@ncukondo/search-hub 0.5.0 → 0.7.0

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

@@ -1,4 +1,5 @@
 import { Article } from '../../providers/base/types.js';
+import { QueryAST, FieldType } from '../../query/types.js';
 export interface DiffResult {
     session1Count: number;
     session2Count: number;
@@ -15,9 +16,63 @@ export interface DiffResult {
  */
 export declare function computeDiff(session1: Article[], session2: Article[]): DiffResult;
 export type ShowFilter = 'added' | 'removed' | 'common';
+/**
+ * Options for formatting diff with query information.
+ */
+export interface FormatDiffOptions {
+    queryDiff?: QueryDiff | undefined;
+    noQueryDiff?: boolean | undefined;
+    showQueryDiffPlaceholder?: boolean | undefined;
+}
 /**
  * Format diff result as human-readable text.
  */
-export declare function formatDiff(diff: DiffResult, session1Id: string, session2Id: string, show?: ShowFilter): string;
-export declare function formatDiffJson(diff: DiffResult, session1Id: string, session2Id: string, show?: ShowFilter): string;
+export declare function formatDiff(diff: DiffResult, session1Id: string, session2Id: string, show?: ShowFilter, options?: FormatDiffOptions): string;
+export declare function formatDiffJson(diff: DiffResult, session1Id: string, session2Id: string, show?: ShowFilter, options?: FormatDiffOptions): string;
+/**
+ * Diff result for a single query block.
+ */
+export interface BlockDiff {
+    index: number;
+    field: FieldType;
+    added: string[];
+    removed: string[];
+    meshAdded?: string[];
+    meshRemoved?: string[];
+    emtreeAdded?: string[];
+    emtreeRemoved?: string[];
+    excludeAdded?: string[];
+    excludeRemoved?: string[];
+    hasChanges: boolean;
+    isNew?: boolean;
+    isRemoved?: boolean;
+}
+/**
+ * Diff result for query filters.
+ */
+export interface FilterDiff {
+    yearFromChanged: boolean;
+    oldYearFrom?: number | undefined;
+    newYearFrom?: number | undefined;
+    yearToChanged: boolean;
+    oldYearTo?: number | undefined;
+    newYearTo?: number | undefined;
+    languagesAdded: string[];
+    languagesRemoved: string[];
+}
+/**
+ * Complete query diff result.
+ */
+export interface QueryDiff {
+    blocks: BlockDiff[];
+    filters: FilterDiff;
+}
+/**
+ * Compute the diff between two QueryAST objects.
+ */
+export declare function computeQueryDiff(query1: QueryAST, query2: QueryAST): QueryDiff;
+/**
+ * Format query diff as human-readable text.
+ */
+export declare function formatQueryDiff(queryDiff: QueryDiff): string;
 //# sourceMappingURL=diff.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"diff.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/diff.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,+BAA+B,CAAC;AAC7D,OAAO,KAAK,EAAE,QAAQ,EAAE,SAAS,EAAa,MAAM,sBAAsB,CAAC;AAG3E,MAAM,WAAW,UAAU;IACzB,aAAa,EAAE,MAAM,CAAC;IACtB,aAAa,EAAE,MAAM,CAAC;IACtB,KAAK,EAAE,OAAO,EAAE,CAAC;IACjB,OAAO,EAAE,OAAO,EAAE,CAAC;IACnB,MAAM,EAAE,OAAO,EAAE,CAAC;CACnB;AAED;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,OAAO,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,GAAG,UAAU,CAyDhF;AAED,MAAM,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,GAAG,QAAQ,CAAC;AAoBxD;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC;IAClC,WAAW,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAClC,wBAAwB,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAChD;AAED;;GAEG;AACH,wBAAgB,UAAU,CACxB,IAAI,EAAE,UAAU,EAChB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,EAClB,IAAI,CAAC,EAAE,UAAU,EACjB,OAAO,CAAC,EAAE,iBAAiB,GAC1B,MAAM,CAyDR;AAqBD,wBAAgB,cAAc,CAC5B,IAAI,EAAE,UAAU,EAChB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,EAClB,IAAI,CAAC,EAAE,UAAU,EACjB,OAAO,CAAC,EAAE,iBAAiB,GAC1B,MAAM,CA6BR;AAED;;GAEG;AACH,MAAM,WAAW,SAAS;IACxB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,SAAS,CAAC;IACjB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;IACrB,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,aAAa,CAAC,EAAE,MAAM,EAAE,CAAC;IACzB,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B,UAAU,EAAE,OAAO,CAAC;IACpB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAED;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,eAAe,EAAE,OAAO,CAAC;IACzB,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACjC,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACjC,aAAa,EAAE,OAAO,CAAC;IACvB,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,gBAAgB,EAAE,MAAM,EAAE,CAAC;CAC5B;AAED;;GAEG;AACH,MAAM,WAAW,SAAS;IACxB,MAAM,EAAE,SAAS,EAAE,CAAC;IACpB,OAAO,EAAE,UAAU,CAAC;CACrB;AA2ED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,GAAG,SAAS,CAqC9E;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,SAAS,EAAE,SAAS,GAAG,MAAM,CAuG5D"}

