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},
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{
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Id: "5",
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CreatedAt: timestamppb.New(time.Time{}),
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UpdatedAt: timestamppb.New(time.Time{}),
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Title: "Deep Research (Powered by XtraMCP)",
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Content: "First, understand my paper and extract the key ideas into an optimized query. Do deep research and compare my paper against others.",
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Title: "Generate Citations (XtraMCP's Reviewer)",
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Content: "Call `generate_citations` to create properly formatted citations for my paper based on the provided references.\n\nTool parameters:\n- links: [\n\t# paste URLs, arXiv IDs, DOIs, or titles\n\t# eg.: XtraGPT: Context-Aware and Controllable Academic Paper Revision\n\t...\n]",
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IsUserPrompt: false,
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},
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{
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Id: "6",
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CreatedAt: timestamppb.New(time.Time{}),
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UpdatedAt: timestamppb.New(time.Time{}),
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Title: "Online Research (Powered by XtraMCP)",
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Content: "Understand my paper and run online search to find the latest papers related to my work.",
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Title: "Deep Research (XtraMCP's Researcher)",
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Content: "You are a research assistant helping to retrieve related academic papers to prepare for Deep Research.\n\nStep 1 — Query synthesis:\nCarefully read the provided paper content.\nExtract the core technical ideas, methods, problem setting, and application domain.\nProduce ONE concise, high-signal search query optimized for academic paper retrieval.\n- Prefer technical keywords and established terminology\n- Include model names, task names, or methodological frameworks when applicable\n- Avoid unnecessary elaboration, prose, or citations\n\nStep 2 — Tool invocation:\nCall `deep_research` using the synthesized query.\n\nTool parameters:\n- query: <your synthesized query>",
62+
IsUserPrompt: false,
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},
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{
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Id: "7",
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CreatedAt: timestamppb.New(time.Time{}),
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UpdatedAt: timestamppb.New(time.Time{}),
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Title: "Online Research (XtraMCP's Researcher)",
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Content: "You are a research assistant assisting with a recency-focused academic literature search.\n\nStep 1 — Keyword extraction:\nCarefully read the paper and extract a set of high-recall search keywords, including:\n- core task names and problem statements\n- methodological approaches and system types\n- application domains\n- commonly used synonyms and alternative phrasings\n- well-known model or framework names if relevant and widely used\n\nPrefer established terminology used in paper titles and abstracts.\nAvoid internal project names or marketing labels.\n\nStep 2 — Query construction:\nConstruct a keyword-based search query optimized for lexical search:\n- Use keyword phrases rather than full sentences\n- Combine terms using natural keyword adjacency (not prose)\n- Bias toward recall over precision\n\nStep 3 — Online retrieval:\nCall `online_search_papers` using the constructed query to find recent papers outside the internal database.",
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IsUserPrompt: false,
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},
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}

‎webapp/_webapp/src/components/message-entry-container/tools/tools.tsx‎

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Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@ import { ReviewPaperCard } from "./xtramcp/review-paper";
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import { SearchRelevantPapersCard } from "./xtramcp/search-relevant-papers";
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import { OnlineSearchPapersCard } from "./xtramcp/online-search-papers";
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import { VerifyCitationsCard } from "./xtramcp/verify-citations";
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import { GenerateCitationsCard } from "./xtramcp/generate-citations";
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import { isXtraMcpTool } from "./xtramcp/utils/common";
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import { GeneralToolCard } from "./general";
1314

@@ -67,6 +68,10 @@ export default function Tools({ messageId, functionName, message, error, prepari
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return (
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<VerifyCitationsCard functionName={functionName} message={message} preparing={preparing} animated={animated} />
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);
71+
} else if (functionName === "generate_citations") {
72+
return (
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<GenerateCitationsCard functionName={functionName} message={message} preparing={preparing} animated={animated} />
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);
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}
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// Generic XtraMCP tool (not specialized)

‎webapp/_webapp/src/components/message-entry-container/tools/xtramcp/generate-citations.tsx‎

