@ncukondo/search-hub 0.9.4 → 0.10.0

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

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

@@ -28,6 +28,31 @@ function getArticleId(article) {
   if (article.ericId) return article.ericId;
   return article.title;
 }
+function getBasisGuidanceComment(basis) {
+  switch (basis) {
+    case "title":
+      return [
+        "# Screening by title only.",
+        '# Mark clearly irrelevant items as "exclude" with a comment explaining the reason.',
+        '# Leave everything else as "uncertain".',
+        ""
+      ].join("\n");
+    case "abstract":
+      return [
+        "# Screening by title and abstract.",
+        '# You should be able to decide "include" or "exclude" for most items at this stage.',
+        '# Mark remaining ambiguous items as "uncertain" with a comment explaining why.',
+        ""
+      ].join("\n");
+    case "fulltext":
+      return [
+        "# Screening by full text. This is the final decision stage.",
+        '# Decide "include" or "exclude" for each item.',
+        '# Use "uncertain" only when absolutely unavoidable, with a comment explaining why.',
+        ""
+      ].join("\n");
+  }
+}
 function sortArticles(articles, sort, seed) {
   switch (sort) {
     case "year":
@@ -105,7 +130,8 @@ async function executeReviewExtract(options, sessionsDir) {
     const yamlContent = stringify(workFile, {
       lineWidth: 0
     });
-    finalContent = yamlContent;
+    const guidanceComment = getBasisGuidanceComment(options.basis);
+    finalContent = guidanceComment + yamlContent;
   } else {
     if (!options.reviewer) {
       throw new Error("--reviewer is required for review file extract");

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

@@ -1 +1 @@
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'';\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 ?? 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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, 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\"). 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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 ?? 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package/dist/cli/commands/review/merge.d.ts

@@ -8,6 +8,12 @@ export interface ReviewMergeOptions {
 export interface ReviewMergeResult {
     reviewsAdded: number;
     decisionsSet: number;
+    includeCount: number;
+    excludeCount: number;
+    uncertainCount: number;
+    finalDecisionsSet: number;
+    finalDecisionsIncludeCount: number;
+    finalDecisionsExcludeCount: number;
     warnings: string[];
 }
 /**