package/dist/cli/commands/diff.js

@@ -57,12 +57,22 @@ function formatArticleLine(prefix, article) {
   const yearPart = year ? `[${year}] ` : "";
   return `  ${prefix} ${yearPart}${article.title}`;
 }
-function formatDiff(diff, session1Id, session2Id, show) {
+function formatDiff(diff, session1Id, session2Id, show, options) {
   const lines = [];
   lines.push(`Diff: ${session1Id} → ${session2Id}`);
   lines.push(`  Session 1: ${diff.session1Count} articles (${session1Id})`);
   lines.push(`  Session 2: ${diff.session2Count} articles (${session2Id})`);
   lines.push("");
+  const shouldShowQueryDiff = options?.queryDiff && !options?.noQueryDiff;
+  const shouldShowPlaceholder = options?.showQueryDiffPlaceholder && !options?.queryDiff && !options?.noQueryDiff;
+  if (shouldShowPlaceholder) {
+    lines.push("Query changes: (query data not available)");
+    lines.push("");
+  } else if (shouldShowQueryDiff) {
+    lines.push(formatQueryDiff(options.queryDiff));
+    lines.push("");
+    lines.push("Result changes:");
+  }
   lines.push(`  Common:  ${diff.common.length} articles`);
   lines.push(`  Added:   ${diff.added.length} articles (in ${session2Id} but not ${session1Id})`);
   lines.push(`  Removed: ${diff.removed.length} articles (in ${session1Id} but not ${session2Id})`);
@@ -92,7 +102,7 @@ function formatDiff(diff, session1Id, session2Id, show) {
   }
   return lines.join("\n");
 }
-function formatDiffJson(diff, session1Id, session2Id, show) {
+function formatDiffJson(diff, session1Id, session2Id, show, options) {
   const result = {
     session1: session1Id,
     session2: session2Id,
@@ -104,6 +114,9 @@ function formatDiffJson(diff, session1Id, session2Id, show) {
       removedCount: diff.removed.length
     }
   };
+  if (options?.queryDiff && !options?.noQueryDiff) {
+    result.queryDiff = options.queryDiff;
+  }
   if (!show || show === "added") {
     result.added = diff.added;
   }
@@ -115,9 +128,167 @@ function formatDiffJson(diff, session1Id, session2Id, show) {
   }
   return JSON.stringify(result, null, 2);
 }
+function setDiff(arr1, arr2) {
+  const set1 = new Set(arr1);
+  return arr2.filter((item) => !set1.has(item));
+}
+function compareBlocks(block1, block2, index, field) {
+  const emptyTerms = { keywords: [], mesh: [], emtree: [], exclude: [] };
+  const terms1 = block1 ?? emptyTerms;
+  const terms2 = block2 ?? emptyTerms;
+  const added = setDiff(terms1.keywords, terms2.keywords);
+  const removed = setDiff(terms2.keywords, terms1.keywords);
+  const meshAdded = setDiff(terms1.mesh ?? [], terms2.mesh ?? []);
+  const meshRemoved = setDiff(terms2.mesh ?? [], terms1.mesh ?? []);
+  const emtreeAdded = setDiff(terms1.emtree ?? [], terms2.emtree ?? []);
+  const emtreeRemoved = setDiff(terms2.emtree ?? [], terms1.emtree ?? []);
+  const excludeAdded = setDiff(terms1.exclude ?? [], terms2.exclude ?? []);
+  const excludeRemoved = setDiff(terms2.exclude ?? [], terms1.exclude ?? []);
+  const hasChanges = added.length > 0 || removed.length > 0 || meshAdded.length > 0 || meshRemoved.length > 0 || emtreeAdded.length > 0 || emtreeRemoved.length > 0 || excludeAdded.length > 0 || excludeRemoved.length > 0;
+  const result = {
+    index,
+    field,
+    added,
+    removed,
+    hasChanges
+  };
+  if (meshAdded.length > 0 || meshRemoved.length > 0) {
+    result.meshAdded = meshAdded;
+    result.meshRemoved = meshRemoved;
+  }
+  if (emtreeAdded.length > 0 || emtreeRemoved.length > 0) {
+    result.emtreeAdded = emtreeAdded;
+    result.emtreeRemoved = emtreeRemoved;
+  }
+  if (excludeAdded.length > 0 || excludeRemoved.length > 0) {
+    result.excludeAdded = excludeAdded;
+    result.excludeRemoved = excludeRemoved;
+  }
+  if (!block1) {
+    result.isNew = true;
+    result.hasChanges = true;
+  }
+  if (!block2) {
+    result.isRemoved = true;
+    result.hasChanges = true;
+  }
+  return result;
+}
+function computeQueryDiff(query1, query2) {
+  const blocks = [];
+  const maxBlocks = Math.max(query1.blocks.length, query2.blocks.length);
+  for (let i = 0; i < maxBlocks; i++) {
+    const block1 = query1.blocks[i];
+    const block2 = query2.blocks[i];
+    const field = block2?.field ?? block1?.field ?? "all";
+    const blockDiff = compareBlocks(
+      block1?.terms,
+      block2?.terms,
+      i,
+      field
+    );
+    blocks.push(blockDiff);
+  }
+  const filters = {
+    yearFromChanged: query1.filters.yearFrom !== query2.filters.yearFrom,
+    yearToChanged: query1.filters.yearTo !== query2.filters.yearTo,
+    languagesAdded: setDiff(query1.filters.languages ?? [], query2.filters.languages ?? []),
+    languagesRemoved: setDiff(query2.filters.languages ?? [], query1.filters.languages ?? [])
+  };
+  if (filters.yearFromChanged) {
+    filters.oldYearFrom = query1.filters.yearFrom;
+    filters.newYearFrom = query2.filters.yearFrom;
+  }
+  if (filters.yearToChanged) {
+    filters.oldYearTo = query1.filters.yearTo;
+    filters.newYearTo = query2.filters.yearTo;
+  }
+  return { blocks, filters };
+}
+function formatQueryDiff(queryDiff) {
+  const lines = [];
+  lines.push("Query changes:");
+  for (const block of queryDiff.blocks) {
+    const blockNum = block.index + 1;
+    let blockHeader = `  Block ${blockNum} (${block.field})`;
+    if (block.isNew) {
+      blockHeader += " (new block)";
+    } else if (block.isRemoved) {
+      blockHeader += " (removed block)";
+    }
+    if (!block.hasChanges) {
+      lines.push(`${blockHeader}: no changes`);
+    } else {
+      lines.push(`${blockHeader}:`);
+      for (const keyword of block.added) {
+        lines.push(`    + ${keyword}`);
+      }
+      for (const keyword of block.removed) {
+        lines.push(`    - ${keyword}`);
+      }
+      if (block.meshAdded) {
+        for (const term of block.meshAdded) {
+          lines.push(`    + [MeSH] ${term}`);
+        }
+      }
+      if (block.meshRemoved) {
+        for (const term of block.meshRemoved) {
+          lines.push(`    - [MeSH] ${term}`);
+        }
+      }
+      if (block.emtreeAdded) {
+        for (const term of block.emtreeAdded) {
+          lines.push(`    + [Emtree] ${term}`);
+        }
+      }
+      if (block.emtreeRemoved) {
+        for (const term of block.emtreeRemoved) {
+          lines.push(`    - [Emtree] ${term}`);
+        }
+      }
+      if (block.excludeAdded) {
+        for (const term of block.excludeAdded) {
+          lines.push(`    + [exclude] ${term}`);
+        }
+      }
+      if (block.excludeRemoved) {
+        for (const term of block.excludeRemoved) {
+          lines.push(`    - [exclude] ${term}`);
+        }
+      }
+    }
+  }
+  const hasFilterChanges = queryDiff.filters.yearFromChanged || queryDiff.filters.yearToChanged || queryDiff.filters.languagesAdded.length > 0 || queryDiff.filters.languagesRemoved.length > 0;
