@ncukondo/search-hub 0.10.0 → 0.12.0

package/dist/cli/commands/review/extract.js.map

@@ -1 +1 @@
-{"version":3,"file":"extract.js","sources":["../../../../src/cli/commands/review/extract.ts"],"sourcesContent":["/**\n * review extract command - Extract subset of articles for distributed review\n */\n\nimport { join, dirname } from 'node:path';\nimport { readFile, writeFile, mkdir, copyFile, access } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport { classifyStatus, type ReviewFile, type ArticleEntry, type ReviewStatus, type ReviewBasis, type WorkFile, type WorkFileArticle } from './types.js';\n\nexport type SortOption = 'year' | 'title' | 'random' | 'none';\n\nexport interface ReviewExtractOptions {\n  sessionId: string;\n  filter?: ReviewStatus[];\n  sort?: SortOption;\n  seed?: number;\n  limit?: number;\n  offset?: number;\n  /** Basis for the review (title, abstract). When specified, outputs work file format. */\n  basis?: ReviewBasis;\n  /** Reviewer identifier (e.g., \"ai:claude\"). Required for all extract modes. */\n  reviewer?: string;\n  /** Name for the review subset (output goes to for-review/<name>/review.yaml) */\n  name: string;\n}\n\n\nexport interface ReviewExtractResult {\n  outputPath: string;\n  extractedCount: number;\n  totalMatching: number;\n}\n\n/**\n * Load review file from session directory\n */\nasync function loadReviewFile(sessionDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Seeded random number generator (Fisher-Yates shuffle with LCG)\n */\nfunction seededShuffle<T>(array: T[], seed: number): T[] {\n  const result = [...array];\n  let currentSeed = seed;\n\n  // Linear congruential generator\n  function random(): number {\n    currentSeed = (currentSeed * 1664525 + 1013904223) % 4294967296;\n    return currentSeed / 4294967296;\n  }\n\n  // Fisher-Yates shuffle\n  for (let i = result.length - 1; i > 0; i--) {\n    const j = Math.floor(random() * (i + 1));\n    [result[i], result[j]] = [result[j]!, result[i]!];\n  }\n\n  return result;\n}\n\n/**\n * Get the best identifier for an article (doi > pmid > scopusId > arxivId > ericId > title)\n */\nfunction getArticleId(article: ArticleEntry): string {\n  if (article.doi) return article.doi;\n  if (article.pmid) return article.pmid;\n  if (article.scopusId) return article.scopusId;\n  if (article.arxivId) return article.arxivId;\n  if (article.ericId) return article.ericId;\n  return article.title;\n}\n\nfunction getBasisGuidanceComment(basis: ReviewBasis): string {\n  switch (basis) {\n    case 'title':\n      return [\n        '# Screening by title only.',\n        '# Mark clearly irrelevant items as \"exclude\" with a comment explaining the reason.',\n        '# Leave everything else as \"uncertain\".',\n        '',\n      ].join('\\n');\n    case 'abstract':\n      return [\n        '# Screening by title and abstract.',\n        '# You should be able to decide \"include\" or \"exclude\" for most items at this stage.',\n        '# Mark remaining ambiguous items as \"uncertain\" with a comment explaining why.',\n        '',\n      ].join('\\n');\n    case 'fulltext':\n      return [\n        '# Screening by full text. This is the final decision stage.',\n        '# Decide \"include\" or \"exclude\" for each item.',\n        '# Use \"uncertain\" only when absolutely unavoidable, with a comment explaining why.',\n        '',\n      ].join('\\n');\n  }\n}\n\n/**\n * Sort articles based on sort option\n */\nfunction sortArticles(articles: ArticleEntry[], sort: SortOption, seed?: number): ArticleEntry[] {\n  switch (sort) {\n    case 'year':\n      return [...articles].sort((a, b) => {\n        const yearA = a.year ?? '';\n        const yearB = b.year ?? '';\n        return yearA.localeCompare(yearB);\n      });\n    case 'title':\n      return [...articles].sort((a, b) => a.title.localeCompare(b.title));\n    case 'random':\n      return seededShuffle(articles, seed ?? Date.now());\n    case 'none':\n    default:\n      return articles;\n  }\n}\n\n/**\n * Validate the name parameter for extract\n */\nexport function validateName(name: string): void {\n  if (!name || name.trim() === '') {\n    throw new Error('--name must not be empty');\n  }\n  if (name.includes('/') || name.includes('\\\\')) {\n    throw new Error(`--name must not contain path separators: \"${name}\"`);\n  }\n  if (name.includes('..')) {\n    throw new Error(`--name must not contain \"..\": \"${name}\"`);\n  }\n}\n\n/**\n * Execute review extract command\n */\nexport async function executeReviewExtract(\n  options: ReviewExtractOptions,\n  sessionsDir: string\n): Promise<ReviewExtractResult> {\n  validateName(options.name);\n\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const outputPath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n  const reviewFile = await loadReviewFile(sessionDir);\n\n  // Filter articles by status\n  const reviewers = reviewFile.reviewers;\n  let filtered: ArticleEntry[];\n  if (options.filter && options.filter.length > 0) {\n    filtered = reviewFile.articles.filter((article) => {\n      const status = classifyStatus(article, reviewers);\n      return options.filter!.includes(status);\n    });\n  } else {\n    filtered = [...reviewFile.articles];\n  }\n\n  const totalMatching = filtered.length;\n\n  // Sort articles\n  const sorted = sortArticles(filtered, options.sort ?? 'none', options.seed);\n\n  // Apply pagination\n  let paginated = sorted;\n  if (options.offset !== undefined && options.offset > 0) {\n    paginated = paginated.slice(options.offset);\n  }\n  if (options.limit !== undefined && options.limit > 0) {\n    paginated = paginated.slice(0, options.limit);\n  }\n\n  let finalContent: string;\n\n  // If basis is specified, output work file format\n  if (options.basis && options.reviewer) {\n    const workFile: WorkFile = {\n      sessionId: options.sessionId,\n      basis: options.basis,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => {\n        const workArticle: WorkFileArticle = {\n          id: getArticleId(article),\n          title: article.title,\n          decision: 'uncertain',\n          comment: '',\n        };\n        // Include abstract for abstract and fulltext basis\n        if ((options.basis === 'abstract' || options.basis === 'fulltext') && article.abstract) {\n          workArticle.abstract = article.abstract;\n        }\n        // Include fulltext dirName for fulltext basis\n        if (options.basis === 'fulltext' && article.fulltext) {\n          workArticle.fulltext = article.fulltext.dirName;\n        }\n        return workArticle;\n      }),\n    };\n\n    const yamlContent = stringifyYaml(workFile, {\n      lineWidth: 0,\n    });\n\n    // Add basis-specific guidance comment at the top\n    const guidanceComment = getBasisGuidanceComment(options.basis);\n    finalContent = guidanceComment + yamlContent;\n  } else {\n    if (!options.reviewer) {\n      throw new Error('--reviewer is required for review file extract');\n    }\n    // Build output review file with reviewHistory separation\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      ...(options.reviewer && { reviewer: options.reviewer }),\n      articles: paginated.map((article) => ({\n        ...article,\n        reviewHistory: article.reviews ?? [],\n        reviews: [],\n        finalDecision: null,\n      })),\n    };\n\n    // Generate YAML with schema reference\n    const yamlContent = stringifyYaml(outputFile, {\n      lineWidth: 0,\n    });\n\n    // Replace finalDecision: null with a commented placeholder for user guidance\n    const yamlWithComments = yamlContent.replace(\n      /^(\\s*)finalDecision: null$/gm,\n      '$1finalDecision: # include / exclude'\n    );\n\n    // Schema reference pointing to adjacent file\n    const schemaComment = `# yaml-language-server: $schema=./review.schema.json\\n`;\n    finalContent = schemaComment + yamlWithComments;\n  }\n\n  // Ensure output directory exists\n  const outputDir = dirname(outputPath);\n  await mkdir(outputDir, { recursive: true });\n\n  // Write output YAML\n  await writeFile(outputPath, finalContent, 'utf-8');\n\n  // Copy schema file to output directory if it exists\n  const schemasDir = join(dirname(sessionsDir), '.search-hub', 'schemas');\n  const 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+{"version":3,"file":"extract.js","sources":["../../../../src/cli/commands/review/extract.ts"],"sourcesContent":["/**\n * review extract command - Extract subset of articles for distributed review\n */\n\nimport { join, dirname } from 'node:path';\nimport { readFile, writeFile, mkdir, copyFile, access } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport { classifyStatus, type ReviewFile, type ArticleEntry, type ReviewStatus, type ReviewBasis } from './types.js';\n\nexport type SortOption = 'year' | 'title' | 'random' | 'none';\n\nexport interface ReviewExtractOptions {\n  sessionId: string;\n  filter?: ReviewStatus[];\n  sort?: SortOption;\n  seed?: number;\n  limit?: number;\n  offset?: number;\n  /** Basis for the review (title, abstract, fulltext). When specified, outputs screening format. */\n  basis?: ReviewBasis;\n  /** Reviewer identifier (e.g., \"ai:claude\"). Required for all extract modes. */\n  reviewer?: string;\n  /** Name for the review subset (output goes to for-review/<name>/review.yaml) */\n  name: string;\n  /** When true, outputs final decision format with reviewHistory and finalDecision fields. */\n  finalize?: boolean;\n}\n\n\nexport interface ReviewExtractResult {\n  outputPath: string;\n  extractedCount: number;\n  totalMatching: number;\n}\n\n/**\n * Load review file from session directory\n */\nasync function loadReviewFile(sessionDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Seeded random number generator (Fisher-Yates shuffle with LCG)\n */\nfunction seededShuffle<T>(array: T[], seed: number): T[] {\n  const result = [...array];\n  let currentSeed = seed;\n\n  // Linear congruential generator\n  function random(): number {\n    currentSeed = (currentSeed * 1664525 + 1013904223) % 4294967296;\n    return currentSeed / 4294967296;\n  }\n\n  // Fisher-Yates shuffle\n  for (let i = result.length - 1; i > 0; i--) {\n    const j = Math.floor(random() * (i + 1));\n    [result[i], result[j]] = [result[j]!, result[i]!];\n  }\n\n  return result;\n}\n\n/**\n * Get the best identifier for an article (doi > pmid > scopusId > arxivId > ericId > title)\n */\nfunction getArticleId(article: ArticleEntry): string {\n  if (article.doi) return article.doi;\n  if (article.pmid) return article.pmid;\n  if (article.scopusId) return article.scopusId;\n  if (article.arxivId) return article.arxivId;\n  if (article.ericId) return article.ericId;\n  return article.title;\n}\n\nfunction getBasisGuidanceComment(basis: ReviewBasis): string {\n  const schemaLine = '# yaml-language-server: $schema=./review.schema.json';\n  switch (basis) {\n    case 'title':\n      return [\n        schemaLine,\n        '# Screening by title only.',\n        '# Mark clearly irrelevant items as \"exclude\" with a comment explaining the reason.',\n        '# Leave everything else as \"uncertain\".',\n        '',\n      ].join('\\n');\n    case 'abstract':\n      return [\n        schemaLine,\n        '# Screening by title and abstract.',\n        '# You should be able to decide \"include\" or \"exclude\" for most items at this stage.',\n        '# Mark remaining ambiguous items as \"uncertain\" with a comment explaining why.',\n        '',\n      ].join('\\n');\n    case 'fulltext':\n      return [\n        schemaLine,\n        '# Screening by full text. This is the final decision stage.',\n        '# Decide \"include\" or \"exclude\" for each item.',\n        '# Use \"uncertain\" only when absolutely unavoidable, with a comment explaining why.',\n        '',\n      ].join('\\n');\n  }\n}\n\nfunction getDecisionInlineComment(basis: ReviewBasis): string {\n  switch (basis) {\n    case 'title':\n      return '# exclude / uncertain';\n    case 'abstract':\n    case 'fulltext':\n      return '# include / exclude / uncertain';\n  }\n}\n\n/** Build a screening article for --basis mode: only include fields relevant to the basis */\nfunction buildScreeningArticle(article: ArticleEntry, basis: ReviewBasis): ArticleEntry {\n  // Start with identifiers\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Include abstract for abstract and fulltext basis\n  if ((basis === 'abstract' || basis === 'fulltext') && article.abstract) {\n    result.abstract = article.abstract;\n  }\n\n  // Include fulltext ref for fulltext basis\n  if (basis === 'fulltext' && article.fulltext) {\n    result.fulltext = article.fulltext;\n  }\n\n  // Pre-populate reviews (reviewer omitted; filled from top-level field on merge)\n  result.reviews = [{ decision: 'uncertain' as const, comment: '' } as ArticleEntry['reviews'][0]];\n\n  return result;\n}\n\n/** Build a finalize article with reviewHistory and finalDecision, optionally scoped by basis */\nfunction buildFinalizeArticle(article: ArticleEntry, basis?: ReviewBasis): ArticleEntry {\n  const result: ArticleEntry = { title: article.title, reviews: [] };\n\n  // Always include identifiers\n  if (article.doi) result.doi = article.doi;\n  if (article.pmid) result.pmid = article.pmid;\n  if (article.scopusId) result.scopusId = article.scopusId;\n  if (article.arxivId) result.arxivId = article.arxivId;\n  if (article.ericId) result.ericId = article.ericId;\n\n  // Always include bibliographic metadata\n  if (article.authors) result.authors = article.authors;\n  if (article.year) result.year = article.year;\n\n  // Scope content by basis (or include all if no basis)\n  if (!basis || basis === 'abstract' || basis === 'fulltext') {\n    if (article.abstract) result.abstract = article.abstract;\n  }\n  if (!basis || basis === 'fulltext') {\n    if (article.fulltext) result.fulltext = article.fulltext;\n  }\n\n  // Add reviewHistory (existing reviews, read-only)\n  result.reviewHistory = article.reviews ?? [];\n\n  // Empty reviews for new reviews\n  result.reviews = [];\n\n  // Null finalDecision as placeholder\n  result.finalDecision = null;\n\n  return result;\n}\n\nfunction getFinalDecisionGuidanceComment(): string {\n  return [\n    '# yaml-language-server: $schema=./review.schema.json',\n    '# Final decision file: set finalDecision on each article',\n    '# Valid decisions: include / exclude / null',\n    '',\n  ].join('\\n');\n}\n\n/**\n * Sort articles based on sort option\n */\nfunction sortArticles(articles: ArticleEntry[], sort: SortOption, seed?: number): ArticleEntry[] {\n  switch (sort) {\n    case 'year':\n      return [...articles].sort((a, b) => {\n        const yearA = a.year ?? '';\n        const yearB = b.year ?? '';\n        return yearA.localeCompare(yearB);\n      });\n    case 'title':\n      return [...articles].sort((a, b) => a.title.localeCompare(b.title));\n    case 'random':\n      return seededShuffle(articles, seed ?? Date.now());\n    case 'none':\n    default:\n      return articles;\n  }\n}\n\n/**\n * Validate the name parameter for extract\n */\nexport function validateName(name: string): void {\n  if (!name || name.trim() === '') {\n    throw new Error('--name must not be empty');\n  }\n  if (name.includes('/') || name.includes('\\\\')) {\n    throw new Error(`--name must not contain path separators: \"${name}\"`);\n  }\n  if (name.includes('..')) {\n    throw new Error(`--name must not contain \"..\": \"${name}\"`);\n  }\n}\n\n/**\n * Execute review extract command\n */\nexport async function executeReviewExtract(\n  options: ReviewExtractOptions,\n  sessionsDir: string\n): Promise<ReviewExtractResult> {\n  validateName(options.name);\n\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const outputPath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n  const reviewFile = await loadReviewFile(sessionDir);\n\n  // Filter articles by status\n  const reviewers = reviewFile.reviewers;\n  let filtered: ArticleEntry[];\n  if (options.filter && options.filter.length > 0) {\n    filtered = reviewFile.articles.filter((article) => {\n      const status = classifyStatus(article, reviewers);\n      return options.filter!.includes(status);\n    });\n  } else {\n    filtered = [...reviewFile.articles];\n  }\n\n  const totalMatching = filtered.length;\n\n  // Sort articles\n  const sorted = sortArticles(filtered, options.sort ?? 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yamlWithComments = yamlContent.replace(\n      /^(\\s*-?\\s*)decision: uncertain$/gm,\n      `$1decision: uncertain          ${decisionComment}`\n    );\n\n    const guidanceComment = getBasisGuidanceComment(options.basis);\n    finalContent = guidanceComment + yamlWithComments;\n  } else {\n    // Final decision mode: --finalize, or no --basis (backward compat)\n    const outputFile: ReviewFile = {\n      sessionId: options.sessionId,\n      reviewer: options.reviewer,\n      articles: paginated.map((article) => buildFinalizeArticle(article, options.basis)),\n    };\n\n    const yamlContent = stringifyYaml(outputFile, { lineWidth: 0 });\n\n    // Replace finalDecision: null with a commented placeholder for user guidance\n    const yamlWithComments = yamlContent.replace(\n      /^(\\s*)finalDecision: null$/gm,\n      '$1finalDecision: # include / exclude'\n    );\n\n    const guidanceComment = getFinalDecisionGuidanceComment();\n    finalContent = guidanceComment + yamlWithComments;\n  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package/dist/cli/commands/review/mark.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands/review/mark.js

