@markuxt/markuxt 0.1.15 → 0.1.16

package/README.md

@@ -1,7 +1,7 @@
 # Markuxt
 
 <div align="center">
-  <img src="src/public/images/logo.png" alt="Markuxt" width="360" />
+  <img src="https://raw.githubusercontent.com/markuxt/markuxt/main/src/public/images/logo.png" alt="Markuxt" width="360" />
   <!-- <h1>Markuxt</h1> -->
 </div>
 

package/action.yml

@@ -0,0 +1,24 @@
+name: 'Sync Publications from OpenAlex'
+description: 'Fetches publications from OpenAlex based on member ORCIDs and syncs to content directory'
+
+inputs:
+  ror_id:
+    description: 'ROR ID of the institution (e.g., https://ror.org/03y4dt428)'
+    required: true
+  contact_email:
+    description: 'Contact email for OpenAlex API requests'
+    required: true
+  content_dir:
+    description: 'Path to content directory (default: src)'
+    required: false
+    default: 'src'
+
+outputs:
+  new_publications_count:
+    description: 'Number of new publication files added'
+  new_publications_files:
+    description: 'List of new publication file paths'
+
+runs:
+  using: 'node20'
+  main: 'src/actions/sync-publications/index.ts'

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@markuxt/markuxt",
-  "version": "0.1.15",
+  "version": "0.1.16",
   "description": "A Markdown-first academic portal framework for laboratories, research groups, and knowledge communities, powered by Nuxt.",
   "author": "hnrobert",
   "license": "Apache-2.0",
@@ -14,6 +14,7 @@
     "access": "public"
   },
   "files": [
+    "action.yml",
     "nuxt.config.ts",
     "app.config.ts",
     "app.config.d.ts",
@@ -30,6 +31,7 @@
     "@icon-park/vue-next": "^1.4.2",
     "@nuxt/content": "^2.13.2",
     "@nuxtjs/i18n": "^10.4.0",
+    "glob": "^13.0.6",
     "katex": "0.16.47",
     "mermaid": "11.15.0",
     "nuxt": "^3.15.1",
@@ -38,7 +40,11 @@
   },
   "devDependencies": {
     "@types/node": "^25.2.3",
+    "tsx": "^4.19.0",
     "typescript": "^5.7.3",
     "vue-tsc": "^3.2.4"
+  },
+  "bin": {
+    "markuxt-sync-publications": "./src/actions/sync-publications/index.ts"
   }
 }