+  if (hasFilterChanges) {
+    lines.push("");
+    lines.push("  Filters:");
+    if (queryDiff.filters.yearFromChanged) {
+      const oldVal = queryDiff.filters.oldYearFrom ?? "(none)";
+      const newVal = queryDiff.filters.newYearFrom ?? "(none)";
+      lines.push(`    yearFrom: ${oldVal} → ${newVal}`);
+    }
+    if (queryDiff.filters.yearToChanged) {
+      const oldVal = queryDiff.filters.oldYearTo ?? "(none)";
+      const newVal = queryDiff.filters.newYearTo ?? "(none)";
+      lines.push(`    yearTo: ${oldVal} → ${newVal}`);
+    }
+    if (queryDiff.filters.languagesAdded.length > 0 || queryDiff.filters.languagesRemoved.length > 0) {
+      lines.push("    languages:");
+      for (const lang of queryDiff.filters.languagesAdded) {
+        lines.push(`      + ${lang}`);
+      }
+      for (const lang of queryDiff.filters.languagesRemoved) {
+        lines.push(`      - ${lang}`);
+      }
+    }
+  }
+  return lines.join("\n");
+}
 export {
   computeDiff,
+  computeQueryDiff,
   formatDiff,
-  formatDiffJson
+  formatDiffJson,
+  formatQueryDiff
 };
 //# sourceMappingURL=diff.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"diff.js","sources":["../../../src/cli/commands/diff.ts"],"sourcesContent":["import type { Article } from '../../providers/base/types.js';\nimport { getArticleKeys } from './session-utils.js';\n\nexport interface DiffResult {\n  session1Count: number;\n  session2Count: number;\n  added: Article[];\n  removed: Article[];\n  common: Article[];\n}\n\n/**\n * Compute the diff between two sets of articles.\n *\n * Articles are matched by identifiers (DOI, PMID, arXiv ID, Scopus ID, ERIC ID).\n * Two articles are considered the same if they share any identifier.\n * Articles without identifiers cannot be matched.\n */\nexport function computeDiff(session1: Article[], session2: Article[]): DiffResult {\n  // Build a set of all identifier keys from session1\n  const session1Keys = new Set<string>();\n  for (const article of session1) {\n    for (const key of getArticleKeys(article)) {\n      session1Keys.add(key);\n    }\n  }\n\n  // Build a set of all identifier keys from session2\n  const session2Keys = new Set<string>();\n  for (const article of session2) {\n    for (const key of getArticleKeys(article)) {\n      session2Keys.add(key);\n    }\n  }\n\n  // Classify session1 articles as common or removed\n  const common: Article[] = [];\n  const removed: Article[] = [];\n  for (const article of session1) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n      // No identifiers - cannot match, treat as removed\n      removed.push(article);\n      continue;\n    }\n    const isInSession2 = keys.some((key) => session2Keys.has(key));\n    if (isInSession2) {\n      common.push(article);\n    } else {\n      removed.push(article);\n    }\n  }\n\n  // Classify session2 articles as added (those not in session1)\n  const added: Article[] = [];\n  for (const article of session2) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n      // No identifiers - cannot match, treat as added\n      added.push(article);\n      continue;\n    }\n    const isInSession1 = keys.some((key) => session1Keys.has(key));\n    if (!isInSession1) {\n      added.push(article);\n    }\n  }\n\n  return {\n    session1Count: session1.length,\n    session2Count: session2.length,\n    added,\n    removed,\n    common,\n  };\n}\n\nexport type ShowFilter = 'added' | 'removed' | 'common';\n\n/**\n * Extract a year string from publicationDate, or return empty string.\n */\nfunction extractYear(publicationDate: string | undefined): string {\n  if (!publicationDate) return '';\n  const year = publicationDate.substring(0, 4);\n  return /^\\d{4}$/.test(year) ? year : '';\n}\n\n/**\n * Format an article line for display.\n */\nfunction formatArticleLine(prefix: string, article: Article): string {\n  const year = extractYear(article.publicationDate);\n  const yearPart = year ? `[${year}] ` : '';\n  return `  ${prefix} ${yearPart}${article.title}`;\n}\n\n/**\n * Format diff result as human-readable text.\n */\nexport function formatDiff(\n  diff: DiffResult,\n  session1Id: string,\n  session2Id: string,\n  show?: ShowFilter,\n): string {\n  const lines: string[] = [];\n\n  // Header\n  lines.push(`Diff: ${session1Id} → ${session2Id}`);\n  lines.push(`  Session 1: ${diff.session1Count} articles (${session1Id})`);\n  lines.push(`  Session 2: ${diff.session2Count} articles (${session2Id})`);\n  lines.push('');\n\n  // Summary counts\n  lines.push(`  Common:  ${diff.common.length} articles`);\n  lines.push(`  Added:   ${diff.added.length} articles (in ${session2Id} but not ${session1Id})`);\n  lines.push(`  Removed: ${diff.removed.length} articles (in ${session1Id} but not ${session2Id})`);\n\n  // Article lists based on show filter\n  const showAdded = !show || show === 'added';\n  const showRemoved = !show || show === 'removed';\n  const showCommon = show === 'common';\n\n  if (showAdded && diff.added.length > 0) {\n    lines.push('');\n    lines.push(`Added (+${diff.added.length}):`);\n    for (const article of diff.added) {\n      lines.push(formatArticleLine('+', article));\n    }\n  }\n\n  if (showRemoved && diff.removed.length > 0) {\n    lines.push('');\n    lines.push(`Removed (-${diff.removed.length}):`);\n    for (const article of diff.removed) {\n      lines.push(formatArticleLine('-', article));\n    }\n  }\n\n  if (showCommon && diff.common.length > 0) {\n    lines.push('');\n    lines.push(`Common (${diff.common.length}):`);\n    for (const article of diff.common) {\n      lines.push(formatArticleLine('=', article));\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format diff result as JSON.\n */\ninterface DiffJsonOutput {\n  session1: string;\n  session2: string;\n  summary: {\n    session1Count: number;\n    session2Count: number;\n    commonCount: number;\n    addedCount: number;\n    removedCount: number;\n  };\n  added?: Article[];\n  removed?: Article[];\n  common?: Article[];\n}\n\nexport function formatDiffJson(\n  diff: DiffResult,\n  session1Id: string,\n  session2Id: string,\n  show?: ShowFilter,\n): string {\n  const result: DiffJsonOutput = {\n    session1: session1Id,\n    session2: session2Id,\n    summary: {\n      session1Count: diff.session1Count,\n      session2Count: diff.session2Count,\n      commonCount: diff.common.length,\n      addedCount: diff.added.length,\n      removedCount: diff.removed.length,\n    },\n  };\n\n  if (!show || show === 'added') {\n    result.added = diff.added;\n  }\n  if (!show || show === 'removed') {\n    result.removed = diff.removed;\n  }\n  if (!show || show === 'common') {\n    result.common = diff.common;\n  }\n\n  return JSON.stringify(result, null, 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+{"version":3,"file":"diff.js","sources":["../../../src/cli/commands/diff.ts"],"sourcesContent":["import type { Article } from '../../providers/base/types.js';\nimport type { QueryAST, FieldType, TermBlock } from '../../query/types.js';\nimport { getArticleKeys } from './session-utils.js';\n\nexport interface DiffResult {\n  session1Count: number;\n  session2Count: number;\n  added: Article[];\n  removed: Article[];\n  common: Article[];\n}\n\n/**\n * Compute the diff between two sets of articles.