@@ -1,36 +1,83 @@
 import { readFile, writeFile } from "node:fs/promises";
 import { parse, stringify } from "yaml";
-async function loadWorkFile(filePath) {
-  const content = await readFile(filePath, "utf-8");
-  const workFile = parse(content);
-  if (!workFile.basis) {
-    throw new Error('Invalid work file: missing "basis" field. This command only works with work files generated by "review extract --basis".');
+function extractLeadingComments(content) {
+  const lines = content.split("\n");
+  const commentLines = [];
+  for (const line of lines) {
+    if (line.startsWith("#") || line.trim() === "") {
+      commentLines.push(line);
+    } else {
+      break;
+    }
   }
-  return workFile;
+  if (commentLines.length === 0) return "";
+  return commentLines.join("\n") + "\n";
 }
-async function saveWorkFile(filePath, workFile) {
-  const content = stringify(workFile, { lineWidth: 0 });
-  await writeFile(filePath, content, "utf-8");
+function isWorkFile(file) {
+  if (typeof file !== "object" || file === null || !("basis" in file) || !("articles" in file) || !Array.isArray(file.articles)) {
+    return false;
+  }
+  const articles = file.articles;
+  if (articles.length === 0) return false;
+  const first = articles[0];
+  return "id" in first && "decision" in first && !("reviews" in first);
+}
+function findArticleByIdentifier(id, articles) {
+  for (const article of articles) {
+    if (article.doi && article.doi.toLowerCase() === id.toLowerCase()) return article;
+    if (article.pmid && article.pmid === id) return article;
+    if (article.scopusId && article.scopusId === id) return article;
+    if (article.arxivId && article.arxivId === id) return article;
+    if (article.ericId && article.ericId === id) return article;
+    if (article.title.toLowerCase() === id.toLowerCase()) return article;
+  }
+  return void 0;
 }
 async function executeReviewMark(options) {
-  const workFile = await loadWorkFile(options.file);
+  if (!options.id || !options.decision) {
+    throw new Error("--id and --decision must be specified");
+  }
+  const rawContent = await readFile(options.file, "utf-8");
+  const parsed = parse(rawContent);
   const result = {
     marked: 0,
     warnings: []
   };
-  if (!options.id || !options.decision) {
-    throw new Error("--id and --decision must be specified");
-  }
-  const article = workFile.articles.find((a) => a.id === options.id);
-  if (!article) {
-    throw new Error(`Article not found: ${options.id}`);
-  }
-  article.decision = options.decision;
-  if (options.comment !== void 0) {
-    article.comment = options.comment;
+  if (isWorkFile(parsed)) {
+    const workFile = parsed;
+    const article = workFile.articles.find((a) => a.id === options.id);
+    if (!article) {
+      throw new Error(`Article not found: ${options.id}`);
+    }
+    article.decision = options.decision;
+    if (options.comment !== void 0) {
+      article.comment = options.comment;
+    }
+    result.marked = 1;
+    const yamlContent = stringify(workFile, { lineWidth: 0 });
+    const leadingComments = extractLeadingComments(rawContent);
+    await writeFile(options.file, leadingComments + yamlContent, "utf-8");
+  } else {
+    const reviewFile = parsed;
+    if (!reviewFile.basis) {
+      throw new Error('Invalid review file: missing "basis" field. This command only works with files generated by "review extract --basis".');
+    }
+    const article = findArticleByIdentifier(options.id, reviewFile.articles);
+    if (!article) {
+      throw new Error(`Article not found: ${options.id}`);
+    }
+    if (!article.reviews || article.reviews.length === 0) {
+      article.reviews = [{ decision: "uncertain", comment: "" }];
+    }
+    article.reviews[0].decision = options.decision;
+    if (options.comment !== void 0) {
+      article.reviews[0].comment = options.comment;
+    }
+    result.marked = 1;
+    const yamlContent = stringify(reviewFile, { lineWidth: 0 });
+    const leadingComments = extractLeadingComments(rawContent);
+    await writeFile(options.file, leadingComments + yamlContent, "utf-8");
   }
-  result.marked = 1;
-  await saveWorkFile(options.file, workFile);
   return result;
 }
 export {

