@ncukondo/search-hub 0.10.0 → 0.12.0

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

@@ -0,0 +1,82 @@
+import { Article, ProviderName } from '../../providers/base/types.js';
+import { SessionFile, SessionSource } from '../../session/types.js';
+/**
+ * Result of merging articles from multiple sessions.
+ */
+export interface MergeResult {
+    /** All unique articles after deduplication */
+    articles: Article[];
+    /** Articles grouped by provider */
+    byProvider: Map<ProviderName, Article[]>;
+    /** Total article count before deduplication */
+    totalBefore: number;
+    /** Total unique article count after deduplication */
+    totalAfter: number;
+    /** Number of duplicates removed */
+    duplicatesRemoved: number;
+    /** Per-session article counts (before dedup) */
+    perSession: Map<string, number>;
+}
+/**
+ * Options for creating a merged session.
+ */
+export interface CreateMergedSessionOptions {
+    name: string;
+    sources: SessionSource[];
+    byProvider: Map<ProviderName, Article[]>;
+    totalRetrieved: number;
+    sessionsDir: string;
+    sourceSessionIds: string[];
+}
+/**
+ * Validation result for merge sources.
+ */
+export interface MergeValidationResult {
+    valid: boolean;
+    error?: string;
+    expandedCommand?: string;
+}
+/**
+ * Output data for formatting merge results.
+ */
+export interface MergeOutputData {
+    sessionId: string;
+    totalBefore: number;
+    totalAfter: number;
+    duplicatesRemoved: number;
+    sources: Array<{
+        id: string;
+        name: string;
+        count: number;
+    }>;
+    byProvider: Map<string, number>;
+}
+/**
+ * Merge articles from multiple sessions with identifier-based deduplication.
+ *
+ * When duplicates are found (same DOI, PMID, etc.), the article with
+ * richer metadata is kept.
+ */
+export declare function mergeArticles(sessionArticles: Map<string, Article[]>): MergeResult;
+/**
+ * Copy source session provenance files to sources/ subdirectory.
+ * Copies session.yaml, query_common.yaml, and query text files.
+ */
+export declare function copySourceProvenance(sourceSessionId: string, sessionsDir: string, mergedSessionDir: string): Promise<void>;
+/**
+ * Validate that all source sessions are valid for merging.
+ */
+export declare function validateMergeSources(sessions: Map<string, SessionFile>): MergeValidationResult;
+/**
+ * Create a merged session on disk.
+ */
+export declare function createMergedSession(options: CreateMergedSessionOptions): Promise<SessionFile>;
+/**
+ * Format merge result as human-readable text.
+ */
+export declare function formatMergeOutput(data: MergeOutputData): string;
+/**
+ * Format merge result as JSON.
+ */
+export declare function formatMergeJson(data: MergeOutputData): string;
+//# sourceMappingURL=merge.d.ts.map

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

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package/dist/cli/commands/merge.js