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

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

@@ -70,6 +70,12 @@ function processWorkFile(workFile, mainFile, options) {
   const result = {
     reviewsAdded: 0,
     decisionsSet: 0,
+    includeCount: 0,
+    excludeCount: 0,
+    uncertainCount: 0,
+    finalDecisionsSet: 0,
+    finalDecisionsIncludeCount: 0,
+    finalDecisionsExcludeCount: 0,
     warnings: []
   };
   const timestamp = (/* @__PURE__ */ new Date()).toISOString();
@@ -101,6 +107,9 @@ function processWorkFile(workFile, mainFile, options) {
       mainArticle.reviews.push(review);
     }
     result.reviewsAdded++;
+    if (workArticle.decision === "include") result.includeCount++;
+    else if (workArticle.decision === "exclude") result.excludeCount++;
+    else if (workArticle.decision === "uncertain") result.uncertainCount++;
   }
   return result;
 }
@@ -108,6 +117,12 @@ function processReviewFile(extractedFile, mainFile, options) {
   const result = {
     reviewsAdded: 0,
     decisionsSet: 0,
+    includeCount: 0,
+    excludeCount: 0,
+    uncertainCount: 0,
+    finalDecisionsSet: 0,
+    finalDecisionsIncludeCount: 0,
+    finalDecisionsExcludeCount: 0,
     warnings: []
   };
   const timestamp = (/* @__PURE__ */ new Date()).toISOString();
@@ -139,12 +154,18 @@ function processReviewFile(extractedFile, mainFile, options) {
         registerReviewer(mainFile, reviewer, basis);
       }
       result.reviewsAdded++;
+      if (review.decision === "include") result.includeCount++;
+      else if (review.decision === "exclude") result.excludeCount++;
+      else if (review.decision === "uncertain") result.uncertainCount++;
     }
     if (extracted.finalDecision !== void 0 && extracted.finalDecision !== null) {
       if (!options.dryRun) {
         mainArticle.finalDecision = extracted.finalDecision;
       }
       result.decisionsSet++;
+      result.finalDecisionsSet++;
+      if (extracted.finalDecision === "include") result.finalDecisionsIncludeCount++;
+      else if (extracted.finalDecision === "exclude") result.finalDecisionsExcludeCount++;
     }
   }
   return result;
@@ -182,8 +203,29 @@ function formatMergeOutput(result, dryRun) {
     lines.push("");
   }
   lines.push("Merge Summary:");
-  lines.push(`  Reviews added:    ${result.reviewsAdded}`);
-  lines.push(`  Decisions set:    ${result.decisionsSet}`);
+  if (result.reviewsAdded === 0) {
+    lines.push(`  Reviews added: 0`);
+  } else {
+    const parts = [];
+    if (result.excludeCount > 0) parts.push(`${result.excludeCount} exclude`);
+    if (result.includeCount > 0) parts.push(`${result.includeCount} include`);
+    if (result.uncertainCount > 0) parts.push(`${result.uncertainCount} uncertain`);
+    if (parts.length > 0) {
+      lines.push(`  Reviews added: ${result.reviewsAdded} (${parts.join(", ")})`);
+    } else {
+      lines.push(`  Reviews added: ${result.reviewsAdded}`);
+    }
+  }
+  if (result.finalDecisionsSet > 0) {
+    const parts = [];
+    if (result.finalDecisionsIncludeCount > 0) parts.push(`${result.finalDecisionsIncludeCount} include`);
+    if (result.finalDecisionsExcludeCount > 0) parts.push(`${result.finalDecisionsExcludeCount} exclude`);
+    if (parts.length > 0) {
+      lines.push(`  Final decisions set: ${result.finalDecisionsSet} (${parts.join(", ")})`);
+    } else {
+      lines.push(`  Final decisions set: ${result.finalDecisionsSet}`);
+    }
+  }
   if (result.warnings.length > 0) {
     lines.push("");
     lines.push("Warnings:");

