@ncukondo/reference-manager 0.25.0 → 0.26.0

package/dist/chunks/checker-CKfdG8Ia.js

@@ -0,0 +1,170 @@
+async function checkReference(item, config) {
+  const id = item.id;
+  const uuid = item.custom?.uuid ?? "";
+  const checkedAt = (/* @__PURE__ */ new Date()).toISOString();
+  const findings = [];
+  const checkedSources = [];
+  const hasDoi = !!item.DOI;
+  const hasPmid = !!item.PMID;
+  if (!hasDoi && !hasPmid) {
+    return { id, uuid, status: "skipped", findings: [], checkedAt, checkedSources: [] };
+  }
+  let crossrefMetadata;
+  if (hasDoi) {
+    checkedSources.push("crossref");
+    const crossrefResult = await checkCrossref(item.DOI, config);
+    findings.push(...crossrefResult.findings);
+    crossrefMetadata = crossrefResult.metadata;
+  }
+  if (hasPmid) {
+    checkedSources.push("pubmed");
+    const pubmedFindings = await checkPubmed(item.PMID, config);
+    addUniqueFindings(findings, pubmedFindings);
+  }
+  const metadataFinding = await checkMetadata(item, config, crossrefMetadata, hasPmid, hasDoi);
+  if (metadataFinding) {
+    findings.push(metadataFinding);
+  }
+  const status = findings.length > 0 ? "warning" : "ok";
+  return { id, uuid, status, findings, checkedAt, checkedSources };
+}
+function addUniqueFindings(target, source) {
+  for (const finding of source) {
+    if (!target.some((f) => f.type === finding.type)) {
+      target.push(finding);
+    }
+  }
+}
+async function checkMetadata(item, config, crossrefMetadata, hasPmid, hasDoi) {
+  if (config?.metadata === false) return null;
+  if (crossrefMetadata) {
+    return compareItemMetadata(item, crossrefMetadata);
+  }
+  if (hasPmid && !hasDoi) {
+    return comparePubmedMetadata(item, config);
+  }
+  return null;
+}
+async function checkCrossref(doi, config) {
+  const { queryCrossref } = await import("./crossref-client-Gs75LMVf.js");
+  const crossrefConfig = config?.email ? { email: config.email } : void 0;
+  const result = await queryCrossref(doi, crossrefConfig);
+  if (!result.success) return { findings: [] };
+  const findings = [];
+  for (const update of result.updates) {
+    const finding = mapCrossrefUpdate(update);
+    if (finding) {
+      findings.push(finding);
+    }
+  }
+  return result.metadata ? { findings, metadata: result.metadata } : { findings };
+}
+async function compareItemMetadata(item, remoteMetadata) {
+  const { compareMetadata } = await import("./metadata-comparator-C5zfoYdK.js");
+  const local = extractLocalMetadata(item);
+  const comparison = compareMetadata(local, remoteMetadata);
+  if (comparison.classification === "no_change") return null;
+  const type = comparison.classification;
+  const message = type === "metadata_mismatch" ? "Local metadata significantly differs from the remote record" : "Remote metadata has been updated since import";
+  return {
+    type,
+    message,
+    details: {
+      updatedFields: comparison.changedFields,
+      fieldDiffs: comparison.fieldDiffs
+    }
+  };
+}
+async function comparePubmedMetadata(item, config) {
+  const { fetchPmids } = await import("./index-of6eJn8N.js").then((n) => n.y);
+  const pubmedConfig = config?.pubmed ?? {};
+  const results = await fetchPmids([item.PMID], pubmedConfig);
+  const result = results[0];
+  if (!result || !result.success) {
+    console.error(
+      `PubMed metadata fetch failed for PMID ${item.PMID}: ${result?.error ?? "unknown error"}`
+    );
+    return null;
+  }
+  const remoteMetadata = cslItemToRemoteMetadata(result.item);
+  return compareItemMetadata(item, remoteMetadata);
+}
+function cslItemToRemoteMetadata(item) {
+  const metadata = {};
+  if (item.title !== void 0) metadata.title = item.title;
+  if (item.author !== void 0) {
+    metadata.author = item.author;
+  }
+  if (item["container-title"] !== void 0) metadata.containerTitle = item["container-title"];
+  if (item.type !== void 0) metadata.type = item.type;
+  if (item.page !== void 0) metadata.page = item.page;
+  if (item.volume !== void 0) metadata.volume = item.volume;
+  if (item.issue !== void 0) metadata.issue = item.issue;
+  if (item.issued !== void 0) {
