@ncukondo/reference-manager 0.27.2 → 0.28.1

package/dist/chunks/{fix-interaction-BCtx4Q9F.js.map → fix-interaction-pDdwGbp1.js.map}

@@ -1 +1 @@
-{"version":3,"file":"fix-interaction-BCtx4Q9F.js","sources":["../../src/features/check/fix-actions.ts","../../src/features/check/fix-interaction.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport type { CheckFinding } from \"./types.js\";\n\nexport type FixActionType =\n  | \"add_retracted_tag\"\n  | \"add_retraction_note\"\n  | \"remove_from_library\"\n  | \"update_from_published\"\n  | \"add_version_tag\"\n  | \"add_concern_tag\"\n  | \"add_concern_note\"\n  | \"update_all_fields\"\n  | \"update_selected_fields\"\n  | \"skip\";\n\nexport interface FixAction {\n  type: FixActionType;\n  label: string;\n}\n\nexport interface FixActionResult {\n  applied: boolean;\n  message: string;\n  removed?: boolean;\n}\n\nexport function getFixActionsForFinding(finding: CheckFinding): FixAction[] {\n  switch (finding.type) {\n    case \"retracted\":\n      return [\n        { type: \"add_retracted_tag\", label: 'Add tag \"retracted\"' },\n        { type: \"add_retraction_note\", label: \"Add note with retraction details\" },\n        { type: \"remove_from_library\", label: \"Remove from library\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"version_changed\":\n      return [\n        { type: \"update_from_published\", label: \"Update metadata from published version\" },\n        { type: \"add_version_tag\", label: 'Add tag \"has-published-version\"' },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"concern\":\n      return [\n        { type: \"add_concern_tag\", label: 'Add tag \"expression-of-concern\"' },\n        { type: \"add_concern_note\", label: \"Add note with concern details\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"metadata_mismatch\":\n    case \"metadata_outdated\":\n      return [\n        { type: \"update_all_fields\", label: \"Update all changed fields from remote\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    default:\n      return [];\n  }\n}\n\nfunction addTag(item: CslItem, tag: string): string[] {\n  const existing = (item.custom?.tags as string[] | undefined) ?? [];\n  if (existing.includes(tag)) {\n    return existing;\n  }\n  return [...existing, tag];\n}\n\nfunction buildNoteText(prefix: string, finding: CheckFinding): string {\n  const parts = [prefix];\n  if (finding.details?.retractionDate) {\n    parts.push(`Date: ${finding.details.retractionDate}`);\n  }\n  if (finding.details?.retractionDoi) {\n    parts.push(`DOI: ${finding.details.retractionDoi}`);\n  }\n  return parts.join(\". \");\n}\n\nfunction appendNote(existingNote: string | undefined, newNote: string): string {\n  if (existingNote) {\n    return `${existingNote}\\n\\n${newNote}`;\n  }\n  return newNote;\n}\n\nasync function applyTagAction(\n  library: ILibrary,\n  item: CslItem,\n  tag: string\n): Promise<FixActionResult> {\n  const tags = addTag(item, tag);\n  await library.update(item.id, { custom: { ...item.custom, tags } } as Partial<CslItem>, {\n    idType: \"id\",\n  });\n  await library.save();\n  return { applied: true, message: `Added tag \"${tag}\"` };\n}\n\nasync function applyNoteAction(\n  library: ILibrary,\n  item: CslItem,\n  prefix: string,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const noteText = buildNoteText(prefix, finding);\n  const note = appendNote(item.note, noteText);\n  await library.update(item.id, { note } as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Added note: ${noteText}` };\n}\n\nasync function applyUpdateFromPublished(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const newDoi = finding.details?.newDoi;\n  if (!newDoi) {\n    return { applied: false, message: \"No published DOI available in finding details\" };\n  }\n  const { fetchDoi } = await import(\"../import/fetcher.js\");\n  const fetchResult = await fetchDoi(newDoi);\n  if (!fetchResult.success) {\n    return {\n      applied: false,\n      message: `Failed to fetch metadata for ${newDoi}: ${fetchResult.error}`,\n    };\n  }\n  const { id: _id, custom: _custom, ...metadata } = fetchResult.item;\n  await library.update(item.id, metadata as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Updated metadata from ${newDoi}` };\n}\n\nasync function applyUpdateAllFields(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  let fetchedItem: CslItem;\n\n  if (item.DOI) {\n    const { fetchDoi } = await import(\"../import/fetcher.js\");\n    const fetchResult = await fetchDoi(item.DOI);\n    if (!fetchResult.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for DOI ${item.DOI}: ${fetchResult.error}`,\n      };\n    }\n    fetchedItem = fetchResult.item;\n  } else if (item.PMID) {\n    const { fetchPmids } = await import(\"../import/fetcher.js\");\n    const results = await fetchPmids([item.PMID], {});\n    const result = results[0];\n    if (!result || !result.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for PMID ${item.PMID}: ${result?.error ?? \"unknown error\"}`,\n      };\n    }\n    fetchedItem = result.item;\n  } else {\n    return { applied: false, message: \"No DOI or PMID available for metadata update\" };\n  }\n\n  const updatedFields = finding.details?.updatedFields ?? [];\n  const updates: Partial<CslItem> = {};\n  for (const field of updatedFields) {\n    if (field in fetchedItem) {\n      (updates as Record<string, unknown>)[field] = (fetchedItem as Record<string, unknown>)[field];\n    }\n  }\n  if (Object.keys(updates).length === 0) {\n    return { applied: false, message: \"No fields to update\" };\n  }\n  await library.update(item.id, updates, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Updated fields: ${updatedFields.join(\", \")}` };\n}\n\nexport async function applyFixAction(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding,\n  actionType: FixActionType\n): Promise<FixActionResult> {\n  switch (actionType) {\n    case \"add_retracted_tag\":\n      return applyTagAction(library, item, \"retracted\");\n\n    case \"add_retraction_note\":\n      return applyNoteAction(library, item, \"RETRACTED\", finding);\n\n    case \"add_concern_tag\":\n      return applyTagAction(library, item, \"expression-of-concern\");\n\n    case \"add_concern_note\":\n      return applyNoteAction(library, item, \"EXPRESSION OF CONCERN\", finding);\n\n    case \"add_version_tag\":\n      return applyTagAction(library, item, \"has-published-version\");\n\n    case \"remove_from_library\": {\n      const removeResult = await library.remove(item.id, { idType: \"id\" });\n      if (!removeResult.removed) {\n        return { applied: false, message: `Failed to remove ${item.id}` };\n      }\n      await library.save();\n      return { applied: true, message: `Removed ${item.id}`, removed: true };\n    }\n\n    case \"update_from_published\":\n      return applyUpdateFromPublished(library, item, finding);\n\n    case \"update_all_fields\":\n      return applyUpdateAllFields(library, item, finding);\n\n    // Placeholder for programmatic API (MCP/server) use.