@@ -0,0 +1,221 @@
+import { mkdir, writeFile, copyFile, readdir } from "node:fs/promises";
+import { join } from "node:path";
+import { createHash } from "node:crypto";
+import { stringify } from "yaml";
+import { isMergedSession } from "../../session/types.js";
+import { sanitizeName } from "../../session/manager.js";
+import { convertResultsToYaml } from "../../session/results-io.js";
+import { getArticleKeys } from "./session-utils.js";
+function countMetadataFields(article) {
+  let count = 0;
+  if (article.doi) count++;
+  if (article.pmid) count++;
+  if (article.arxivId) count++;
+  if (article.scopusId) count++;
+  if (article.ericId) count++;
+  if (article.abstract) count++;
+  if (article.publicationDate) count++;
+  if (article.journal) count++;
+  if (article.volume) count++;
+  if (article.issue) count++;
+  if (article.pages) count++;
+  if (article.authors.length > 0) count++;
+  return count;
+}
+function mergeArticles(sessionArticles) {
+  const keyToIndex = /* @__PURE__ */ new Map();
+  const unique = [];
+  let totalBefore = 0;
+  let duplicatesRemoved = 0;
+  const perSession = /* @__PURE__ */ new Map();
+  for (const [sessionId, articles] of sessionArticles) {
+    perSession.set(sessionId, articles.length);
+    totalBefore += articles.length;
+    for (const article of articles) {
+      const keys = getArticleKeys(article);
+      if (keys.length === 0) {
+        unique.push(article);
+        continue;
+      }
+      let existingIndex;
+      for (const key of keys) {
+        const idx = keyToIndex.get(key);
+        if (idx !== void 0) {
+          existingIndex = idx;
+          break;
+        }
+      }
+      if (existingIndex !== void 0) {
+        const existing = unique[existingIndex];
+        if (countMetadataFields(article) > countMetadataFields(existing)) {
+          unique[existingIndex] = article;
+          const newKeys = getArticleKeys(article);
+          for (const key of newKeys) {
+            keyToIndex.set(key, existingIndex);
+          }
+        }
+        duplicatesRemoved++;
+      } else {
+        const index = unique.length;
+        unique.push(article);
+        for (const key of keys) {
+          keyToIndex.set(key, index);
+        }
+      }
+    }
+  }
+  const byProvider = /* @__PURE__ */ new Map();
+  for (const article of unique) {
+    const existing = byProvider.get(article.source) ?? [];
+    existing.push(article);
+    byProvider.set(article.source, existing);
+  }
+  return {
+    articles: unique,
+    byProvider,
+    totalBefore,
+    totalAfter: unique.length,
+    duplicatesRemoved,
+    perSession
+  };
+}
+async function copySourceProvenance(sourceSessionId, sessionsDir, mergedSessionDir) {
+  const sourceDir = join(sessionsDir, sourceSessionId);
+  const targetDir = join(mergedSessionDir, "sources", sourceSessionId);
+  await mkdir(targetDir, { recursive: true });
+  for (const file of ["session.yaml", "query_common.yaml"]) {
+    try {
+      await copyFile(join(sourceDir, file), join(targetDir, file));
+    } catch {
+    }
+  }
+  const entries = await readdir(sourceDir);
+  for (const entry of entries) {
+    if (entry.startsWith("query_") && entry.endsWith(".txt")) {
+      await copyFile(join(sourceDir, entry), join(targetDir, entry));
+    }
+  }
+}
+function validateMergeSources(sessions) {
+  for (const [sessionId, session] of sessions) {
+    if (isMergedSession(session)) {
+      const originalSources = session.sources?.map((s) => s.id) ?? [];
+      const otherIds = [...sessions.keys()].filter((id) => id !== sessionId);
+      const allSources = [.../* @__PURE__ */ new Set([...originalSources, ...otherIds])];
+      const expandedCommand = `search-hub merge ${allSources.join(" ")}`;
+      return {
+        valid: false,
+        error: `Session '${sessionId}' is a merged session (sources: ${originalSources.join(", ")}).
+  Merge the original sources directly:
+  ${expandedCommand}`,
+        expandedCommand
+      };
+    }
+  }
+  for (const [sessionId, session] of sessions) {
+    if (session.summary.status !== "completed") {
+      return {
+        valid: false,
+        error: `Session '${sessionId}' is not completed (status: ${session.summary.status}). Only completed sessions can be merged.`
+      };
+    }
+  }
+  return { valid: true };
+}
+function generateMergedSessionId(name, sourceIds) {
+  const date = (/* @__PURE__ */ new Date()).toISOString().slice(0, 10).replace(/-/g, "");
+  const sanitized = sanitizeName(name);