+    metadata.issued = item.issued;
+  }
+  return metadata;
+}
+function extractLocalMetadata(item) {
+  const local = {};
+  if (item.title !== void 0) local.title = item.title;
+  if (item.author !== void 0)
+    local.author = item.author;
+  if (item["container-title"] !== void 0) local["container-title"] = item["container-title"];
+  if (item.type !== void 0) local.type = item.type;
+  if (item.page !== void 0) local.page = item.page;
+  if (item.volume !== void 0) local.volume = item.volume;
+  if (item.issue !== void 0) local.issue = item.issue;
+  if (item.issued !== void 0) local.issued = item.issued;
+  return local;
+}
+async function checkPubmed(pmid, config) {
+  const { queryPubmed } = await import("./pubmed-client-CGReJIOz.js");
+  const result = await queryPubmed(pmid, config?.pubmed);
+  if (!result.success) return [];
+  const findings = [];
+  if (result.isRetracted) {
+    findings.push({
+      type: "retracted",
+      message: "This article is marked as retracted in PubMed"
+    });
+  }
+  if (result.hasConcern) {
+    findings.push({
+      type: "concern",
+      message: "Expression of concern noted in PubMed"
+    });
+  }
+  return findings;
+}
+function mapCrossrefUpdate(update) {
+  const doiDetail = update.doi ? { retractionDoi: update.doi } : {};
+  const dateDetail = update.date ? { retractionDate: update.date } : {};
+  const newDoiDetail = update.doi ? { newDoi: update.doi } : {};
+  switch (update.type) {
+    case "retraction":
+      return {
+        type: "retracted",
+        message: update.date ? `This article was retracted on ${update.date}` : "This article was retracted",
+        details: { ...doiDetail, ...dateDetail }
+      };
+    case "expression-of-concern":
+      return {
+        type: "concern",
+        message: update.date ? `Expression of concern issued on ${update.date}` : "Expression of concern issued",
+        details: { ...doiDetail, ...dateDetail }
+      };
+    case "new_version":
+      return {
+        type: "version_changed",
+        message: update.doi ? `Published version available: ${update.doi}` : "Published version available",
+        details: newDoiDetail
+      };
+    default:
+      return null;
+  }
+}
+export {
+  checkReference
+};
+//# sourceMappingURL=checker-CKfdG8Ia.js.map

package/dist/chunks/checker-CKfdG8Ia.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"checker-CKfdG8Ia.js","sources":["../../src/features/check/checker.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { CrossrefUpdateInfo, RemoteMetadata } from \"./crossref-client.js\";\nimport type { CheckFinding, CheckResult } from \"./types.js\";\n\nexport interface CheckConfig {\n  email?: string;\n  pubmed?: { email?: string; apiKey?: string };\n  metadata?: boolean;\n}\n\ninterface CrossrefCheckResult {\n  findings: CheckFinding[];\n  metadata?: RemoteMetadata;\n}\n\n/**\n * Check a single reference against external sources for status changes.\n *\n * @param item - The CSL-JSON item to check\n * @param config - Optional config for API credentials\n * @returns Check result with findings\n */\nexport async function checkReference(item: CslItem, config?: CheckConfig): Promise<CheckResult> {\n  const id = item.id;\n  const uuid = (item.custom?.uuid as string) ?? \"\";\n  const checkedAt = new Date().toISOString();\n  const findings: CheckFinding[] = [];\n  const checkedSources: string[] = [];\n\n  const hasDoi = !!item.DOI;\n  const hasPmid = !!item.PMID;\n\n  // Skip references with neither DOI nor PMID\n  if (!hasDoi && !hasPmid) {\n    return { id, uuid, status: \"skipped\", findings: [], checkedAt, checkedSources: [] };\n  }\n\n  let crossrefMetadata: RemoteMetadata | undefined;\n\n  // Query Crossref if DOI is present\n  if (hasDoi) {\n    checkedSources.push(\"crossref\");\n    const crossrefResult = await checkCrossref(item.DOI as string, config);\n    findings.push(...crossrefResult.findings);\n    crossrefMetadata = crossrefResult.metadata;\n  }\n\n  // Query PubMed if PMID is present\n  if (hasPmid) {\n    checkedSources.push(\"pubmed\");\n    const pubmedFindings = await checkPubmed(item.PMID as string, config);\n    addUniqueFindings(findings, pubmedFindings);\n  }\n\n  // Metadata comparison (default: enabled)\n  const metadataFinding = await checkMetadata(item, config, crossrefMetadata, hasPmid, hasDoi);\n  if (metadataFinding) {\n    findings.push(metadataFinding);\n  }\n\n  const status = findings.length > 0 ? \"warning\" : \"ok\";\n  return { id, uuid, status, findings, checkedAt, checkedSources };\n}\n\n/**\n * Add findings that aren't already present (by type) to the target list.