\n *\n * Articles are matched by identifiers (DOI, PMID, arXiv ID, Scopus ID, ERIC ID).\n * Two articles are considered the same if they share any identifier.\n * Articles without identifiers cannot be matched.\n */\nexport function computeDiff(session1: Article[], session2: Article[]): DiffResult {\n  // Build a set of all identifier keys from session1\n  const session1Keys = new Set<string>();\n  for (const article of session1) {\n    for (const key of getArticleKeys(article)) {\n      session1Keys.add(key);\n    }\n  }\n\n  // Build a set of all identifier keys from session2\n  const session2Keys = new Set<string>();\n  for (const article of session2) {\n    for (const key of getArticleKeys(article)) {\n      session2Keys.add(key);\n    }\n  }\n\n  // Classify session1 articles as common or removed\n  const common: Article[] = [];\n  const removed: Article[] = [];\n  for (const article of session1) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n      // No identifiers - cannot match, treat as removed\n      removed.push(article);\n      continue;\n    }\n    const isInSession2 = keys.some((key) => session2Keys.has(key));\n    if (isInSession2) {\n      common.push(article);\n    } else {\n      removed.push(article);\n    }\n  }\n\n  // Classify session2 articles as added (those not in session1)\n  const added: Article[] = [];\n  for (const article of session2) {\n    const keys = getArticleKeys(article);\n    if (keys.length === 0) {\n      // No identifiers - cannot match, treat as added\n      added.push(article);\n      continue;\n    }\n    const isInSession1 = keys.some((key) => session1Keys.has(key));\n    if (!isInSession1) {\n      added.push(article);\n    }\n  }\n\n  return {\n    session1Count: session1.length,\n    session2Count: session2.length,\n    added,\n    removed,\n    common,\n  };\n}\n\nexport type ShowFilter = 'added' | 'removed' | 'common';\n\n/**\n * Extract a year string from publicationDate, or return empty string.\n */\nfunction extractYear(publicationDate: string | undefined): string {\n  if (!publicationDate) return '';\n  const year = publicationDate.substring(0, 4);\n  return /^\\d{4}$/.test(year) ? year : '';\n}\n\n/**\n * Format an article line for display.\n */\nfunction formatArticleLine(prefix: string, article: Article): string {\n  const year = extractYear(article.publicationDate);\n  const yearPart = year ? `[${year}] ` : '';\n  return `  ${prefix} ${yearPart}${article.title}`;\n}\n\n/**\n * Options for formatting diff with query information.\n */\nexport interface FormatDiffOptions {\n  queryDiff?: QueryDiff | undefined;\n  noQueryDiff?: boolean | undefined;\n  showQueryDiffPlaceholder?: boolean | undefined;\n}\n\n/**\n * Format diff result as human-readable text.\n */\nexport function formatDiff(\n  diff: DiffResult,\n  session1Id: string,\n  session2Id: string,\n  show?: ShowFilter,\n  options?: FormatDiffOptions,\n): string {\n  const lines: string[] = [];\n\n  // Header\n  lines.push(`Diff: ${session1Id} → ${session2Id}`);\n  lines.push(`  Session 1: ${diff.session1Count} articles (${session1Id})`);\n  lines.push(`  Session 2: ${diff.session2Count} articles (${session2Id})`);\n  lines.push('');\n\n  // Query changes section (if available and not disabled)\n  const shouldShowQueryDiff = options?.queryDiff && !options?.noQueryDiff;\n  const shouldShowPlaceholder = options?.showQueryDiffPlaceholder && !options?.queryDiff && !options?.noQueryDiff;\n\n  if (shouldShowPlaceholder) {\n    lines.push('Query changes: (query data not available)');\n    lines.push('');\n  } else if (shouldShowQueryDiff) {\n    lines.push(formatQueryDiff(options.queryDiff!));\n    lines.push('');\n    lines.push('Result changes:');\n  }\n\n  // Summary counts\n  lines.push(`  Common:  ${diff.common.length} articles`);\n  lines.push(`  Added:   ${diff.added.length} articles (in ${session2Id} but not ${session1Id})`);\n  lines.push(`  Removed: ${diff.removed.length} articles (in ${session1Id} but not ${session2Id})`);\n\n  // Article lists based on show filter\n  const showAdded = !show || show === 'added';\n  const showRemoved = !show || show === 'removed';\n  const showCommon = show === 'common';\n\n  if (showAdded && diff.added.length > 0) {\n    lines.push('');\n    lines.push(`Added (+${diff.added.length}):`);\n    for (const article of diff.added) {\n      lines.push(formatArticleLine('+', article));\n    }\n  }\n\n  if (showRemoved && diff.removed.length > 0) {\n    lines.push('');\n    lines.push(`Removed (-${diff.removed.length}):`);\n    for (const article of diff.removed) {\n      lines.push(formatArticleLine('-', article));\n    }\n  }\n\n  if (showCommon && diff.common.length > 0) {\n    lines.push('');\n    lines.push(`Common (${diff.common.length}):`);\n    for (const article of diff.common) {\n      lines.push(formatArticleLine('=', article));\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Format diff result as JSON.\n */\ninterface DiffJsonOutput {\n  session1: string;\n  session2: string;\n  summary: {\n    session1Count: number;\n    session2Count: number;\n    commonCount: number;\n    addedCount: number;\n    removedCount: number;\n  };\n  queryDiff?: QueryDiff;\n  added?: Article[];\n  removed?: Article[];\n  common?: Article[];\n}\n\nexport function formatDiffJson(\n  diff: DiffResult,\n  session1Id: string,\n  session2Id: string,\n  show?: ShowFilter,\n  options?: FormatDiffOptions,\n): string {\n  const result: DiffJsonOutput = {\n    session1: session1Id,\n    session2: session2Id,\n    summary: {\n      session1Count: diff.session1Count,\n      session2Count: diff.session2Count,\n      commonCount: diff.common.length,\n      addedCount: diff.added.length,\n      removedCount: diff.removed.length,\n    },\n  };\n\n  // Add queryDiff if available and not disabled\n  if (options?.queryDiff && !options?.noQueryDiff) {\n    result.queryDiff = options.queryDiff;\n  }\n\n  if (!show || show === 'added') {\n    result.added = diff.added;\n  }\n  if (!show || show === 'removed') {\n    result.removed = diff.removed;\n  }\n  if (!show || show === 'common') {\n    result.common = diff.common;\n  }\n\n  return JSON.stringify(result, null, 2);\n}\n\n/**\n * Diff result for a single query block.