package/src/actions/sync-publications/index.ts

@@ -0,0 +1,488 @@
+#!/usr/bin/env -S node --loader tsx
+
+/**
+ * markuxt-sync-publications
+ *
+ * GitHub Action to sync publications from OpenAlex based on member ORCIDs.
+ * Fetches publications for all members with ORCID, deduplicates against existing
+ * content, and writes new markdown files to <content_dir>/publications/<year>/<openalex_id>/index.md
+ *
+ * Usage: Called via GitHub Action (see action.yml) or directly:
+ *   ROR_ID="https://ror.org/..." CONTACT_EMAIL="..." CONTENT_DIR="src" tsx index.ts
+ */
+
+import { readFileSync, writeFileSync, mkdirSync, existsSync } from 'fs'
+import { join } from 'path'
+import { glob } from 'glob'
+
+// Inputs from GitHub Actions (passed as environment variables)
+const ROR_ID = process.env.INPUT_ROR_ID || ''
+const CONTACT_EMAIL = process.env.INPUT_CONTACT_EMAIL || ''
+const CONTENT_DIR = process.env.INPUT_CONTENT_DIR || 'src'
+const GITHUB_OUTPUT = process.env.GITHUB_OUTPUT || ''
+
+if (!ROR_ID) {
+  console.error('Error: INPUT_ROR_ID is required')
+  process.exit(1)
+}
+
+if (!CONTACT_EMAIL) {
+  console.error('Error: INPUT_CONTACT_EMAIL is required')
+  process.exit(1)
+}
+
+const OPENALEX_BASE = 'https://api.openalex.org'
+const PUBLICATIONS_DIR = join(CONTENT_DIR, 'publications')
+const MEMBERS_DIR = join(CONTENT_DIR, 'members')
+
+// ---------------------------------------------------------------------------
+// Types
+// ---------------------------------------------------------------------------
+
+interface ExistingPublication {
+  openalexId?: string
+  doi?: string
+  title?: string
+  year?: number
+  authors?: string[]
+}
+
+interface PendingPublication {
+  openalexId: string
+  title: string
+  authors: string[]
+  authorsOrcid: (string | null)[]
+  year: number
+  doi: string | null
+  venue: string | null
+  keywords: string[]
+  abstract: string | null
+  hidden: boolean
+}
+
+interface MemberInfo {
+  name: string
+  orcid: string
+}
+
+// ---------------------------------------------------------------------------
+// YAML / Markdown helpers
+// ---------------------------------------------------------------------------
+
+function parseYamlFrontmatter(content: string): Record<string, unknown> {
+  const match = content.match(/^---\r?\n([\s\S]*?)\r?\n---/)
+  if (!match) return {}
+  const result: Record<string, unknown> = {}
+  const lines = match[1].split('\n')
+  let currentKey = ''
+  let currentList: string[] | null = null
+  for (const line of lines) {
+    const listItem = line.match(/^  - (.+)$/)
+    if (listItem && currentList !== null) {
+      currentList.push(listItem[1].trim().replace(/^["']|["']$/g, ''))
+      continue
+    }
+    if (currentList !== null) {
+      result[currentKey] = currentList
+      currentList = null
+    }
+    const kv = line.match(/^(\w[\w_]*)\s*:\s*(.*)$/)
+    if (!kv) continue
+    const [, key, val] = kv
+    const trimmed = val.trim()
+    if (trimmed === '') {
+      currentKey = key
+      currentList = []
+    } else {
+      result[key] = trimmed.replace(/^["']|["']$/g, '')
+    }
+  }
+  if (currentList !== null) result[currentKey] = currentList
+  return result
+}
+
+function yamlStr(value: string): string {
+  if (/[:#\[\]{}&*!,|>'"?%@`]/.test(value) || value.startsWith(' ') || value.endsWith(' ')) {
+    return `"${value.replace(/\\/g, '\\\\').replace(/"/g, '\\"')}"`
+  }
+  return value
+}
+
+// ---------------------------------------------------------------------------
+// Deduplication helpers
+// ---------------------------------------------------------------------------
+
+const STOP_WORDS = new Set([
+  'a','an','the','of','in','on','for','to','and','or','with','by','from',
+  'at','is','are','was','were','be','been','being','that','this','these',
+  'those','it','its'
+])
+
+function tokenize(title: string): Set<string> {
+  return new Set(
+    title.toLowerCase()
+      .replace(/[^a-z0-9\s]/g, ' ')
+      .split(/\s+/)