+  const hash = createHash("sha256").update(sourceIds.join(",")).digest("hex").slice(0, 6);
+  return `${date}_${sanitized}_${hash}`;
+}
+async function createMergedSession(options) {
+  const { name, sources, byProvider, totalRetrieved, sessionsDir, sourceSessionIds } = options;
+  const id = generateMergedSessionId(name, sourceSessionIds);
+  const sessionDir = join(sessionsDir, id);
+  const now = (/* @__PURE__ */ new Date()).toISOString();
+  await mkdir(sessionDir, { recursive: true });
+  const databases = {};
+  for (const [provider, articles] of byProvider) {
+    const jsonlFilename = `${provider}_results.jsonl`;
+    const yamlFilename = `${provider}_results.yaml`;
+    const jsonlPath = join(sessionDir, jsonlFilename);
+    const jsonlContent = articles.map((a) => JSON.stringify(a)).join("\n") + "\n";
+    await writeFile(jsonlPath, jsonlContent, "utf-8");
+    const yamlPath = join(sessionDir, yamlFilename);
+    await convertResultsToYaml(jsonlPath, yamlPath, {
+      provider,
+      queryName: name
+    });
+    databases[provider] = {
+      status: "completed",
+      retrievedCount: articles.length,
+      files: {
+        query: "",
+        results: jsonlFilename,
+        resultsYaml: yamlFilename
+      }
+    };
+  }
+  const sessionFile = {
+    version: 1,
+    id,
+    name,
+    type: "merge",
+    createdAt: now,
+    updatedAt: now,
+    sources,
+    databases,
+    summary: {
+      totalHits: 0,
+      totalRetrieved,
+      status: "completed"
+    }
+  };
+  await writeFile(
+    join(sessionDir, "session.yaml"),
+    stringify(sessionFile),
+    "utf-8"
+  );
+  for (const sourceId of sourceSessionIds) {
+    await copySourceProvenance(sourceId, sessionsDir, sessionDir);
+  }
+  return sessionFile;
+}
+function formatMergeOutput(data) {
+  const lines = [];
+  lines.push(`Merged session: ${data.sessionId}`);
+  lines.push("");
+  lines.push("Sources:");
+  for (const source of data.sources) {
+    lines.push(`  ${source.id} (${source.name}): ${source.count} articles`);
+  }
+  lines.push("");
+  lines.push(`Total articles: ${data.totalBefore} → ${data.totalAfter} unique (${data.duplicatesRemoved} duplicates removed)`);
+  if (data.byProvider.size > 0) {
+    lines.push("");
+    lines.push("By database:");
+    for (const [provider, count] of data.byProvider) {
+      lines.push(`  ${provider}: ${count} articles`);
+    }
+  }
+  return lines.join("\n");
+}
+function formatMergeJson(data) {
+  return JSON.stringify({
+    sessionId: data.sessionId,
+    totalBefore: data.totalBefore,
+    totalAfter: data.totalAfter,
+    duplicatesRemoved: data.duplicatesRemoved,
+    sources: data.sources,
+    byProvider: Object.fromEntries(data.byProvider)
+  }, null, 2);
+}
+export {
+  copySourceProvenance,
+  createMergedSession,
+  formatMergeJson,
+  formatMergeOutput,
+  mergeArticles,
+  validateMergeSources
+};
+//# sourceMappingURL=merge.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"merge.js","sources":["../../../src/cli/commands/merge.ts"],"sourcesContent":["import { mkdir, writeFile, readFile, readdir, copyFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { createHash } from 'node:crypto';\nimport { stringify as stringifyYaml } from 'yaml';\nimport type { Article, ProviderName } from '../../providers/base/types.js';\nimport type { SessionFile, SessionSource, DatabaseStatus } from '../../session/types.js';\nimport { isMergedSession } from '../../session/types.js';\nimport { sanitizeName } from '../../session/manager.js';\nimport { convertResultsToYaml } from '../../session/results-io.js';\nimport { getArticleKeys } from './session-utils.js';\n\n/**\n * Result of merging articles from multiple sessions.\n */\nexport interface MergeResult {\n  /** All unique articles after deduplication */\n  articles: Article[];\n  /** Articles grouped by provider */\n  byProvider: Map<ProviderName, Article[]>;\n  /** Total article count before deduplication */\n  totalBefore: number;\n  /** Total unique article count after deduplication */\n  totalAfter: number;\n  /** Number of duplicates removed */\n  duplicatesRemoved: number;\n  /** Per-session article counts (before dedup) */\n  perSession: Map<string, number>;\n}\n\n/**\n * Options for creating a merged session.\n */\nexport interface CreateMergedSessionOptions {\n  name: string;\n  sources: SessionSource[];\n  byProvider: Map<ProviderName, Article[]>;\n  totalRetrieved: number;\n  sessionsDir: string;\n  sourceSessionIds: string[];\n}\n\n/**\n * Validation result for merge sources.