package/dist/cli/commands/review/mark.js.map

@@ -1 +1 @@
-{"version":3,"file":"mark.js","sources":["../../../../src/cli/commands/review/mark.ts"],"sourcesContent":["/**\n * review mark command - Mark decisions in work files\n */\n\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { ReviewDecision, WorkFile } from './types.js';\n\n\nexport interface ReviewMarkOptions {\n  /** Path to the work file */\n  file: string;\n  /** Article ID to mark */\n  id?: string;\n  /** Decision to apply */\n  decision?: ReviewDecision;\n  /** Optional comment */\n  comment?: string;\n}\n\nexport interface ReviewMarkResult {\n  /** Number of articles marked */\n  marked: number;\n  /** Warnings (e.g., articles not found) */\n  warnings: string[];\n}\n\n/**\n * Load work file\n */\nasync function loadWorkFile(filePath: string): Promise<WorkFile> {\n  const content = await readFile(filePath, 'utf-8');\n  const workFile = parseYaml(content) as WorkFile;\n\n  // Validate that this is a work file (has basis field)\n  if (!workFile.basis) {\n    throw new Error('Invalid work file: missing \"basis\" field. This command only works with work files generated by \"review extract --basis\".');\n  }\n\n  return workFile;\n}\n\n/**\n * Save work file\n */\nasync function saveWorkFile(filePath: string, workFile: WorkFile): Promise<void> {\n  const content = stringifyYaml(workFile, { lineWidth: 0 });\n  await writeFile(filePath, content, 'utf-8');\n}\n\n/**\n * Execute review mark command\n */\nexport async function executeReviewMark(options: ReviewMarkOptions): Promise<ReviewMarkResult> {\n  const workFile = await loadWorkFile(options.file);\n\n  const result: ReviewMarkResult = {\n    marked: 0,\n    warnings: [],\n  };\n\n  if (!options.id || !options.decision) {\n    throw new Error('--id and --decision must be specified');\n  }\n\n  const article = workFile.articles.find((a) => a.id === options.id);\n  if (!article) {\n    throw new Error(`Article not found: ${options.id}`);\n  }\n\n  article.decision = options.decision;\n  if (options.comment !== undefined) {\n    article.comment = options.comment;\n  }\n  result.marked = 1;\n\n  await saveWorkFile(options.file, workFile);\n\n  return result;\n}\n"],"names":["parseYaml","stringifyYaml"],"mappings":";;AA8BA,eAAe,aAAa,UAAqC;AAC/D,QAAM,UAAU,MAAM,SAAS,UAAU,OAAO;AAChD,QAAM,WAAWA,MAAU,OAAO;AAGlC,MAAI,CAAC,SAAS,OAAO;AACnB,UAAM,IAAI,MAAM,0HAA0H;AAAA,EAC5I;AAEA,SAAO;AACT;AAKA,eAAe,aAAa,UAAkB,UAAmC;AAC/E,QAAM,UAAUC,UAAc,UAAU,EAAE,WAAW,GAAG;AACxD,QAAM,UAAU,UAAU,SAAS,OAAO;AAC5C;AAKA,eAAsB,kBAAkB,SAAuD;AAC7F,QAAM,WAAW,MAAM,aAAa,QAAQ,IAAI;AAEhD,QAAM,SAA2B;AAAA,IAC/B,QAAQ;AAAA,IACR,UAAU,CAAA;AAAA,EAAC;AAGb,MAAI,CAAC,QAAQ,MAAM,CAAC,QAAQ,UAAU;AACpC,UAAM,IAAI,MAAM,uCAAuC;AAAA,EACzD;AAEA,QAAM,UAAU,SAAS,SAAS,KAAK,CAAC,MAAM,EAAE,OAAO,QAAQ,EAAE;AACjE,MAAI,CAAC,SAAS;AACZ,UAAM,IAAI,MAAM,sBAAsB,QAAQ,EAAE,EAAE;AAAA,EACpD;AAEA,UAAQ,WAAW,QAAQ;AAC3B,MAAI,QAAQ,YAAY,QAAW;AACjC,YAAQ,UAAU,QAAQ;AAAA,EAC5B;AACA,SAAO,SAAS;AAEhB,QAAM,aAAa,QAAQ,MAAM,QAAQ;AAEzC,SAAO;AACT;"}
+{"version":3,"file":"mark.js","sources":["../../../../src/cli/commands/review/mark.ts"],"sourcesContent":["/**\n * review mark command - Mark decisions in review/work files\n */\n\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { ReviewDecision, ReviewFile, WorkFile, ArticleEntry } from './types.js';\n\n\nexport interface ReviewMarkOptions {\n  /** Path to the work file */\n  file: string;\n  /** Article ID to mark */\n  id?: string;\n  /** Decision to apply */\n  decision?: ReviewDecision;\n  /** Optional comment */\n  comment?: string;\n}\n\nexport interface ReviewMarkResult {\n  /** Number of articles marked */\n  marked: number;\n  /** Warnings (e.g., articles not found) */\n  warnings: string[];\n}\n\n/**\n * Extract leading comment lines from YAML content (lines starting with #)\n */\nfunction extractLeadingComments(content: string): string {\n  const lines = content.split('\\n');\n  const commentLines: string[] = [];\n  for (const line of lines) {\n    if (line.startsWith('#') || line.trim() === '') {\n      commentLines.push(line);\n    } else {\n      break;\n    }\n  }\n  // Return empty string if no comments found\n  if (commentLines.length === 0) return '';\n  return commentLines.join('\\n') + '\\n';\n}\n\n/** @deprecated Detects old WorkFile format (flat id/decision fields). Kept for backward compat. */\nfunction isWorkFile(file: unknown): file is WorkFile {\n  if (\n    typeof file !== 'object' ||\n    file === null ||\n    !('basis' in file) ||\n    !('articles' in file) ||\n    !Array.isArray((file as WorkFile).articles)\n  ) {\n    return false;\n  }\n  const articles = (file as WorkFile).articles;\n  if (articles.length === 0) return false;\n  const first = articles[0]!;\n  return 'id' in first && 'decision' in first && !('reviews' in first);\n}\n\n/**\n * Find article by identifier (doi, pmid, scopusId, arxivId, ericId, title)\n */\nfunction findArticleByIdentifier(\n  id: string,\n  articles: ArticleEntry[]\n): ArticleEntry | undefined {\n  for (const article of articles) {\n    if (article.doi && article.doi.toLowerCase() === id.toLowerCase()) return article;\n    if (article.pmid && article.pmid === id) return article;\n    if (article.scopusId && article.scopusId === id) return article;\n    if (article.arxivId && article.arxivId === id) return article;\n    if (article.ericId && article.ericId === id) return article;\n    if (article.title.toLowerCase() === id.toLowerCase()) return article;\n  }\n  return undefined;\n}\n\n/**\n * Execute review mark command\n */\nexport async function executeReviewMark(options: ReviewMarkOptions): Promise<ReviewMarkResult> {\n  if (!options.id || !options.decision) {\n    throw new Error('--id and --decision must be specified');\n  }\n\n  const rawContent = await readFile(options.file, 'utf-8');\n  const parsed = parseYaml(rawContent);\n\n  const result: ReviewMarkResult = {\n    marked: 0,\n    warnings: [],\n  };\n\n  if (isWorkFile(parsed)) {\n    // Old WorkFile format (backward compat)\n    const workFile = parsed as WorkFile;\n    const article = workFile.articles.find((a) => a.id === options.id);\n    if (!article) {\n      throw new Error(`Article not found: ${options.id}`);\n    }\n    article.decision = options.decision;\n    if (options.comment !== undefined) {\n      article.comment = options.comment;\n    }\n    result.marked = 1;\n\n    const yamlContent = stringifyYaml(workFile, { lineWidth: 0 });\n    const leadingComments = extractLeadingComments(rawContent);\n    await writeFile(options.file, leadingComments + yamlContent, 'utf-8');\n  } else {\n    // New ReviewFile screening format\n    const reviewFile = parsed as ReviewFile;\n\n    if (!reviewFile.basis) {\n      throw new Error('Invalid review file: missing \"basis\" field. This command only works with files generated by \"review extract --basis\".');\n    }\n\n    const article = findArticleByIdentifier(options.id, reviewFile.articles);\n    if (!article) {\n      throw new Error(`Article not found: ${options.id}`);\n    }\n\n    // Ensure reviews array exists with at least one entry\n    if (!article.reviews || article.reviews.length === 0) {\n      article.reviews = [{ decision: 'uncertain', comment: '' } as ArticleEntry['reviews'][0]];\n    }\n\n    // Update first review entry\n    article.reviews[0]!.decision = options.decision;\n    if (options.comment !== undefined) {\n      article.reviews[0]!.comment = options.comment;\n    }\n    result.marked = 1;\n\n    const yamlContent = stringifyYaml(reviewFile, { lineWidth: 0 });\n    const leadingComments = extractLeadingComments(rawContent);\n    await writeFile(options.file, leadingComments + yamlContent, 'utf-8');\n  }\n\n  return result;\n}\n"],"names":["parseYaml","stringifyYaml"],"mappings":";;AA8BA,SAAS,uBAAuB,SAAyB;AACvD,QAAM,QAAQ,QAAQ,MAAM,IAAI;AAChC,QAAM,eAAyB,CAAA;AAC/B,aAAW,QAAQ,OAAO;AACxB,QAAI,KAAK,WAAW,GAAG,KAAK,KAAK,KAAA,MAAW,IAAI;AAC9C,mBAAa,KAAK,IAAI;AAAA,IACxB,OAAO;AACL;AAAA,IACF;AAAA,EACF;AAEA,MAAI,aAAa,WAAW,EAAG,QAAO;AACtC,SAAO,aAAa,KAAK,IAAI,IAAI;AACnC;AAGA,SAAS,WAAW,MAAiC;AACnD,MACE,OAAO,SAAS,YAChB,SAAS,QACT,EAAE,WAAW,SACb,EAAE,cAAc,SAChB,CAAC,MAAM,QAAS,KAAkB,QAAQ,GAC1C;AACA,WAAO;AAAA,EACT;AACA,QAAM,WAAY,KAAkB;AACpC,MAAI,SAAS,WAAW,EAAG,QAAO;AAClC,QAAM,QAAQ,SAAS,CAAC;AACxB,SAAO,QAAQ,SAAS,cAAc,SAAS,EAAE,aAAa;AAChE;AAKA,SAAS,wBACP,IACA,UAC0B;AAC1B,aAAW,WAAW,UAAU;AAC9B,QAAI,QAAQ,OAAO,QAAQ,IAAI,kBAAkB,GAAG,YAAA,EAAe,QAAO;AAC1E,QAAI,QAAQ,QAAQ,QAAQ,SAAS,GAAI,QAAO;AAChD,QAAI,QAAQ,YAAY,QAAQ,aAAa,GAAI,QAAO;AACxD,QAAI,QAAQ,WAAW,QAAQ,YAAY,GAAI,QAAO;AACtD,QAAI,QAAQ,UAAU,QAAQ,WAAW,GAAI,QAAO;AACpD,QAAI,QAAQ,MAAM,YAAA,MAAkB,GAAG,YAAA,EAAe,QAAO;AAAA,EAC/D;AACA,SAAO;AACT;AAKA,eAAsB,kBAAkB,SAAuD;AAC7F,MAAI,CAAC,QAAQ,MAAM,CAAC,QAAQ,UAAU;AACpC,UAAM,IAAI,MAAM,uCAAuC;AAAA,EACzD;AAEA,QAAM,aAAa,MAAM,SAAS,QAAQ,MAAM,OAAO;AACvD,QAAM,SAASA,MAAU,UAAU;AAEnC,QAAM,SAA2B;AAAA,IAC/B,QAAQ;AAAA,IACR,UAAU,CAAA;AAAA,EAAC;AAGb,MAAI,WAAW,MAAM,GAAG;AAEtB,UAAM,WAAW;AACjB,UAAM,UAAU,SAAS,SAAS,KAAK,CAAC,MAAM,EAAE,OAAO,QAAQ,EAAE;AACjE,QAAI,CAAC,SAAS;AACZ,YAAM,IAAI,MAAM,sBAAsB,QAAQ,EAAE,EAAE;AAAA,IACpD;AACA,YAAQ,WAAW,QAAQ;AAC3B,QAAI,QAAQ,YAAY,QAAW;AACjC,cAAQ,UAAU,QAAQ;AAAA,IAC5B;AACA,WAAO,SAAS;AAEhB,UAAM,cAAcC,UAAc,UAAU,EAAE,WAAW,GAAG;AAC5D,UAAM,kBAAkB,uBAAuB,UAAU;AACzD,UAAM,UAAU,QAAQ,MAAM,kBAAkB,aAAa,OAAO;AAAA,EACtE,OAAO;AAEL,UAAM,aAAa;AAEnB,QAAI,CAAC,WAAW,OAAO;AACrB,YAAM,IAAI,MAAM,uHAAuH;AAAA,IACzI;AAEA,UAAM,UAAU,wBAAwB,QAAQ,IAAI,WAAW,QAAQ;AACvE,QAAI,CAAC,SAAS;AACZ,YAAM,IAAI,MAAM,sBAAsB,QAAQ,EAAE,EAAE;AAAA,IACpD;AAGA,QAAI,CAAC,QAAQ,WAAW,QAAQ,QAAQ,WAAW,GAAG;AACpD,cAAQ,UAAU,CAAC,EAAE,UAAU,aAAa,SAAS,IAAkC;AAAA,IACzF;AAGA,YAAQ,QAAQ,CAAC,EAAG,WAAW,QAAQ;AACvC,QAAI,QAAQ,YAAY,QAAW;AACjC,cAAQ,QAAQ,CAAC,EAAG,UAAU,QAAQ;AAAA,IACxC;AACA,WAAO,SAAS;AAEhB,UAAM,cAAcA,UAAc,YAAY,EAAE,WAAW,GAAG;AAC9D,UAAM,kBAAkB,uBAAuB,UAAU;AACzD,UAAM,UAAU,QAAQ,MAAM,kBAAkB,aAAa,OAAO;AAAA,EACtE;AAEA,SAAO;AACT;"}