\n    // Individual field selection is not available in interactive CLI mode,\n    // but can be used via the MCP tool or HTTP server API.\n    case \"update_selected_fields\":\n      return { applied: false, message: \"Field selection not available in CLI mode\" };\n\n    case \"skip\":\n      return { applied: true, message: \"Skipped\" };\n\n    default:\n      return { applied: false, message: `Unknown action: ${actionType}` };\n  }\n}\n","import { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { restoreStdinAfterInk } from \"../interactive/alternate-screen.js\";\nimport { Select } from \"../interactive/components/index.js\";\nimport type { SelectOption } from \"../interactive/components/index.js\";\nimport { type FixActionType, applyFixAction, getFixActionsForFinding } from \"./fix-actions.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface FixInteractionResult {\n  totalFindings: number;\n  applied: number;\n  skipped: number;\n  removed: string[];\n}\n\nfunction selectFixAction(\n  message: string,\n  options: SelectOption<FixActionType>[]\n): Promise<FixActionType | null> {\n  return new Promise<FixActionType | null>((resolve) => {\n    let selected: FixActionType | null = null;\n\n    const { waitUntilExit } = render(\n      createElement(Select<FixActionType>, {\n        options,\n        message,\n        onSelect: (value: FixActionType) => {\n          selected = value;\n        },\n        onCancel: () => {\n          selected = null;\n        },\n      })\n    );\n\n    waitUntilExit()\n      .then(() => {\n        restoreStdinAfterInk();\n        resolve(selected);\n      })\n      .catch(() => {\n        restoreStdinAfterInk();\n        resolve(null);\n      });\n  });\n}\n\nfunction getStatusLabel(type: string): string {\n  switch (type) {\n    case \"retracted\":\n      return \"RETRACTED\";\n    case \"concern\":\n      return \"CONCERN\";\n    case \"version_changed\":\n      return \"VERSION\";\n    case \"metadata_mismatch\":\n      return \"MISMATCH\";\n    case \"metadata_outdated\":\n      return \"OUTDATED\";\n    default:\n      return \"WARNING\";\n  }\n}\n\nfunction buildSelectOptions(finding: CheckFinding): SelectOption<FixActionType>[] {\n  return getFixActionsForFinding(finding).map((a) => ({\n    label: a.label,\n    value: a.type,\n  }));\n}\n\nasync function processFinding(\n  result: FixInteractionResult,\n  library: ILibrary,\n  item: CslItem,\n  resultId: string,\n  finding: CheckFinding\n): Promise<void> {\n  result.totalFindings++;\n  const options = buildSelectOptions(finding);\n  if (options.length === 0) return;\n\n  const label = getStatusLabel(finding.type);\n  const message = `[${label}] ${resultId}: ${finding.message}`;\n  const selectedAction = await selectFixAction(message, options);\n\n  if (selectedAction === null) {\n    result.skipped++;\n    return;\n  }\n\n  const actionResult = await applyFixAction(library, item, finding, selectedAction);\n\n  if (!actionResult.applied) {\n    process.stderr.write(`  Error: ${actionResult.message}\\n`);\n    return;\n  }\n\n  process.stderr.write(`  ${actionResult.message}\\n`);\n  if (selectedAction === \"skip\") {\n    result.skipped++;\n  } else {\n    result.applied++;\n    if (actionResult.removed) {\n      result.removed.push(resultId);\n    }\n  }\n}\n\nexport async function runFixInteraction(\n  results: CheckResult[],\n  library: ILibrary,\n  findItem: (id: string) => CslItem | undefined\n): Promise<FixInteractionResult> {\n  const interactionResult: FixInteractionResult = {\n    totalFindings: 0,\n    applied: 0,\n    skipped: 0,\n    removed: [],\n  };\n\n  const warningResults = results.filter((r) => r.status === \"warning\");\n\n  for (const checkResult of warningResults) {\n    const item = findItem(checkResult.id);\n    if (!item) continue;\n\n    for (const finding of checkResult.findings) {\n      await processFinding(interactionResult, library, item, checkResult.id, finding);\n    }\n  }\n\n  return interactionResult;\n}\n"],"names":[],"mappings":";;;AA2BO,SAAS,wBAAwB,SAAoC;AAC1E,UAAQ,QAAQ,MAAA;AAAA,IACd,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,qBAAqB,OAAO,sBAAA;AAAA,QACpC,EAAE,MAAM,uBAAuB,OAAO,mCAAA;AAAA,QACtC,EAAE,MAAM,uBAAuB,OAAO,sBAAA;AAAA,QACtC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,yBAAyB,OAAO,yCAAA;AAAA,QACxC,EAAE,MAAM,mBAAmB,OAAO,kCAAA;AAAA,QAClC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,mBAAmB,OAAO,kCAAA;AAAA,QAClC,EAAE,MAAM,oBAAoB,OAAO,gCAAA;AAAA,QACnC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC,KAAK;AAAA,IACL,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,qBAAqB,OAAO,wCAAA;AAAA,QACpC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC;AACE,aAAO,CAAA;AAAA,EAAC;AAEd;AAEA,SAAS,OAAO,MAAe,KAAuB;AACpD,QAAM,WAAY,KAAK,QAAQ,QAAiC,CAAA;AAChE,MAAI,SAAS,SAAS,GAAG,GAAG;AAC1B,WAAO;AAAA,EACT;AACA,SAAO,CAAC,GAAG,UAAU,GAAG;AAC1B;AAEA,SAAS,cAAc,QAAgB,SAA+B;AACpE,QAAM,QAAQ,CAAC,MAAM;AACrB,MAAI,QAAQ,SAAS,gBAAgB;AACnC,UAAM,KAAK,SAAS,QAAQ,QAAQ,cAAc,EAAE;AAAA,EACtD;AACA,MAAI,QAAQ,SAAS,eAAe;AAClC,UAAM,KAAK,QAAQ,QAAQ,QAAQ,aAAa,EAAE;AAAA,EACpD;AACA,SAAO,MAAM,KAAK,IAAI;AACxB;AAEA,SAAS,WAAW,cAAkC,SAAyB;AAC7E,MAAI,cAAc;AAChB,WAAO,GAAG,YAAY;AAAA;AAAA,EAAO,OAAO;AAAA,EACtC;AACA,SAAO;AACT;AAEA,eAAe,eACb,SACA,MACA,KAC0B;AAC1B,QAAM,OAAO,OAAO,MAAM,GAAG;AAC7B,QAAM,QAAQ,OAAO,KAAK,IAAI,EAAE,QAAQ,EAAE,GAAG,KAAK,QAAQ,KAAA,EAAK,GAAyB;AAAA,IACtF,QAAQ;AAAA,EAAA,CACT;AACD,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,cAAc,GAAG,IAAA;AACpD;AAEA,eAAe,gBACb,SACA,MACA,QACA,SAC0B;AAC1B,QAAM,WAAW,cAAc,QAAQ,OAAO;AAC9C,QAAM,OAAO,WAAW,KAAK,MAAM,QAAQ;AAC3C,QAAM,QAAQ,OAAO,KAAK,IAAI,EAAE,QAA4B,EAAE,QAAQ,MAAM;AAC5E,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,eAAe,QAAQ,GAAA;AAC1D;AAEA,eAAe,yBACb,SACA,MACA,SAC0B;AAC1B,QAAM,SAAS,QAAQ,SAAS;AAChC,MAAI,CAAC,QAAQ;AACX,WAAO,EAAE,SAAS,OAAO,SAAS,gDAAA;AAAA,EACpC;AACA,QAAM,EAAE,SAAA,IAAa,MAAM,OAAO,qBAAsB,EAAA,KAAA,OAAA,EAAA,CAAA;AACxD,QAAM,cAAc,MAAM,SAAS,MAAM;AACzC,MAAI,CAAC,YAAY,SAAS;AACxB,WAAO;AAAA,MACL,SAAS;AAAA,MACT,SAAS,gCAAgC,MAAM,KAAK,YAAY,KAAK;AAAA,IAAA;AAAA,EAEzE;AACA,QAAM,EAAE,