@ncukondo/reference-manager 0.25.0 → 0.26.0

package/dist/features/check/fix-interaction.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"fix-interaction.d.ts","sourceRoot":"","sources":["../../../src/features/check/fix-interaction.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iCAAiC,CAAC;AAKhE,OAAO,KAAK,EAAgB,WAAW,EAAE,MAAM,YAAY,CAAC;AAE5D,MAAM,WAAW,oBAAoB;IACnC,aAAa,EAAE,MAAM,CAAC;IACtB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,EAAE,CAAC;CACnB;AAgGD,wBAAsB,iBAAiB,CACrC,OAAO,EAAE,WAAW,EAAE,EACtB,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,CAAC,EAAE,EAAE,MAAM,KAAK,OAAO,GAAG,SAAS,GAC5C,OAAO,CAAC,oBAAoB,CAAC,CAoB/B"}

package/dist/features/check/metadata-comparator.d.ts

@@ -0,0 +1,37 @@
+/**
+ * Metadata comparator for classifying differences between local and remote metadata.
+ */
+import type { RemoteMetadata } from "./crossref-client.js";
+export interface MetadataComparisonResult {
+    classification: "metadata_mismatch" | "metadata_outdated" | "no_change";
+    changedFields: string[];
+    fieldDiffs: Array<{
+        field: string;
+        local: string | null;
+        remote: string | null;
+    }>;
+}
+/**
+ * Local item fields relevant for metadata comparison.
+ */
+export interface LocalMetadataFields {
+    title?: string;
+    author?: Array<{
+        family?: string;
+        given?: string;
+    }>;
+    "container-title"?: string;
+    type?: string;
+    page?: string;
+    volume?: string;
+    issue?: string;
+    issued?: {
+        "date-parts"?: number[][];
+    };
+}
+/**
+ * Compare local metadata fields against remote (Crossref) metadata.
+ * Classifies differences as metadata_mismatch, metadata_outdated, or no_change.
+ */
+export declare function compareMetadata(local: LocalMetadataFields, remote: RemoteMetadata): MetadataComparisonResult;
+//# sourceMappingURL=metadata-comparator.d.ts.map

package/dist/features/check/metadata-comparator.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"metadata-comparator.d.ts","sourceRoot":"","sources":["../../../src/features/check/metadata-comparator.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,MAAM,WAAW,wBAAwB;IACvC,cAAc,EAAE,mBAAmB,GAAG,mBAAmB,GAAG,WAAW,CAAC;IACxE,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,UAAU,EAAE,KAAK,CAAC;QAChB,KAAK,EAAE,MAAM,CAAC;QACd,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;QACrB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;KACvB,CAAC,CAAC;CACJ;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,KAAK,CAAC;QAAE,MAAM,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACpD,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE;QAAE,YAAY,CAAC,EAAE,MAAM,EAAE,EAAE,CAAA;KAAE,CAAC;CACxC;AAsHD;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,KAAK,EAAE,mBAAmB,EAC1B,MAAM,EAAE,cAAc,GACrB,wBAAwB,CAe1B"}

package/dist/features/check/metadata-similarity.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Metadata similarity functions for comparing local vs remote reference metadata.
+ */
+type AuthorName = {
+    family?: string;
+    given?: string;
+};
+/**
+ * Check if two titles are similar using Jaccard similarity and Containment coefficient.
+ * Returns true (similar) if Jaccard >= 0.5 OR Containment >= 0.8.
+ * Returns true if either title is empty/undefined (not enough data to compare).
+ */
+export declare function isTitleSimilar(local: string | undefined, remote: string | undefined): boolean;
+/**
+ * Check if author lists are similar using family name overlap ratio.
+ * Overlap = |local_families ∩ remote_families| / |local_families|
+ * Returns true (similar) if overlap >= 0.5.
+ * Returns true if either side has no authors (not enough data).
+ */
+export declare function isAuthorSimilar(local: AuthorName[] | undefined, remote: AuthorName[] | undefined): boolean;
+export {};
+//# sourceMappingURL=metadata-similarity.d.ts.map