\n */\nfunction addUniqueFindings(target: CheckFinding[], source: CheckFinding[]): void {\n  for (const finding of source) {\n    if (!target.some((f) => f.type === finding.type)) {\n      target.push(finding);\n    }\n  }\n}\n\n/**\n * Perform metadata comparison if enabled.\n */\nasync function checkMetadata(\n  item: CslItem,\n  config: CheckConfig | undefined,\n  crossrefMetadata: RemoteMetadata | undefined,\n  hasPmid: boolean,\n  hasDoi: boolean\n): Promise<CheckFinding | null> {\n  if (config?.metadata === false) return null;\n\n  if (crossrefMetadata) {\n    // DOI-based: compare against Crossref metadata\n    return compareItemMetadata(item, crossrefMetadata);\n  }\n\n  if (hasPmid && !hasDoi) {\n    // PubMed-only: fetch remote CSL-JSON via PubMed and compare\n    return comparePubmedMetadata(item, config);\n  }\n\n  return null;\n}\n\n/**\n * Query Crossref and return findings plus metadata.\n */\nasync function checkCrossref(doi: string, config?: CheckConfig): Promise<CrossrefCheckResult> {\n  const { queryCrossref } = await import(\"./crossref-client.js\");\n  const crossrefConfig = config?.email ? { email: config.email } : undefined;\n  const result = await queryCrossref(doi, crossrefConfig);\n  if (!result.success) return { findings: [] };\n\n  const findings: CheckFinding[] = [];\n  for (const update of result.updates) {\n    const finding = mapCrossrefUpdate(update);\n    if (finding) {\n      findings.push(finding);\n    }\n  }\n  return result.metadata ? { findings, metadata: result.metadata } : { findings };\n}\n\n/**\n * Compare item metadata against Crossref metadata.\n */\nasync function compareItemMetadata(\n  item: CslItem,\n  remoteMetadata: RemoteMetadata\n): Promise<CheckFinding | null> {\n  const { compareMetadata } = await import(\"./metadata-comparator.js\");\n\n  const local = extractLocalMetadata(item);\n  const comparison = compareMetadata(local, remoteMetadata);\n\n  if (comparison.classification === \"no_change\") return null;\n\n  const type = comparison.classification;\n  const message =\n    type === \"metadata_mismatch\"\n      ? \"Local metadata significantly differs from the remote record\"\n      : \"Remote metadata has been updated since import\";\n\n  return {\n    type,\n    message,\n    details: {\n      updatedFields: comparison.changedFields,\n      fieldDiffs: comparison.fieldDiffs,\n    },\n  };\n}\n\n/**\n * Fetch PubMed CSL-JSON and compare metadata for PMID-only references.\n */\nasync function comparePubmedMetadata(\n  item: CslItem,\n  config?: CheckConfig\n): Promise<CheckFinding | null> {\n  const { fetchPmids } = await import(\"../import/fetcher.js\");\n  const pubmedConfig = config?.pubmed ?? {};\n  const results = await fetchPmids([item.PMID as string], pubmedConfig);\n  const result = results[0];\n  if (!result || !result.success) {\n    console.error(\n      `PubMed metadata fetch failed for PMID ${item.PMID}: ${result?.error ?? \"unknown error\"}`\n    );\n    return null;\n  }\n\n  const remoteMetadata = cslItemToRemoteMetadata(result.item);\n  return compareItemMetadata(item, remoteMetadata);\n}\n\n/**\n * Convert a CslItem (from PubMed) to RemoteMetadata format for comparison.\n */\nfunction cslItemToRemoteMetadata(item: CslItem): RemoteMetadata {\n  const metadata: RemoteMetadata = {};\n  if (item.title !== undefined) metadata.title = item.title;\n  if (item.author !== undefined) {\n    metadata.author = item.author as Array<{ family?: string; given?: string }>;\n  }\n  if (item[\"container-title\"] !== undefined) metadata.containerTitle = item[\"container-title\"];\n  if (item.type !