\n */\nexport interface MergeValidationResult {\n  valid: boolean;\n  error?: string;\n  expandedCommand?: string;\n}\n\n/**\n * Output data for formatting merge results.\n */\nexport interface MergeOutputData {\n  sessionId: string;\n  totalBefore: number;\n  totalAfter: number;\n  duplicatesRemoved: number;\n  sources: Array<{ id: string; name: string; count: number }>;\n  byProvider: Map<string, number>;\n}\n\n/**\n * Count metadata fields for comparing article richness.\n */\nfunction countMetadataFields(article: Article): number {\n  let count = 0;\n  if (article.doi) count++;\n  if (article.pmid) count++;\n  if (article.arxivId) count++;\n  if (article.scopusId) count++;\n  if (article.ericId) count++;\n  if (article.abstract) count++;\n  if (article.publicationDate) count++;\n  if (article.journal) count++;\n  if (article.volume) count++;\n  if (article.issue) count++;\n  if (article.pages) count++;\n  if (article.authors.length > 0) count++;\n  return count;\n}\n\n/**\n * Merge articles from multiple sessions with identifier-based deduplication.\n *\n * When duplicates are found (same DOI, PMID, etc.), the article with\n * richer metadata is kept.\n */\nexport function mergeArticles(\n  sessionArticles: Map<string, Article[]>,\n): MergeResult {\n  const keyToIndex = new Map<string, number>();\n  const unique: Article[] = [];\n  let totalBefore = 0;\n  let duplicatesRemoved = 0;\n  const perSession = new Map<string, number>();\n\n  for (const [sessionId, articles] of sessionArticles) {\n    perSession.set(sessionId, articles.length);\n    totalBefore += articles.length;\n\n    for (const article of articles) {\n      const keys = getArticleKeys(article);\n\n      if (keys.length === 0) {\n        unique.push(article);\n        continue;\n      }\n\n      let existingIndex: number | undefined;\n      for (const key of keys) {\n        const idx = keyToIndex.get(key);\n        if (idx !== undefined) {\n          existingIndex = idx;\n          break;\n        }\n      }\n\n      if (existingIndex !== undefined) {\n        const existing = unique[existingIndex]!;\n        if (countMetadataFields(article) > countMetadataFields(existing)) {\n          unique[existingIndex] = article;\n          const newKeys = getArticleKeys(article);\n          for (const key of newKeys) {\n            keyToIndex.set(key, existingIndex);\n          }\n        }\n        duplicatesRemoved++;\n      } else {\n        const index = unique.length;\n        unique.push(article);\n        for (const key of keys) {\n          keyToIndex.set(key, index);\n        }\n      }\n    }\n  }\n\n  // Group by provider\n  const byProvider = new Map<ProviderName, Article[]>();\n  for (const article of unique) {\n    const existing = byProvider.get(article.source) ?? [];\n    existing.push(article);\n    byProvider.set(article.source, existing);\n  }\n\n  return {\n    articles: unique,\n    byProvider,\n    totalBefore,\n    totalAfter: unique.length,\n    duplicatesRemoved,\n    perSession,\n  };\n}\n\n/**\n * Copy source session provenance files to sources/ subdirectory.\n * Copies session.yaml, query_common.yaml, and query text files.\n */\nexport async function copySourceProvenance(\n  sourceSessionId: string,\n  sessionsDir: string,\n  mergedSessionDir: string,\n): Promise<void> {\n  const sourceDir = join(sessionsDir, sourceSessionId);\n  const targetDir = join(mergedSessionDir, 'sources', sourceSessionId);\n  await mkdir(targetDir, { recursive: true });\n\n  // Copy session.yaml and query_common.yaml\n  for (const file of ['session.yaml', 'query_common.yaml']) {\n    try {\n      await copyFile(join(sourceDir, file), join(targetDir, file));\n    } catch {\n      // Skip if file doesn't exist\n    }\n  }\n\n  // Copy query text files (query_*.txt)\n  const entries = await readdir(sourceDir);\n  for (const entry of entries) {\n    if (entry.startsWith('query_') && entry.endsWith('.txt')) {\n      await copyFile(join(sourceDir, entry), join(targetDir, entry));\n    }\n  }\n}\n\n/**\n * Validate that all source sessions are valid for merging.\n */\nexport function validateMergeSources(\n  sessions: Map<string, SessionFile>,\n): MergeValidationResult {\n  // Check for merged sessions as sources\n  for (const [sessionId, session] of sessions) {\n    if (isMergedSession(session)) {\n      // Collect original sources from the merged session\n      const originalSources = session.sources?.map((s) => s.id) ?? [];\n      // Collect non-merged session IDs\n      const otherIds = [...sessions.keys()].filter((id) => id !