IAAI,KAAK,QAAQ,SAAS,GAAG,SAAA,IAAa,YAAY;AAC9D,QAAM,QAAQ,OAAO,KAAK,IAAI,UAA8B,EAAE,QAAQ,MAAM;AAC5E,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,yBAAyB,MAAM,GAAA;AAClE;AAEA,eAAe,qBACb,SACA,MACA,SAC0B;AAC1B,MAAI;AAEJ,MAAI,KAAK,KAAK;AACZ,UAAM,EAAE,SAAA,IAAa,MAAM,OAAO,qBAAsB,EAAA,KAAA,OAAA,EAAA,CAAA;AACxD,UAAM,cAAc,MAAM,SAAS,KAAK,GAAG;AAC3C,QAAI,CAAC,YAAY,SAAS;AACxB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,oCAAoC,KAAK,GAAG,KAAK,YAAY,KAAK;AAAA,MAAA;AAAA,IAE/E;AACA,kBAAc,YAAY;AAAA,EAC5B,WAAW,KAAK,MAAM;AACpB,UAAM,EAAE,WAAA,IAAe,MAAM,OAAO,qBAAsB,EAAA,KAAA,OAAA,EAAA,CAAA;AAC1D,UAAM,UAAU,MAAM,WAAW,CAAC,KAAK,IAAI,GAAG,EAAE;AAChD,UAAM,SAAS,QAAQ,CAAC;AACxB,QAAI,CAAC,UAAU,CAAC,OAAO,SAAS;AAC9B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,qCAAqC,KAAK,IAAI,KAAK,QAAQ,SAAS,eAAe;AAAA,MAAA;AAAA,IAEhG;AACA,kBAAc,OAAO;AAAA,EACvB,OAAO;AACL,WAAO,EAAE,SAAS,OAAO,SAAS,+CAAA;AAAA,EACpC;AAEA,QAAM,gBAAgB,QAAQ,SAAS,iBAAiB,CAAA;AACxD,QAAM,UAA4B,CAAA;AAClC,aAAW,SAAS,eAAe;AACjC,QAAI,SAAS,aAAa;AACvB,cAAoC,KAAK,IAAK,YAAwC,KAAK;AAAA,IAC9F;AAAA,EACF;AACA,MAAI,OAAO,KAAK,OAAO,EAAE,WAAW,GAAG;AACrC,WAAO,EAAE,SAAS,OAAO,SAAS,sBAAA;AAAA,EACpC;AACA,QAAM,QAAQ,OAAO,KAAK,IAAI,SAAS,EAAE,QAAQ,MAAM;AACvD,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,mBAAmB,cAAc,KAAK,IAAI,CAAC,GAAA;AAC9E;AAEA,eAAsB,eACpB,SACA,MACA,SACA,YAC0B;AAC1B,UAAQ,YAAA;AAAA,IACN,KAAK;AACH,aAAO,eAAe,SAAS,MAAM,WAAW;AAAA,IAElD,KAAK;AACH,aAAO,gBAAgB,SAAS,MAAM,aAAa,OAAO;AAAA,IAE5D,KAAK;AACH,aAAO,eAAe,SAAS,MAAM,uBAAuB;AAAA,IAE9D,KAAK;AACH,aAAO,gBAAgB,SAAS,MAAM,yBAAyB,OAAO;AAAA,IAExE,KAAK;AACH,aAAO,eAAe,SAAS,MAAM,uBAAuB;AAAA,IAE9D,KAAK,uBAAuB;AAC1B,YAAM,eAAe,MAAM,QAAQ,OAAO,KAAK,IAAI,EAAE,QAAQ,MAAM;AACnE,UAAI,CAAC,aAAa,SAAS;AACzB,eAAO,EAAE,SAAS,OAAO,SAAS,oBAAoB,KAAK,EAAE,GAAA;AAAA,MAC/D;AACA,YAAM,QAAQ,KAAA;AACd,aAAO,EAAE,SAAS,MAAM,SAAS,WAAW,KAAK,EAAE,IAAI,SAAS,KAAA;AAAA,IAClE;AAAA,IAEA,KAAK;AACH,aAAO,yBAAyB,SAAS,MAAM,OAAO;AAAA,IAExD,KAAK;AACH,aAAO,qBAAqB,SAAS,MAAM,OAAO;AAAA;AAAA;AAAA;AAAA,IAKpD,KAAK;AACH,aAAO,EAAE,SAAS,OAAO,SAAS,4CAAA;AAAA,IAEpC,KAAK;AACH,aAAO,EAAE,SAAS,MAAM,SAAS,UAAA;AAAA,IAEnC;AACE,aAAO,EAAE,SAAS,OAAO,SAAS,mBAAmB,UAAU,GAAA;AAAA,EAAG;AAExE;ACrNA,SAAS,gBACP,SACA,SAC+B;AAC/B,SAAO,IAAI,QAA8B,CAAC,YAAY;AACpD,QAAI,WAAiC;AAErC,UAAM,EAAE,kBAAkB;AAAA,MACxB,cAAc,QAAuB;AAAA,QACnC;AAAA,QACA;AAAA,QACA,UAAU,CAAC,UAAyB;AAClC,qBAAW;AAAA,QACb;AAAA,QACA,UAAU,MAAM;AACd,qBAAW;AAAA,QACb;AAAA,MAAA,CACD;AAAA,IAAA;AAGH,kBAAA,EACG,KAAK,MAAM;AACV,2BAAA;AACA,cAAQ,QAAQ;AAAA,IAClB,CAAC,EACA,MAAM,MAAM;AACX,2BAAA;AACA,cAAQ,IAAI;AAAA,IACd,CAAC;AAAA,EACL,CAAC;AACH;AAEA,SAAS,eAAe,MAAsB;AAC5C,UAAQ,MAAA;AAAA,IACN,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT;AACE,aAAO;AAAA,EAAA;AAEb;AAEA,SAAS,mBAAmB,SAAsD;AAChF,SAAO,wBAAwB,OAAO,EAAE,IAAI,CAAC,OAAO;AAAA,IAClD,OAAO,EAAE;AAAA,IACT,OAAO,EAAE;AAAA,EAAA,EACT;AACJ;AAEA,eAAe,eACb,QACA,SACA,MACA,UACA,SACe;AACf,SAAO;AACP,QAAM,UAAU,mBAAmB,OAAO;AAC1C,MAAI,QAAQ,WAAW,EAAG;AAE1B,QAAM,QAAQ,eAAe,QAAQ,IAAI;AACzC,QAAM,UAAU,IAAI,KAAK,KAAK,QAAQ,KAAK,QAAQ,OAAO;AAC1D,QAAM,iBAAiB,MAAM,gBAAgB,SAAS,OAAO;AAE7D,MAAI,mBAAmB,MAAM;AAC3B,WAAO;AACP;AAAA,EACF;AAEA,QAAM,eAAe,MAAM,eAAe,SAAS,MAAM,SAAS,cAAc;AAEhF,MAAI,CAAC,aAAa,SAAS;AACzB,YAAQ,OAAO,MAAM,YAAY,aAAa,OAAO;AAAA,CAAI;AACzD;AAAA,EACF;AAEA,UAAQ,OAAO,MAAM,KAAK,aAAa,OAAO;AAAA,CAAI;AAClD,MAAI,mBAAmB,QAAQ;AAC7B,WAAO;AAAA,EACT,OAAO;AACL,WAAO;AACP,QAAI,aAAa,SAAS;AACxB,aAAO,QAAQ,KAAK,QAAQ;AAAA,IAC9B;AAAA,EACF;AACF;AAEA,eAAsB,kBACpB,SACA,SACA,UAC+B;AAC/B,QAAM,oBAA0C;AAAA,IAC9C,eAAe;AAAA,IACf,SAAS;AAAA,IACT,SAAS;AAAA,IACT,SAAS,CAAA;AAAA,EAAC;AAGZ,QAAM,iBAAiB,QAAQ,OAAO,CAAC,MAAM,EAAE,WAAW,SAAS;AAEnE,aAAW,eAAe,gBAAgB;AACxC,UAAM,OAAO,SAAS,YAAY,EAAE;AACpC,QAAI,CAAC,KAAM;AAEX,eAAW,WAAW,YAAY,UAAU;AAC1C,YAAM,eAAe,mBAAmB,SAAS,MAAM,YAAY,IAAI,OAAO;AAAA,IAChF;AAAA,EACF;AAEA,SAAO;AACT;"}
+{"version":3,"file":"fix-interaction-pDdwGbp1.js","sources":["../../src/features/check/fix-actions.ts","../../src/features/check/fix-interaction.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport type { CheckFinding } from \"./types.js\";\n\nexport type FixActionType =\n  | \"add_retracted_tag\"\n  | \"add_retraction_note\"\n  | \"remove_from_library\"\n  | \"update_from_published\"\n  | \"add_version_tag\"\n  | \"add_concern_tag\"\n  | \"add_concern_note\"\n  | \"update_all_fields\"\n  | \"update_selected_fields\"\n  | \"skip\";\n\nexport interface FixAction {\n  type: FixActionType;\n  label: string;\n}\n\nexport interface FixActionResult {\n  applied: boolean;\n  message: string;\n  removed?: boolean;\n}\n\nexport function getFixActionsForFinding(finding: CheckFinding): FixAction[] {\n  switch (finding.type) {\n    case \"retracted\":\n      return [\n        { type: \"add_retracted_tag\", label: 'Add tag \"retracted\"' },\n        { type: \"add_retraction_note\", label: \"Add note with retraction details\" },\n        { type: \"remove_from_library\", label: \"Remove from library\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"version_changed\":\n      return [\n        { type: \"update_from_published\", label: \"Update metadata from published version\" },\n        { type: \"add_version_tag\", label: 'Add tag \"has-published-version\"' },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"concern\":\n      return [\n        { type: \"add_concern_tag\", label: 'Add tag \"expression-of-concern\"' },\n        { type: \"add_concern_note\", label: \"Add note with concern details\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    case \"metadata_mismatch\":\n    case \"metadata_outdated\":\n      return [\n        { type: \"update_all_fields\", label: \"Update all changed fields from remote\" },\n        { type: \"skip\", label: \"Skip\" },\n      ];\n    default:\n      return [];\n  }\n}\n\nfunction addTag(item: CslItem, tag: string): string[] {\n  const existing = (item.custom?.tags as string[] | undefined) ?? [];\n  if (existing.includes(tag)) {\n    return existing;\n  }\n  return [...existing, tag];\n}\n\nfunction buildNoteText(prefix: string, finding: CheckFinding): string {\n  const parts = [prefix];\n  if (finding.details?.retractionDate) {\n    parts.push(`Date: ${finding.details.retractionDate}`);\n  }\n  if (finding.details?.retractionDoi) {\n    parts.push(`DOI: ${finding.details.retractionDoi}`);\n  }\n  return parts.join(\". \");\n}\n\nfunction appendNote(existingNote: string | undefined, newNote: string): string {\n  if (existingNote) {\n    return `${existingNote}\\n\\n${newNote}`;\n  }\n  return newNote;\n}\n\nasync function applyTagAction(\n  library: ILibrary,\n  item: CslItem,\n  tag: string\n): Promise<FixActionResult> {\n  const tags = addTag(item, tag);\n  await library.update(item.id, { custom: { ...item.custom, tags } } as Partial<CslItem>, {\n    idType: \"id\",\n  });\n  await library.save();\n  return { applied: true, message: `Added tag \"${tag}\"` };\n}\n\nasync function applyNoteAction(\n  library: ILibrary,\n  item: CslItem,\n  prefix: string,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const noteText = buildNoteText(prefix, finding);\n  const note = appendNote(item.note, noteText);\n  await library.update(item.id, { note } as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Added note: ${noteText}` };\n}\n\nasync function applyUpdateFromPublished(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  const newDoi = finding.details?.newDoi;\n  if (!newDoi) {\n    return { applied: false, message: \"No published DOI available in finding details\" };\n  }\n  const { fetchDoi } = await import(\"../import/fetcher.js\");\n  const fetchResult = await fetchDoi(newDoi);\n  if (!fetchResult.success) {\n    return {\n      applied: false,\n      message: `Failed to fetch metadata for ${newDoi}: ${fetchResult.error}`,\n    };\n  }\n  const { id: _id, custom: _custom, ...metadata } = fetchResult.item;\n  await library.update(item.id, metadata as Partial<CslItem>, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Updated metadata from ${newDoi}` };\n}\n\nasync function applyUpdateAllFields(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding\n): Promise<FixActionResult> {\n  let fetchedItem: CslItem;\n\n  if (item.DOI) {\n    const { fetchDoi } = await import(\"../import/fetcher.js\");\n    const fetchResult = await fetchDoi(item.DOI);\n    if (!fetchResult.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for DOI ${item.DOI}: ${fetchResult.error}`,\n      };\n    }\n    fetchedItem = fetchResult.item;\n  } else if (item.PMID) {\n    const { fetchPmids } = await import(\"../import/fetcher.js\");\n    const results = await fetchPmids([item.PMID], {});\n    const result = results[0];\n    if (!result || !result.success) {\n      return {\n        applied: false,\n        message: `Failed to fetch metadata for PMID ${item.PMID}: ${result?.error ?? \"unknown error\"}`,\n      };\n    }\n    fetchedItem = result.item;\n  } else {\n    return { applied: false, message: \"No DOI or PMID available for metadata update\" };\n  }\n\n  const updatedFields = finding.details?.updatedFields ?? [];\n  const updates: Partial<CslItem> = {};\n  for (const field of updatedFields) {\n    if (field in fetchedItem) {\n      (updates as Record<string, unknown>)[field] = (fetchedItem as Record<string, unknown>)[field];\n    }\n  }\n  if (Object.keys(updates).length === 0) {\n    return { applied: false, message: \"No fields to update\" };\n  }\n  await library.update(item.id, updates, { idType: \"id\" });\n  await library.save();\n  return { applied: true, message: `Updated fields: ${updatedFields.join(\", \")}` };\n}\n\nexport async function applyFixAction(\n  library: ILibrary,\n  item: CslItem,\n  finding: CheckFinding,\n  actionType: FixActionType\n): Promise<FixActionResult> {\n  switch (actionType) {\n    case \"add_retracted_tag\":\n      return applyTagAction(library, item, \"retracted\");\n\n    case \"add_retraction_note\":\n      return applyNoteAction(library, item, \"RETRACTED\", finding);\n\n    case \"add_concern_tag\":\n      return applyTagAction(library, item, \"expression-of-concern\");\n\n    case \"add_concern_note\":\n      return applyNoteAction(library, item, \"EXPRESSION OF CONCERN\", finding);\n\n    case \"add_version_tag\":\n      return applyTagAction(library, item, \"has-published-version\");\n\n    case \"remove_from_library\": {\n      const removeResult = await library.remove(item.id, { idType: \"id\" });\n      if (!removeResult.removed) {\n        return { applied: false, message: `Failed to remove ${item.id}` };\n      }\n      await library.save();\n      return { applied: true, message: `Removed ${item.id}`, removed: true };\n    }\n\n    case \"update_from_published\":\n      return applyUpdateFromPublished(library, item, finding);\n\n    case \"update_all_fields\":\n      return applyUpdateAllFields(library, item, finding);\n\n    // Placeholder for programmatic API (MCP/server) use.\n    // Individual field selection is not available in interactive CLI mode,\n    // but can be used via the MCP tool or HTTP server API.\n    case \"update_selected_fields\":\n      return { applied: false, message: \"Field selection not available in CLI mode\" };\n\n    case \"skip\":\n      return { applied: true, message: \"Skipped\" };\n\n    default:\n      return { applied: false, message: `Unknown action: ${actionType}` };\n  }\n}\n","import { render } from \"ink\";\nimport { createElement } from \"react\";\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { ILibrary } from \"../../core/library-interface.js\";\nimport { restoreStdinAfterInk } from \"../interactive/alternate-screen.js\";\nimport { Select } from \"../interactive/components/index.js\";\nimport type { SelectOption } from \"../interactive/components/index.js\";\nimport { type FixActionType, applyFixAction, getFixActionsForFinding } from \"./fix-actions.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface FixInteractionResult {\n  totalFindings: number;\n  applied: number;\n  skipped: number;\n  removed: string[];\n}\n\nfunction selectFixAction(\n  message: string,\n  options: SelectOption<FixActionType>[]\n): Promise<FixActionType | null> {\n  return new Promise<FixActionType | null>((resolve) => {\n    let selected: FixActionType | null = null;\n\n    const { waitUntilExit } = render(\n      createElement(Select<FixActionType>, {\n        options,\n        message,\n        onSelect: (value: FixActionType) => {\n          selected = value;\n        },\n        onCancel: () => {\n          selected = null;\n        },\n      })\n    );\n\n    waitUntilExit()\n      .then(() => {\n        restoreStdinAfterInk();\n        resolve(selected);\n      })\n      .catch(() => {\n        restoreStdinAfterInk();\n        resolve(null);\n      });\n  });\n}\n\nfunction getStatusLabel(type: string): string {\n  switch (type) {\n    case \"retracted\":\n      return \"RETRACTED\";\n    case \"concern\":\n      return \"CONCERN\";\n    case \"version_changed\":\n      return \"VERSION\";\n    case \"metadata_mismatch\":\n      return \"MISMATCH\";\n    case \"metadata_outdated\":\n      return \"OUTDATED\";\n    default:\n      return \"WARNING\";\n  }\n}\n\nfunction buildSelectOptions(finding: CheckFinding): SelectOption<FixActionType>[] {\n  