\n */\nexport interface BlockDiff {\n  index: number;\n  field: FieldType;\n  added: string[];\n  removed: string[];\n  meshAdded?: string[];\n  meshRemoved?: string[];\n  emtreeAdded?: string[];\n  emtreeRemoved?: string[];\n  excludeAdded?: string[];\n  excludeRemoved?: string[];\n  hasChanges: boolean;\n  isNew?: boolean;\n  isRemoved?: boolean;\n}\n\n/**\n * Diff result for query filters.\n */\nexport interface FilterDiff {\n  yearFromChanged: boolean;\n  oldYearFrom?: number | undefined;\n  newYearFrom?: number | undefined;\n  yearToChanged: boolean;\n  oldYearTo?: number | undefined;\n  newYearTo?: number | undefined;\n  languagesAdded: string[];\n  languagesRemoved: string[];\n}\n\n/**\n * Complete query diff result.\n */\nexport interface QueryDiff {\n  blocks: BlockDiff[];\n  filters: FilterDiff;\n}\n\n/**\n * Compute the set difference: elements in arr2 not in arr1.\n */\nfunction setDiff(arr1: string[], arr2: string[]): string[] {\n  const set1 = new Set(arr1);\n  return arr2.filter((item) => !set1.has(item));\n}\n\n/**\n * Compare two query blocks and return the differences.\n */\nfunction compareBlocks(\n  block1: TermBlock | undefined,\n  block2: TermBlock | undefined,\n  index: number,\n  field: FieldType,\n): BlockDiff {\n  const emptyTerms = { keywords: [] as string[], mesh: [] as string[], emtree: [] as string[], exclude: [] as string[] };\n  const terms1 = block1 ?? emptyTerms;\n  const terms2 = block2 ?? emptyTerms;\n\n  const added = setDiff(terms1.keywords, terms2.keywords);\n  const removed = setDiff(terms2.keywords, terms1.keywords);\n  const meshAdded = setDiff(terms1.mesh ?? [], terms2.mesh ?? []);\n  const meshRemoved = setDiff(terms2.mesh ?? [], terms1.mesh ?? []);\n  const emtreeAdded = setDiff(terms1.emtree ?? [], terms2.emtree ?? []);\n  const emtreeRemoved = setDiff(terms2.emtree ?? [], terms1.emtree ?? []);\n  const excludeAdded = setDiff(terms1.exclude ?? [], terms2.exclude ?? []);\n  const excludeRemoved = setDiff(terms2.exclude ?? [], terms1.exclude ?? []);\n\n  const hasChanges =\n    added.length > 0 ||\n    removed.length > 0 ||\n    meshAdded.length > 0 ||\n    meshRemoved.length > 0 ||\n    emtreeAdded.length > 0 ||\n    emtreeRemoved.length > 0 ||\n    excludeAdded.length > 0 ||\n    excludeRemoved.length > 0;\n\n  const result: BlockDiff = {\n    index,\n    field,\n    added,\n    removed,\n    hasChanges,\n  };\n\n  if (meshAdded.length > 0 || meshRemoved.length > 0) {\n    result.meshAdded = meshAdded;\n    result.meshRemoved = meshRemoved;\n  }\n  if (emtreeAdded.length > 0 || emtreeRemoved.length > 0) {\n    result.emtreeAdded = emtreeAdded;\n    result.emtreeRemoved = emtreeRemoved;\n  }\n  if (excludeAdded.length > 0 || excludeRemoved.length > 0) {\n    result.excludeAdded = excludeAdded;\n    result.excludeRemoved = excludeRemoved;\n  }\n\n  if (!block1) {\n    result.isNew = true;\n    result.hasChanges = true;\n  }\n  if (!block2) {\n    result.isRemoved = true;\n    result.hasChanges = true;\n  }\n\n  return result;\n}\n\n/**\n * Compute the diff between two QueryAST objects.\n */\nexport function computeQueryDiff(query1: QueryAST, query2: QueryAST): QueryDiff {\n  const blocks: BlockDiff[] = [];\n\n  const maxBlocks = Math.max(query1.blocks.length, query2.blocks.length);\n\n  for (let i = 0; i < maxBlocks; i++) {\n    const block1 = query1.blocks[i];\n    const block2 = query2.blocks[i];\n\n    const field = block2?.field ?? block1?.field ?? 'all';\n    const blockDiff = compareBlocks(\n      block1?.terms,\n      block2?.terms,\n      i,\n      field,\n    );\n    blocks.push(blockDiff);\n  }\n\n  // Compare filters\n  const filters: FilterDiff = {\n    yearFromChanged: query1.filters.yearFrom !== query2.filters.yearFrom,\n    yearToChanged: query1.filters.yearTo !== query2.filters.yearTo,\n    languagesAdded: setDiff(query1.filters.languages ?? [], query2.filters.languages ?? []),\n    languagesRemoved: setDiff(query2.filters.languages ?? [], query1.filters.languages ?? []),\n  };\n\n  if (filters.yearFromChanged) {\n    filters.oldYearFrom = query1.filters.yearFrom;\n    filters.newYearFrom = query2.filters.yearFrom;\n  }\n  if (filters.yearToChanged) {\n    filters.oldYearTo = query1.filters.yearTo;\n    filters.newYearTo = query2.filters.yearTo;\n  }\n\n  return { blocks, filters };\n}\n\n/**\n * Format query diff as human-readable text.\n */\nexport function formatQueryDiff(queryDiff: QueryDiff): string {\n  const lines: string[] = [];\n\n  lines.push('Query changes:');\n\n  // Format block changes\n  for (const block of queryDiff.blocks) {\n    const blockNum = block.index + 1;\n    let blockHeader = `  Block ${blockNum} (${block.field})`;\n    if (block.isNew) {\n      blockHeader += ' (new block)';\n    } else if (block.isRemoved) {\n      blockHeader += ' (removed block)';\n    }\n\n    if (!block.hasChanges) {\n      lines.push(`${blockHeader}: no changes`);\n    } else {\n      lines.push(`${blockHeader}:`);\n\n      // Added keywords\n      for (const keyword of block.added) {\n        lines.push(`    + ${keyword}`);\n      }\n\n      // Removed keywords\n      for (const keyword of block.removed) {\n        lines.push(`    - ${keyword}`);\n      }\n\n      // MeSH changes\n      if (block.meshAdded) {\n        for (const term of block.meshAdded) {\n          lines.push(`    + [MeSH] ${term}`);\n        }\n      }\n      if (block.meshRemoved) {\n        for (const term of block.meshRemoved) {\n          lines.push(`    - [MeSH] ${term}`);\n        }\n      }\n\n      // Emtree changes\n      if (block.emtreeAdded) {\n        for (const term of block.emtreeAdded) {\n          lines.push(`    + [Emtree] ${term}`);\n        }\n      }\n      if (block.emtreeRemoved) {\n        for (const term of block.emtreeRemoved) {\n          lines.push(`    - [Emtree] ${term}`);\n        }\n      }\n\n      // Exclude changes\n      if (block.excludeAdded) {\n        for (const term of block.excludeAdded) {\n          lines.push(`    + [exclude] ${term}`);\n        }\n      }\n      if (block.excludeRemoved) {\n        for (const term of block.excludeRemoved) {\n          lines.push(`    - [exclude] ${term}`);\n        }\n      }\n    }\n  }\n\n  // Format filter changes\n  const hasFilterChanges =\n    queryDiff.filters.yearFromChanged ||\n    queryDiff.filters.yearToChanged ||\n    queryDiff.filters.languagesAdded.length > 0 ||\n    queryDiff.filters.languagesRemoved.length > 0;\n\n  if (hasFilterChanges) {\n    lines.push('');\n    lines.push('  Filters:');\n\n    if (queryDiff.filters.yearFromChanged) {\n      const oldVal = queryDiff.filters.oldYearFrom ?? 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package/dist/cli/commands/query/init.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands/query/init.js