package/dist/cli/commands/review/merge.d.ts.map

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package/dist/cli/commands/review/merge.js

@@ -3,7 +3,13 @@ import { readFile, writeFile } from "node:fs/promises";
 import { parse, stringify } from "yaml";
 import { validateName } from "./extract.js";
 function isWorkFile(file) {
-  return typeof file === "object" && file !== null && "basis" in file && "reviewer" in file && "articles" in file && Array.isArray(file.articles);
+  if (typeof file !== "object" || file === null || !("basis" in file) || !("reviewer" in file) || !("articles" in file) || !Array.isArray(file.articles)) {
+    return false;
+  }
+  const articles = file.articles;
+  if (articles.length === 0) return false;
+  const first = articles[0];
+  return "id" in first && "decision" in first && !("reviews" in first);
 }
 async function loadReviewFile(path) {
   const content = await readFile(path, "utf-8");
@@ -142,7 +148,7 @@ function processReviewFile(extractedFile, mainFile, options) {
       if (!reviewer) {
         throw new Error("reviewer is required: set reviewer on individual review or top-level ReviewFile");
       }
-      const basis = review.basis ?? detectBasis(extracted);
+      const basis = review.basis ?? extractedFile.basis ?? detectBasis(extracted);
       if (!options.dryRun) {
         const mergedReview = {
           ...review,