+      .filter(w => w.length > 1 && !STOP_WORDS.has(w))
+  )
+}
+
+function jaccardSimilarity(a: Set<string>, b: Set<string>): number {
+  if (a.size === 0 && b.size === 0) return 1
+  let intersection = 0
+  for (const w of a) if (b.has(w)) intersection++
+  const union = a.size + b.size - intersection
+  return union === 0 ? 0 : intersection / union
+}
+
+function authorOverlap(a: string[], b: string[]): number {
+  if (!a.length || !b.length) return 0
+  const normalize = (name: string) => name.toLowerCase().replace(/[^a-z]/g, '')
+  const setA = new Set(a.map(normalize))
+  const setB = new Set(b.map(normalize))
+  let intersection = 0
+  for (const n of setA) if (setB.has(n)) intersection++
+  const union = setA.size + setB.size - intersection
+  return union === 0 ? 0 : intersection / union
+}
+
+function isDuplicate(
+  candidate: { title: string; year: number; authors: string[] },
+  existing: { title: string; year: number; authors: string[] }
+): boolean {
+  if (candidate.title.toLowerCase().trim() === existing.title.toLowerCase().trim()) return true
+  if (Math.abs(candidate.year - existing.year) > 1) return false
+  const titleSim = jaccardSimilarity(tokenize(candidate.title), tokenize(existing.title))
+  const authorSim = authorOverlap(candidate.authors, existing.authors)
+  return titleSim >= 0.85 && authorSim >= 0.5
+}
+
+// ---------------------------------------------------------------------------
+// Abstract reconstruction from inverted index
+// ---------------------------------------------------------------------------
+
+function reconstructAbstract(invertedIndex: Record<string, number[]> | null): string | null {
+  if (!invertedIndex) return null
+  const entries: [string, number][] = []
+  for (const [word, positions] of Object.entries(invertedIndex)) {
+    for (const pos of positions) entries.push([word, pos])
+  }
+  entries.sort((a, b) => a[1] - b[1])
+  return entries.map(e => e[0]).join(' ')
+}
+
+// ---------------------------------------------------------------------------
+// Author name formatting: OpenAlex display_name → "LastName, FirstName"
+// ---------------------------------------------------------------------------
+
+function formatAuthorName(displayName: string): string {
+  const parts = displayName.trim().split(/\s+/)
+  if (parts.length === 1) return parts[0]
+  const last = parts[parts.length - 1]
+  const first = parts.slice(0, -1).join(' ')
+  return `${last}, ${first}`
+}
+
+function extractOrcidId(orcidUrl: string | null): string | null {
+  if (!orcidUrl) return null
+  const m = orcidUrl.match(/(\d{4}-\d{4}-\d{4}-\d{3}[\dX])/)
+  return m ? m[1] : null
+}
+
+// ---------------------------------------------------------------------------
+// Markdown file builder
+// ---------------------------------------------------------------------------
+
+function buildMarkdown(pub: PendingPublication): string {
+  const lines: string[] = ['---', `_hidden: ${pub.hidden}`]
+  lines.push(`title: ${yamlStr(pub.title)}`)
+  lines.push('authors:')
+  for (const a of pub.authors) lines.push(`  - ${yamlStr(a)}`)
+  lines.push('authors_orcid:')
+  for (const o of pub.authorsOrcid) lines.push(`  - ${o ?? 'null'}`)
+  lines.push(`year: ${pub.year}`)
+  lines.push(`doi: ${pub.doi ? yamlStr(pub.doi) : ''}`)
+  lines.push(`openalex_id: ${pub.openalexId}`)
+  lines.push(`venue: ${pub.venue ? yamlStr(pub.venue) : ''}`)
+  if (pub.keywords.length) {
+    lines.push('keywords:')
+    for (const k of pub.keywords) lines.push(`  - ${yamlStr(k)}`)
+  } else {
+    lines.push('keywords: []')
+  }
+  lines.push('---', '')
+  if (pub.abstract) lines.push(pub.abstract, '')
+  return lines.join('\n')
+}
+
+// ---------------------------------------------------------------------------
+// OpenAlex API helpers
+// ---------------------------------------------------------------------------
+
+async function oaFetch(path: string): Promise<unknown> {
+  const sep = path.includes('?') ? '&' : '?'