@@ -10,6 +10,8 @@ query:
         - "search term 2"
       # mesh:                 # PubMed MeSH terms (optional)
       #   - "MeSH Heading"
+      # eric:                 # ERIC Descriptors (optional, ERIC only)
+      #   - "ERIC Descriptor"
       exclude: []             # Terms to exclude (NOT operator)
       # Tip: Use exclude to filter out false matches from short keywords/acronyms
       # exclude:

package/dist/cli/commands/query/init.js.map

@@ -1 +1 @@
-{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/query/init.ts"],"sourcesContent":["/**\n * Query init command implementation.\n *\n * Generates a skeleton YAML query file with helpful comments.\n */\nimport { writeFile as fsWriteFile, access } from \"node:fs/promises\";\n\n/**\n * The YAML template string with comments preserved.\n * This is a raw string (not generated by a YAML library) so comments are kept.\n */\n// prettier-ignore\nconst QUERY_TEMPLATE =\n  \"name: my_search\\n\" +\n  \"description: \\\"\\\"\\n\" +\n  \"\\n\" +\n  \"query:\\n\" +\n  \"  - field: title_abstract    # title, abstract, title_abstract, author, keyword, all\\n\" +\n  \"    terms:\\n\" +\n  \"      keywords:\\n\" +\n  \"        - \\\"search term 1\\\"\\n\" +\n  \"        - \\\"search term 2\\\"\\n\" +\n  \"      # mesh:                 # PubMed MeSH terms (optional)\\n\" +\n  \"      #   - \\\"MeSH Heading\\\"\\n\" +\n  \"      exclude: []             # Terms to exclude (NOT operator)\\n\" +\n  \"      # Tip: Use exclude to filter out false matches from short keywords/acronyms\\n\" +\n  \"      # exclude:\\n\" +\n  \"      #   - \\\"unwanted term\\\"\\n\" +\n  \"      #   - \\\"irrelevant topic\\\"\\n\" +\n  \"    operator: OR             # How to combine terms within this block\\n\" +\n  \"\\n\" +\n  \"  # Add more blocks — blocks are AND'd together\\n\" +\n  \"  # - field: title_abstract\\n\" +\n  \"  #   terms:\\n\" +\n  \"  #     keywords:\\n\" +\n  \"  #       - \\\"another term\\\"\\n\" +\n  \"  #   operator: OR\\n\" +\n  \"\\n\" +\n  \"# filters:                   # Optional: apply to all databases\\n\" +\n  \"#   year_from: 2020\\n\" +\n  \"#   year_to: 2026\\n\" +\n  \"#   language:\\n\" +\n  \"#     - en\\n\" +\n  \"#   publication_types:\\n\" +\n  \"#     exclude:\\n\" +\n  \"#       - \\\"Review\\\"\\n\" +\n  \"#       - \\\"Comment\\\"\\n\" +\n  \"\\n\" +\n  \"# overrides:                 # Optional: database-specific settings\\n\" +\n  \"#   pubmed:\\n\" +\n  \"#     filters:\\n\" +\n  \"#       publication_types:\\n\" +\n  \"#         exclude:\\n\" +\n  \"#           - \\\"Letter\\\"\\n\";\n\n/**\n * Generate the query template YAML string.\n *\n * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(): string {\n  return QUERY_TEMPLATE;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n * @param options - Output options\n * @param options.output - File path to write to (if omitted, returns template in message)\n * @param options.force - Whether to overwrite existing files\n * @returns Result with success status and message\n */\nexport async function writeQueryTemplate(options: {\n  output?: string;\n  force?: boolean;\n}): Promise<{ success: boolean; message: string }> {\n  const template = generateQueryTemplate();\n\n  if (!options.output) {\n    // No output file specified, return template as message\n    return { success: true, message: template };\n  }\n\n  // Check if file exists (unless force is set)\n  if (!options.force) {\n    try {\n      await access(options.output);\n      // File exists and force is not set\n      return {\n        success: false,\n        message: `File already exists: ${options.output}. Use --force to overwrite.`,\n      };\n    } catch {\n      // File does not exist, proceed\n    }\n  }\n\n  // Write to file\n  await fsWriteFile(options.output, template, \"utf-8\");\n  return {\n    success: true,\n    message: `Template written to ${options.output}`,\n  };\n}\n"],"names":["fsWriteFile"],"mappings":";AAYA,MAAM,iBACJ;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AA+CK,SAAS,wBAAgC;AAC9C,SAAO;AACT;AAUA,eAAsB,mBAAmB,SAGU;AACjD,QAAM,WAAW,sBAAA;AAEjB,MAAI,CAAC,QAAQ,QAAQ;AAEnB,WAAO,EAAE,SAAS,MAAM,SAAS,SAAA;AAAA,EACnC;AAGA,MAAI,CAAC,QAAQ,OAAO;AAClB,QAAI;AACF,YAAM,OAAO,QAAQ,MAAM;AAE3B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,wBAAwB,QAAQ,MAAM;AAAA,MAAA;AAAA,IAEnD,QAAQ;AAAA,IAER;AAAA,EACF;AAGA,QAAMA,UAAY,QAAQ,QAAQ,UAAU,OAAO;AACnD,SAAO;AAAA,IACL,SAAS;AAAA,IACT,SAAS,uBAAuB,QAAQ,MAAM;AAAA,EAAA;AAElD;"}
+{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/query/init.ts"],"sourcesContent":["/**\n * Query init command implementation.\n *\n * Generates a skeleton YAML query file with helpful comments.\n */\nimport { writeFile as fsWriteFile, access } from \"node:fs/promises\";\n\n/**\n * The YAML template string with comments preserved.\n * This is a raw string (not generated by a YAML library) so comments are kept.\n */\n// prettier-ignore\nconst QUERY_TEMPLATE =\n  \"name: my_search\\n\" +\n  \"description: \\\"\\\"\\n\" +\n  \"\\n\" +\n  \"query:\\n\" +\n  \"  - field: title_abstract    # title, abstract, title_abstract, author, keyword, all\\n\" +\n  \"    terms:\\n\" +\n  \"      keywords:\\n\" +\n  \"        - \\\"search term 1\\\"\\n\" +\n  \"        - \\\"search term 2\\\"\\n\" +\n  \"      # mesh:                 # PubMed MeSH terms (optional)\\n\" +\n  \"      #   - \\\"MeSH Heading\\\"\\n\" +\n  \"      # eric:                 # ERIC Descriptors (optional, ERIC only)\\n\" +\n  \"      #   - \\\"ERIC Descriptor\\\"\\n\" +\n  \"      exclude: []             # Terms to exclude (NOT operator)\\n\" +\n  \"      # Tip: Use exclude to filter out false matches from short keywords/acronyms\\n\" +\n  \"      # exclude:\\n\" +\n  \"      #   - \\\"unwanted term\\\"\\n\" +\n  \"      #   - \\\"irrelevant topic\\\"\\n\" +\n  \"    operator: OR             # How to combine terms within this block\\n\" +\n  \"\\n\" +\n  \"  # Add more blocks — blocks are AND'd together\\n\" +\n  \"  # - field: title_abstract\\n\" +\n  \"  #   terms:\\n\" +\n  \"  #     keywords:\\n\" +\n  \"  #       - \\\"another term\\\"\\n\" +\n  \"  #   operator: OR\\n\" +\n  \"\\n\" +\n  \"# filters:                   # Optional: apply to all databases\\n\" +\n  \"#   year_from: 2020\\n\" +\n  \"#   year_to: 2026\\n\" +\n  \"#   language:\\n\" +\n  \"#     - en\\n\" +\n  \"#   publication_types:\\n\" +\n  \"#     exclude:\\n\" +\n  \"#       - \\\"Review\\\"\\n\" +\n  \"#       - \\\"Comment\\\"\\n\" +\n  \"\\n\" +\n  \"# overrides:                 # Optional: database-specific settings\\n\" +\n  \"#   pubmed:\\n\" +\n  \"#     filters:\\n\" +\n  \"#       publication_types:\\n\" +\n  \"#         exclude:\\n\" +\n  \"#           - \\\"Letter\\\"\\n\";\n\n/**\n * Generate the query template YAML string.\n *\n * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(): string {\n  return QUERY_TEMPLATE;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n * @param options - Output options\n * @param options.output - File path to write to (if omitted, returns template in message)\n * @param options.force - Whether to overwrite existing files\n * @returns Result with success status and message\n */\nexport async function writeQueryTemplate(options: {\n  output?: string;\n  force?: boolean;\n}): Promise<{ success: boolean; message: string }> {\n  const template = generateQueryTemplate();\n\n  if (!options.output) {\n    // No output file specified, return template as message\n    return { success: true, message: template };\n  }\n\n  // Check if file exists (unless force is set)\n  if (!options.force) {\n    try {\n      await access(options.output);\n      // File exists and force is not set\n      return {\n        success: false,\n        message: `File already exists: ${options.output}. Use --force to overwrite.`,\n      };\n    } catch {\n      // File does not exist, proceed\n    }\n  }\n\n  // Write to file\n  await fsWriteFile(options.output, template, \"utf-8\");\n  return {\n    success: true,\n    message: `Template written to ${options.output}`,\n  };\n}\n"],"names":["fsWriteFile"],"mappings":";AAYA,MAAM,iBACJ;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAiDK,SAAS,wBAAgC;AAC9C,SAAO;AACT;AAUA,eAAsB,mBAAmB,SAGU;AACjD,QAAM,WAAW,sBAAA;AAEjB,MAAI,CAAC,QAAQ,QAAQ;AAEnB,WAAO,EAAE,SAAS,MAAM,SAAS,SAAA;AAAA,EACnC;AAGA,MAAI,CAAC,QAAQ,OAAO;AAClB,QAAI;AACF,YAAM,OAAO,QAAQ,MAAM;AAE3B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,wBAAwB,QAAQ,MAAM;AAAA,MAAA;AAAA,IAEnD,QAAQ;AAAA,IAER;AAAA,EACF;AAGA,QAAMA,UAAY,QAAQ,QAAQ,UAAU,OAAO;AACnD,SAAO;AAAA,IACL,SAAS;AAAA,IACT,SAAS,uBAAuB,QAAQ,MAAM;AAAA,EAAA;AAElD;"}

package/dist/cli/commands/register.js

@@ -98,7 +98,7 @@ function getAlternativeIds(article) {
   return ids;
 }
 async function hasReviewFile(sessionId, sessionsDir) {
-  const reviewsPath = join(sessionsDir, sessionId, "reviews.yaml");
+  const reviewsPath = join(sessionsDir, sessionId, ".internal", "reviews.yaml");
   try {
     await access(reviewsPath, constants.R_OK);
     return true;
@@ -107,7 +107,7 @@ async function hasReviewFile(sessionId, sessionsDir) {
   }
 }
 async function loadReviewFile(sessionId, sessionsDir) {
-  const reviewsPath = join(sessionsDir, sessionId, "reviews.yaml");
+  const reviewsPath = join(sessionsDir, sessionId, ".internal", "reviews.yaml");
   const content = await readFile(reviewsPath, "utf-8");
   return parse(content);
 }