package/dist/cli/commands/review/merge.js.map

@@ -1 +1 @@
-{"version":3,"file":"merge.js","sources":["../../../../src/cli/commands/review/merge.ts"],"sourcesContent":["/**\n * review merge command - Merge edited file back into main reviews.yaml\n */\n\nimport { join } from 'node:path';\nimport { readFile, writeFile } from 'node:fs/promises';\nimport { parse as parseYaml, stringify as stringifyYaml } from 'yaml';\nimport type { ReviewFile, ArticleEntry, Review, WorkFile, ReviewBasis } from './types.js';\nimport { validateName } from './extract.js';\n\n\n/**\n * Check if a file is a work file (has basis field)\n */\nfunction isWorkFile(file: unknown): file is WorkFile {\n  return (\n    typeof file === 'object' &&\n    file !== null &&\n    'basis' in file &&\n    'reviewer' in file &&\n    'articles' in file &&\n    Array.isArray((file as WorkFile).articles)\n  );\n}\n\nexport interface ReviewMergeOptions {\n  sessionId: string;\n  /** Name of the review subset (reads from for-review/<name>/review.yaml) */\n  name: string;\n  dryRun?: boolean;\n}\n\nexport interface ReviewMergeResult {\n  reviewsAdded: number;\n  decisionsSet: number;\n  includeCount: number;\n  excludeCount: number;\n  uncertainCount: number;\n  finalDecisionsSet: number;\n  finalDecisionsIncludeCount: number;\n  finalDecisionsExcludeCount: number;\n  warnings: string[];\n}\n\n/**\n * Load review file from path\n */\nasync function loadReviewFile(path: string): Promise<ReviewFile> {\n  const content = await readFile(path, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Auto-detect review basis from article data: fulltext > abstract > title\n */\nfunction detectBasis(article: ArticleEntry): ReviewBasis {\n  if (article.fulltext) return 'fulltext';\n  if (article.abstract) return 'abstract';\n  return 'title';\n}\n\n/**\n * Register a reviewer in the review file's reviewers registry.\n * Deduplicates by name+basis pair.\n */\nexport function registerReviewer(reviewFile: ReviewFile, name: string, basis: ReviewBasis): void {\n  if (!reviewFile.reviewers) {\n    reviewFile.reviewers = [];\n  }\n  const exists = reviewFile.reviewers.some((r) => r.name === name && r.basis === basis);\n  if (!exists) {\n    reviewFile.reviewers.push({ name, basis });\n  }\n}\n\n/**\n * Match article from extracted file to main file\n */\nfunction findMatchingArticle(\n  extracted: ArticleEntry,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  // Try matching by various identifiers\n  for (const main of mainArticles) {\n    if (extracted.pmid && main.pmid && extracted.pmid === main.pmid) {\n      return main;\n    }\n    if (extracted.doi && main.doi && extracted.doi.toLowerCase() === main.doi.toLowerCase()) {\n      return main;\n    }\n    if (extracted.scopusId && main.scopusId && extracted.scopusId === main.scopusId) {\n      return main;\n    }\n    if (extracted.arxivId && main.arxivId && extracted.arxivId === main.arxivId) {\n      return main;\n    }\n    if (extracted.ericId && main.ericId && extracted.ericId === main.ericId) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Match work file article by id to main file\n * The id can be a DOI, PMID, ScopusId, ArxivId, EricId, or title\n */\nfunction findMatchingArticleById(\n  id: string,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  for (const main of mainArticles) {\n    // Match by DOI (case-insensitive)\n    if (main.doi && main.doi.toLowerCase() === id.toLowerCase()) {\n      return main;\n    }\n    // Match by PMID\n    if (main.pmid && main.pmid === id) {\n      return main;\n    }\n    // Match by ScopusId\n    if (main.scopusId && main.scopusId === id) {\n      return main;\n    }\n    // Match by ArxivId\n    if (main.arxivId && main.arxivId === id) {\n      return main;\n    }\n    // Match by EricId\n    if (main.ericId && main.ericId === id) {\n      return main;\n    }\n    // Match by title (fallback, case-insensitive)\n    if (main.title.toLowerCase() === id.toLowerCase()) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Process work file format (with basis/reviewer)\n */\nfunction processWorkFile(\n  workFile: WorkFile,\n  mainFile: ReviewFile,\n  options: ReviewMergeOptions\n): ReviewMergeResult {\n  const result: ReviewMergeResult = {\n    reviewsAdded: 0,\n    decisionsSet: 0,\n    includeCount: 0,\n    excludeCount: 0,\n    uncertainCount: 0,\n    finalDecisionsSet: 0,\n    finalDecisionsIncludeCount: 0,\n    finalDecisionsExcludeCount: 0,\n    warnings: [],\n  };\n\n  const timestamp = new Date().toISOString();\n\n  // Register the reviewer for this work file's basis\n  if (!options.dryRun) {\n    registerReviewer(mainFile, workFile.reviewer, workFile.basis);\n  }\n\n  for (const workArticle of workFile.articles) {\n    // Skip articles with null decision (not yet reviewed)\n    if (workArticle.decision === null) {\n      continue;\n    }\n\n    const mainArticle = findMatchingArticleById(workArticle.id, mainFile.articles);\n\n    if (!mainArticle) {\n      result.warnings.push(`Article not found in main file: id=\"${workArticle.id}\"`);\n      continue;\n    }\n\n    // Ensure mainArticle.reviews is an array\n    if (!mainArticle.reviews) {\n      mainArticle.reviews = [];\n    }\n\n    // Create review from work file article\n    const review: Review = {\n      reviewer: workFile.reviewer,\n      decision: workArticle.decision,\n      basis: workFile.basis,\n      timestamp,\n    };\n\n    // Add comment if provided\n    if (workArticle.comment) {\n      review.comment = workArticle.comment;\n    }\n\n    if (!options.dryRun) {\n      mainArticle.reviews.push(review);\n    }\n    result.reviewsAdded++;\n\n    // Count decision types\n    if (workArticle.decision === 'include') result.includeCount++;\n    else if (workArticle.decision === 'exclude') result.excludeCount++;\n    else if (workArticle.decision === 'uncertain') result.uncertainCount++;\n  }\n\n  return result;\n}\n\n/**\n 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Kept for backward compat. */\nfunction isWorkFile(file: unknown): file is WorkFile {\n  if (\n    typeof file !== 'object' ||\n    file === null ||\n    !('basis' in file) ||\n    !('reviewer' in file) ||\n    !('articles' in file) ||\n    !Array.isArray((file as WorkFile).articles)\n  ) {\n    return false;\n  }\n  // Distinguish from new ReviewFile-with-basis: old WorkFile has articles with flat `id` + `decision` fields\n  const articles = (file as WorkFile).articles;\n  if (articles.length === 0) return false;\n  const first = articles[0]!;\n  return 'id' in first && 'decision' in first && !('reviews' in first);\n}\n\nexport interface ReviewMergeOptions {\n  sessionId: string;\n  /** Name of the review subset (reads from for-review/<name>/review.yaml) */\n  name: string;\n  dryRun?: boolean;\n}\n\nexport interface ReviewMergeResult {\n  reviewsAdded: number;\n  decisionsSet: number;\n  includeCount: number;\n  excludeCount: number;\n  uncertainCount: number;\n  finalDecisionsSet: 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reviewFile.reviewers.push({ name, basis });\n  }\n}\n\n/**\n * Match article from extracted file to main file\n */\nfunction findMatchingArticle(\n  extracted: ArticleEntry,\n  mainArticles: ArticleEntry[]\n): ArticleEntry | undefined {\n  // Try matching by various identifiers\n  for (const main of mainArticles) {\n    if (extracted.pmid && main.pmid && extracted.pmid === main.pmid) {\n      return main;\n    }\n    if (extracted.doi && main.doi && extracted.doi.toLowerCase() === main.doi.toLowerCase()) {\n      return main;\n    }\n    if (extracted.scopusId && main.scopusId && extracted.scopusId === main.scopusId) {\n      return main;\n    }\n    if (extracted.arxivId && main.arxivId && extracted.arxivId === main.arxivId) {\n      return main;\n    }\n    if (extracted.ericId && main.ericId && extracted.ericId === main.ericId) {\n      return main;\n    }\n  }\n  return undefined;\n}\n\n/**\n * Match work file article by id to main file\n * The id can be a DOI, PMID, ScopusId, 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schemaComment = `# yaml-language-server: $schema=${schemaPath}\\n`;\n    const finalContent = schemaComment + yamlContent;\n\n    await writeFile(mainReviewsPath, finalContent, 'utf-8');\n  }\n\n  return result;\n}\n\n/**\n * Format merge result as human-readable string\n */\nexport function formatMergeOutput(result: ReviewMergeResult, dryRun: boolean): string {\n  const lines: string[] = [];\n\n  if (dryRun) {\n    lines.push('Dry run - no changes made');\n    lines.push('');\n  }\n\n  lines.push('Merge Summary:');\n\n  // Build reviews line with decision breakdown\n  if (result.reviewsAdded === 0) {\n    lines.push(`  Reviews added: 0`);\n  } else {\n    const parts: string[] = [];\n    if (result.excludeCount > 0) parts.push(`${result.excludeCount} exclude`);\n    if (result.includeCount > 0) parts.push(`${result.includeCount} include`);\n    if (result.uncertainCount > 0) parts.push(`${result.uncertainCount} uncertain`);\n\n    if (parts.length > 0) {\n      lines.push(`  Reviews 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package/dist/cli/commands/review/types.d.ts

@@ -63,6 +63,8 @@ export interface ReviewFile {
     criteria?: string;
     /** Reviewer identifier (only in extracted ReviewFiles) */
     reviewer?: string;
+    /** Basis level for screening (only in extracted ReviewFiles) */
+    basis?: ReviewBasis;
     articles: ArticleEntry[];
     /** Registry of reviewers who participated at each basis level */
     reviewers?: ReviewerRecord[];
@@ -70,6 +72,7 @@ export interface ReviewFile {
 /**
  * Work file article entry for AI agent workflow
  */
+/** @deprecated Use ReviewFile format with reviews[] instead. Kept for backward compatibility. */
 export interface WorkFileArticle {
     id: string;
     title: string;
@@ -82,6 +85,7 @@ export interface WorkFileArticle {
 /**
  * Work file structure for AI agent workflow
  */
+/** @deprecated Use ReviewFile format with basis field instead. Kept for backward compatibility. */
 export interface WorkFile {
     sessionId: string;
     basis: ReviewBasis;

package/dist/cli/commands/review/types.d.ts.map

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package/dist/cli/commands/review/types.js

