feat: Generate Citations

.github/workflows/build-backend-prd.yml

@@ -65,6 +65,7 @@ jobs:
           XTRAMCP_OPENREVIEW_PASSWORD: ${{ secrets.XTRAMCP_OPENREVIEW_PASSWORD_PRD }}
           XTRAMCP_CROSSREF_EMAIL_ADDRESS: ${{ secrets.XTRAMCP_CROSSREF_EMAIL_ADDRESS_PRD }}
           XTRAMCP_DOI_EMAIL_ADDRESS: ${{ secrets.XTRAMCP_DOI_EMAIL_ADDRESS_PRD }}
+          XTRAMCP_ACL_METADATA_DB_URL: ${{ secrets.XTRAMCP_ACL_METADATA_DB_URL_PRD }}
           XTRAMCP_ARXIV_METADATA_DB_URL: ${{ secrets.XTRAMCP_ARXIV_METADATA_DB_URL_PRD }}
           XTRAMCP_MONGO_URI: ${{ secrets.XTRAMCP_MONGO_URI_PRD }}
           MONGO_URI: ${{ secrets.MONGO_URI_PRD }}

.github/workflows/build-backend-stg.yml

@@ -65,6 +65,7 @@ jobs:
           XTRAMCP_OPENREVIEW_PASSWORD: ${{ secrets.XTRAMCP_OPENREVIEW_PASSWORD_STG }}
           XTRAMCP_CROSSREF_EMAIL_ADDRESS: ${{ secrets.XTRAMCP_CROSSREF_EMAIL_ADDRESS_STG }}
           XTRAMCP_DOI_EMAIL_ADDRESS: ${{ secrets.XTRAMCP_DOI_EMAIL_ADDRESS_STG }}
+          XTRAMCP_ACL_METADATA_DB_URL: ${{ secrets.XTRAMCP_ACL_METADATA_DB_URL_PRD }}
           XTRAMCP_ARXIV_METADATA_DB_URL: ${{ secrets.XTRAMCP_ARXIV_METADATA_DB_URL_STG }}
           XTRAMCP_MONGO_URI: ${{ secrets.XTRAMCP_MONGO_URI_STG }}
           MONGO_URI: ${{ secrets.MONGO_URI_STG }}

hack/prd.sh

@@ -18,6 +18,7 @@ XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-dummy-XTRAMCP_OPENREV
 XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-dummy-XTRAMCP_OPENREVIEW_PASSWORD}
 XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-dummy-crossref-email-address}
 XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-dummy-doi-email-address}
+XTRAMCP_ACL_METADATA_DB_URL=${XTRAMCP_ACL_METADATA_DB_URL:-postgresql://dummy-acl-metadata-db-url}
 XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-postgresql://dummy-arxiv-metadata-db-url}
 XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-mongodb://dummy-mongo-uri}
 PAPERDEBUGGER_IMAGE=${PAPERDEBUGGER_IMAGE:-ghcr.io/paperdebugger/sharelatex-paperdebugger:latest}
@@ -42,6 +43,7 @@ helm template $ROOT_DIR/helm-chart \
     --set-string xtramcp_openreview_password=$XTRAMCP_OPENREVIEW_PASSWORD \
     --set-string xtramcp_crossref_email_address=$XTRAMCP_CROSSREF_EMAIL_ADDRESS \
     --set-string xtramcp_doi_email_address=$XTRAMCP_DOI_EMAIL_ADDRESS \
+    --set-string xtramcp_acl_metadata_db_url=$XTRAMCP_ACL_METADATA_DB_URL \
     --set-string xtramcp_arxiv_metadata_db_url=$XTRAMCP_ARXIV_METADATA_DB_URL \
     --set-string xtramcp_mongo_uri=$XTRAMCP_MONGO_URI \
     --set-string paperdebugger.image=$PAPERDEBUGGER_IMAGE \

hack/stg.sh

@@ -18,6 +18,7 @@ XTRAMCP_OPENREVIEW_USERNAME=${XTRAMCP_OPENREVIEW_USERNAME:-dummy-XTRAMCP_OPENREV
 XTRAMCP_OPENREVIEW_PASSWORD=${XTRAMCP_OPENREVIEW_PASSWORD:-dummy-XTRAMCP_OPENREVIEW_PASSWORD}
 XTRAMCP_CROSSREF_EMAIL_ADDRESS=${XTRAMCP_CROSSREF_EMAIL_ADDRESS:-dummy-crossref-email-address}
 XTRAMCP_DOI_EMAIL_ADDRESS=${XTRAMCP_DOI_EMAIL_ADDRESS:-dummy-doi-email-address}
+XTRAMCP_ACL_METADATA_DB_URL=${XTRAMCP_ACL_METADATA_DB_URL:-postgresql://dummy-acl-metadata-db-url}
 XTRAMCP_ARXIV_METADATA_DB_URL=${XTRAMCP_ARXIV_METADATA_DB_URL:-postgresql://dummy-arxiv-metadata-db-url}
 XTRAMCP_MONGO_URI=${XTRAMCP_MONGO_URI:-mongodb://dummy-mongo-uri}
 PAPERDEBUGGER_IMAGE=${PAPERDEBUGGER_IMAGE:-ghcr.io/paperdebugger/sharelatex-paperdebugger:latest}
@@ -42,6 +43,7 @@ helm template $ROOT_DIR/helm-chart \
     --set-string xtramcp_openreview_password=$XTRAMCP_OPENREVIEW_PASSWORD \
     --set-string xtramcp_crossref_email_address=$XTRAMCP_CROSSREF_EMAIL_ADDRESS \
     --set-string xtramcp_doi_email_address=$XTRAMCP_DOI_EMAIL_ADDRESS \
+    --set-string xtramcp_acl_metadata_db_url=$XTRAMCP_ACL_METADATA_DB_URL \
     --set-string xtramcp_arxiv_metadata_db_url=$XTRAMCP_ARXIV_METADATA_DB_URL \
     --set-string xtramcp_mongo_uri=$XTRAMCP_MONGO_URI \
     --set-string paperdebugger.image=$PAPERDEBUGGER_IMAGE \