+  const url = `${OPENALEX_BASE}${path}${sep}mailto=${encodeURIComponent(CONTACT_EMAIL)}`
+  const res = await fetch(url, {
+    headers: { 'User-Agent': `markuxt-sync-publications/1.0 (mailto:${CONTACT_EMAIL})` }
+  })
+  if (!res.ok) throw new Error(`OpenAlex ${res.status}: ${url}`)
+  return res.json()
+}
+
+async function getInstitutionId(rorId: string): Promise<string> {
+  const data = await oaFetch(
+    `/institutions?filter=ror:${encodeURIComponent(rorId)}&select=id`
+  ) as { results: { id: string }[] }
+  if (!data.results?.length) throw new Error(`Institution not found for ROR: ${rorId}`)
+  return data.results[0].id
+}
+
+async function getAuthorId(orcid: string): Promise<string | null> {
+  const data = await oaFetch(
+    `/authors?filter=orcid:${encodeURIComponent(orcid)}&select=id`
+  ) as { results: { id: string }[] }
+  return data.results?.[0]?.id ?? null
+}
+
+async function getWorksForAuthor(authorId: string, institutionId: string): Promise<unknown[]> {
+  const works: unknown[] = []
+  let cursor = '*'
+  const fields = 'id,title,authorships,publication_year,doi,primary_location,keywords,abstract_inverted_index'
+  while (true) {
+    const data = await oaFetch(
+      `/works?filter=author.id:${encodeURIComponent(authorId)},institution.id:${encodeURIComponent(institutionId)}&per_page=200&cursor=${cursor}&select=${fields}`
+    ) as { results: unknown[]; meta: { next_cursor: string | null } }
+    works.push(...data.results)
+    if (!data.meta?.next_cursor) break
+    cursor = data.meta.next_cursor
+  }
+  return works
+}
+
+// ---------------------------------------------------------------------------
+// Scan existing publications
+// ---------------------------------------------------------------------------
+
+async function scanExistingPublications(): Promise<ExistingPublication[]> {
+  const files = await glob('**/*.md', { cwd: PUBLICATIONS_DIR, absolute: true })
+  const existing: ExistingPublication[] = []
+  for (const file of files) {
+    const content = readFileSync(file, 'utf-8')
+    const fm = parseYamlFrontmatter(content)
+    if (fm._hidden === 'true' || fm._hidden === true) continue
+    const openalexId = typeof fm.openalex_id === 'string'
+      ? fm.openalex_id.replace(/^W/, '') : undefined
+    const doi = typeof fm.doi === 'string' && fm.doi ? fm.doi : undefined
+    const title = typeof fm.title === 'string' ? fm.title : undefined
+    const year = typeof fm.year === 'string'
+      ? parseInt(fm.year) : (typeof fm.year === 'number' ? fm.year : undefined)
+    const authors = Array.isArray(fm.authors) ? fm.authors as string[] : undefined
+    existing.push({ openalexId, doi, title, year, authors })
+  }
+  return existing
+}
+
+// ---------------------------------------------------------------------------
+// Scan members with ORCID
+// ---------------------------------------------------------------------------
+
+async function scanMembersWithOrcid(): Promise<MemberInfo[]> {
+  const files = await glob('**/*.md', { cwd: MEMBERS_DIR, absolute: true })
+  const members: MemberInfo[] = []
+  for (const file of files) {
+    const content = readFileSync(file, 'utf-8')
+    const fm = parseYamlFrontmatter(content)
+    if (fm._hidden === 'true' || fm._hidden === true) continue
+    if (typeof fm.orcid === 'string' && fm.orcid.trim()) {
+      members.push({ name: String(fm.name ?? 'Unknown'), orcid: fm.orcid.trim() })
+    }
+  }
+  return members
+}
+
+// ---------------------------------------------------------------------------
+// Parse OpenAlex work → PendingPublication
+// ---------------------------------------------------------------------------
+
+function parseWork(work: Record<string, unknown>): PendingPublication | null {
+  const rawId = typeof work.id === 'string'
+    ? work.id.replace('https://openalex.org/', '') : null
+  if (!rawId) return null
+
+  const title = typeof work.title === 'string' ? work.title.trim() : null
+  if (!title) return null
+
+  const year = typeof work.publication_year === 'number' ? work.publication_year : null