@@ -17,10 +17,17 @@ function classifyStatus(entry, registeredReviewers) {
   }
   if (registeredReviewers && registeredReviewers.length > 0) {
     const reviewerNames = new Set(reviews.map((r) => r.reviewer));
-    const hasAllReviewers = registeredReviewers.every(
+    let highestReviewedRank = 0;
+    for (const r of reviews) {
+      highestReviewedRank = Math.max(highestReviewedRank, basisRank(r.basis));
+    }
+    const applicableReviewers = highestReviewedRank === 0 ? registeredReviewers : registeredReviewers.filter(
+      (reg) => basisRank(reg.basis) <= highestReviewedRank
+    );
+    const hasAllReviewers = applicableReviewers.every(
       (reg) => reviewerNames.has(reg.name)
     );
-    if (!hasAllReviewers) {
+    if (applicableReviewers.length > 0 && !hasAllReviewers) {
       return "incomplete";
     }
   }
@@ -52,7 +59,7 @@ function classifyStatus(entry, registeredReviewers) {
   }
   const effectiveDecisions = [];
   for (const { decision, rank } of reviewerMap.values()) {
-    if (decision === "uncertain" && rank < highestDefinitiveRank) {
+    if (rank < highestDefinitiveRank) {
       continue;
     }
     effectiveDecisions.push(decision);

package/dist/cli/commands/review/types.js.map

@@ -1 +1 @@
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+{"version":3,"file":"types.js","sources":["../../../../src/cli/commands/review/types.ts"],"sourcesContent":["/**\n * Review workflow types for article assessment tracking\n */\n\nimport type { ArticleFulltextRef } from '../../../fulltext/types.js';\n\nexport type ReviewDecision = 'include' | 'exclude' | 'uncertain';\n\n/**\n * Basis of the review decision (what information was used)\n */\nexport type ReviewBasis = 'title' | 'abstract' | 'fulltext';\n\n/**\n * Individual assessment of an article by a reviewer\n */\nexport interface Review {\n  /** Reviewer identifier: \"human:name\" or \"ai:name\" */\n  reviewer: string;\n  /** Assessment decision */\n  decision?: ReviewDecision;\n  /** Basis of the decision (what information was used) */\n  basis?: ReviewBasis;\n  /** Optional comment or reason */\n  comment?: string;\n  /** ISO 8601 timestamp (optional - auto-assigned on merge if not provided) */\n  timestamp?: string;\n}\n\n/**\n * Source information for merged duplicates\n */\nexport interface MergedSource {\n  source: string;\n  pmid?: string;\n  doi?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n}\n\n/**\n * Article entry with identifiers, bibliographic info, and reviews\n */\nexport interface ArticleEntry {\n  // Identifiers (at least one required for matching)\n  doi?: string;\n  pmid?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n\n  // Bibliographic info (for reviewer reference)\n  title: string;\n  authors?: string;\n  year?: string;\n  abstract?: string;\n\n  // Deduplication tracking\n  mergedFrom?: MergedSource[];\n\n  // Review data\n  reviews: Review[];\n  /** Historical reviews (only in extracted ReviewFiles, never in master file) */\n  reviewHistory?: Review[];\n  finalDecision?: 'include' | 'exclude' | null;\n\n  // Fulltext reference (set by fulltext init/sync)\n  fulltext?: ArticleFulltextRef;\n}\n\n/**\n * Top-level structure of the reviews.yaml file\n */\nexport interface ReviewerRecord {\n  name: string;\n  basis: ReviewBasis;\n}\n\nexport interface ReviewFile {\n  sessionId: string;\n  /** Path to inclusion criteria file */\n  criteria?: string;\n  /** Reviewer identifier (only in extracted ReviewFiles) */\n  reviewer?: string;\n  /** Basis level for screening (only in extracted ReviewFiles) */\n  basis?: ReviewBasis;\n  articles: ArticleEntry[];\n  /** Registry of reviewers who participated at each basis level */\n  reviewers?: ReviewerRecord[];\n}\n\n/**\n * Work file article entry for AI agent workflow\n */\n/** @deprecated Use ReviewFile format with reviews[] instead. 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package/dist/cli/commands/status.js

@@ -43,7 +43,7 @@ async function getSessionDetails(sessionId, sessionsDir) {
       status: session.summary.status,
       createdAt: session.createdAt,
       updatedAt: session.updatedAt,
-      queryFile: session.query.file,
+      queryFile: session.query?.file ?? "",
       totalHits: session.summary.totalHits,
       totalRetrieved: session.summary.totalRetrieved,
       databases