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

@@ -1 +1 @@
-{"version":3,"file":"register.js","sources":["../../../src/cli/commands/register.ts"],"sourcesContent":["/**\n * Register command for reference-manager integration.\n * Registers search results with reference-manager CLI.\n */\n\nimport { join } from 'node:path';\nimport { readFile, access } from 'node:fs/promises';\nimport { constants } from 'node:fs';\nimport { createInterface } from 'node:readline';\nimport { parse as parseYaml } from 'yaml';\nimport type { ProviderName, Article, Author } from '../../providers/base/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\nimport { classifyStatus, type ReviewFile } from './review/types.js';\n\nexport interface RegisterCommandOptions {\n  sessionId: string;\n  providers?: ProviderName[];\n  dryRun: boolean;\n  withAbstracts: boolean;\n  /** Register only reviewed articles with finalDecision='include' */\n  reviewed?: boolean;\n  /** Register all articles, ignoring reviews */\n  all?: boolean;\n  /** Skip confirmation prompts */\n  force?: boolean;\n  /** Suppress tips and suggestions */\n  quiet?: boolean;\n}\n\nexport interface CommandLineOptions {\n  db?: string | undefined;\n  dryRun?: boolean | undefined;\n  withAbstracts?: boolean | undefined;\n  reviewed?: boolean | undefined;\n  all?: boolean | undefined;\n  force?: boolean | undefined;\n  quiet?: boolean | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\n/**\n * Parse command line options into RegisterCommandOptions.\n */\nexport function parseRegisterOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): RegisterCommandOptions {\n  const result: RegisterCommandOptions = {\n    sessionId,\n    dryRun: options.dryRun ?? false,\n    withAbstracts: options.withAbstracts ?? false,\n    reviewed: options.reviewed ?? false,\n    all: options.all ?? false,\n    force: options.force ?? false,\n    quiet: options.quiet ?? false,\n  };\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  return result;\n}\n\n/**\n * Validate register command input.\n */\nexport function validateRegisterInput(options: RegisterCommandOptions): 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\n/**\n * Format registration summary for CLI output.\n */\nexport function formatRegistrationSummary(summary: {\n  total: number;\n  added: number;\n  skipped: number;\n  failed: number;\n  noId: number;\n}): string {\n  const lines: string[] = ['Registration complete:'];\n\n  // Added\n  lines.push(`  ✓ ${summary.added} added`);\n\n  // Duplicates (skipped)\n  if (summary.skipped > 0) {\n    lines.push(`  ⚠ ${summary.skipped} duplicates (already in library)`);\n  }\n\n  // Failed\n  if (summary.failed > 0) {\n    lines.push(`  ✗ ${summary.failed} failed`);\n  }\n\n  // No ID (skipped)\n  if (summary.noId > 0) {\n    lines.push(`  - ${summary.noId} skipped (no identifier)`);\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get registration identifier for an article.\n * PMID is preferred over DOI for better metadata quality.\n */\nfunction getRegistrationId(article: Article): string | null {\n  if (article.pmid) {\n    return `pmid:${article.pmid}`;\n  }\n  if (article.doi) {\n    return article.doi;\n  }\n  return null;\n}\n\n/**\n * Format dry run output showing what would be registered.\n */\nexport function formatDryRunOutput(articles: Article[]): string {\n  const withId: Array<{ article: Article; id: string }> = [];\n  const withoutId: Article[] = [];\n\n  for (const article of articles) {\n    const id = getRegistrationId(article);\n    if (id) {\n      withId.push({ article, id });\n    } else {\n      withoutId.push(article);\n    }\n  }\n\n  const lines: string[] = [];\n\n  // Summary\n  lines.push(\n    `Would register ${withId.length} reference${withId.length !== 1 ? 's' : ''}:`\n  );\n\n  // List articles with IDs\n  for (const { id, article } of withId) {\n    const title = article.title.length > 60\n      ? article.title.substring(0, 57) + '...'\n      : article.title;\n    lines.push(`  - ${id}: ${title}`);\n  }\n\n  // Details about articles without DOI/PMID\n  if (withoutId.length > 0) {\n    lines.push('');\n    lines.push(\n      `${withoutId.length} article${withoutId.length !== 1 ? 's' : ''} will be skipped (no DOI or PMID):`\n    );\n\n    const maxDisplay = 10;\n    const displayed = withoutId.slice(0, maxDisplay);\n\n    for (const article of displayed) {\n      const truncatedTitle = article.title.length > 50\n        ? article.title.substring(0, 50) + '...'\n        : article.title;\n\n      const altIds = getAlternativeIds(article);\n      const hasAltIds = altIds.length > 0 ? `, has: ${altIds.join(', ')}` : '';\n\n      lines.push(`  - \"${truncatedTitle}\" (source: ${article.source}${hasAltIds})`);\n    }\n\n    if (withoutId.length > maxDisplay) {\n      lines.push(`  ... and ${withoutId.length - maxDisplay} more`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get alternative (non-DOI/PMID) identifiers for an article.\n */\nfunction getAlternativeIds(article: Article): string[] {\n  const ids: string[] = [];\n  if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n  if (article.ericId) ids.push(`eric:${article.ericId}`);\n  if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n  return ids;\n}\n\n/**\n * Summary of review decisions for a session.\n */\nexport interface ReviewSummary {\n  /** Total articles in review file */\n  total: number;\n  /** Articles with finalDecision='include' */\n  included: number;\n  /** Articles with finalDecision='exclude' */\n  excluded: number;\n  /** Articles without finalDecision (pending, needs-final, conflicting) */\n  pending: number;\n}\n\n/**\n * Check if a session has a reviews.yaml file.\n */\nexport async function hasReviewFile(sessionId: string, sessionsDir: string): Promise<boolean> {\n  const reviewsPath = join(sessionsDir, sessionId, 'reviews.yaml');\n  try {\n    await access(reviewsPath, constants.R_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Load and parse the review file for a session.\n */\nasync function loadReviewFile(sessionId: string, sessionsDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionsDir, sessionId, 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Get review summary (counts) for a session.\n * Throws if reviews.yaml does not exist.\n */\nexport async function getReviewSummary(sessionId: string, sessionsDir: string): Promise<ReviewSummary> {\n  const reviewFile = await loadReviewFile(sessionId, sessionsDir);\n  const articles = reviewFile.articles ?? [];\n\n  const summary: ReviewSummary = {\n    total: articles.length,\n    included: 0,\n    excluded: 0,\n    pending: 0,\n  };\n\n  for (const article of articles) {\n    const status = classifyStatus(article);\n\n    if (status === 'finalized') {\n      if (article.finalDecision === 'include') {\n        summary.included++;\n      } else {\n        summary.excluded++;\n      }\n    } else {\n      // pending, needs-final, conflicting all count as pending for registration\n      summary.pending++;\n    }\n  }\n\n  return summary;\n}\n\n/**\n * Parse author name string into Author object.\n * Simple heuristic: last word is family name, rest is given name.\n */\nfunction parseAuthorName(name: string): Author {\n  const parts = name.trim().split(/\\s+/);\n  if (parts.length === 1) {\n    return { family: parts[0] ?? '' };\n  }\n  // Last part is family name (most common pattern in scientific citations)\n  const family = parts.pop() ?? '';\n  const given = parts.join(' ');\n  return { family, given };\n}\n\n/**\n * Get articles with finalDecision='include' from review file.\n * Converts from ArticleEntry format to Article format.\n *\n * @throws Error if mergedFrom is missing or empty (indicates legacy review file)\n */\nexport async function getIncludedArticles(sessionId: string, sessionsDir: string): Promise<Article[]> {\n  const reviewFile = await loadReviewFile(sessionId, sessionsDir);\n  const articles = reviewFile.articles ?? [];\n\n  return articles\n    .filter((entry) => entry.finalDecision === 'include')\n    .map((entry): Article => {\n      // Validate mergedFrom exists\n      if (!entry.mergedFrom) {\n        throw new Error(\n          `Article \"${entry.title}\" has mergedFrom missing. ` +\n            `This may be a legacy review file created before source tracking was fixed. ` +\n            `Please re-run 'review init' to regenerate the review file with source tracking.