== undefined) metadata.type = item.type;\n  if (item.page !== undefined) metadata.page = item.page;\n  if (item.volume !== undefined) metadata.volume = item.volume;\n  if (item.issue !== undefined) metadata.issue = item.issue;\n  if (item.issued !== undefined) {\n    metadata.issued = item.issued as { \"date-parts\"?: number[][] };\n  }\n  return metadata;\n}\n\n/**\n * Extract local metadata fields from a CslItem for comparison.\n */\nfunction extractLocalMetadata(\n  item: CslItem\n): import(\"./metadata-comparator.js\").LocalMetadataFields {\n  const local: import(\"./metadata-comparator.js\").LocalMetadataFields = {};\n  if (item.title !== undefined) local.title = item.title;\n  if (item.author !== undefined)\n    local.author = item.author as Array<{ family?: string; given?: string }>;\n  if (item[\"container-title\"] !== undefined) local[\"container-title\"] = item[\"container-title\"];\n  if (item.type !== undefined) local.type = item.type;\n  if (item.page !== undefined) local.page = item.page;\n  if (item.volume !== undefined) local.volume = item.volume;\n  if (item.issue !== undefined) local.issue = item.issue;\n  if (item.issued !== undefined) local.issued = item.issued as { \"date-parts\"?: number[][] };\n  return local;\n}\n\n/**\n * Query PubMed and return findings.\n */\nasync function checkPubmed(pmid: string, config?: CheckConfig): Promise<CheckFinding[]> {\n  const { queryPubmed } = await import(\"./pubmed-client.js\");\n  const result = await queryPubmed(pmid, config?.pubmed);\n  if (!result.success) return [];\n\n  const findings: CheckFinding[] = [];\n  if (result.isRetracted) {\n    findings.push({\n      type: \"retracted\",\n      message: \"This article is marked as retracted in PubMed\",\n    });\n  }\n  if (result.hasConcern) {\n    findings.push({\n      type: \"concern\",\n      message: \"Expression of concern noted in PubMed\",\n    });\n  }\n  return findings;\n}\n\n/**\n * Map a Crossref update-to entry to a CheckFinding.\n */\nfunction mapCrossrefUpdate(update: CrossrefUpdateInfo): CheckFinding | null {\n  const doiDetail = update.doi ? { retractionDoi: update.doi } : {};\n  const dateDetail = update.date ? { retractionDate: update.date } : {};\n  const newDoiDetail = update.doi ? { newDoi: update.doi } : {};\n\n  switch (update.type) {\n    case \"retraction\":\n      return {\n        type: \"retracted\",\n        message: update.date\n          ? `This article was retracted on ${update.date}`\n          : \"This article was retracted\",\n        details: { ...doiDetail, ...dateDetail },\n      };\n    case \"expression-of-concern\":\n      return {\n        type: \"concern\",\n        message: update.date\n          ? `Expression of concern issued on ${update.date}`\n          : \"Expression of concern issued\",\n        details: { ...doiDetail, ...dateDetail },\n      };\n    case \"new_version\":\n      return {\n        type: \"version_changed\",\n        message: update.doi\n          ? `Published 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package/dist/chunks/crossref-client-Gs75LMVf.js

@@ -0,0 +1,94 @@
+import { g as getRateLimiter } from "./index-of6eJn8N.js";
+const CROSSREF_API_BASE = "https://api.crossref.org/works";
+function formatDateParts(updated) {
+  if (!updated || typeof updated !== "object") return {};
+  const dateParts = updated["date-parts"];
+  if (!Array.isArray(dateParts) || dateParts.length === 0) return {};
+  const parts = dateParts[0];
+  if (!Array.isArray(parts) || parts.length === 0) return {};
+  const [year, month, day] = parts;
+  const m = String(month ?? 1).padStart(2, "0");
+  const d = String(day ?? 1).padStart(2, "0");
+  return { date: `${year}-${m}-${d}` };
+}
+function extractMetadata(message) {
+  if (!message) return void 0;
+  const metadata = {};
+  const titleArr = message.title;
+  const firstTitle = Array.isArray(titleArr) ? titleArr[0] : void 0;
+  if (firstTitle) {
+    metadata.title = firstTitle;
+  }
+  const authorArr = message.author;
+  if (Array.isArray(authorArr) && authorArr.length > 0) {
+    metadata.author = authorArr.map((a) => ({