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@@ -0,0 +1,116 @@
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import { cn } from "@heroui/react";
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import { LoadingIndicator } from "../../../loading-indicator";
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import MarkdownComponent from "../../../markdown";
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import { useState } from "react";
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import { XtraMcpToolCardProps, parseXtraMcpToolResult, CollapseArrowButton, CollapseWrapper } from "./utils/common";
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export const GenerateCitationsCard = ({ functionName, message, preparing, animated }: XtraMcpToolCardProps) => {
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const [isMetadataCollapsed, setIsMetadataCollapsed] = useState(false);
9+
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// Loading state (tool executing)
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if (preparing) {
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return (
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<div className={cn("tool-card", { animated: animated })}>
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<div className="flex items-center justify-between">
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<h3 className="tool-card-title">Generating your citations..</h3>
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</div>
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<LoadingIndicator text="Processing ..." estimatedSeconds={35} />
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</div>
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);
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}
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// Parse XtraMCP ToolResult format
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const result = parseXtraMcpToolResult(message);
24+
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// No result or not ToolResult format - minimal display
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if (!result) {
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return (
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<div className={cn("tool-card noselect narrow", { animated: animated })}>
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<div className="flex items-center justify-between">
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<h3 className="tool-card-title">{functionName}</h3>
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</div>
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</div>
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);
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}
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// Error state
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if (result.error || result.success === false) {
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return (
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<div className={cn("tool-card noselect narrow", { animated: animated })}>
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{/* Header with Error label and arrow button */}
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<div
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className="flex items-center justify-between cursor-pointer"
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onClick={() => setIsMetadataCollapsed(!isMetadataCollapsed)}
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>
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<h3 className="tool-card-title">{functionName}</h3>
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<div className="flex items-center gap-2">
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<span className="text-red-500 text-sm font-medium">Error</span>
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<CollapseArrowButton
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isCollapsed={isMetadataCollapsed}
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ariaLabel={isMetadataCollapsed ? "Expand error" : "Collapse error"}
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/>
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</div>
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</div>
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{/* Error message dropdown */}
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<CollapseWrapper isCollapsed={isMetadataCollapsed}>
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<div className="text-xs text-red-600 mt-2 pt-2 border-t border-red-200">
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{result.error || "Tool execution failed"}
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</div>
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</CollapseWrapper>
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</div>
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);
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}
64+
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// Success state - verbatim mode (guaranteed for this tool on success)
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// Display compact card + content below
67+
if (typeof result.content === "string") {
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return (
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<>
70+
{/* COMPACT TOOL CARD - Just title + metadata dropdown */}
71+
<div className={cn("tool-card noselect narrow", { animated: animated })}>
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{/* Header with arrow button */}
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<div
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className="flex items-center justify-between cursor-pointer"
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onClick={() => setIsMetadataCollapsed(!isMetadataCollapsed)}
76+
>
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<h3 className="tool-card-title">{functionName}</h3>
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<CollapseArrowButton
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isCollapsed={isMetadataCollapsed}
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ariaLabel={isMetadataCollapsed ? "Expand metadata" : "Collapse metadata"}
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/>
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</div>
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{/* Metadata dropdown - INSIDE the tool card */}
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{result.metadata && Object.keys(result.metadata).length > 0 && (
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<CollapseWrapper isCollapsed={isMetadataCollapsed}>
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<div className="text-xs text-gray-600 mt-2 pt-2 border-t border-gray-200">
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{/* Custom metadata rendering */}
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<div className="mb-2 italic">⚠️ [Experimental Feature] Some BibTeX entries may not be able to be generated.<br />Report if you encounter an unknown issue.</div>
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{result.metadata.total_links !== undefined && (
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<div>
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<span className="font-medium">Total Links/IDs/Info:</span> {result.metadata.total_links}
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</div>
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)}
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</div>
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</CollapseWrapper>
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)}
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</div>
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{/* CONTENT - OUTSIDE/BELOW the tool card, always visible */}
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<div className="canselect text-sm mt-2">
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<MarkdownComponent animated={animated}>{result.content}</MarkdownComponent>
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</div>
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</>
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);
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}
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// Fallback - unknown format
109+
return (
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<div className={cn("tool-card noselect narrow", { animated: animated })}>
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<div className="flex items-center justify-between">
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<h3 className="tool-card-title">{functionName}</h3>
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</div>
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</div>
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);
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};

‎webapp/_webapp/src/components/message-entry-container/tools/xtramcp/search-relevant-papers.tsx‎

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Original file line numberDiff line numberDiff line change
@@ -93,7 +93,10 @@ export const SearchRelevantPapersCard = ({ functionName, message, preparing, ani
9393
{result.metadata && Object.keys(result.metadata).length > 0 && (
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<CollapseWrapper isCollapsed={isMetadataCollapsed}>
9595
<div className="text-xs text-gray-600 mt-2 pt-2 border-t border-gray-200">
96-
{/* Custom metadata rendering */}
96+
{/* Custom metadata rendering; NOTE: hard-coded the CAA date */}
97+
<div className="mb-2">
98+
<span className="font-medium">⚠️ Papers searched from a pool updated as of 31st Dec 2025.</span>
99+
</div>
97100
{result.metadata.query && (
98101
<div className="mb-2">
99102
<span className="font-medium">Query Used:</span> "{result.metadata.query}"

‎webapp/_webapp/src/components/message-entry-container/tools/xtramcp/utils/common.tsx‎

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Original file line numberDiff line numberDiff line change
@@ -27,11 +27,12 @@ const XTRA_MCP_TOOL_NAMES = [
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// REVIEWER TOOLS
2828
"review_paper",
2929
"verify_citations",
30+
"generate_citations",
3031
// ENHANCER TOOLS
3132
// "enhance_academic_writing",
3233
// OPENREVIEW ONLINE TOOLS
33-
// "search_user",
34-
// "get_user_papers"
34+
"search_user",
35+
"get_user_papers"
3536
];
3637

3738
export const isXtraMcpTool = (functionName: string): boolean => {

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