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

@@ -1 +1 @@
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boolean;\n}\n\nexport interface ReviewMergeResult {\n  reviewsAdded: number;\n  decisionsSet: 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    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=\"${workArticle.id}\"`);\n      continue;\n    }\n\n    // Ensure mainArticle.reviews is an array\n    if (!mainArticle.reviews) {\n      mainArticle.reviews = [];\n    }\n\n    // Create review from work file article\n    const review: Review = {\n      reviewer: workFile.reviewer,\n      decision: workArticle.decision,\n      basis: workFile.basis,\n      timestamp,\n    };\n\n    // Add comment if provided\n    if (workArticle.comment) {\n      review.comment = workArticle.comment;\n    }\n\n    if (!options.dryRun) {\n      mainArticle.reviews.push(review);\n    }\n    result.reviewsAdded++;\n  }\n\n  return result;\n}\n\n/**\n * Process review file format (with reviewHistory separation)\n */\nfunction processReviewFile(\n  extractedFile: ReviewFile,\n  mainFile: ReviewFile,\n  options: ReviewMergeOptions\n): ReviewMergeResult {\n  const result: ReviewMergeResult = {\n    reviewsAdded: 0,\n    decisionsSet: 0,\n    warnings: [],\n  };\n\n  const timestamp = new Date().toISOString();\n  const topLevelReviewer = extractedFile.reviewer;\n\n  for (const extracted of extractedFile.articles) {\n    const mainArticle = findMatchingArticle(extracted, mainFile.articles);\n\n    if (!mainArticle) {\n      result.warnings.push(`Article not found in main file: \"${extracted.title}\"`);\n      continue;\n    }\n\n    // Merge only reviews[] (reviewHistory is ignored)\n    const extractedReviews = extracted.reviews ?? [];\n\n    // Ensure mainArticle.reviews is an array\n    if (!mainArticle.reviews) {\n      mainArticle.reviews = [];\n    }\n\n    for (const review of extractedReviews) {\n      // Fill in reviewer from top-level field if not on individual review\n      const reviewer = review.reviewer ?? topLevelReviewer;\n      if (!reviewer) {\n        throw new Error('reviewer is required: set reviewer on individual review or top-level ReviewFile');\n      }\n      // Fill in basis from review or auto-detect from article data\n      const basis = review.basis ?? detectBasis(extracted);\n\n      if (!options.dryRun) {\n        const mergedReview: Review = {\n          ...review,\n          reviewer,\n          basis,\n          timestamp: review.timestamp ?? timestamp,\n        };\n        mainArticle.reviews.push(mergedReview);\n\n        // Register reviewer\n        registerReviewer(mainFile, reviewer, basis);\n      }\n      result.reviewsAdded++;\n    }\n\n    // Overwrite finalDecision if set in extracted (null means unset)\n    if (extracted.finalDecision !== undefined && extracted.finalDecision !== null) {\n      if (!options.dryRun) {\n        mainArticle.finalDecision = extracted.finalDecision;\n      }\n      result.decisionsSet++;\n    }\n  }\n\n  return result;\n}\n\n/**\n * Execute review merge command\n */\nexport async function executeReviewMerge(\n  options: ReviewMergeOptions,\n  sessionsDir: string\n): Promise<ReviewMergeResult> {\n  validateName(options.name);\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const mainReviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const filePath = join(sessionDir, 'for-review', options.name, 'review.yaml');\n\n  // Load both files\n  const mainFile = await loadReviewFile(mainReviewsPath);\n  const content = await readFile(filePath, 'utf-8');\n  const inputFile = parseYaml(content);\n\n  let result: ReviewMergeResult;\n\n  // Detect file format and process accordingly\n  if (isWorkFile(inputFile)) {\n    result = processWorkFile(inputFile, mainFile, options);\n  } else {\n    result = processReviewFile(inputFile as ReviewFile, mainFile, options);\n  }\n\n  // Write back if not dry-run\n  if (!options.dryRun) {\n    const yamlContent = stringifyYaml(mainFile, {\n      lineWidth: 0,\n    });\n\n    // Preserve schema reference comment\n    // Path from sessions/{id}/.internal/ to .search-hub/schemas/\n    const schemaPath = '../../../../.search-hub/schemas/review.schema.json';\n    const 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 - 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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 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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() === 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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 added: 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package/dist/cli/commands/review/types.d.ts

@@ -88,6 +88,7 @@ export interface WorkFile {
     reviewer: string;
     articles: WorkFileArticle[];
 }
+export declare function basisRank(basis: ReviewBasis | undefined): number;
 /**
  * Review status classification (7-state model)
  */