+      ...a.family ? { family: a.family } : {},
+      ...a.given ? { given: a.given } : {}
+    }));
+  }
+  const containerArr = message["container-title"];
+  const firstContainer = Array.isArray(containerArr) ? containerArr[0] : void 0;
+  if (firstContainer) {
+    metadata.containerTitle = firstContainer;
+  }
+  if (typeof message.type === "string") {
+    metadata.type = message.type;
+  }
+  if (typeof message.page === "string") metadata.page = message.page;
+  if (typeof message.volume === "string") metadata.volume = message.volume;
+  if (typeof message.issue === "string") metadata.issue = message.issue;
+  const issued = message.issued;
+  if (issued && Array.isArray(issued["date-parts"])) {
+    metadata.issued = issued;
+  }
+  if (Object.keys(metadata).length === 0) return void 0;
+  return metadata;
+}
+async function queryCrossref(doi, config) {
+  const rateLimiter = getRateLimiter("crossref", {});
+  await rateLimiter.acquire();
+  try {
+    const url = new URL(`${CROSSREF_API_BASE}/${encodeURIComponent(doi)}`);
+    if (config?.email) {
+      url.searchParams.set("mailto", config.email);
+    }
+    const response = await fetch(url.toString());
+    if (!response.ok) {
+      return {
+        success: false,
+        error: `Crossref API returned ${response.status} ${response.statusText}`
+      };
+    }
+    const data = await response.json();
+    const message = data.message;
+    const updateTo = message?.["update-to"] ?? [];
+    const updatedBy = message?.["updated-by"] ?? [];
+    const allEntries = [...updateTo, ...updatedBy].map((e) => {
+      const datePart = formatDateParts(e.updated);
+      return {
+        type: String(e.type ?? ""),
+        ...e.DOI ? { doi: String(e.DOI) } : {},
+        ...e.label ? { label: String(e.label) } : {},
+        ...datePart.date ? { date: datePart.date } : {}
+      };
+    });
+    const seen = /* @__PURE__ */ new Set();
+    const updates = allEntries.filter((e) => {
+      const key = `${e.type}:${e.doi ?? ""}`;
+      if (seen.has(key)) return false;
+      seen.add(key);
+      return true;
+    });
+    const metadata = extractMetadata(message);
+    return metadata ? { success: true, updates, metadata } : { success: true, updates };
+  } catch (error) {
+    return {
+      success: false,
+      error: error instanceof Error ? error.message : String(error)
+    };
+  }
+}
+export {
+  queryCrossref
+};
+//# sourceMappingURL=crossref-client-Gs75LMVf.js.map

package/dist/chunks/crossref-client-Gs75LMVf.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"crossref-client-Gs75LMVf.js","sources":["../../src/features/check/crossref-client.ts"],"sourcesContent":["import { getRateLimiter } from \"../import/rate-limiter.js\";\n\nconst CROSSREF_API_BASE = \"https://api.crossref.org/works\";\n\nexport interface CrossrefUpdateInfo {\n  type: string;\n  doi?: string;\n  label?: string;\n  date?: string;\n}\n\nexport interface RemoteMetadata {\n  title?: string;\n  author?: Array<{ family?: string; given?: string }>;\n  containerTitle?: string;\n  type?: string;\n  page?: string;\n  volume?: string;\n  issue?: string;\n  issued?: { \"date-parts\"?: number[][] };\n}\n\nexport type CrossrefResult =\n  | { success: true; updates: CrossrefUpdateInfo[]; metadata?: RemoteMetadata }\n  | { success: false; error: string };\n\n/**\n * Format date-parts from Crossref API response to ISO date string.\n */\nfunction formatDateParts(updated: unknown): { date?: string } {\n  if (!updated || typeof updated !== \"object\") return {};\n  const dateParts = (updated as Record<string, unknown>)[\"date-parts\"];\n  if (!Array.isArray(dateParts) || dateParts.length === 0) return {};\n  const parts = dateParts[0] as number[];\n  if (!Array.isArray(parts) || parts.length === 0) return {};\n  const [year, month, day] = parts;\n  const m = String(month ?? 1).padStart(2, \"0\");\n  const d = String(day ?? 1).padStart(2, \"0\");\n  return { date: `${year}-${m}-${d}` };\n}\n\n/**\n * Extract comparable metadata fields from a Crossref message object.