feat: add PubMed and software citation format support

Extends bibliography smart import capabilities with additional citation.js plugins:
- @citation-js/plugin-pubmed: Support for PubMed IDs (PMID/PMCID)
- @citation-js/plugin-software-formats: Support for software citations (CFF, GitHub, npm, Zenodo)

Updates smart-parser.ts to recognize and validate Zenodo DOI format (10.5281/zenodo.xxxxx).
Improves input type detection for better user feedback.

Includes code formatting improvements to bibliographyStore.ts for consistency.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

package-lock.json

@@ -12,7 +12,9 @@
         "@citation-js/plugin-bibtex": "^0.7.18",
         "@citation-js/plugin-csl": "^0.7.18",
         "@citation-js/plugin-doi": "^0.7.18",
+        "@citation-js/plugin-pubmed": "^0.3.0",
         "@citation-js/plugin-ris": "^0.7.18",
+        "@citation-js/plugin-software-formats": "^0.6.1",
         "@emotion/react": "^11.11.3",
         "@emotion/styled": "^11.11.0",
         "@mui/icons-material": "^5.15.10",
@@ -377,6 +379,18 @@
         "@citation-js/core": "^0.7.0"
       }
     },
+    "node_modules/@citation-js/plugin-cff": {
+      "version": "0.6.1",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-cff/-/plugin-cff-0.6.1.tgz",
+      "integrity": "sha512-tLjTgsfzNOdQWGn5mNc2NAaydHnlRucSERoyAXLN7u0BQBfp7j5zwdxCmxcQD/N7hH3fpDKMG+qDzbqpJuKyNA==",
+      "dependencies": {
+        "@citation-js/date": "^0.5.0",
+        "@citation-js/plugin-yaml": "^0.6.1"
+      },
+      "engines": {
+        "node": ">=14.0.0"
+      }
+    },
     "node_modules/@citation-js/plugin-csl": {
       "version": "0.7.18",
       "resolved": "https://registry.npmjs.org/@citation-js/plugin-csl/-/plugin-csl-0.7.18.tgz",
@@ -406,6 +420,41 @@
         "@citation-js/core": "^0.7.0"
       }
     },
+    "node_modules/@citation-js/plugin-github": {
+      "version": "0.6.1",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-github/-/plugin-github-0.6.1.tgz",
+      "integrity": "sha512-1ZeSgQ5AoYsa8n2acVooUeRk76oA8rLszYNBjzj5z6MPa11BZlQJ9O+Gy4tHjlImvsENLbLPx5f8/V1VHXaCfQ==",
+      "dependencies": {
+        "@citation-js/date": "^0.5.0",
+        "@citation-js/name": "^0.4.2"
+      },
+      "engines": {
+        "node": ">=14.0.0"
+      }
+    },
+    "node_modules/@citation-js/plugin-npm": {
+      "version": "0.6.1",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-npm/-/plugin-npm-0.6.1.tgz",
+      "integrity": "sha512-rojJA+l/p2KBpDoY+8n0YfNyQO1Aw03fQR5BN+gXD1LNAP1V+8wqvdPsaHnzPsrhrd4ZXDR7ch/Nk0yynPkJ3Q==",
+      "dependencies": {
+        "@citation-js/date": "^0.5.0",
+        "@citation-js/name": "^0.4.2"
+      },
+      "engines": {
+        "node": ">=14.0.0"
+      }
+    },
+    "node_modules/@citation-js/plugin-pubmed": {
+      "version": "0.3.0",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-pubmed/-/plugin-pubmed-0.3.0.tgz",
+      "integrity": "sha512-E3l83VP5UnTh6lLJaTaNBIkNgIx3U6IjDNf7j5l4geBOaOwDIhkl9X+Ss33/MMNEIMNDsBoodoMJTZ8Cq+C/ug==",
+      "engines": {
+        "node": ">=14"
+      },
+      "peerDependencies": {
+        "@citation-js/core": ">=0.5.1 <=0.6"
+      }
+    },
     "node_modules/@citation-js/plugin-ris": {
       "version": "0.7.18",
       "resolved": "https://registry.npmjs.org/@citation-js/plugin-ris/-/plugin-ris-0.7.18.tgz",
@@ -421,6 +470,44 @@
         "@citation-js/core": "^0.7.0"
       }
     },