+  if (!year) return null
+
+  const authorships = Array.isArray(work.authorships)
+    ? work.authorships as Record<string, unknown>[] : []
+
+  const authors = authorships.map(a => {
+    const author = a.author as Record<string, unknown> | undefined
+    return author?.display_name ? formatAuthorName(String(author.display_name)) : null
+  }).filter((n): n is string => n !== null)
+
+  const authorsOrcid = authorships.map(a => {
+    const author = a.author as Record<string, unknown> | undefined
+    return extractOrcidId(author?.orcid ? String(author.orcid) : null)
+  })
+
+  const doiRaw = typeof work.doi === 'string' ? work.doi : null
+  const doi = doiRaw
+    ? (doiRaw.startsWith('http') ? doiRaw : `https://doi.org/${doiRaw}`) : null
+
+  const primaryLocation = work.primary_location as Record<string, unknown> | undefined
+  const source = primaryLocation?.source as Record<string, unknown> | undefined
+  const venue = source?.display_name ? String(source.display_name) : null
+
+  const keywordsRaw = Array.isArray(work.keywords)
+    ? work.keywords as Record<string, unknown>[] : []
+  const keywords = keywordsRaw.map(k => String(k.display_name ?? '')).filter(Boolean)
+
+  const abstract = reconstructAbstract(
+    work.abstract_inverted_index as Record<string, number[]> | null
+  )
+
+  return { openalexId: rawId, title, authors, authorsOrcid, year, doi, venue, keywords, abstract, hidden: false }
+}
+
+// ---------------------------------------------------------------------------
+// Set GitHub Actions output
+// ---------------------------------------------------------------------------
+
+function setOutput(name: string, value: string): void {
+  if (GITHUB_OUTPUT) {
+    appendFileSync(GITHUB_OUTPUT, `${name}=${value}\n`)
+  }
+  console.log(`::set-output name=${name}::${value}`)
+}
+
+function appendFileSync(file: string, data: string): void {
+  const fd = require('fs').openSync(file, 'a')
+  require('fs').writeSync(fd, data)
+  require('fs').closeSync(fd)
+}
+
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+
+async function main() {
+  console.log(`[markuxt-sync-publications] Starting...`)
+  console.log(`[markuxt-sync-publications] ROR ID: ${ROR_ID}`)
+  console.log(`[markuxt-sync-publications] Content dir: ${CONTENT_DIR}`)
+
+  // 1. Resolve institution OpenAlex ID
+  const institutionId = await getInstitutionId(ROR_ID)
+  console.log(`[markuxt-sync-publications] Institution ID: ${institutionId}`)
+
+  // 2. Scan existing publications
+  const existing = await scanExistingPublications()
+  const existingOpenalexIds = new Set(
+    existing.map(p => p.openalexId).filter((id): id is string => !!id)
+  )
+  const existingDois = new Set(
+    existing
+      .map(p => p.doi?.toLowerCase().replace(/https?:\/\/doi\.org\//i, ''))
+      .filter((d): d is string => !!d)
+  )
+  console.log(`[markuxt-sync-publications] Found ${existing.length} existing publications`)
+
+  // 3. Scan members with ORCID
+  const members = await scanMembersWithOrcid()
+  console.log(`[markuxt-sync-publications] Found ${members.length} members with ORCID`)
+
+  // 4. Fetch works from OpenAlex for each member
+  const allWorks = new Map<string, PendingPublication>()
+  for (const member of members) {
+    console.log(`[markuxt-sync-publications] Processing ${member.name} (${member.orcid})...`)
+    const authorId = await getAuthorId(member.orcid)
+    if (!authorId) {
+      console.warn(`  → Not found on OpenAlex: ${member.orcid}`)
+      continue
+    }
+    console.log(`  → Author ID: ${authorId}`)
+    const works = await getWorksForAuthor(authorId, institutionId)
+    console.log(`  → ${works.length} works`)
+    for (const w of works) {
+      const pub = parseWork(w as Record<string, unknown>)
+      if (!pub) continue
+      if (!allWorks.has(pub.openalexId)) allWorks.set(pub.openalexId, pub)
+    }
+  }
+  console.log(`[markuxt-sync-publications] Total unique works from OpenAlex: ${allWorks.size}`)