return getFixActionsForFinding(finding).map((a) => ({\n    label: a.label,\n    value: a.type,\n  }));\n}\n\nasync function processFinding(\n  result: FixInteractionResult,\n  library: ILibrary,\n  item: CslItem,\n  resultId: string,\n  finding: CheckFinding\n): Promise<void> {\n  result.totalFindings++;\n  const options = buildSelectOptions(finding);\n  if (options.length === 0) return;\n\n  const label = getStatusLabel(finding.type);\n  const message = `[${label}] ${resultId}: ${finding.message}`;\n  const selectedAction = await selectFixAction(message, options);\n\n  if (selectedAction === null) {\n    result.skipped++;\n    return;\n  }\n\n  const actionResult = await applyFixAction(library, item, finding, selectedAction);\n\n  if (!actionResult.applied) {\n    process.stderr.write(`  Error: ${actionResult.message}\\n`);\n    return;\n  }\n\n  process.stderr.write(`  ${actionResult.message}\\n`);\n  if (selectedAction === \"skip\") {\n    result.skipped++;\n  } else {\n    result.applied++;\n    if (actionResult.removed) {\n      result.removed.push(resultId);\n    }\n  }\n}\n\nexport async function runFixInteraction(\n  results: CheckResult[],\n  library: ILibrary,\n  findItem: (id: string) => CslItem | undefined\n): Promise<FixInteractionResult> {\n  const interactionResult: FixInteractionResult = {\n    totalFindings: 0,\n    applied: 0,\n    skipped: 0,\n    removed: [],\n  };\n\n  const warningResults = results.filter((r) => r.status === \"warning\");\n\n  for (const checkResult of warningResults) {\n    const item = findItem(checkResult.id);\n    if (!item) continue;\n\n    for (const finding of checkResult.findings) {\n      await processFinding(interactionResult, library, item, checkResult.id, finding);\n    }\n  }\n\n  return interactionResult;\n}\n"],"names":[],"mappings":";;;AA2BO,SAAS,wBAAwB,SAAoC;AAC1E,UAAQ,QAAQ,MAAA;AAAA,IACd,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,qBAAqB,OAAO,sBAAA;AAAA,QACpC,EAAE,MAAM,uBAAuB,OAAO,mCAAA;AAAA,QACtC,EAAE,MAAM,uBAAuB,OAAO,sBAAA;AAAA,QACtC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,yBAAyB,OAAO,yCAAA;AAAA,QACxC,EAAE,MAAM,mBAAmB,OAAO,kCAAA;AAAA,QAClC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,mBAAmB,OAAO,kCAAA;AAAA,QAClC,EAAE,MAAM,oBAAoB,OAAO,gCAAA;AAAA,QACnC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC,KAAK;AAAA,IACL,KAAK;AACH,aAAO;AAAA,QACL,EAAE,MAAM,qBAAqB,OAAO,wCAAA;AAAA,QACpC,EAAE,MAAM,QAAQ,OAAO,OAAA;AAAA,MAAO;AAAA,IAElC;AACE,aAAO,CAAA;AAAA,EAAC;AAEd;AAEA,SAAS,OAAO,MAAe,KAAuB;AACpD,QAAM,WAAY,KAAK,QAAQ,QAAiC,CAAA;AAChE,MAAI,SAAS,SAAS,GAAG,GAAG;AAC1B,WAAO;AAAA,EACT;AACA,SAAO,CAAC,GAAG,UAAU,GAAG;AAC1B;AAEA,SAAS,cAAc,QAAgB,SAA+B;AACpE,QAAM,QAAQ,CAAC,MAAM;AACrB,MAAI,QAAQ,SAAS,gBAAgB;AACnC,UAAM,KAAK,SAAS,QAAQ,QAAQ,cAAc,EAAE;AAAA,EACtD;AACA,MAAI,QAAQ,SAAS,eAAe;AAClC,UAAM,KAAK,QAAQ,QAAQ,QAAQ,aAAa,EAAE;AAAA,EACpD;AACA,SAAO,MAAM,KAAK,IAAI;AACxB;AAEA,SAAS,WAAW,cAAkC,SAAyB;AAC7E,MAAI,cAAc;AAChB,WAAO,GAAG,YAAY;AAAA;AAAA,EAAO,OAAO;AAAA,EACtC;AACA,SAAO;AACT;AAEA,eAAe,eACb,SACA,MACA,KAC0B;AAC1B,QAAM,OAAO,OAAO,MAAM,GAAG;AAC7B,QAAM,QAAQ,OAAO,KAAK,IAAI,EAAE,QAAQ,EAAE,GAAG,KAAK,QAAQ,KAAA,EAAK,GAAyB;AAAA,IACtF,QAAQ;AAAA,EAAA,CACT;AACD,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,cAAc,GAAG,IAAA;AACpD;AAEA,eAAe,gBACb,SACA,MACA,QACA,SAC0B;AAC1B,QAAM,WAAW,cAAc,QAAQ,OAAO;AAC9C,QAAM,OAAO,WAAW,KAAK,MAAM,QAAQ;AAC3C,QAAM,QAAQ,OAAO,KAAK,IAAI,EAAE,QAA4B,EAAE,QAAQ,MAAM;AAC5E,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,eAAe,QAAQ,GAAA;AAC1D;AAEA,eAAe,yBACb,SACA,MACA,SAC0B;AAC1B,QAAM,SAAS,QAAQ,SAAS;AAChC,MAAI,CAAC,QAAQ;AACX,WAAO,EAAE,SAAS,OAAO,SAAS,gDAAA;AAAA,EACpC;AACA,QAAM,EAAE,SAAA,IAAa,MAAM,OAAO,qBAAsB,EAAA,KAAA,OAAA,EAAA,CAAA;AACxD,QAAM,cAAc,MAAM,SAAS,MAAM;AACzC,MAAI,CAAC,YAAY,SAAS;AACxB,WAAO;AAAA,MACL,SAAS;AAAA,MACT,SAAS,gCAAgC,MAAM,KAAK,YAAY,KAAK;AAAA,IAAA;AAAA,EAEzE;AACA,QAAM,EAAE,IAAI,KAAK,QAAQ,SAAS,GAAG,SAAA,IAAa,YAAY;AAC9D,QAAM,QAAQ,OAAO,KAAK,IAAI,UAA8B,EAAE,QAAQ,MAAM;AAC5E,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,yBAAyB,MAAM,GAAA;AAClE;AAEA,eAAe,qBACb,SACA,MACA,SAC0B;AAC1B,MAAI;AAEJ,MAAI,KAAK,KAAK;AACZ,UAAM,EAAE,SAAA,IAAa,MAAM,OAAO,qBAAsB,EAAA,KAAA,OAAA,EAAA,CAAA;AACxD,UAAM,cAAc,MAAM,SAAS,KAAK,GAAG;AAC3C,QAAI,CAAC,YAAY,SAAS;AACxB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,oCAAoC,KAAK,GAAG,KAAK,YAAY,KAAK;AAAA,MAAA;AAAA,IAE/E;AACA,kBAAc,YAAY;AAAA,EAC5B,WAAW,KAAK,MAAM;AACpB,UAAM,EAAE,WAAA,IAAe,MAAM,OAAO,qBAAsB,EAAA,KAAA,OAAA,EAAA,CAAA;AAC1D,UAAM,UAAU,MAAM,WAAW,CAAC,KAAK,IAAI,GAAG,EAAE;AAChD,UAAM,SAAS,QAAQ,CAAC;AACxB,QAAI,CAAC,UAAU,CAAC,OAAO,SAAS;AAC9B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,qCAAqC,KAAK,IAAI,KAAK,QAAQ,SAAS,eAAe;AAAA,MAAA;AAAA,IAEhG;AACA,kBAAc,OAAO;AAAA,EACvB,OAAO;AACL,WAAO,EAAE,SAAS,OAAO,SAAS,+CAAA;AAAA,EACpC;AAEA,QAAM,gBAAgB,QAAQ,SAAS,iBAAiB,CAAA;AACxD,QAAM,UAA4B,CAAA;AAClC,aAAW,SAAS,eAAe;AACjC,QAAI,SAAS,aAAa;AACvB,cAAoC,KAAK,IAAK,YAAwC,KAAK;AAAA,IAC9F;AAAA,EACF;AACA,MAAI,OAAO,KAAK,OAAO,EAAE,WAAW,GAAG;AACrC,WAAO,EAAE,SAAS,OAAO,SAAS,sBAAA;AAAA,EACpC;AACA,QAAM,QAAQ,OAAO,KAAK,IAAI,SAAS,EAAE,QAAQ,MAAM;AACvD,QAAM,QAAQ,KAAA;AACd,SAAO,EAAE,SAAS,MAAM,SAAS,mBAAmB,cAAc,KAAK,IAAI,CAAC,GAAA;AAC9E;AAEA,eAAsB,eACpB,SACA,MACA,SACA,YAC0B;AAC1B,UAAQ,YAAA;AAAA,IACN,KAAK;AACH,aAAO,eAAe,SAAS,MAAM,WAAW;AAAA,IAElD,KAAK;AACH,aAAO,gBAAgB,SAAS,MAAM,aAAa,OAAO;AAAA,IAE5D,KAAK;AACH,aAAO,eAAe,SAAS,MAAM,uBAAuB;AAAA,IAE9D,KAAK;AACH,aAAO,gBAAgB,SAAS,MAAM,yBAAyB,OAAO;AAAA,IAExE,KAAK;AACH,aAAO,eAAe,SAAS,MAAM,uBAAuB;AAAA,IAE9D,KAAK,uBAAuB;AAC1B,YAAM,eAAe,MAAM,QAAQ,OAAO,KAAK,IAAI,EAAE,QAAQ,MAAM;AACnE,UAAI,CAAC,aAAa,SAAS;AACzB,eAAO,EAAE,SAAS,OAAO,SAAS,oBAAoB,KAAK,EAAE,GAAA;AAAA,MAC/D;AACA,YAAM,QAAQ,KAAA;AACd,aAAO,EAAE,SAAS,MAAM,SAAS,WAAW,KAAK,EAAE,IAAI,SAAS,KAAA;AAAA,IAClE;AAAA,IAEA,KAAK;AACH,aAAO,yBAAyB,SAAS,MAAM,OAAO;AAAA,IAExD,KAAK;AACH,aAAO,qBAAqB,SAAS,MAAM,OAAO;AAAA;AAAA;AAAA;AAAA,IAKpD,KAAK;AACH,aAAO,EAAE,SAAS,OAAO,SAAS,4CAAA;AAAA,IAEpC,KAAK;AACH,aAAO,EAAE,SAAS,MAAM,SAAS,UAAA;AAAA,IAEnC;AACE,aAAO,EAAE,SAAS,OAAO,SAAS,mBAAmB,UAAU,GAAA;AAAA,EAAG;AAExE;ACrNA,SAAS,gBACP,SACA,SAC+B;AAC/B,SAAO,IAAI,QAA8B,CAAC,YAAY;AACpD,QAAI,WAAiC;AAErC,UAAM,EAAE,kBAAkB;AAAA,MACxB,cAAc,QAAuB;AAAA,QACnC;AAAA,QACA;AAAA,QACA,UAAU,CAAC,UAAyB;AAClC,qBAAW;AAAA,QACb;AAAA,QACA,UAAU,MAAM;AACd,qBAAW;AAAA,QACb;AAAA,MAAA,CACD;AAAA,IAAA;AAGH,kBAAA,EACG,KAAK,MAAM;AACV,2BAAA;AACA,cAAQ,QAAQ;AAAA,IAClB,CAAC,EACA,MAAM,MAAM;AACX,2BAAA;AACA,cAAQ,IAAI;AAAA,IACd,CAAC;AAAA,EACL,CAAC;AACH;AAEA,SAAS,eAAe,MAAsB;AAC5C,UAAQ,MAAA;AAAA,IACN,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT,KAAK;AACH,aAAO;AAAA,IACT;AACE,aAAO;AAAA,EAAA;AAEb;AAEA,SAAS,mBAAmB,SAAsD;AAChF,SAAO,wBAAwB,OAAO,EAAE,IAAI,CAAC,OAAO;AAAA,IAClD,OAAO,EAAE;AAAA,IACT,OAAO,EAAE;AAAA,EAAA,EACT;AACJ;AAEA,eAAe,eACb,QACA,SACA,MACA,UACA,SACe;AACf,SAAO;AACP,QAAM,UAAU,mBAAmB,OAAO;AAC1C,MAAI,QAAQ,WAAW,EAAG;AAE1B,QAAM,QAAQ,eAAe,QAAQ,IAAI;AACzC,QAAM,UAAU,IAAI,KAAK,KAAK,QAAQ,KAAK,QAAQ,OAAO;AAC1D,QAAM,iBAAiB,MAAM,gBAAgB,SAAS,OAAO;AAE7D,MAAI,mBAAmB,MAAM;AAC3B,WAAO;AACP;AAAA,EACF;AAEA,QAAM,eAAe,MAAM,eAAe,SAAS,MAAM,SAAS,cAAc;AAEhF,MAAI,CAAC,aAAa,SAAS;AACzB,YAAQ,OAAO,MAAM,YAAY,aAAa,OAAO;AAAA,CAAI;AACzD;AAAA,EACF;AAEA,UAAQ,OAAO,MAAM,KAAK,aAAa,OAAO;AAAA,CAAI;AAClD,MAAI,mBAAmB,QAAQ;AAC7B,WAAO;AAAA,EACT,OAAO;AACL,WAAO;AACP,QAAI,aAAa,SAAS;AACxB,aAAO,QAAQ,KAAK,QAAQ;AAAA,IAC9B;AAAA,EACF;AACF;AAEA,eAAsB,kBACpB,SACA,SACA,UAC+B;AAC/B,QAAM,oBAA0C;AAAA,IAC9C,eAAe;AAAA,IACf,SAAS;AAAA,IACT,SAAS;AAAA,IACT,SAAS,CAAA;AAAA,EAAC;AAGZ,QAAM,iBAAiB,QAAQ,OAAO,CAAC,MAAM,EAAE,WAAW,SAAS;AAEnE,aAAW,eAAe,gBAAgB;AACxC,UAAM,OAAO,SAAS,YAAY,EAAE;AACpC,QAAI,CAAC,KAAM;AAEX,eAAW,WAAW,YAAY,UAAU;AAC1C,YAAM,eAAe,mBAAmB,SAAS,MAAM,YAAY,IAAI,OAAO;AAAA,IAChF;AAAA,EACF;AAEA,SAAO;AACT;"}

package/dist/chunks/{index-SwsAKyQr.js → index-DM3Q5lW4.js}

@@ -1,5 +1,5 @@
-import { a } from "./index-BdLVfbj0.js";
-import { d, g, l, o, s } from "./index-DkJT7s7N.js";
+import { a } from "./index-T-edKSzd.js";
+import { d, g, l, o, s } from "./index-Dk83ayti.js";
 export {
   a as addAttachment,
   d as detachAttachment,
@@ -8,4 +8,4 @@ export {
   o as openAttachment,
   s as syncAttachments
 };
-//# sourceMappingURL=index-SwsAKyQr.js.map
+//# sourceMappingURL=index-DM3Q5lW4.js.map

package/dist/chunks/index-DM3Q5lW4.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index-DM3Q5lW4.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;"}

package/dist/chunks/{index-DkJT7s7N.js → index-Dk83ayti.js}

@@ -1,13 +1,13 @@
 import { Command, Option } from "commander";
-import { i as isEqual, M as MANAGED_CUSTOM_FIELDS, w as writeFileAtomic, L as Library, h as CslItemSchema, p as pickDefined, a as sortOrderSchema, z as paginationOptionsSchema, F as FileWatcher, b as sortFieldSchema, y as searchSortFieldSchema } from "./file-watcher-Dlx0PolG.js";
+import { i as isEqual, M as MANAGED_CUSTOM_FIELDS, w as writeFileAtomic, L as Library, h as CslItemSchema, p as pickDefined, a as sortOrderSchema, z as paginationOptionsSchema, F as FileWatcher, b as sortFieldSchema, y as searchSortFieldSchema } from "./file-watcher-CWHg1yol.js";
 import * as fs from "node:fs";
 import { promises, readFileSync, existsSync, mkdirSync, writeFileSync } from "node:fs";
 import * as os from "node:os";
 import * as path from "node:path";
 import path__default, { join, basename, dirname } from "node:path";
-import { n as normalizePathForOutput, d as deleteDirectoryIfEmpty, p as parseFilename, i as isReservedRole, e as ensureDirectory, a as addAttachment, R as RESERVED_ROLES, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as fulltextGet, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-BdLVfbj0.js";
+import { n as normalizePathForOutput, d as deleteDirectoryIfEmpty, p as parseFilename, i as isReservedRole, e as ensureDirectory, a as addAttachment, R as RESERVED_ROLES, b as generateFilename, c as findFulltextFiles, h as findFulltextFile, j as extensionToFormat, k as fulltextAttach, l as fulltextDiscover, m as fulltextFetch, o as fulltextConvert, q as fulltextGet, r as getExtension, s as getDefaultExportFromCjs, B as BUILTIN_STYLES, t as getFulltextAttachmentTypes, u as startServerWithFileWatcher } from "./index-T-edKSzd.js";
 import { readFile, unlink, stat, readdir, rename } from "node:fs/promises";
-import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-B-fte1uv.js";
+import { o as openWithSystemApp, l as loadConfig, e as getDefaultCurrentDirConfigFilename, h as getDefaultUserConfigPath } from "./loader-B6sytmQd.js";
 import { spawn, spawnSync } from "node:child_process";
 import process$1, { stdin, stdout } from "node:process";
 import * as readline from "node:readline";
@@ -19,7 +19,7 @@ import "@citation-js/plugin-csl";
 import { ZodOptional as ZodOptional$2, z } from "zod";
 import { serve } from "@hono/node-server";
 const name = "@ncukondo/reference-manager";
-const version$1 = "0.27.2";
+const version$1 = "0.28.1";
 const description$1 = "A local reference management tool using CSL-JSON as the single source of truth";
 const packageJson = {
   name,
@@ -802,10 +802,9 @@ async function resolveDirectory(ref2, attachmentsDirectory) {
   }
   return { dirPath, directoryCreated };
 }
-async function updateDirectoryMetadata(library, ref2, dirPath) {
+async function updateDirectoryMetadata(library, item, dirPath) {
   const dirName = basename(dirPath);
-  const item = ref2;
-  await library.update(ref2.id, {
+  await library.update(item.id, {
     custom: {
       ...item.custom,
       attachments: {
@@ -860,7 +859,7 @@ async function openAttachment(library, options) {
   const attachments = ref2.custom?.attachments;
   const { dirPath, directoryCreated } = await resolveDirectory(ref2, attachmentsDirectory);
   if (directoryCreated && !attachments?.directory) {
-    await updateDirectoryMetadata(library, ref2, dirPath);
+    await updateDirectoryMetadata(library, item, dirPath);
   }
   const targetResult = await resolveTargetPath(dirPath, filename, role, attachments);
   if ("error" in targetResult) {
@@ -902,15 +901,15 @@ class OperationsLibrary {
   }
   // High-level operations
   async search(options) {
-    const { searchReferences } = await import("./index-BdLVfbj0.js").then((n) => n.E);
+    const { searchReferences } = await import("./index-T-edKSzd.js").then((n) => n.E);
     return searchReferences(this.library, options);
   }
   async list(options) {
-    const { listReferences } = await import("./index-BdLVfbj0.js").then((n) => n.D);
+    const { listReferences } = await import("./index-T-edKSzd.js").then((n) => n.D);
     return listReferences(this.library, options ?? {});
   }
   async cite(options) {
-    const { citeReferences } = await import("./index-BdLVfbj0.js").then((n) => n.C);
+    const { citeReferences } = await import("./index-T-edKSzd.js").then((n) => n.C);
     const defaultStyle = options.defaultStyle ?? this.citationConfig?.defaultStyle;
     const cslDirectory = options.cslDirectory ?? this.citationConfig?.cslDirectory;
     const mergedOptions = {
@@ -921,36 +920,36 @@ class OperationsLibrary {
     return citeReferences(this.library, mergedOptions);
   }
   async import(inputs, options) {
-    const { addReferences } = await import("./index-BdLVfbj0.js").then((n) => n.z);
+    const { addReferences } = await import("./index-T-edKSzd.js").then((n) => n.z);