package/dist/features/check/metadata-similarity.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"metadata-similarity.d.ts","sourceRoot":"","sources":["../../../src/features/check/metadata-similarity.ts"],"names":[],"mappings":"AAAA;;GAEG;AAIH,KAAK,UAAU,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAAC;AAWtD;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,SAAS,EAAE,MAAM,EAAE,MAAM,GAAG,SAAS,GAAG,OAAO,CAuB7F;AAeD;;;;;GAKG;AACH,wBAAgB,eAAe,CAC7B,KAAK,EAAE,UAAU,EAAE,GAAG,SAAS,EAC/B,MAAM,EAAE,UAAU,EAAE,GAAG,SAAS,GAC/B,OAAO,CAoBT"}

package/dist/features/check/types.d.ts

@@ -1,7 +1,7 @@
 /**
  * Check feature types
  */
-export type CheckStatus = "ok" | "retracted" | "concern" | "version_changed" | "metadata_changed";
+export type CheckStatus = "ok" | "retracted" | "concern" | "version_changed" | "metadata_mismatch" | "metadata_outdated";
 export interface CheckFinding {
     type: CheckStatus;
     message: string;
@@ -10,6 +10,11 @@ export interface CheckFinding {
         retractionDate?: string;
         newDoi?: string;
         updatedFields?: string[];
+        fieldDiffs?: Array<{
+            field: string;
+            local: string | null;
+            remote: string | null;
+        }>;
     };
 }
 export interface CheckResult {

package/dist/features/check/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/features/check/types.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,MAAM,MAAM,WAAW,GACnB,IAAI,GACJ,WAAW,GACX,SAAS,GACT,iBAAiB,GACjB,mBAAmB,GACnB,mBAAmB,CAAC;AAExB,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,WAAW,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE;QACR,aAAa,CAAC,EAAE,MAAM,CAAC;QACvB,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,aAAa,CAAC,EAAE,MAAM,EAAE,CAAC;QACzB,UAAU,CAAC,EAAE,KAAK,CAAC;YACjB,KAAK,EAAE,MAAM,CAAC;YACd,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;YACrB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;SACvB,CAAC,CAAC;KACJ,CAAC;CACH;AAED,MAAM,WAAW,WAAW;IAC1B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,IAAI,GAAG,SAAS,GAAG,SAAS,CAAC;IACrC,QAAQ,EAAE,YAAY,EAAE,CAAC;IACzB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,EAAE,CAAC;CAC1B"}

package/dist/features/operations/check.d.ts

@@ -7,6 +7,7 @@ export interface CheckOperationOptions {
     searchQuery?: string;
     skipDays?: number;
     save?: boolean;
+    metadata?: boolean;
     config?: {
         email?: string;
         pubmed?: {

package/dist/features/operations/check.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/features/operations/check.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,QAAQ,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAChF,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAErD,MAAM,WAAW,qBAAqB;IACpC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,MAAM,CAAC,EAAE,cAAc,CAAC;IACxB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,MAAM,CAAC,EAAE;YAAE,KAAK,CAAC,EAAE,MAAM,CAAC;YAAC,MAAM,CAAC,EAAE,MAAM,CAAA;SAAE,CAAA;KAAE,CAAC;CAC3E;AAED,MAAM,WAAW,oBAAoB;IACnC,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,OAAO,EAAE;QACP,KAAK,EAAE,MAAM,CAAC;QACd,EAAE,EAAE,MAAM,CAAC;QACX,QAAQ,EAAE,MAAM,CAAC;QACjB,OAAO,EAAE,MAAM,CAAC;KACjB,CAAC;CACH;AAiBD,wBAAsB,eAAe,CACnC,OAAO,EAAE,QAAQ,EACjB,OAAO,EAAE,qBAAqB,GAC7B,OAAO,CAAC,oBAAoB,CAAC,CAwB/B"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/features/operations/check.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,QAAQ,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAChF,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAErD,MAAM,WAAW,qBAAqB;IACpC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,MAAM,CAAC,EAAE,cAAc,CAAC;IACxB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,MAAM,CAAC,EAAE;YAAE,KAAK,CAAC,EAAE,MAAM,CAAC;YAAC,MAAM,CAAC,EAAE,MAAM,CAAA;SAAE,CAAA;KAAE,CAAC;CAC3E;AAED,MAAM,WAAW,oBAAoB;IACnC,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,OAAO,EAAE;QACP,KAAK,EAAE,MAAM,CAAC;QACd,EAAE,EAAE,MAAM,CAAC;QACX,QAAQ,EAAE,MAAM,CAAC;QACjB,OAAO,EAAE,MAAM,CAAC;KACjB,CAAC;CACH;AAiBD,wBAAsB,eAAe,CACnC,OAAO,EAAE,QAAQ,EACjB,OAAO,EAAE,qBAAqB,GAC7B,OAAO,CAAC,oBAAoB,CAAC,CA4B/B"}