== sessionId);\n      // Build expanded command with original sources + other sessions\n      const allSources = [...new Set([...originalSources, ...otherIds])];\n      const expandedCommand = `search-hub merge ${allSources.join(' ')}`;\n\n      return {\n        valid: false,\n        error: `Session '${sessionId}' is a merged session (sources: ${originalSources.join(', ')}).\\n  Merge the original sources directly:\\n  ${expandedCommand}`,\n        expandedCommand,\n      };\n    }\n  }\n\n  // Check that all sessions are completed\n  for (const [sessionId, session] of sessions) {\n    if (session.summary.status !== 'completed') {\n      return {\n        valid: false,\n        error: `Session '${sessionId}' is not completed (status: ${session.summary.status}). Only completed sessions can be merged.`,\n      };\n    }\n  }\n\n  return { valid: true };\n}\n\n/**\n * Generate a session ID for a merged session.\n */\nfunction generateMergedSessionId(name: string, sourceIds: string[]): string {\n  const date = new Date().toISOString().slice(0, 10).replace(/-/g, '');\n  const sanitized = sanitizeName(name);\n  const hash = createHash('sha256').update(sourceIds.join(',')).digest('hex').slice(0, 6);\n  return `${date}_${sanitized}_${hash}`;\n}\n\n/**\n * Create a merged session on disk.\n */\nexport async function createMergedSession(\n  options: CreateMergedSessionOptions,\n): Promise<SessionFile> {\n  const { name, sources, byProvider, totalRetrieved, sessionsDir, sourceSessionIds } = options;\n\n  const id = generateMergedSessionId(name, sourceSessionIds);\n  const sessionDir = join(sessionsDir, id);\n  const now = new Date().toISOString();\n\n  await mkdir(sessionDir, { recursive: true });\n\n  // Build database statuses and write result files\n  const databases: Partial<Record<ProviderName, DatabaseStatus>> = {};\n\n  for (const [provider, articles] of byProvider) {\n    const jsonlFilename = `${provider}_results.jsonl`;\n    const yamlFilename = `${provider}_results.yaml`;\n    const jsonlPath = join(sessionDir, jsonlFilename);\n\n    // Write JSONL results\n    const jsonlContent = articles\n      .map((a) => JSON.stringify(a))\n      .join('\\n') + '\\n';\n    await writeFile(jsonlPath, jsonlContent, 'utf-8');\n\n    // Convert to YAML\n    const yamlPath = join(sessionDir, yamlFilename);\n    await convertResultsToYaml(jsonlPath, yamlPath, {\n      provider,\n      queryName: name,\n    });\n\n    databases[provider] = {\n      status: 'completed',\n      retrievedCount: articles.length,\n      files: {\n        query: '',\n        results: jsonlFilename,\n        resultsYaml: yamlFilename,\n      },\n    };\n  }\n\n  // Create session file\n  const sessionFile: SessionFile = {\n    version: 1,\n    id,\n    name,\n    type: 'merge',\n    createdAt: now,\n    updatedAt: now,\n    sources,\n    databases,\n    summary: {\n      totalHits: 0,\n      totalRetrieved: totalRetrieved,\n      status: 'completed',\n    },\n  };\n\n  // Write session.yaml\n  await writeFile(\n    join(sessionDir, 'session.yaml'),\n    stringifyYaml(sessionFile),\n    'utf-8',\n  );\n\n  // Copy provenance from source sessions\n  for (const sourceId of sourceSessionIds) {\n    await copySourceProvenance(sourceId, sessionsDir, sessionDir);\n  }\n\n  return sessionFile;\n}\n\n/**\n * Format merge result as human-readable text.\n */\nexport function formatMergeOutput(data: MergeOutputData): string {\n  const lines: string[] = [];\n\n  lines.push(`Merged session: ${data.sessionId}`);\n  lines.push('');\n  lines.push('Sources:');\n  for (const source of data.sources) {\n    lines.push(`  ${source.id} (${source.name}): ${source.count} articles`);\n  }\n  lines.push('');\n  lines.push(`Total articles: ${data.totalBefore} → ${data.totalAfter} unique (${data.duplicatesRemoved} duplicates removed)`);\n\n  if (data.byProvider.size > 0) {\n    lines.push('');\n    lines.push('By database:');\n    for (const [provider, count] of data.byProvider) {\n      lines.push(`  ${provider}: ${count} articles`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format merge result as JSON.\n */\nexport function formatMergeJson(data: MergeOutputData): string {\n  return JSON.stringify({\n    sessionId: data.sessionId,\n    totalBefore: data.totalBefore,\n    totalAfter: data.totalAfter,\n    duplicatesRemoved: data.duplicatesRemoved,\n    sources: data.sources,\n    byProvider: Object.fromEntries(data.byProvider),\n  }, null, 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package/dist/cli/commands/resume.d.ts.map