     return addReferences(inputs, this.library, options ?? {});
   }
   async check(options) {
-    const { checkReferences } = await import("./index-BdLVfbj0.js").then((n) => n.A);
+    const { checkReferences } = await import("./index-T-edKSzd.js").then((n) => n.A);
     return checkReferences(this.library, options);
   }
   // Attachment operations
   async attachAdd(options) {
-    const { addAttachment: addAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { addAttachment: addAttachment2 } = await import("./index-DM3Q5lW4.js");
     return addAttachment2(this.library, options);
   }
   async attachList(options) {
-    const { listAttachments: listAttachments2 } = await import("./index-SwsAKyQr.js");
+    const { listAttachments: listAttachments2 } = await import("./index-DM3Q5lW4.js");
     return listAttachments2(this.library, options);
   }
   async attachGet(options) {
-    const { getAttachment: getAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { getAttachment: getAttachment2 } = await import("./index-DM3Q5lW4.js");
     return getAttachment2(this.library, options);
   }
   async attachDetach(options) {
-    const { detachAttachment: detachAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { detachAttachment: detachAttachment2 } = await import("./index-DM3Q5lW4.js");
     return detachAttachment2(this.library, options);
   }
   async attachSync(options) {
-    const { syncAttachments: syncAttachments2 } = await import("./index-SwsAKyQr.js");
+    const { syncAttachments: syncAttachments2 } = await import("./index-DM3Q5lW4.js");
     return syncAttachments2(this.library, options);
   }
   async attachOpen(options) {
-    const { openAttachment: openAttachment2 } = await import("./index-SwsAKyQr.js");
+    const { openAttachment: openAttachment2 } = await import("./index-DM3Q5lW4.js");
     return openAttachment2(this.library, options);
   }
 }
@@ -1806,7 +1805,7 @@ function getAttachExitCode(result) {
 }
 async function executeInteractiveSelect$2(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-9GUq-x2d.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -2471,7 +2470,7 @@ async function handleCheckAction(identifiers, options, globalOpts) {
     const jsonOptions = buildJsonOptionsFromRefs(options, outputFormat, result, allRefs);
     outputCheckResult(result, outputFormat, jsonOptions);
     if (options.fix && result.summary.warnings > 0 && allRefs) {
-      const { runFixInteraction } = await import("./fix-interaction-BCtx4Q9F.js");
+      const { runFixInteraction } = await import("./fix-interaction-pDdwGbp1.js");
       const findItem = (id2) => allRefs.find((item) => item.id === id2);
       const fixResult = await runFixInteraction(result.results, context.library, findItem);
       const removedSuffix = fixResult.removed.length > 0 ? `, ${fixResult.removed.length} removed` : "";
@@ -2539,7 +2538,7 @@ function outputCheckError(error, format2) {
 }
 async function selectReferencesInteractively(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-9GUq-x2d.js");
   const allReferences = await context.library.getAll();
   if (allReferences.length === 0) {
     process.stderr.write("No references in library.\n");
@@ -2607,10 +2606,10 @@ function getCiteExitCode(result) {
 }
 async function executeInteractiveCite(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runCiteFlow } = await import("./index-Cf5bYLrr.js");
-  const { buildStyleChoices, listCustomStyles } = await import("./style-select-AvDsSnlB.js");
-  const { search } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.B);
-  const { tokenize } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.A);
+  const { runCiteFlow } = await import("./index-gwWeJC-c.js");
+  const { buildStyleChoices, listCustomStyles } = await import("./style-select-DvH9N4Jg.js");
+  const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
+  const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
   checkTTY();
   const allReferences = await context.library.getAll();
@@ -7209,7 +7208,7 @@ function formatEditOutput(result) {
 }
 async function executeInteractiveEdit(options, context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-9GUq-x2d.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: true }, config2.cli.tui)
@@ -10771,7 +10770,7 @@ function getFulltextExitCode(result) {
 }
 async function executeInteractiveSelect$1(context, config2, multiSelect = false) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-9GUq-x2d.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect }, config2.cli.tui)
@@ -11211,6 +11210,7 @@ function buildResourceIndicators(item) {
   return labels.join(" ");
 }
 function formatAuthor(author) {
+  if (author.literal) return author.literal;
   const family = author.family || "";
   const givenInitial = author.given ? `${author.given.charAt(0)}.` : "";
   return givenInitial ? `${family}, ${givenInitial}` : family;
@@ -32225,7 +32225,7 @@ async function mcpStart(options) {
 async function executeRemove(options, context) {
   const { identifier, idType = "id", fulltextDirectory, deleteFulltext = false } = options;
   if (context.mode === "local" && deleteFulltext && fulltextDirectory) {
-    const { removeReference } = await import("./index-BdLVfbj0.js").then((n) => n.x);
+    const { removeReference } = await import("./index-T-edKSzd.js").then((n) => n.x);
     return removeReference(context.library, {
       identifier,
       idType,
@@ -32280,7 +32280,7 @@ Continue?`;
 }
 async function executeInteractiveRemove(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferenceItemsOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferenceItemsOrExit } = await import("./reference-select-9GUq-x2d.js");
   const allReferences = await context.library.getAll();
   const selectedItems = await withAlternateScreen2(
     () => selectReferenceItemsOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -32505,9 +32505,9 @@ async function executeInteractiveSearch(options, context, config2) {
   validateInteractiveOptions(options);
   const { checkTTY } = await import("./tty-BMyaEOhX.js");
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { runSearchFlow } = await import("./index-Cf5bYLrr.js");
-  const { search } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.B);
-  const { tokenize } = await import("./file-watcher-Dlx0PolG.js").then((n) => n.A);
+  const { runSearchFlow } = await import("./index-gwWeJC-c.js");
+  const { search } = await import("./file-watcher-CWHg1yol.js").then((n) => n.B);