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

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

@@ -1,3 +1,12 @@
+const BASIS_RANK = {
+  title: 1,
+  abstract: 2,
+  fulltext: 3
+};
+function basisRank(basis) {
+  if (basis === void 0) return 0;
+  return BASIS_RANK[basis] ?? 0;
+}
 function classifyStatus(entry, registeredReviewers) {
   if (entry.finalDecision !== void 0 && entry.finalDecision !== null) {
     return "finalized";
@@ -15,25 +24,58 @@ function classifyStatus(entry, registeredReviewers) {
       return "incomplete";
     }
   }
-  const decisions = reviews.filter((r) => r.decision !== void 0).map((r) => r.decision);
-  if (decisions.length === 0) {
+  const reviewsWithDecisions = reviews.filter((r) => r.decision !== void 0);
+  if (reviewsWithDecisions.length === 0) {
+    return "pending";
+  }
+  let highestDefinitiveRank = 0;
+  for (const r of reviewsWithDecisions) {
+    if (r.decision !== "uncertain") {
+      highestDefinitiveRank = Math.max(highestDefinitiveRank, basisRank(r.basis));
+    }
+  }
+  const reviewerMap = /* @__PURE__ */ new Map();
+  for (const r of reviewsWithDecisions) {
+    const rank = basisRank(r.basis);
+    const existing = reviewerMap.get(r.reviewer);
+    if (!existing) {
+      reviewerMap.set(r.reviewer, { decision: r.decision, rank });
+    } else {
+      if (r.decision !== "uncertain" && existing.decision === "uncertain") {
+        reviewerMap.set(r.reviewer, { decision: r.decision, rank });
+      } else if (r.decision !== "uncertain" && existing.decision !== "uncertain" && rank > existing.rank) {
+        reviewerMap.set(r.reviewer, { decision: r.decision, rank });
+      } else if (r.decision === "uncertain" && existing.decision === "uncertain" && rank > existing.rank) {
+        reviewerMap.set(r.reviewer, { decision: r.decision, rank });
+      }
+    }
+  }
+  const effectiveDecisions = [];
+  for (const { decision, rank } of reviewerMap.values()) {
+    if (decision === "uncertain" && rank < highestDefinitiveRank) {
+      continue;
+    }
+    effectiveDecisions.push(decision);
+  }
+  if (effectiveDecisions.length === 0) {
     return "pending";
   }
-  const hasInclude = decisions.includes("include");
-  const hasExclude = decisions.includes("exclude");
+  const hasInclude = effectiveDecisions.includes("include");
+  const hasExclude = effectiveDecisions.includes("exclude");
   if (hasInclude && hasExclude) {
     return "conflicting";
   }
-  const hasUncertain = decisions.includes("uncertain");
+  const hasUncertain = effectiveDecisions.includes("uncertain");
   if (hasUncertain) {
     return "uncertain";
   }
-  if (decisions.every((d) => d === "include")) {
+  if (effectiveDecisions.every((d) => d === "include")) {
     return "agreed-include";
   }
   return "agreed-exclude";
 }
 export {
+  basisRank,
   classifyStatus
 };
 //# sourceMappingURL=types.js.map