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package/dist/cli/commands/resume.js

@@ -1,4 +1,5 @@
 import { loadSession, getResumableProviders } from "../../session/manager.js";
+import { isMergedSession } from "../../session/types.js";
 import { parseProviderNames } from "../utils/validation.js";
 function parseResumeOptions(sessionId, options) {
   const result = {
@@ -24,6 +25,12 @@ function validateResumeInput(options) {
 async function getResumableProvidersForCommand(sessionId, sessionsDir, options) {
   try {
     const session = await loadSession(sessionId, sessionsDir);
+    if (isMergedSession(session)) {
+      return {
+        success: false,
+        error: `Cannot resume merged session '${sessionId}'. Merged sessions are created from other sessions and cannot be resumed.`
+      };
+    }
     let resumable = getResumableProviders(session);
     if (options.providers && options.providers.length > 0) {
       resumable = resumable.filter((r) => options.providers.includes(r.provider));

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

@@ -1 +1 @@
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+{"version":3,"file":"resume.js","sources":["../../../src/cli/commands/resume.ts"],"sourcesContent":["import { loadSession, getResumableProviders } from '../../session/manager.js';\nimport type { ProviderName, ResumableProvider } from '../../session/types.js';\nimport { isMergedSession } from '../../session/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\n\nexport interface ResumeCommandOptions {\n  sessionId: string;\n  providers?: ProviderName[];\n  retryFailed?: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  retryFailed?: boolean | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\nexport interface ResumeResult {\n  success: boolean;\n  providers?: ResumableProvider[];\n  error?: string;\n}\n\nexport function parseResumeOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): ResumeCommandOptions {\n  const result: ResumeCommandOptions = {\n    sessionId,\n  };\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  if (options.retryFailed) {\n    result.retryFailed = true;\n  }\n\n  return result;\n}\n\nexport function validateResumeInput(options: ResumeCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  return { valid: true };\n}\n\nexport async function getResumableProvidersForCommand(\n  sessionId: string,\n  sessionsDir: string,\n  options: { providers?: ProviderName[] | undefined; retryFailed?: boolean | undefined }\n): Promise<ResumeResult> {\n  try {\n    const session = await loadSession(sessionId, sessionsDir);\n\n    // Reject merged sessions\n    if (isMergedSession(session)) {\n      return {\n        success: false,\n        error: `Cannot resume merged session '${sessionId}'. Merged sessions are created from other sessions and cannot be resumed.`,\n      };\n    }\n\n    let resumable = getResumableProviders(session);\n\n    // Filter by specific providers if requested\n    if (options.providers && options.providers.length > 0) {\n      resumable = resumable.filter((r) => options.providers!.includes(r.provider));\n    }\n\n    // Filter to only retry strategies if retryFailed is true\n    if (options.retryFailed) {\n      resumable = resumable.filter((r) => r.strategy === 'retry');\n    }\n\n    return {\n      success: true,\n      providers: resumable,\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"],"names":[],"mappings":";;;AA2BO,SAAS,mBACd,WACA,SACsB;AACtB,QAAM,SAA+B;AAAA,IACnC;AAAA,EAAA;AAGF,MAAI,QAAQ,IAAI;AACd,WAAO,YAAY,mBAAmB,QAAQ,EAAE;AAAA,EAClD;AAEA,MAAI,QAAQ,aAAa;AACvB,WAAO,cAAc;AAAA,EACvB;AAEA,SAAO;AACT;AAEO,SAAS,oBAAoB,SAAiD;AACnF,MAAI,CAAC,QAAQ,aAAa,QAAQ,UAAU,KAAA,MAAW,IAAI;AACzD,WAAO;AAAA,MACL,OAAO;AAAA,MACP,OAAO;AAAA,IAAA;AAAA,EAEX;AAEA,SAAO,EAAE,OAAO,KAAA;AAClB;AAEA,eAAsB,gCACpB,WACA,aACA,SACuB;AACvB,MAAI;AACF,UAAM,UAAU,MAAM,YAAY,WAAW,WAAW;AAGxD,QAAI,gBAAgB,OAAO,GAAG;AAC5B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,OAAO,iCAAiC,SAAS;AAAA,MAAA;AAAA,IAErD;AAEA,QAAI,YAAY,sBAAsB,OAAO;AAG7C,QAAI,QAAQ,aAAa,QAAQ,UAAU,SAAS,GAAG;AACrD,kBAAY,UAAU,OAAO,CAAC,MAAM,QAAQ,UAAW,SAAS,EAAE,QAAQ,CAAC;AAAA,IAC7E;AAGA,QAAI,QAAQ,aAAa;AACvB,kBAAY,UAAU,OAAO,CAAC,MAAM,EAAE,aAAa,OAAO;AAAA,IAC5D;AAEA,WAAO;AAAA,MACL,SAAS;AAAA,MACT,WAAW;AAAA,IAAA;AAAA,EAEf,SAAS,OAAO;AACd,UAAM,UAAU,iBAAiB,QAAQ,MAAM,UAAU;AACzD,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO;AAAA,IAAA;AAAA,EAEX;AACF;"}

