research-copilot 0.2.16 → 0.2.17

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "research-copilot",
-  "version": "0.2.16",
+  "version": "0.2.17",
   "description": "AI-powered research assistant for scientists — literature search, data analysis, academic writing, and project management",
   "type": "module",
   "bin": {
@@ -12,6 +12,7 @@
     "app/build/",
     "app/package.json",
     "lib/skills/",
+    "scripts/",
     "README.md",
     "LICENSE"
   ],

package/scripts/backfill-papers.mjs

@@ -0,0 +1,142 @@
+#!/usr/bin/env node
+// Backfill paper artifacts from existing literature-run review.json files.
+// Usage: node scripts/backfill-papers.mjs <projectPath>
+import { readFileSync, writeFileSync, mkdirSync, readdirSync, existsSync } from 'fs'
+import { join } from 'path'
+import { randomUUID } from 'crypto'
+
+const projectPath = process.argv[2]
+if (!projectPath) {
+  console.error('Usage: node scripts/backfill-papers.mjs <projectPath>')
+  process.exit(1)
+}
+
+const litRunsDir = join(projectPath, '.research-pilot/literature-runs')
+const papersDir = join(projectPath, '.research-pilot/artifacts/papers')
+mkdirSync(papersDir, { recursive: true })
+
+// Load existing papers for dedup
+const existingPapers = []
+if (existsSync(papersDir)) {
+  for (const f of readdirSync(papersDir)) {
+    if (!f.endsWith('.json')) continue
+    try {
+      const p = JSON.parse(readFileSync(join(papersDir, f), 'utf-8'))
+      existingPapers.push(p)
+    } catch {}
+  }
+}
+
+function normalizeTitle(t) {
+  return t.toLowerCase().replace(/[^\w\s]/g, ' ').replace(/\s+/g, ' ').trim()
+}
+
+function isDuplicate(title, year) {
+  const nt = normalizeTitle(title)
+  return existingPapers.some(p => {
+    const pt = normalizeTitle(p.title)
+    if (pt !== nt) return false
+    if (!year || !p.year) return true
+    return p.year === year
+  })
+}
+
+function generateCiteKey(authors, year) {
+  const firstAuthor = (authors?.[0] ?? 'unknown').split(/\s+/).pop()?.toLowerCase() ?? 'unknown'
+  return `${firstAuthor}${year ?? 'nd'}`
+}
+
+const AUTO_SAVE_THRESHOLD = 7
+let saved = 0
+let skippedDup = 0
+let skippedScore = 0
+
+if (!existsSync(litRunsDir)) {
+  console.error(`No literature-runs dir at ${litRunsDir}`)
+  process.exit(1)
+}
+
+const runs = readdirSync(litRunsDir)
+for (const runId of runs) {
+  const reviewPath = join(litRunsDir, runId, 'review.json')
+  if (!existsSync(reviewPath)) continue
+
+  let data
+  try {
+    data = JSON.parse(readFileSync(reviewPath, 'utf-8'))
+  } catch { continue }
+
+  const papers = data.review?.relevantPapers ?? []
+  const subTopics = data.plan?.subTopics ?? []
+  const roundLabel = `R-${runId}`
+
+  for (const paper of papers) {
+    if ((paper.relevanceScore ?? 0) < AUTO_SAVE_THRESHOLD) {
+      skippedScore++
+      continue
+    }
+    if (isDuplicate(paper.title, paper.year)) {
+      skippedDup++
+      continue
+    }
+
+    const authors = paper.authors?.length > 0 ? paper.authors : ['Unknown']
+    const citeKey = generateCiteKey(authors, paper.year)
+    const doi = (paper.doi ?? '').trim() || `unknown:${citeKey}`
+    const now = new Date().toISOString()
+    const id = randomUUID()
+
+    // Match subtopic
+    const matchedSubTopic = subTopics.find(st =>
+      paper.relevanceJustification?.toLowerCase().includes(st.name.toLowerCase())
+    )?.name
+
+    const artifact = {
+      id,
+      type: 'paper',
+      title: paper.title,
+      authors,
+      abstract: paper.abstract ?? '',
+      citeKey,
+      doi,
+      bibtex: `@article{${citeKey},\n  title = {${paper.title}},\n  author = {${authors.join(' and ')}},${paper.year ? `\n  year = {${paper.year}},` : ''}${paper.venue ? `\n  journal = {${paper.venue}},` : ''}${doi ? `\n  doi = {${doi}},` : ''}${paper.url ? `\n  url = {${paper.url}},` : ''}\n}`,
+      year: paper.year ?? undefined,
+      venue: paper.venue ?? undefined,
+      url: paper.url ?? undefined,
+      tags: [],
+      provenance: {
+        source: 'agent',
+        sessionId: 'backfill',
+        agentId: 'literature-team',
+        extractedFrom: 'agent-response'
+      },
+      createdAt: now,
+      updatedAt: now,
+      externalSource: paper.source,
+      relevanceScore: paper.relevanceScore,
+      citationCount: paper.citationCount ?? undefined,
+      relevanceJustification: paper.relevanceJustification,
+      subTopic: matchedSubTopic,
+      addedInRound: roundLabel,
+      addedByTask: 'deep_literature_study',
+      identityConfidence: paper.doi ? 'high' : 'medium',
+      semanticScholarId: paper.source === 'semantic_scholar' ? paper.id : undefined,
+      arxivId: paper.source === 'arxiv' ? paper.id : undefined,
+    }
+
+    // Remove undefined keys for clean JSON
+    for (const [k, v] of Object.entries(artifact)) {
+      if (v === undefined) delete artifact[k]
+    }
+
+    const filePath = join(papersDir, `${id}.json`)
+    writeFileSync(filePath, JSON.stringify(artifact, null, 2), 'utf-8')
+
+    // Track for dedup within this run
+    existingPapers.push(artifact)
+    saved++
+    console.log(`  + ${paper.title.slice(0, 80)}  (score: ${paper.relevanceScore})`)
+  }
+}
+
+console.log(`\nDone: ${saved} papers saved, ${skippedDup} duplicates skipped, ${skippedScore} below threshold (< ${AUTO_SAVE_THRESHOLD})`)

package/scripts/fix-node-pty-perms.mjs

@@ -0,0 +1,32 @@
+import { chmodSync, readdirSync, statSync } from 'node:fs'
+import { createRequire } from 'node:module'
+import path from 'node:path'
+
+// spawn-helper is only used on Unix platforms; Windows uses conpty.
+if (process.platform === 'win32') process.exit(0)
+
+const require = createRequire(import.meta.url)
+
+try {
+  // Resolve from package.json so we rely only on node-pty's public layout,
+  // not internal modules or runtime-loaded native bindings.
+  const ptyDir = path.dirname(require.resolve('node-pty/package.json'))
+  const prebuildsDir = path.join(ptyDir, 'prebuilds')
+
+  for (const entry of readdirSync(prebuildsDir, { withFileTypes: true })) {
+    if (!entry.isDirectory()) continue
+    const helper = path.join(prebuildsDir, entry.name, 'spawn-helper')
+    try {
+      const stat = statSync(helper)
+      if ((stat.mode & 0o111) !== 0o111) {
+        chmodSync(helper, stat.mode | 0o755)
+        console.log(`[postinstall] fixed node-pty helper permissions: ${helper}`)
+      }
+    } catch {
+      // Arch dirs without spawn-helper (e.g., win32-*) — skip silently.
+    }
+  }
+} catch (error) {
+  const message = error instanceof Error ? error.message : String(error)
+  console.warn(`[postinstall] skipped node-pty helper permission fix: ${message}`)
+}