\n */\nfunction extractMetadata(message: Record<string, unknown> | undefined): RemoteMetadata | undefined {\n  if (!message) return undefined;\n\n  const metadata: RemoteMetadata = {};\n\n  // Title: array in Crossref, take first element\n  const titleArr = message.title as string[] | undefined;\n  const firstTitle = Array.isArray(titleArr) ? titleArr[0] : undefined;\n  if (firstTitle) {\n    metadata.title = firstTitle;\n  }\n\n  // Author\n  const authorArr = message.author as Array<{ family?: string; given?: string }> | undefined;\n  if (Array.isArray(authorArr) && authorArr.length > 0) {\n    metadata.author = authorArr.map((a) => ({\n      ...(a.family ? { family: a.family } : {}),\n      ...(a.given ? { given: a.given } : {}),\n    }));\n  }\n\n  // Container title: array in Crossref, take first\n  const containerArr = message[\"container-title\"] as string[] | undefined;\n  const firstContainer = Array.isArray(containerArr) ? containerArr[0] : undefined;\n  if (firstContainer) {\n    metadata.containerTitle = firstContainer;\n  }\n\n  // Type\n  if (typeof message.type === \"string\") {\n    metadata.type = message.type;\n  }\n\n  // Page, volume, issue\n  if (typeof message.page === \"string\") metadata.page = message.page;\n  if (typeof message.volume === \"string\") metadata.volume = message.volume;\n  if (typeof message.issue === \"string\") metadata.issue = message.issue;\n\n  // Issued\n  const issued = message.issued as { \"date-parts\"?: number[][] } | undefined;\n  if (issued && Array.isArray(issued[\"date-parts\"])) {\n    metadata.issued = issued;\n  }\n\n  // Return undefined if no metadata fields were populated (prevents spurious diffs)\n  if (Object.keys(metadata).length === 0) return undefined;\n\n  return metadata;\n}\n\n/**\n * Query Crossref REST API for a DOI and extract update-to information.\n *\n * @param doi - The DOI to query\n * @param config - Optional config with email for polite pool\n * @returns Crossref result with update information\n */\nexport async function queryCrossref(\n  doi: string,\n  config?: { email?: string }\n): Promise<CrossrefResult> {\n  const rateLimiter = getRateLimiter(\"crossref\", {});\n  await rateLimiter.acquire();\n\n  try {\n    const url = new URL(`${CROSSREF_API_BASE}/${encodeURIComponent(doi)}`);\n    if (config?.email) {\n      url.searchParams.set(\"mailto\", config.email);\n    }\n    const response = await fetch(url.toString());\n\n    if (!response.ok) {\n      return {\n        success: false,\n        error: `Crossref API returned ${response.status} ${response.statusText}`,\n      };\n    }\n\n    const data = (await response.json()) as Record<string, unknown>;\n    const message = data.message as Record<string, unknown> | undefined;\n\n    const updateTo = (message?.[\"update-to\"] ?? []) as Record<string, unknown>[];\n    const updatedBy = (message?.[\"updated-by\"] ?? []) as Record<string, unknown>[];\n    const allEntries: CrossrefUpdateInfo[] = [...updateTo, ...updatedBy].map((e) => {\n      const datePart = formatDateParts(e.updated);\n      return {\n        type: String(e.type ?? \"\"),\n        ...(e.DOI ? { doi: String(e.DOI) } : {}),\n        ...(e.label ? { label: String(e.label) } : {}),\n        ...(datePart.date ? { date: datePart.date } : {}),\n      };\n    });\n\n    const seen = new Set<string>();\n    const updates = allEntries.filter((e) => {\n      const key = `${e.type}:${e.doi ?? \"\"}`;\n      if (seen.has(key)) return false;\n      seen.add(key);\n      return true;\n    });\n\n    const metadata = extractMetadata(message);\n\n    return metadata ? { success: true, updates, metadata } : { success: true, updates };\n  } catch (error) {\n    return {\n      success: false,\n      error: error instanceof Error ? error.message : String(error),\n    };\n  }\n}\n"],"names":[],"mappings":";AAEA,MAAM,oBAAoB;AA2B1B,SAAS,gBAAgB,SAAqC;AAC5D,MAAI,CAAC,WAAW,OAAO,YAAY,iBAAiB,CAAA;AACpD,QAAM,YAAa,QAAoC,YAAY;AACnE,MAAI,CAAC,MAAM,QAAQ,SAAS,KAAK,UAAU,WAAW,EAAG,QAAO,CAAA;AAChE,QAAM,QAAQ,UAAU,CAAC;AACzB,MAAI,CAAC,MAAM,QAAQ,KAAK,KAAK,MAAM,WAAW,EAAG,QAAO,CAAA;AACxD,QAAM,CAAC,MAAM,OAAO,GAAG,IAAI;AAC3B,QAAM,IAAI,OAAO,SAAS,CAAC,EAAE,SAAS,GAAG,GAAG;AAC5C,QAAM,IAAI,OAAO,OAAO,CAAC,EAAE,SAAS,GAAG,GAAG;AAC1C,SAAO,EAAE,MAAM,GAAG,IAAI,IAAI,CAAC,IAAI,CAAC,GAAA;AAClC;AAKA,SAAS,gBAAgB,SAA0E;AACjG,MAAI,CAAC,QAAS,QAAO;AAErB,QAAM,WAA2B,CAAA;AAGjC,QAAM,WAAW,QAAQ;AACzB,QAAM,aAAa,MAAM,QAAQ,QAAQ,IAAI,SAAS,CAAC,IAAI;AAC3D,MAAI,YAAY;AACd,aAAS,QAAQ;AAAA,EACnB;AAGA,QAAM,YAAY,QAAQ;AAC1B,MAAI,MAAM,QAAQ,SAAS,KAAK,UAAU,SAAS,GAAG;AACpD,aAAS,SAAS,UAAU,IAAI,CAAC,OAAO;AAAA,MACtC,GAAI,EAAE,SAAS,EAAE,QAAQ,EAAE,OAAA,IAAW,CAAA;AAAA,MACtC,GAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAA,IAAU,CAAA;AAAA,IAAC,EACpC;AAAA,EACJ;AAGA,QAAM,eAAe,QAAQ,iBAAiB;AAC9C,QAAM,iBAAiB,MAAM,QAAQ,YAAY,IAAI,aAAa,CAAC,IAAI;AACvE,MAAI,gBAAgB;AAClB,aAAS,iBAAiB;AAAA,EAC5B;AAGA,MAAI,OAAO,QAAQ,SAAS,UAAU;AACpC,aAAS,OAAO,QAAQ;AAAA,EAC1B;AAGA,MAAI,OAAO,QAAQ,SAAS,SAAU,UAAS,OAAO,QAAQ;AAC9D,MAAI,OAAO,QAAQ,WAAW,SAAU,UAAS,SAAS,QAAQ;AAClE,MAAI,OAAO,QAAQ,UAAU,SAAU,UAAS,QAAQ,QAAQ;AAGhE,QAAM,SAAS,QAAQ;AACvB,MAAI,UAAU,MAAM,QAAQ,OAAO,YAAY,CAAC,GAAG;AACjD,aAAS,SAAS;AAAA,EACpB;AAGA,MAAI,OAAO,KAAK,QAAQ,EAAE,WAAW,EAAG,QAAO;AAE/C,SAAO;AACT;AASA,eAAsB,cACpB,KACA,QACyB;AACzB,QAAM,cAAc,eAAe,YAAY,EAAE;AACjD,QAAM,YAAY,QAAA;AAElB,MAAI;AACF,UAAM,MAAM,IAAI,IAAI,GAAG,iBAAiB,IAAI,mBAAmB,GAAG,CAAC,EAAE;AACrE,QAAI,QAAQ,OAAO;AACjB,UAAI,aAAa,IAAI,UAAU,OAAO,KAAK;AAAA,IAC7C;AACA,UAAM,WAAW,MAAM,MAAM,IAAI,UAAU;AAE3C,QAAI,CAAC,SAAS,IAAI;AAChB,aAAO;AAAA,QACL,SAAS;AAAA,QACT,OAAO,yBAAyB,SAAS,MAAM,IAAI,SAAS,UAAU;AAAA,MAAA;AAAA,IAE1E;AAEA,UAAM,OAAQ,MAAM,SAAS,KAAA;AAC7B,UAAM,UAAU,KAAK;AAErB,UAAM,WAAY,UAAU,WAAW,KAAK,CAAA;AAC5C,UAAM,YAAa,UAAU,YAAY,KAAK,CAAA;AAC9C,UAAM,aAAmC,CAAC,GAAG,UAAU,GAAG,SAAS,EAAE,IAAI,CAAC,MAAM;AAC9E,YAAM,WAAW,gBAAgB,EAAE,OAAO;AAC1C,aAAO;AAAA,QACL,MAAM,OAAO,EAAE,QAAQ,EAAE;AAAA,QACzB,GAAI,EAAE,MAAM,EAAE,KAAK,OAAO,EAAE,GAAG,EAAA,IAAM,CAAA;AAAA,QACrC,GAAI,EAAE,QAAQ,EAAE,OAAO,OAAO,EAAE,KAAK,EAAA,IAAM,CAAA;AAAA,QAC3C,GAAI,SAAS,OAAO,EAAE,MAAM,SAAS,KAAA,IAAS,CAAA;AAAA,MAAC;AAAA,IAEnD,CAAC;AAED,UAAM,2BAAW,IAAA;AACjB,UAAM,UAAU,WAAW,OAAO,CAAC,MAAM;AACvC,YAAM,MAAM,GAAG,EAAE,IAAI,IAAI,EAAE,OAAO,EAAE;AACpC,UAAI,KAAK,IAAI,GAAG,EAAG,QAAO;AAC1B,WAAK,IAAI,GAAG;AACZ,aAAO;AAAA,IACT,CAAC;AAED,UAAM,WAAW,gBAAgB,OAAO;AAExC,WAAO,WAAW,EAAE,SAAS,MAAM,SAAS,aAAa,EAAE,SAAS,MAAM,QAAA;AAAA,EAC5E,SAAS,OAAO;AACd,WAAO;AAAA,MACL,SAAS;AAAA,MACT,OAAO,iBAAiB,QAAQ,MAAM,UAAU,OAAO,KAAK;AAAA,IAAA;AAAA,EAEhE;AACF;"}

package/dist/chunks/{fix-interaction-BpfMLRNY.js → fix-interaction-DNXbmlPr.js}

@@ -1,6 +1,6 @@
 import { render } from "ink";
 import { createElement } from "react";
-import { S as Select, r as restoreStdinAfterInk } from "./index-QTYx5RaF.js";
+import { S as Select, r as restoreStdinAfterInk } from "./index-BEQ4YIXx.js";
 function getFixActionsForFinding(finding) {
   switch (finding.type) {
     case "retracted":
@@ -22,6 +22,12 @@ function getFixActionsForFinding(finding) {
         { type: "add_concern_note", label: "Add note with concern details" },
         { type: "skip", label: "Skip" }
       ];
+    case "metadata_mismatch":
+    case "metadata_outdated":
+      return [
+        { type: "update_all_fields", label: "Update all changed fields from remote" },
+        { type: "skip", label: "Skip" }
+      ];
     default:
       return [];
   }
@@ -66,6 +72,64 @@ async function applyNoteAction(library, item, prefix, finding) {
   await library.save();
   return { applied: true, message: `Added note: ${noteText}` };
 }
+async function applyUpdateFromPublished(library, item, finding) {
+  const newDoi = finding.details?.newDoi;
+  if (!newDoi) {
+    return { applied: false, message: "No published DOI available in finding details" };
+  }
+  const { fetchDoi } = await import("./index-of6eJn8N.js").then((n) => n.y);
+  const fetchResult = await fetchDoi(newDoi);
+  if (!fetchResult.success) {
+    return {
+      applied: false,
+      message: `Failed to fetch metadata for ${newDoi}: ${fetchResult.error}`
+    };
+  }
+  const { id: _id, custom: _custom, ...metadata } = fetchResult.item;
+  await library.update(item.id, metadata, { idType: "id" });
+  await library.save();
+  return { applied: true, message: `Updated metadata from ${newDoi}` };
+}