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

@@ -7,12 +7,14 @@ export interface ReviewExtractOptions {
     seed?: number;
     limit?: number;
     offset?: number;
-    /** Basis for the review (title, abstract). When specified, outputs work file format. */
+    /** Basis for the review (title, abstract, fulltext). When specified, outputs screening format. */
     basis?: ReviewBasis;
     /** Reviewer identifier (e.g., "ai:claude"). Required for all extract modes. */
     reviewer?: string;
     /** Name for the review subset (output goes to for-review/<name>/review.yaml) */
     name: string;
+    /** When true, outputs final decision format with reviewHistory and finalDecision fields. */
+    finalize?: boolean;
 }
 export interface ReviewExtractResult {
     outputPath: string;

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

@@ -1 +1 @@
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+{"version":3,"file":"extract.d.ts","sourceRoot":"","sources":["../../../../src/cli/commands/review/extract.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,OAAO,EAAsD,KAAK,YAAY,EAAE,KAAK,WAAW,EAAE,MAAM,YAAY,CAAC;AAErH,MAAM,MAAM,UAAU,GAAG,MAAM,GAAG,OAAO,GAAG,QAAQ,GAAG,MAAM,CAAC;AAE9D,MAAM,WAAW,oBAAoB;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,YAAY,EAAE,CAAC;IACxB,IAAI,CAAC,EAAE,UAAU,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,kGAAkG;IAClG,KAAK,CAAC,EAAE,WAAW,CAAC;IACpB,+EAA+E;IAC/E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gFAAgF;IAChF,IAAI,EAAE,MAAM,CAAC;IACb,4FAA4F;IAC5F,QAAQ,CAAC,EAAE,OAAO,CAAC;CACpB;AAGD,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,cAAc,EAAE,MAAM,CAAC;IACvB,aAAa,EAAE,MAAM,CAAC;CACvB;AAgLD;;GAEG;AACH,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAU/C;AAED;;GAEG;AACH,wBAAsB,oBAAoB,CACxC,OAAO,EAAE,oBAAoB,EAC7B,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,mBAAmB,CAAC,CAuG9B"}