+    "node_modules/@citation-js/plugin-software-formats": {
+      "version": "0.6.1",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-software-formats/-/plugin-software-formats-0.6.1.tgz",
+      "integrity": "sha512-BDF9rqi56K0hoTgYTVANCFVRSbWKC9V06Uap7oa8SjqCTgnHJAy8t/F3NxsyYPPG+zmRsLW9VNbcIsJOl0eu/w==",
+      "dependencies": {
+        "@citation-js/plugin-cff": "^0.6.1",
+        "@citation-js/plugin-github": "^0.6.1",
+        "@citation-js/plugin-npm": "^0.6.1",
+        "@citation-js/plugin-yaml": "^0.6.1",
+        "@citation-js/plugin-zenodo": "^0.6.1"
+      },
+      "engines": {
+        "node": ">=14.0.0"
+      }
+    },
+    "node_modules/@citation-js/plugin-yaml": {
+      "version": "0.6.1",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-yaml/-/plugin-yaml-0.6.1.tgz",
+      "integrity": "sha512-XEVVks1cJTqRbjy+nmthfw/puR6NwRB3fyJWi1tX13UYXlkhP/h45nsv4zjgLLGekdcMHQvhad9MAYunOftGKA==",
+      "dependencies": {
+        "js-yaml": "^4.0.0"
+      },
+      "engines": {
+        "node": ">=14.0.0"
+      }
+    },
+    "node_modules/@citation-js/plugin-zenodo": {
+      "version": "0.6.1",
+      "resolved": "https://registry.npmjs.org/@citation-js/plugin-zenodo/-/plugin-zenodo-0.6.1.tgz",
+      "integrity": "sha512-bUybENHoZqJ6gheUqgkumjI+mu+fA2bg6VoniDmZTb7Qng9iEpi+IWEAR26/vBE0gK0EWrJjczyDW3HCwrhvVw==",
+      "dependencies": {
+        "@citation-js/date": "^0.5.0",
+        "@citation-js/name": "^0.4.2"
+      },
+      "engines": {
+        "node": ">=14.0.0"
+      }
+    },
     "node_modules/@emotion/babel-plugin": {
       "version": "11.13.5",
       "resolved": "https://registry.npmjs.org/@emotion/babel-plugin/-/babel-plugin-11.13.5.tgz",
@@ -2103,6 +2190,7 @@
       "version": "18.3.26",
       "resolved": "https://registry.npmjs.org/@types/react/-/react-18.3.26.tgz",
       "integrity": "sha512-RFA/bURkcKzx/X9oumPG9Vp3D3JUgus/d0b67KB0t5S/raciymilkOa66olh78MUI92QLbEJevO7rvqU/kjwKA==",
+      "dev": true,
       "dependencies": {
         "@types/prop-types": "*",
         "csstype": "^3.0.2"
@@ -2436,8 +2524,7 @@
     "node_modules/argparse": {
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/argparse/-/argparse-2.0.1.tgz",
-      "integrity": "sha512-8+9WqebbFzpX9OR+Wa6O29asIogeRMzcGtAINdpMHHyAg10f05aSFVBbcEqGf/PXw1EjAZ+q2/bEBg3DvurK3Q==",
+      "integrity": "sha512-8+9WqebbFzpX9OR+Wa6O29asIogeRMzcGtAINdpMHHyAg10f05aSFVBbcEqGf/PXw1EjAZ+q2/bEBg3DvurK3Q=="
-      "dev": true
     },
     "node_modules/array-union": {
       "version": "2.1.0",
@@ -3784,7 +3871,6 @@
       "version": "4.1.0",
       "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.0.tgz",
       "integrity": "sha512-wpxZs9NoxZaJESJGIZTyDEaYpl0FKSA+FB9aJiyemKhMwkxQg63h4T1KJgUGHpTqPDNRcmmYLugrRjJlBtWvRA==",
-      "dev": true,
       "dependencies": {
         "argparse": "^2.0.1"
       },
@@ -5402,20 +5488,6 @@
       "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==",
       "dev": true
     },
-    "node_modules/yaml": {
-      "version": "2.8.1",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.1.tgz",
-      "integrity": "sha512-lcYcMxX2PO9XMGvAJkJ3OsNMw+/7FKes7/hgerGUYWIoWu5j/+YQqcZr5JnPZWzOsEBgMbSbiSTn/dv/69Mkpw==",
-      "dev": true,
-      "optional": true,
-      "peer": true,
-      "bin": {
-        "yaml": "bin.mjs"
-      },
-      "engines": {
-        "node": ">= 14.6"
-      }
-    },
     "node_modules/yocto-queue": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",