+async function applyUpdateAllFields(library, item, finding) {
+  let fetchedItem;
+  if (item.DOI) {
+    const { fetchDoi } = await import("./index-of6eJn8N.js").then((n) => n.y);
+    const fetchResult = await fetchDoi(item.DOI);
+    if (!fetchResult.success) {
+      return {
+        applied: false,
+        message: `Failed to fetch metadata for DOI ${item.DOI}: ${fetchResult.error}`
+      };
+    }
+    fetchedItem = fetchResult.item;
+  } else if (item.PMID) {
+    const { fetchPmids } = await import("./index-of6eJn8N.js").then((n) => n.y);
+    const results = await fetchPmids([item.PMID], {});
+    const result = results[0];
+    if (!result || !result.success) {
+      return {
+        applied: false,
+        message: `Failed to fetch metadata for PMID ${item.PMID}: ${result?.error ?? "unknown error"}`
+      };
+    }
+    fetchedItem = result.item;
+  } else {
+    return { applied: false, message: "No DOI or PMID available for metadata update" };
+  }
+  const updatedFields = finding.details?.updatedFields ?? [];
+  const updates = {};
+  for (const field of updatedFields) {
+    if (field in fetchedItem) {
+      updates[field] = fetchedItem[field];
+    }
+  }
+  if (Object.keys(updates).length === 0) {
+    return { applied: false, message: "No fields to update" };
+  }
+  await library.update(item.id, updates, { idType: "id" });
+  await library.save();
+  return { applied: true, message: `Updated fields: ${updatedFields.join(", ")}` };
+}
 async function applyFixAction(library, item, finding, actionType) {
   switch (actionType) {
     case "add_retracted_tag":
@@ -86,24 +150,15 @@ async function applyFixAction(library, item, finding, actionType) {
       await library.save();
       return { applied: true, message: `Removed ${item.id}`, removed: true };
     }
-    case "update_from_published": {
-      const newDoi = finding.details?.newDoi;
-      if (!newDoi) {
-        return { applied: false, message: "No published DOI available in finding details" };
-      }
-      const { fetchDoi } = await import("./index-D2HsxXnK.js").then((n) => n.y);
-      const fetchResult = await fetchDoi(newDoi);
-      if (!fetchResult.success) {
-        return {
-          applied: false,
-          message: `Failed to fetch metadata for ${newDoi}: ${fetchResult.error}`
-        };
-      }
-      const { id: _id, custom: _custom, ...metadata } = fetchResult.item;
-      await library.update(item.id, metadata, { idType: "id" });
-      await library.save();
-      return { applied: true, message: `Updated metadata from ${newDoi}` };
-    }
+    case "update_from_published":
+      return applyUpdateFromPublished(library, item, finding);
+    case "update_all_fields":
+      return applyUpdateAllFields(library, item, finding);
+    // Placeholder for programmatic API (MCP/server) use.
+    // Individual field selection is not available in interactive CLI mode,
+    // but can be used via the MCP tool or HTTP server API.
+    case "update_selected_fields":
+      return { applied: false, message: "Field selection not available in CLI mode" };
     case "skip":
       return { applied: true, message: "Skipped" };
     default:
@@ -142,6 +197,10 @@ function getStatusLabel(type) {
       return "CONCERN";
     case "version_changed":
       return "VERSION";
+    case "metadata_mismatch":
+      return "MISMATCH";
+    case "metadata_outdated":
+      return "OUTDATED";
     default:
       return "WARNING";
   }
@@ -200,4 +259,4 @@ async function runFixInteraction(results, library, findItem) {
 export {
   runFixInteraction
 };
-//# sourceMappingURL=fix-interaction-BpfMLRNY.js.map
+//# sourceMappingURL=fix-interaction-DNXbmlPr.js.map

package/dist/chunks/fix-interaction-DNXbmlPr.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fix-interaction-DNXbmlPr.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, 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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 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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, 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