package/dist/cli/commands/status.js.map

@@ -1 +1 @@
-{"version":3,"file":"status.js","sources":["../../../src/cli/commands/status.ts"],"sourcesContent":["import { join } from 'node:path';\nimport { listSessions, loadSession } from '../../session/manager.js';\nimport { deduplicateArticles } from './export.js';\nimport { loadNotes, formatNotesList, type NoteEntry } from './notes.js';\nimport { loadResults } from '../../session/results-io.js';\nimport type { ProviderName } from '../../providers/base/types.js';\n\nexport interface SessionListItem {\n  id: string;\n  name: string;\n  status: string;\n  createdAt: string;\n  progress: string;\n}\n\nexport interface DatabaseDetails {\n  provider: string;\n  status: string;\n  totalHits: number;\n  retrievedCount: number;\n  error?: string;\n}\n\nexport interface SessionDetails {\n  id: string;\n  name: string;\n  description?: string;\n  status: string;\n  createdAt: string;\n  updatedAt: string;\n  queryFile: string;\n  totalHits: number;\n  totalRetrieved: number;\n  databases: DatabaseDetails[];\n  uniqueArticles?: number;\n  duplicatesRemoved?: number;\n  notes?: NoteEntry[];\n}\n\nexport interface ListOptions {\n  all: boolean;\n}\n\nexport interface FormatOptions {\n  json: boolean;\n}\n\nexport interface SessionListResult {\n  sessions: SessionListItem[];\n  totalCount: number;\n  filteredCount: number;\n  showingAll: boolean;\n}\n\nexport async function listSessionsForDisplay(\n  sessionsDir: string,\n  options: ListOptions\n): Promise<SessionListResult> {\n  const summaries = await listSessions(sessionsDir);\n\n  const filtered = options.all\n    ? summaries\n    : summaries.filter((s) => s.status !== 'completed');\n\n  const sessions = filtered.map((s) => ({\n    id: s.id,\n    name: s.name,\n    status: s.status,\n    createdAt: s.createdAt,\n    progress: `${s.totalRetrieved}/${s.totalHits}`,\n  }));\n\n  return {\n    sessions,\n    totalCount: summaries.length,\n    filteredCount: filtered.length,\n    showingAll: options.all,\n  };\n}\n\nexport async function getSessionDetails(\n  sessionId: string,\n  sessionsDir: string\n): Promise<{ success: boolean; session?: SessionDetails; error?: string }> {\n  try {\n    const session = await loadSession(sessionId, sessionsDir);\n\n    const databases: DatabaseDetails[] = [];\n    for (const [provider, dbStatus] of Object.entries(session.databases)) {\n      if (!dbStatus) continue;\n      const dbDetail: DatabaseDetails = {\n        provider,\n        status: dbStatus.status,\n        totalHits: dbStatus.totalHits ?? 0,\n        retrievedCount: dbStatus.retrievedCount ?? 0,\n      };\n      if (dbStatus.error?.message) {\n        dbDetail.error = dbStatus.error.message;\n      }\n      databases.push(dbDetail);\n    }\n\n    const sessionDetails: SessionDetails = {\n      id: session.id,\n      name: session.name,\n      status: session.summary.status,\n      createdAt: session.createdAt,\n      updatedAt: session.updatedAt,\n      queryFile: session.query.file,\n      totalHits: session.summary.totalHits,\n      totalRetrieved: session.summary.totalRetrieved,\n      databases,\n    };\n    if (session.description) {\n      sessionDetails.description = session.description;\n    }\n\n    // Load notes (optional - don't fail if notes can't be loaded)\n    try {\n      const sessionDir = join(sessionsDir, sessionId);\n      const notes = await loadNotes(sessionDir);\n      if (notes.length > 0) {\n        sessionDetails.notes = notes;\n      }\n    } catch {\n      // Notes are optional - ignore errors\n    }\n\n    return {\n      success: true,\n      session: sessionDetails,\n    };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Unknown error';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n}\n\nexport async function computeDeduplicationStats(\n  sessionId: string,\n  sessionsDir: string,\n  session: { databases: Record<string, { files?: { results?: string } } | undefined> }\n): Promise<{ uniqueArticles: number; duplicatesRemoved: number }> {\n  const articles: import('../../providers/base/types.js').Article[] = [];\n  const sessionDir = join(sessionsDir, sessionId);\n\n  for (const [providerName] of Object.entries(session.databases)) {\n    const providerArticles = await loadResults(sessionDir, providerName as ProviderName);\n    articles.push(...providerArticles);\n  }\n\n  if (articles.length === 0) {\n    return { uniqueArticles: 0, duplicatesRemoved: 0 };\n  }\n\n  const result = deduplicateArticles(articles);\n  return {\n    uniqueArticles: result.articles.length,\n    duplicatesRemoved: result.duplicatesRemoved,\n  };\n}\n\nexport function formatSessionList(\n  result: SessionListResult,\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(result.sessions, null, 2);\n  }\n\n  if (result.sessions.length === 0) {\n    if (result.totalCount === 0) {\n      return 'No sessions found.';\n    }\n    // Sessions exist but are filtered out (all completed)\n    const completedCount = result.totalCount - result.filteredCount;\n    return `No active sessions. ${completedCount} completed session${completedCount === 1 ? '' : 's'} hidden (use --all to show).`;\n  }\n\n  const header = `${'ID'.padEnd(35)} ${'NAME'.padEnd(20)} ${'STATUS'.padEnd(15)} ${'PROGRESS'.padEnd(12)} CREATED`;\n  const separator = '-'.repeat(100);\n\n  const rows = result.sessions.map((s) => {\n    const date = new Date(s.createdAt).toLocaleDateString();\n    return `${s.id.padEnd(35)} ${s.name.padEnd(20)} ${s.status.padEnd(15)} ${s.progress.padEnd(12)} ${date}`;\n  });\n\n  const lines = [header, separator, ...rows];\n\n  // Show hint about hidden completed sessions if not showing all\n  if (!result.showingAll && result.totalCount > result.filteredCount) {\n    const hiddenCount = result.totalCount - result.filteredCount;\n    lines.push('');\n    lines.push(`(${hiddenCount} completed session${hiddenCount === 1 ? 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+{"version":3,"file":"status.js","sources":["../../../src/cli/commands/status.ts"],"sourcesContent":["import { join } from 'node:path';\nimport { listSessions, loadSession } from '../../session/manager.js';\nimport { deduplicateArticles } from './export.js';\nimport { loadNotes, formatNotesList, type NoteEntry } from './notes.js';\nimport { loadResults } from '../../session/results-io.js';\nimport type { ProviderName } from '../../providers/base/types.js';\n\nexport interface SessionListItem {\n  id: string;\n  name: string;\n  status: string;\n  createdAt: string;\n  progress: string;\n}\n\nexport interface DatabaseDetails {\n  provider: string;\n  status: string;\n  totalHits: number;\n  retrievedCount: number;\n  error?: string;\n}\n\nexport interface SessionDetails {\n  id: string;\n  name: string;\n  description?: string;\n  status: string;\n  createdAt: string;\n  updatedAt: string;\n  queryFile: string;\n  totalHits: number;\n  totalRetrieved: number;\n  databases: DatabaseDetails[];\n  uniqueArticles?: number;\n  duplicatesRemoved?: number;\n  notes?: NoteEntry[];\n}\n\nexport interface ListOptions {\n  all: boolean;\n}\n\nexport interface FormatOptions {\n  json: boolean;\n}\n\nexport interface SessionListResult {\n  sessions: SessionListItem[];\n  totalCount: number;\n  filteredCount: number;\n  showingAll: boolean;\n}\n\nexport async function listSessionsForDisplay(\n  sessionsDir: string,\n  options: ListOptions\n): Promise<SessionListResult> {\n  const summaries = await listSessions(sessionsDir);\n\n  const filtered = options.all\n    ? summaries\n    : summaries.filter((s) => s.status !== 'completed');\n\n  const sessions = filtered.map((s) => ({\n    id: s.id,\n    name: s.name,\n    status: s.status,\n    createdAt: s.createdAt,\n    progress: `${s.totalRetrieved}/${s.totalHits}`,\n  }));\n\n  return {\n    sessions,\n    totalCount: summaries.length,\n    filteredCount: filtered.length,\n    showingAll: options.all,\n  };\n}\n\nexport async function getSessionDetails(\n  sessionId: string,\n  sessionsDir: string\n): Promise<{ success: boolean; session?: SessionDetails; error?: string }> {\n  try {\n    const session = await loadSession(sessionId, sessionsDir);\n\n    const databases: DatabaseDetails[] = [];\n    for (const [provider, dbStatus] of Object.entries(session.databases)) {\n      if (!dbStatus) continue;\n      const dbDetail: DatabaseDetails = {\n        provider,\n        status: dbStatus.status,\n        totalHits: dbStatus.totalHits ?? 0,\n        retrievedCount: dbStatus.retrievedCount ?? 0,\n      };\n      if (dbStatus.error?.message) {\n        dbDetail.error = dbStatus.error.message;\n      }\n      databases.push(dbDetail);\n    }\n\n    const sessionDetails: SessionDetails = {\n      id: session.id,\n      name: session.name,\n      status: session.summary.status,\n      createdAt: session.createdAt,\n      updatedAt: session.updatedAt,\n      queryFile: session.query?.file ?? '',\n      totalHits: session.summary.totalHits,\n      totalRetrieved: session.summary.totalRetrieved,\n      databases,\n    };\n    if (session.description) {\n      sessionDetails.description = session.description;\n    }\n\n    // Load notes (optional - don't fail if notes can't be loaded)\n    try {\n      const sessionDir = join(sessionsDir, sessionId);\n      const notes = await loadNotes(sessionDir);\n      if (notes.length > 0) {\n        sessionDetails.notes = notes;\n      }\n    } catch {\n      // Notes are optional - ignore errors\n    }\n\n    return {\n      success: true,\n      session: sessionDetails,\n    };\n  } catch (error) {\n    const message = error instanceof Error ? error.message : 'Unknown error';\n    return {\n      success: false,\n      error: message,\n    };\n  }\n}\n\nexport async function computeDeduplicationStats(\n  sessionId: string,\n  sessionsDir: string,\n  session: { databases: Record<string, { files?: { results?: string } } | undefined> }\n): Promise<{ uniqueArticles: number; duplicatesRemoved: number }> {\n  const articles: import('../../providers/base/types.js').Article[] = [];\n  const sessionDir = join(sessionsDir, sessionId);\n\n  for (const [providerName] of Object.entries(session.databases)) {\n    const providerArticles = await loadResults(sessionDir, providerName as ProviderName);\n    articles.push(...providerArticles);\n  }\n\n  if (articles.length === 0) {\n    return { uniqueArticles: 0, duplicatesRemoved: 0 };\n  }\n\n  const result = deduplicateArticles(articles);\n  return {\n    uniqueArticles: result.articles.length,\n    duplicatesRemoved: result.duplicatesRemoved,\n  };\n}\n\nexport function formatSessionList(\n  result: SessionListResult,\n  options: FormatOptions\n): string {\n  if (options.json) {\n    return JSON.stringify(result.sessions, null, 2);\n  }\n\n  if (result.sessions.length === 0) {\n    if (result.totalCount === 0) {\n      return 'No sessions found.';\n    }\n    // Sessions exist but are filtered out (all completed)\n    const completedCount = result.totalCount - result.filteredCount;\n    return `No active sessions. ${completedCount} completed session${completedCount === 1 ? 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package/dist/cli/index.d.ts.map

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