+
+  // 5. Filter out already-existing works
+  const pending: PendingPublication[] = []
+  for (const pub of allWorks.values()) {
+    const shortId = pub.openalexId.replace(/^W/, '')
+    if (existingOpenalexIds.has(shortId)) continue
+    const doiKey = pub.doi?.toLowerCase().replace(/https?:\/\/doi\.org\//i, '')
+    if (doiKey && existingDois.has(doiKey)) continue
+    const dupOfExisting = existing.some(e =>
+      e.title && e.year != null &&
+      isDuplicate(
+        { title: pub.title, year: pub.year, authors: pub.authors },
+        { title: e.title, year: e.year, authors: e.authors ?? [] }
+      )
+    )
+    if (dupOfExisting) continue
+    pending.push(pub)
+  }
+  console.log(`[markuxt-sync-publications] After dedup vs existing: ${pending.length} to add`)
+
+  // 6. Dedup within pending list, keep newest per group
+  const toWrite: PendingPublication[] = []
+  const consumed = new Set<number>()
+  for (let i = 0; i < pending.length; i++) {
+    if (consumed.has(i)) continue
+    const group: number[] = [i]
+    for (let j = i + 1; j < pending.length; j++) {
+      if (consumed.has(j)) continue
+      const a = pending[i], b = pending[j]
+      const sameDoi = !!(a.doi && b.doi && a.doi.toLowerCase() === b.doi.toLowerCase())
+      const sameTitle = a.title.toLowerCase().trim() === b.title.toLowerCase().trim()
+      const similar = isDuplicate(
+        { title: a.title, year: a.year, authors: a.authors },
+        { title: b.title, year: b.year, authors: b.authors }
+      )
+      if (sameDoi || sameTitle || similar) {
+        group.push(j)
+        consumed.add(j)
+      }
+    }
+    consumed.add(i)
+    // Sort group: newest first; hide all but the first
+    group.sort((x, y) => pending[y].year - pending[x].year)
+    for (let k = 0; k < group.length; k++) {
+      toWrite.push({ ...pending[group[k]], hidden: k > 0 })
+    }
+  }
+
+  const visible = toWrite.filter(p => !p.hidden).length
+  const hidden = toWrite.filter(p => p.hidden).length
+  console.log(`[markuxt-sync-publications] Writing ${toWrite.length} files (${visible} visible, ${hidden} hidden)`)
+
+  // 7. Write markdown files
+  const newFiles: string[] = []
+  for (const pub of toWrite) {
+    const dir = join(PUBLICATIONS_DIR, String(pub.year), pub.openalexId)
+    if (!existsSync(dir)) mkdirSync(dir, { recursive: true })
+    const filePath = join(dir, 'index.md')
+    writeFileSync(filePath, buildMarkdown(pub), 'utf-8')
+    console.log(`  [${pub.hidden ? 'hidden' : 'visible'}] ${filePath}`)
+    newFiles.push(filePath)
+  }
+
+  // 8. Set GitHub Actions outputs
+  setOutput('count', String(newFiles.length))
+  setOutput('files', newFiles.join('\n'))
+
+  console.log(`[markuxt-sync-publications] Done. Added ${newFiles.length} publication files.`)
+}
+
+main().catch(err => {
+  console.error('[markuxt-sync-publications] Fatal:', err)
+  process.exit(1)
+})

package/src/components/MemberCard.vue

@@ -29,6 +29,17 @@
         >
           <Google class="icon-inline" theme="outline" :size="20" fill="currentColor" :stroke-width="2.5" />
         </a>
+        <a
+          v-if="member.orcid"
+          :href="`https://orcid.org/${member.orcid}`"
+          target="_blank"
+          rel="noopener"
+          class="member-card__action"
+          :aria-label="t('members.orcid')"
+          @click.stop
+        >
+          <Orcid class="icon-inline" theme="outline" :size="20" fill="currentColor" :stroke-width="2.5" />
+        </a>
       </div>
     </div>
     <div class="member-card__content">
@@ -45,6 +56,7 @@
 import { computed } from 'vue'
 import Mail from '@icon-park/vue-next/es/icons/Mail'
 import Google from '@icon-park/vue-next/es/icons/Google'
+import Orcid from '@icon-park/vue-next/es/icons/IdCardH'
 
 interface Member {
   name: string
@@ -52,6 +64,7 @@ interface Member {
   title?: string
   email?: string
   scholar?: string
+  orcid?: string
   image?: string
   interests?: string[]
   category?: string