helm-chart/templates/paperdebugger-xtramcp-server.yaml

@@ -60,3 +60,4 @@ data:
   MONGODB_CONNECTION_STRING: "{{ .Values.xtramcp_mongo_uri }}"
   MONGODB_DATABASE: "paperdebugger"
   ARXIV_METADATA_DB_URL: "{{ .Values.xtramcp_arxiv_metadata_db_url }}"
+  ACL_METADATA_DB_URL: "{{ .Values.xtramcp_acl_metadata_db_url }}"

helm-chart/values.yaml

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

internal/api/user/list_prompts.go

@@ -13,44 +13,60 @@ import (
 )
 
 var defaultPrompts = []*userv1.Prompt{
+	{
+		Id:           "1",
+		CreatedAt:    timestamppb.New(time.Time{}),
+		UpdatedAt:    timestamppb.New(time.Time{}),
+		Title:        "Tool List",
+		Content:      "List available MCP tools with a brief description for each tool.",
+		IsUserPrompt: false,
+	},
 	{
 		Id:           "2",
 		CreatedAt:    timestamppb.New(time.Time{}),
 		UpdatedAt:    timestamppb.New(time.Time{}),
-		Title:        "Search Relevant Papers (Powered by XtraMCP)",
-		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)",
+		Title:        "Search Relevant Papers (XtraMCP's Researcher)",
+		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",
 		IsUserPrompt: false,
 	},
 	{
 		Id:           "3",
 		CreatedAt:    timestamppb.New(time.Time{}),
 		UpdatedAt:    timestamppb.New(time.Time{}),
-		Title:        "Paper Review (Powered by XtraMCP)",
-		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>)",
+		Title:        "Paper Review (XtraMCP's Reviewer)",
+		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>)",
 		IsUserPrompt: false,
 	},
 	{
 		Id:           "4",
 		CreatedAt:    timestamppb.New(time.Time{}),
 		UpdatedAt:    timestamppb.New(time.Time{}),
-		Title:        "Verify Citations (Powered by XtraMCP)",
-		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.",
+		Title:        "Verify Citations (XtraMCP's Reviewer)",
+		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.",
 		IsUserPrompt: false,
 	},
 	{
 		Id:           "5",
 		CreatedAt:    timestamppb.New(time.Time{}),
 		UpdatedAt:    timestamppb.New(time.Time{}),
-		Title:        "Deep Research (Powered by XtraMCP)",
-		Content:      "First, understand my paper and extract the key ideas into an optimized query. Do deep research and compare my paper against others.",
+		Title:        "Generate Citations (XtraMCP's Reviewer)",
+		Content:      "Call `generate_citations` to create properly formatted citations for:\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]",
 		IsUserPrompt: false,
 	},
 	{
 		Id:           "6",
 		CreatedAt:    timestamppb.New(time.Time{}),
 		UpdatedAt:    timestamppb.New(time.Time{}),
-		Title:        "Online Research (Powered by XtraMCP)",
-		Content:      "Understand my paper and run online search to find the latest papers related to my work.",
+		Title:        "Deep Research (XtraMCP's Researcher)",
+		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>",
+		IsUserPrompt: false,
+	},
+	{
+		Id:           "7",
+		CreatedAt:    timestamppb.New(time.Time{}),
+		UpdatedAt:    timestamppb.New(time.Time{}),
+		Title:        "Online Research (XtraMCP's Researcher)",
+		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.",
 		IsUserPrompt: false,
 	},
 }

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

@@ -8,6 +8,7 @@ import { ReviewPaperCard } from "./xtramcp/review-paper";
 import { SearchRelevantPapersCard } from "./xtramcp/search-relevant-papers";
 import { OnlineSearchPapersCard } from "./xtramcp/online-search-papers";
 import { VerifyCitationsCard } from "./xtramcp/verify-citations";
+import { GenerateCitationsCard } from "./xtramcp/generate-citations";
 import { isXtraMcpTool } from "./xtramcp/utils/common";
 import { GeneralToolCard } from "./general";
 
@@ -67,6 +68,10 @@ export default function Tools({ messageId, functionName, message, error, prepari
       return (
         <VerifyCitationsCard functionName={functionName} message={message} preparing={preparing} animated={animated} />
       );
+    } else if (functionName === "generate_citations") {
+      return (
+        <GenerateCitationsCard functionName={functionName} message={message} preparing={preparing} animated={animated} />
+      );
     }
 
     // Generic XtraMCP tool (not specialized)

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

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

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

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

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

@@ -27,11 +27,12 @@ const XTRA_MCP_TOOL_NAMES = [
   // REVIEWER TOOLS
   "review_paper",
   "verify_citations",
+  "generate_citations",
   // ENHANCER TOOLS
   // "enhance_academic_writing",
   // OPENREVIEW ONLINE TOOLS
-  // "search_user",
-  // "get_user_papers"
+  "search_user",
+  "get_user_papers"
 ];
 
 export const isXtraMcpTool = (functionName: string): boolean => {