`\n        );\n      }\n      if (entry.mergedFrom.length === 0) {\n        throw new Error(\n          `Article \"${entry.title}\" has empty mergedFrom array. ` +\n            `This is an invalid state - please re-run 'review init' to regenerate.`\n        );\n      }\n\n      const authors: Author[] = entry.authors\n        ? entry.authors.split(/,\\s*/).map(parseAuthorName)\n        : [];\n\n      // Get source from the first entry in mergedFrom\n      const source = entry.mergedFrom[0]!.source as ProviderName;\n\n      const article: Article = {\n        title: entry.title,\n        authors,\n        source,\n        retrievedAt: new Date().toISOString(),\n      };\n      // Only set optional fields if they have values\n      if (entry.doi) article.doi = entry.doi;\n      if (entry.pmid) article.pmid = entry.pmid;\n      if (entry.scopusId) article.scopusId = entry.scopusId;\n      if (entry.arxivId) article.arxivId = entry.arxivId;\n      if (entry.ericId) article.ericId = entry.ericId;\n      if (entry.abstract) article.abstract = entry.abstract;\n      if (entry.year) article.publicationDate = entry.year;\n      return article;\n    });\n}\n\n/**\n * Format message when reviews exist but no flag specified.\n */\nexport function formatReviewRequiredMessage(summary: ReviewSummary, sessionId: string): string {\n  return `This session has a review file.\n  Status: ${summary.included} include / ${summary.excluded} exclude / ${summary.pending} pending\n\nPlease specify which articles to register:\n  --reviewed   Register ${summary.included} included articles\n  --all        Register all ${summary.total} articles (ignore reviews)\n\nExample:\n  search-hub register ${sessionId} --reviewed`;\n}\n\n/**\n * Format error when --reviewed used but no articles are included.\n */\nexport function formatNoIncludedArticlesError(summary: ReviewSummary, sessionId: string): string {\n  return `Error: No articles marked as 'include' in reviews.\n  Status: ${summary.included} include / ${summary.excluded} exclude / ${summary.pending} pending\n\nRun 'search-hub review status ${sessionId}' for details.`;\n}\n\n/**\n * Format warning when pending articles exist with --reviewed.\n */\nexport function formatPendingWarning(summary: ReviewSummary): string {\n  const articleWord = summary.pending === 1 ? 'article' : 'articles';\n  return `Warning: ${summary.pending} ${articleWord} still pending review (will be skipped).\nRegistering ${summary.included} included articles...\n\nProceed? [Y/n]`;\n}\n\n/**\n * Format tip about review workflow for users who haven't used it.\n */\nexport function formatReviewWorkflowTip(sessionId: string): string {\n  return `\nTip: For systematic reviews, consider using the review workflow:\n  1. search-hub review init ${sessionId}\n  2. (AI/human review in reviews.yaml)\n  3. search-hub register ${sessionId} --reviewed`;\n}\n\n\n/**\n * Format note when --all is used with reviews.yaml present.\n */\nexport function formatIgnoringReviewsNote(total: number): string {\n  return `Note: Ignoring review decisions. Registering all ${total} articles.`;\n}\n\n/**\n * Prompt user for Y/n confirmation.\n * Returns true if user confirms (Y/y/Enter), false otherwise.\n */\nexport async function confirmPrompt(\n  input: NodeJS.ReadableStream = process.stdin,\n  output: NodeJS.WritableStream = process.stdout\n): Promise<boolean> {\n  const rl = createInterface({\n    input,\n    output,\n    terminal: false,\n  });\n\n  return new Promise((resolve) => {\n    rl.question('', (answer) => {\n      rl.close();\n      const trimmed = answer.trim().toLowerCase();\n      // Empty (Enter) or 'y' or 'yes' means confirm\n      resolve(trimmed === '' || trimmed === 'y' || trimmed === 'yes');\n    });\n  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's' : ''}:`\n  );\n\n  // List articles with IDs\n  for (const { id, article } of withId) {\n    const title = article.title.length > 60\n      ? article.title.substring(0, 57) + '...'\n      : article.title;\n    lines.push(`  - ${id}: ${title}`);\n  }\n\n  // Details about articles without DOI/PMID\n  if (withoutId.length > 0) {\n    lines.push('');\n    lines.push(\n      `${withoutId.length} article${withoutId.length !== 1 ? 's' : ''} will be skipped (no DOI or PMID):`\n    );\n\n    const maxDisplay = 10;\n    const displayed = withoutId.slice(0, maxDisplay);\n\n    for (const article of displayed) {\n      const truncatedTitle = article.title.length > 50\n        ? article.title.substring(0, 50) + '...'\n        : article.title;\n\n      const altIds = getAlternativeIds(article);\n      const hasAltIds = altIds.length > 0 ? `, has: ${altIds.join(', ')}` : '';\n\n      lines.push(`  - \"${truncatedTitle}\" (source: ${article.source}${hasAltIds})`);\n    }\n\n    if (withoutId.length > maxDisplay) {\n      lines.push(`  ... and ${withoutId.length - maxDisplay} more`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n\n/**\n * Get alternative (non-DOI/PMID) identifiers for an article.\n */\nfunction getAlternativeIds(article: Article): string[] {\n  const ids: string[] = [];\n  if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n  if (article.ericId) ids.push(`eric:${article.ericId}`);\n  if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n  return ids;\n}\n\n/**\n * Summary of review decisions for a session.\n */\nexport interface ReviewSummary {\n  /** Total articles in review file */\n  total: number;\n  /** Articles with finalDecision='include' */\n  included: number;\n  /** Articles with finalDecision='exclude' */\n  excluded: number;\n  /** Articles without finalDecision (pending, needs-final, conflicting) */\n  pending: number;\n}\n\n/**\n * Check if a session has a reviews.yaml file.\n */\nexport async function hasReviewFile(sessionId: string, sessionsDir: string): Promise<boolean> {\n  const reviewsPath = join(sessionsDir, sessionId, '.internal', 'reviews.yaml');\n  try {\n    await access(reviewsPath, constants.R_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Load and parse the review file for a session.\n */\nasync function loadReviewFile(sessionId: string, sessionsDir: string): Promise<ReviewFile> {\n  const reviewsPath = join(sessionsDir, sessionId, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  return parseYaml(content) as ReviewFile;\n}\n\n/**\n * Get review summary (counts) for a session.\n * Throws if reviews.yaml does not exist.\n */\nexport async function getReviewSummary(sessionId: string, sessionsDir: string): Promise<ReviewSummary> {\n  const reviewFile = await loadReviewFile(sessionId, sessionsDir);\n  const articles = reviewFile.articles ?? 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package/dist/cli/commands/review/export.js

@@ -2,7 +2,7 @@ import { join, dirname } from "node:path";
 import { mkdir, writeFile, readFile } from "node:fs/promises";
 import { stringify, parse } from "yaml";
 async function loadReviewFile(sessionDir) {
-  const reviewsPath = join(sessionDir, "reviews.yaml");
+  const reviewsPath = join(sessionDir, ".internal", "reviews.yaml");
   const content = await readFile(reviewsPath, "utf-8");
   return parse(content);
 }

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

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

@@ -1,4 +1,4 @@
-import { ReviewStatus } from './types.js';
+import { ReviewStatus, ReviewBasis } from './types.js';
 export type SortOption = 'year' | 'title' | 'random' | 'none';
 export interface ReviewExtractOptions {
     sessionId: string;
@@ -7,6 +7,10 @@ export interface ReviewExtractOptions {
     seed?: number;
     limit?: number;
     offset?: number;
+    /** Basis for the review (title, abstract). When specified, outputs work file format. */
+    basis?: ReviewBasis;
+    /** Reviewer identifier (e.g., "ai:claude"). Required when basis is specified. */
+    reviewer?: string;
     output: string;
 }
 export interface ReviewExtractResult {

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

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