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

@@ -20,18 +20,12 @@ function seededShuffle(array, seed) {
   }
   return result;
 }
-function getArticleId(article) {
-  if (article.doi) return article.doi;
-  if (article.pmid) return article.pmid;
-  if (article.scopusId) return article.scopusId;
-  if (article.arxivId) return article.arxivId;
-  if (article.ericId) return article.ericId;
-  return article.title;
-}
 function getBasisGuidanceComment(basis) {
+  const schemaLine = "# yaml-language-server: $schema=./review.schema.json";
   switch (basis) {
     case "title":
       return [
+        schemaLine,
         "# Screening by title only.",
         '# Mark clearly irrelevant items as "exclude" with a comment explaining the reason.',
         '# Leave everything else as "uncertain".',
@@ -39,6 +33,7 @@ function getBasisGuidanceComment(basis) {
       ].join("\n");
     case "abstract":
       return [
+        schemaLine,
         "# 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.',
@@ -46,6 +41,7 @@ function getBasisGuidanceComment(basis) {
       ].join("\n");
     case "fulltext":
       return [
+        schemaLine,
         "# 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.',
@@ -53,6 +49,59 @@ function getBasisGuidanceComment(basis) {
       ].join("\n");
   }
 }
+function getDecisionInlineComment(basis) {
+  switch (basis) {
+    case "title":
+      return "# exclude / uncertain";
+    case "abstract":
+    case "fulltext":
+      return "# include / exclude / uncertain";
+  }
+}
+function buildScreeningArticle(article, basis) {
+  const result = { title: article.title, reviews: [] };
+  if (article.doi) result.doi = article.doi;
+  if (article.pmid) result.pmid = article.pmid;
+  if (article.scopusId) result.scopusId = article.scopusId;
+  if (article.arxivId) result.arxivId = article.arxivId;
+  if (article.ericId) result.ericId = article.ericId;
+  if ((basis === "abstract" || basis === "fulltext") && article.abstract) {
+    result.abstract = article.abstract;
+  }
+  if (basis === "fulltext" && article.fulltext) {
+    result.fulltext = article.fulltext;
+  }
+  result.reviews = [{ decision: "uncertain", comment: "" }];
+  return result;
+}
+function buildFinalizeArticle(article, basis) {
+  const result = { title: article.title, reviews: [] };
+  if (article.doi) result.doi = article.doi;
+  if (article.pmid) result.pmid = article.pmid;
+  if (article.scopusId) result.scopusId = article.scopusId;
+  if (article.arxivId) result.arxivId = article.arxivId;
+  if (article.ericId) result.ericId = article.ericId;
+  if (article.authors) result.authors = article.authors;
+  if (article.year) result.year = article.year;
+  if (!basis || basis === "abstract" || basis === "fulltext") {
+    if (article.abstract) result.abstract = article.abstract;
+  }
+  if (!basis || basis === "fulltext") {
+    if (article.fulltext) result.fulltext = article.fulltext;
+  }
+  result.reviewHistory = article.reviews ?? [];
+  result.reviews = [];
+  result.finalDecision = null;
+  return result;
+}
+function getFinalDecisionGuidanceComment() {
+  return [
+    "# yaml-language-server: $schema=./review.schema.json",
+    "# Final decision file: set finalDecision on each article",
+    "# Valid decisions: include / exclude / null",
+    ""
+  ].join("\n");
+}
 function sortArticles(articles, sort, seed) {
   switch (sort) {
     case "year":
@@ -105,57 +154,38 @@ async function executeReviewExtract(options, sessionsDir) {
   if (options.limit !== void 0 && options.limit > 0) {
     paginated = paginated.slice(0, options.limit);
   }
+  if (!options.reviewer) {
+    throw new Error("--reviewer is required for review file extract");
+  }
   let finalContent;
-  if (options.basis && options.reviewer) {
-    const workFile = {
+  if (options.basis && !options.finalize) {
+    const outputFile = {
       sessionId: options.sessionId,
       basis: options.basis,
       reviewer: options.reviewer,
-      articles: paginated.map((article) => {
-        const workArticle = {
-          id: getArticleId(article),
-          title: article.title,
-          decision: "uncertain",
-          comment: ""
-        };
-        if ((options.basis === "abstract" || options.basis === "fulltext") && article.abstract) {
-          workArticle.abstract = article.abstract;
-        }
-        if (options.basis === "fulltext" && article.fulltext) {
-          workArticle.fulltext = article.fulltext.dirName;
-        }
-        return workArticle;
-      })
+      articles: paginated.map((article) => buildScreeningArticle(article, options.basis))
     };
-    const yamlContent = stringify(workFile, {
-      lineWidth: 0
-    });
+    const yamlContent = stringify(outputFile, { lineWidth: 0 });
+    const decisionComment = getDecisionInlineComment(options.basis);
+    const yamlWithComments = yamlContent.replace(
+      /^(\s*-?\s*)decision: uncertain$/gm,
+      `$1decision: uncertain          ${decisionComment}`
+    );
     const guidanceComment = getBasisGuidanceComment(options.basis);
-    finalContent = guidanceComment + yamlContent;
+    finalContent = guidanceComment + yamlWithComments;
   } else {
-    if (!options.reviewer) {
-      throw new Error("--reviewer is required for review file extract");
-    }
     const outputFile = {
       sessionId: options.sessionId,
-      ...options.reviewer && { reviewer: options.reviewer },
-      articles: paginated.map((article) => ({
-        ...article,
-        reviewHistory: article.reviews ?? [],
-        reviews: [],
-        finalDecision: null
-      }))
+      reviewer: options.reviewer,
+      articles: paginated.map((article) => buildFinalizeArticle(article, options.basis))
     };
-    const yamlContent = stringify(outputFile, {
-      lineWidth: 0
-    });
+    const yamlContent = stringify(outputFile, { lineWidth: 0 });
     const yamlWithComments = yamlContent.replace(
       /^(\s*)finalDecision: null$/gm,
       "$1finalDecision: # include / exclude"
     );
-    const schemaComment = `# yaml-language-server: $schema=./review.schema.json
-`;
-    finalContent = schemaComment + yamlWithComments;
+    const guidanceComment = getFinalDecisionGuidanceComment();
+    finalContent = guidanceComment + yamlWithComments;
   }
   const outputDir = dirname(outputPath);
   await mkdir(outputDir, { recursive: true });