package.json

@@ -14,7 +14,9 @@
     "@citation-js/plugin-bibtex": "^0.7.18",
     "@citation-js/plugin-csl": "^0.7.18",
     "@citation-js/plugin-doi": "^0.7.18",
+    "@citation-js/plugin-pubmed": "^0.3.0",
     "@citation-js/plugin-ris": "^0.7.18",
+    "@citation-js/plugin-software-formats": "^0.6.1",
     "@emotion/react": "^11.11.3",
     "@emotion/styled": "^11.11.0",
     "@mui/icons-material": "^5.15.10",

src/stores/bibliographyStore.ts

@@ -1,18 +1,20 @@
-import { create } from 'zustand';
+import { create } from "zustand";
 // @ts-expect-error - citation.js doesn't have TypeScript definitions
-import { Cite } from '@citation-js/core';
+import { Cite } from "@citation-js/core";
 // Load plugins
-import '@citation-js/plugin-csl';
+import "@citation-js/plugin-csl";
-import '@citation-js/plugin-doi';
+import "@citation-js/plugin-doi";
-import '@citation-js/plugin-bibtex';
+import "@citation-js/plugin-bibtex";
-import '@citation-js/plugin-ris';
+import "@citation-js/plugin-ris";
+import "@citation-js/plugin-pubmed";
+import "@citation-js/plugin-software-formats";
 
 import type {
   BibliographyReference,
   CSLReference,
   ReferenceAppMetadata,
-  BibliographySettings
+  BibliographySettings,
-} from '../types/bibliography';
+} from "../types/bibliography";
 
 interface BibliographyStore {
   // State
@@ -43,18 +45,22 @@ interface BibliographyStore {
   setSettings: (settings: BibliographySettings) => void;
 
   // Citation.js powered operations
-  formatReference: (id: string, style?: string, format?: 'html' | 'text') => string;
+  formatReference: (
-  formatBibliography: (style?: string, format?: 'html' | 'text') => string;
+    id: string,
+    style?: string,
+    format?: "html" | "text",
+  ) => string;
+  formatBibliography: (style?: string, format?: "html" | "text") => string;
   parseInput: (input: string) => Promise<CSLReference[]>;
-  exportAs: (format: 'bibtex' | 'ris' | 'json') => string;
+  exportAs: (format: "bibtex" | "ris" | "json") => string;
 }
 
 export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
   citeInstance: new Cite([]),
   appMetadata: {},
   settings: {
-    defaultStyle: 'apa',
+    defaultStyle: "apa",
-    sortOrder: 'author',
+    sortOrder: "author",
   },
 
   getReferences: () => {
@@ -62,7 +68,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
     const metadata = get().appMetadata;
 
     // Merge CSL data with app metadata
-    return csl.map(ref => ({
+    return csl.map((ref) => ({
       ...ref,
       _app: metadata[ref.id],
     }));
@@ -70,7 +76,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
 
   getReferenceById: (id) => {
     const refs = get().getReferences();
-    return refs.find(ref => ref.id === id);
+    return refs.find((ref) => ref.id === id);
   },
 
   getCSLData: () => {
@@ -81,7 +87,8 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
     const { citeInstance } = get();
 
     // Generate ID if not provided
-    const id = ref.id || `ref-${Date.now()}-${Math.random().toString(36).slice(2, 9)}`;
+    const id =
+      ref.id || `ref-${Date.now()}-${Math.random().toString(36).slice(2, 9)}`;
     const fullRef = { ...ref, id };
 
     // Use citation.js add() method
@@ -89,7 +96,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
 
     // Add app metadata
     const now = new Date().toISOString();
-    set(state => ({
+    set((state) => ({
       appMetadata: {
         ...state.appMetadata,
         [id]: {
@@ -109,15 +116,15 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
     const data = citeInstance.data as CSLReference[];
 