+  const { tokenize } = await import("./file-watcher-CWHg1yol.js").then((n) => n.A);
   checkTTY();
   const allReferences = await context.library.getAll();
   const searchFn = (query) => {
@@ -32524,7 +32524,7 @@ async function executeInteractiveSearch(options, context, config2) {
     })
   );
   if (result.selectedItems && !result.cancelled) {
-    const { isSideEffectAction } = await import("./action-menu-Crcd5X1-.js");
+    const { isSideEffectAction } = await import("./action-menu-BhuUnwdz.js");
     if (isSideEffectAction(result.action)) {
       await executeSideEffectAction(result.action, result.selectedItems, context, config2);
       return { output: "", cancelled: false, action: result.action };
@@ -32540,7 +32540,7 @@ async function executeSideEffectAction(action, items2, context, config2) {
   switch (action) {
     case "open-url": {
       const { resolveDefaultUrl: resolveDefaultUrl2 } = await Promise.resolve().then(() => url);
-      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-B-fte1uv.js").then((n) => n.j);
+      const { openWithSystemApp: openWithSystemApp2 } = await import("./loader-B6sytmQd.js").then((n) => n.j);
       const item = items2[0];
       if (!item) return;
       const url$1 = resolveDefaultUrl2(item);
@@ -32663,12 +32663,29 @@ async function startServerDaemon(options) {
 async function startServerForeground(options) {
   const port = options.port ?? 0;
   const { app, dispose } = await startServerWithFileWatcher(options.library, options.config);
-  const server = serve({
-    fetch: app.fetch,
-    port,
-    hostname: "127.0.0.1"
+  const actualPort = await new Promise((resolve2, reject) => {
+    const server = serve({
+      fetch: app.fetch,
+      port,
+      hostname: "127.0.0.1"
+    });
+    server.on("listening", () => {
+      const addr = server.address();
+      resolve2(addr.port);
+      const cleanup = async () => {
+        process.stdout.write("\nShutting down...\n");
+        server.close();
+        await dispose();
+        await removePortfile(options.portfilePath);
+        setExitCode(ExitCode.SUCCESS);
+      };
+      process.on("SIGINT", cleanup);
+      process.on("SIGTERM", cleanup);
+    });
+    server.on("error", (err) => {
+      reject(err);
+    });
   });
-  const actualPort = server.address().port;
   const pid = process.pid;
   const started_at = (/* @__PURE__ */ new Date()).toISOString();
   await writePortfile(options.portfilePath, actualPort, pid, options.library, started_at);
@@ -32679,15 +32696,6 @@ async function startServerForeground(options) {
   process.stdout.write(`PID: ${pid}
 `);
   process.stdout.write("Press Ctrl+C to stop\n");
-  const cleanup = async () => {
-    process.stdout.write("\nShutting down...\n");
-    server.close();
-    await dispose();
-    await removePortfile(options.portfilePath);
-    setExitCode(ExitCode.SUCCESS);
-  };
-  process.on("SIGINT", cleanup);
-  process.on("SIGTERM", cleanup);
   await new Promise(() => {
   });
 }
@@ -32927,7 +32935,7 @@ function formatUpdateOutput(result, identifier) {
 }
 async function executeInteractiveUpdate(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-9GUq-x2d.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33222,7 +33230,7 @@ function getUrlExitCode(result) {
 }
 async function executeInteractiveSelect(context, config2) {
   const { withAlternateScreen: withAlternateScreen2 } = await Promise.resolve().then(() => alternateScreen);
-  const { selectReferencesOrExit } = await import("./reference-select-Ce9pG8cC.js");
+  const { selectReferencesOrExit } = await import("./reference-select-9GUq-x2d.js");
   const allReferences = await context.library.getAll();
   const identifiers = await withAlternateScreen2(
     () => selectReferencesOrExit(allReferences, { multiSelect: false }, config2.cli.tui)
@@ -33275,7 +33283,16 @@ const LIST_OUTPUT_FORMATS = ["pretty", "json", "bibtex", "ids", "uuid"];
 const MUTATION_OUTPUT_FORMATS = ["json", "text"];
 const CONFIG_OUTPUT_FORMATS = ["text", "json"];
 const LOG_LEVELS = ["silent", "info", "debug"];
-const ADD_INPUT_FORMATS = ["json", "bibtex", "ris", "pmid", "doi", "isbn", "auto"];
+const ADD_INPUT_FORMATS = [
+  "json",
+  "bibtex",
+  "ris",
+  "pmid",
+  "doi",
+  "isbn",
+  "arxiv",
+  "auto"
+];
 const CONFIG_SECTIONS = [
   "backup",
   "citation",
@@ -33770,7 +33787,7 @@ function shouldAutoFetch(cliFlag, configEnabled) {
   return configEnabled;
 }
 async function performAutoFetch(addedItems, context, config2) {
-  const { fulltextFetch: fulltextFetch2 } = await import("./index-BdLVfbj0.js").then((n) => n.w);
+  const { fulltextFetch: fulltextFetch2 } = await import("./index-T-edKSzd.js").then((n) => n.w);
   const fetchResults = await autoFetchFulltext(addedItems, context, {
     fulltextConfig: config2.fulltext,
     fulltextDirectory: config2.attachments.directory,
@@ -33828,7 +33845,11 @@ async function handleAddAction(inputs, options, program) {
   }
 }
 function registerAddCommand(program) {
-  program.command("add").description("Add new reference(s) to the library").argument("[input...]", "File paths or identifiers (PMID/DOI/ISBN), or use stdin").option("-f, --force", "Skip duplicate detection").option("-i, --input <format>", "Input format: json|bibtex|ris|pmid|doi|isbn|auto", "auto").option("--verbose", "Show detailed error information").option("-o, --output <format>", "Output format: json|text", "text").option("--full", "Include full CSL-JSON data in JSON output").option("--fetch-fulltext", "Auto-fetch OA fulltext after adding").option("--no-fetch-fulltext", "Disable auto-fetch fulltext (overrides config)").action(async (inputs, options) => {
+  program.command("add").description("Add new reference(s) to the library").argument("[input...]", "File paths or identifiers (PMID/DOI/ISBN/arXiv), or use stdin").option("-f, --force", "Skip duplicate detection").option(
+    "-i, --input <format>",
+    "Input format: json|bibtex|ris|pmid|doi|isbn|arxiv|auto",
+    "auto"
+  ).option("--verbose", "Show detailed error information").option("-o, --output <format>", "Output format: json|text", "text").option("--full", "Include full CSL-JSON data in JSON output").option("--fetch-fulltext", "Auto-fetch OA fulltext after adding").option("--no-fetch-fulltext", "Disable auto-fetch fulltext (overrides config)").action(async (inputs, options) => {
     await handleAddAction(inputs, options, program);
   });
 }
@@ -34058,4 +34079,4 @@ export {
   restoreStdinAfterInk as r,
   syncAttachments as s
 };
-//# sourceMappingURL=index-DkJT7s7N.js.map
+//# sourceMappingURL=index-Dk83ayti.js.map