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

@@ -1 +1 @@
-{"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  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 */\nexport interface WorkFileArticle {\n  id: string;\n  title: string;\n  abstract?: string;\n  /** Fulltext directory name (only for fulltext basis) */\n  fulltext?: string;\n  decision: ReviewDecision | null;\n  comment: string;\n}\n\n/**\n * Work file structure for AI agent workflow\n */\nexport interface WorkFile {\n  sessionId: string;\n  basis: ReviewBasis;\n  reviewer: string;\n  articles: WorkFileArticle[];\n}\n\n/**\n * Review status classification (7-state model)\n */\nexport type ReviewStatus =\n  | 'pending'\n  | 'incomplete'\n  | 'uncertain'\n  | 'agreed-include'\n  | 'agreed-exclude'\n  | 'conflicting'\n  | 'finalized';\n\n/**\n * Classify the review status of an article entry\n *\n * Classification logic (in order):\n * 1. finalDecision set?           → finalized\n * 2. No reviews?                  → pending\n * 3. Registered reviewer missing? → incomplete\n * 4. include AND exclude present? → conflicting\n * 5. Any uncertain?               → uncertain\n * 6. All include?                 → agreed-include\n * 7. All exclude?                 → agreed-exclude\n */\nexport function classifyStatus(\n  entry: ArticleEntry,\n  registeredReviewers?: ReviewerRecord[]\n): ReviewStatus {\n  // 1. Finalized takes precedence\n  if (entry.finalDecision !== undefined && entry.finalDecision !== null) {\n    return 'finalized';\n  }\n\n  // No reviews = pending (reviews can be null from YAML parsing with only comments)\n  const reviews = entry.reviews ?? [];\n  if (reviews.length === 0) {\n    return 'pending';\n  }\n\n  // 3. 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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  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 */\nexport interface WorkFileArticle {\n  id: string;\n  title: string;\n  abstract?: string;\n  /** Fulltext directory name (only for fulltext basis) */\n  fulltext?: string;\n  decision: ReviewDecision | null;\n  comment: string;\n}\n\n/**\n * Work file structure for AI agent workflow\n */\nexport interface WorkFile {\n  sessionId: string;\n  basis: ReviewBasis;\n  reviewer: string;\n  articles: WorkFileArticle[];\n}\n\n/**\n * Basis priority rank: fulltext > abstract > title > undefined\n */\nconst BASIS_RANK: Record<string, number> = {\n  title: 1,\n  abstract: 2,\n  fulltext: 3,\n};\n\nexport function basisRank(basis: ReviewBasis | undefined): number {\n  if (basis === undefined) return 0;\n  return BASIS_RANK[basis] ?? 0;\n}\n\n/**\n * Review status classification (7-state model)\n */\nexport type ReviewStatus =\n  | 'pending'\n  | 'incomplete'\n  | 'uncertain'\n  | 'agreed-include'\n  | 'agreed-exclude'\n  | 'conflicting'\n  | 'finalized';\n\n/**\n * Classify the review status of an article entry\n *\n * Classification logic (in order):\n * 1. finalDecision set?           → finalized\n * 2. 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package/dist/cli/commands/search-executor.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"search-executor.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/search-executor.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,oBAAoB,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AACpF,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,uBAAuB,CAAC;AACpD,OAAO,KAAK,EAEV,QAAQ,EACR,YAAY,EAEb,MAAM,+BAA+B,CAAC;AAwBvC,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAIrE;;GAEG;AACH,MAAM,WAAW,qBAAqB;IACpC,OAAO,EAAE,OAAO,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC,CAAC;IACnG,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,kBAAkB,CAAC,EAAE,kBAAkB,CAAC;IACxC,aAAa,EAAE,WAAW,GAAG,SAAS,GAAG,QAAQ,CAAC;CACnD;AAOD;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAG,OAAO,CAOhF;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CACpC,IAAI,EAAE,YAAY,EAClB,MAAM,EAAE,MAAM,GACb,QAAQ,GAAG,IAAI,CA2DjB;AAyCD;;GAEG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,EAC7B,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,MAAM,EACd,YAAY,UAAO,GAClB,OAAO,CAAC,qBAAqB,CAAC,CAuVhC;AAED;;;GAGG;AACH,wBAAsB,gBAAgB,CACpC,OAAO,EAAE,oBAAoB,EAC7B,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,WAAW,EAAE,CAAC,CAuExB;AAGD;;GAEG;AACH,wBAAsB,cAAc,CAClC,OAAO,EAAE,oBAAoB,EAC7B,MAAM,EAAE,MAAM,EACd,SAAS,SAAI,GACZ,OAAO,CAAC,aAAa,EAAE,CAAC,CAoF1B"}

package/dist/cli/commands/search-executor.js

@@ -16,7 +16,7 @@ import { translateQuery as translateQuery$1 } from "../../providers/arxiv/transl
 import { translateQuery } from "../../providers/scopus/translator.js";
 import { stringify } from "yaml";
 import { registerArticles, saveRegistrationRecord } from "../../integration/register.js";
-import { buildFailureErrorMessage } from "./search-utils.js";
+import { buildFailureErrorMessage, buildPartialErrorMessage } from "./search-utils.js";
 import { getConfigDir } from "../../config/paths.js";
 import { checkRefAvailable } from "../../integration/ref-cli.js";
 import { convertResultsToYaml, loadResults } from "../../session/results-io.js";
@@ -335,6 +335,15 @@ async function executeSearch(options, sessionsDir, config, showProgress = true)
       error: buildFailureErrorMessage(results)
     };
   }
+  if (options.strict && sessionStatus === "partial") {
+    return {
+      success: false,
+      sessionId,
+      sessionStatus,
+      results,
+      error: buildPartialErrorMessage(results)
+    };
+  }
   let autoRegisterResult;
   if (config.integration.reference_manager.enabled && config.integration.reference_manager.auto_register) {
     const refAvailable = await checkRefAvailable();