     // Find and update the reference
-    const updatedData = data.map(ref =>
+    const updatedData = data.map((ref) =>
-      ref.id === id ? { ...ref, ...updates } : ref
+      ref.id === id ? { ...ref, ...updates } : ref,
     );
 
     // Use citation.js set() method to replace all data
     citeInstance.set(updatedData);
 
     // Update metadata timestamp
-    set(state => ({
+    set((state) => ({
       appMetadata: {
         ...state.appMetadata,
         [id]: {
@@ -133,11 +140,11 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
     const data = citeInstance.data as CSLReference[];
 
     // Remove from citation.js
-    const filteredData = data.filter(ref => ref.id !== id);
+    const filteredData = data.filter((ref) => ref.id !== id);
     citeInstance.set(filteredData);
 
     // Remove metadata
-    set(state => {
+    set((state) => {
       // eslint-disable-next-line @typescript-eslint/no-unused-vars
       const { [id]: _removed, ...rest } = state.appMetadata;
       return { appMetadata: rest };
@@ -146,7 +153,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
 
   duplicateReference: (id) => {
     const original = get().getReferenceById(id);
-    if (!original) return '';
+    if (!original) return "";
 
     const newId = `ref-${Date.now()}-${Math.random().toString(36).slice(2, 9)}`;
     const duplicate = {
@@ -173,7 +180,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
     const metadata: Record<string, ReferenceAppMetadata> = {};
     const now = new Date().toISOString();
 
-    refs.forEach(ref => {
+    refs.forEach((ref) => {
       metadata[ref.id] = {
         id: ref.id,
         tags: [],
@@ -193,9 +200,9 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
 
     // Add metadata for new references
     const now = new Date().toISOString();
-    set(state => {
+    set((state) => {
       const newMetadata = { ...state.appMetadata };
-      refs.forEach(ref => {
+      refs.forEach((ref) => {
         if (!newMetadata[ref.id]) {
           newMetadata[ref.id] = {
             id: ref.id,
@@ -215,7 +222,7 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
   },
 
   updateMetadata: (id, updates) => {
-    set(state => ({
+    set((state) => ({
       appMetadata: {
         ...state.appMetadata,
         [id]: {
@@ -229,34 +236,34 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
 
   setSettings: (settings) => set({ settings }),
 
-  formatReference: (id, style, format = 'html') => {
+  formatReference: (id, style, format = "html") => {
     const { citeInstance, settings } = get();
     const styleToUse = style || settings.defaultStyle;
 
     // Find the reference
-    const ref = (citeInstance.data as CSLReference[]).find(r => r.id === id);
+    const ref = (citeInstance.data as CSLReference[]).find((r) => r.id === id);
-    if (!ref) return '';
+    if (!ref) return "";
 
     // Create temporary Cite instance for single reference
     const cite = new Cite(ref);
 
     // Use citation.js format() method
-    return cite.format('bibliography', {
+    return cite.format("bibliography", {
       format: format,
       template: styleToUse,
-      lang: 'en-US',
+      lang: "en-US",
     });
   },
 
-  formatBibliography: (style, format = 'html') => {
+  formatBibliography: (style, format = "html") => {
     const { citeInstance, settings } = get();
     const styleToUse = style || settings.defaultStyle;
 
     // Use citation.js format() method on entire instance
-    return citeInstance.format('bibliography', {
+    return citeInstance.format("bibliography", {
       format: format,
       template: styleToUse,
-      lang: 'en-US',
+      lang: "en-US",
     });
   },
 
@@ -267,8 +274,8 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
       const cite = await Cite.async(input);
       return cite.data as CSLReference[];
     } catch (error) {
-      console.error('Failed to parse input:', error);
+      console.error("Failed to parse input:", error);
-      throw new Error('Could not parse citation data');
+      throw new Error("Could not parse citation data");
     }
   },
 
@@ -277,14 +284,14 @@ export const useBibliographyStore = create<BibliographyStore>((set, get) => ({
 
     // Use citation.js format() method
     switch (format) {
-      case 'bibtex':
+      case "bibtex":
-        return citeInstance.format('bibtex');
+        return citeInstance.format("bibtex");
-      case 'ris':
+      case "ris":
-        return citeInstance.format('ris');
+        return citeInstance.format("ris");
-      case 'json':
+      case "json":
         return JSON.stringify(citeInstance.data, null, 2);
       default:
-        return '';
+        return "";
     }
   },
 }));
@@ -295,8 +302,8 @@ export const clearBibliographyForDocumentSwitch = () => {
     citeInstance: new Cite([]),
     appMetadata: {},
     settings: {
-      defaultStyle: 'apa',
+      defaultStyle: "apa",
-      sortOrder: 'author',
+      sortOrder: "author",
     },
   });
 };

src/utils/bibliography/smart-parser.ts

@@ -1,17 +1,21 @@
 // @ts-expect-error - citation.js doesn't have TypeScript definitions
-import { Cite } from '@citation-js/core';
+import { Cite } from "@citation-js/core";
-import type { CSLReference } from '../../types/bibliography';
+import type { CSLReference } from "../../types/bibliography";
 
 /**
  * Parse any citation input using citation.js
  * Handles: DOI, URL, BibTeX, RIS, ISBN, PubMed ID, etc.
  */
-export const parseSmartInput = async (input: string): Promise<CSLReference[]> => {
+export const parseSmartInput = async (
+  input: string,
+): Promise<CSLReference[]> => {
   try {
     const cite = await Cite.async(input);
     return cite.data as CSLReference[];
   } catch (error) {
-    throw new Error(`Could not parse input: ${error instanceof Error ? error.message : 'Unknown error'}`);
+    throw new Error(
+      `Could not parse input: ${error instanceof Error ? error.message : "Unknown error"}`,
+    );
   }
 };
 
@@ -46,9 +50,8 @@ export const isValidCitationInput = (input: string): boolean => {
   // Wikidata ID (Q followed by numbers)
   if (/^(wikidata:)?Q\d+$/i.test(trimmed)) return true;
 
-  // Zenodo ID or URL
+  // Zenodo DOI (10.5281/zenodo.xxxxx)
-  if (/^zenodo\.\d+$/i.test(trimmed)) return true;
+  if (/^10\.5281\/zenodo\.\d+/i.test(trimmed)) return true;
-  if (/zenodo\.org\/record\/\d+/i.test(trimmed)) return true;
 
   // CFF (Citation File Format) - YAML-based
   if (/^cff-version:/m.test(trimmed)) return true;
@@ -62,17 +65,16 @@ export const isValidCitationInput = (input: string): boolean => {
 export const getInputTypeHint = (input: string): string => {
   const trimmed = input.trim();
 
-  if (/^10\.\d{4,}\//.test(trimmed)) return 'DOI';
+  if (/^10\.5281\/zenodo\.\d+/i.test(trimmed)) return "Zenodo DOI";
-  if (/zenodo\.org\/record\/\d+/i.test(trimmed)) return 'Zenodo URL';
+  if (/^10\.\d{4,}\//.test(trimmed)) return "DOI";
-  if (/^zenodo\.\d+$/i.test(trimmed)) return 'Zenodo ID';
+  if (/^https?:\/\//.test(trimmed)) return "URL";
-  if (/^https?:\/\//.test(trimmed)) return 'URL';
+  if (/^@\w+\{/.test(trimmed)) return "BibTeX";
-  if (/^@\w+\{/.test(trimmed)) return 'BibTeX';
+  if (/^TY\s+-\s+/m.test(trimmed)) return "RIS Format";
-  if (/^TY\s+-\s+/m.test(trimmed)) return 'RIS Format';
+  if (/^PMID:/i.test(trimmed)) return "PubMed ID (PMID)";
-  if (/^PMID:/i.test(trimmed)) return 'PubMed ID (PMID)';
+  if (/^PMC\d+/i.test(trimmed)) return "PubMed Central ID (PMCID)";
-  if (/^PMC\d+/i.test(trimmed)) return 'PubMed Central ID (PMCID)';
+  if (/^ISBN/i.test(trimmed)) return "ISBN";
-  if (/^ISBN/i.test(trimmed)) return 'ISBN';
+  if (/^(wikidata:)?Q\d+$/i.test(trimmed)) return "Wikidata ID";
-  if (/^(wikidata:)?Q\d+$/i.test(trimmed)) return 'Wikidata ID';
+  if (/^cff-version:/m.test(trimmed)) return "Citation File Format (CFF)";
-  if (/^cff-version:/m.test(trimmed)) return 'Citation File Format (CFF)';
 
-  return 'Unknown';
+  return "Unknown";
 };