package/dist/mcp/tools/check.d.ts

@@ -5,6 +5,7 @@ export interface CheckToolParams {
     all?: boolean | undefined;
     skipDays?: number | undefined;
     save?: boolean | undefined;
+    metadata?: boolean | undefined;
 }
 export declare function registerCheckTool(server: McpServer, getLibraryOperations: () => ILibraryOperations): void;
 //# sourceMappingURL=check.d.ts.map

package/dist/mcp/tools/check.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/mcp/tools/check.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAGzE,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,iDAAiD,CAAC;AAE1F,MAAM,WAAW,eAAe;IAC9B,GAAG,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IAC3B,GAAG,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC1B,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC9B,IAAI,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC3B,QAAQ,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAChC;AAyBD,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,SAAS,EACjB,oBAAoB,EAAE,MAAM,kBAAkB,GAC7C,IAAI,CA0CN"}

package/dist/server/routes/check.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/server/routes/check.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAE5B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AA2BrD,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAsBvD"}
+{"version":3,"file":"check.d.ts","sourceRoot":"","sources":["../../../src/server/routes/check.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAE5B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAC;AA6BrD,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAsBvD"}

package/dist/server.js

@@ -1,6 +1,6 @@
 import "hono";
 import "./chunks/file-watcher-Dlx0PolG.js";
-import { v, u } from "./chunks/index-D2HsxXnK.js";
+import { v, u } from "./chunks/index-of6eJn8N.js";
 export {
   v as createServer,
   u as startServerWithFileWatcher

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ncukondo/reference-manager",
-  "version": "0.25.0",
+  "version": "0.26.0",
   "description": "A local reference management tool using CSL-JSON as the single source of truth",
   "publishConfig": {
     "access": "public"

package/dist/chunks/checker-7pzK2XSC.js

@@ -1,92 +0,0 @@
-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: [] };
-  }
-  if (hasDoi) {
-    checkedSources.push("crossref");
-    const crossrefFindings = await checkCrossref(item.DOI, config);
-    findings.push(...crossrefFindings);
-  }
-  if (hasPmid) {
-    checkedSources.push("pubmed");
-    const pubmedFindings = await checkPubmed(item.PMID, config);
-    for (const pf of pubmedFindings) {
-      if (!findings.some((f) => f.type === pf.type)) {
-        findings.push(pf);
-      }
-    }
-  }
-  const status = findings.length > 0 ? "warning" : "ok";
-  return { id, uuid, status, findings, checkedAt, checkedSources };
-}
-async function checkCrossref(doi, config) {
-  const { queryCrossref } = await import("./crossref-client-DGNz4PNW.js");
-  const crossrefConfig = config?.email ? { email: config.email } : void 0;
-  const result = await queryCrossref(doi, crossrefConfig);
-  if (!result.success) return [];
-  const findings = [];
-  for (const update of result.updates) {
-    const finding = mapCrossrefUpdate(update);
-    if (finding) {
-      findings.push(finding);
-    }
-  }
-  return findings;
-}
-async function checkPubmed(pmid, config) {
-  const { queryPubmed } = await import("./pubmed-client-J18fg3fG.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-7pzK2XSC.js.map

package/dist/chunks/checker-7pzK2XSC.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"checker-7pzK2XSC.js","sources":["../../src/features/check/checker.ts"],"sourcesContent":["import type { CslItem } from \"../../core/csl-json/types.js\";\nimport type { CrossrefUpdateInfo } 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}\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  // Query Crossref if DOI is present\n  if (hasDoi) {\n    checkedSources.push(\"crossref\");\n    const crossrefFindings = await checkCrossref(item.DOI as string, config);\n    findings.push(...crossrefFindings);\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    // Only add PubMed findings that aren't already found via Crossref\n    for (const pf of pubmedFindings) {\n      if (!findings.some((f) => f.type === pf.type)) {\n        findings.push(pf);\n      }\n    }\n  }\n\n  const status = findings.length > 0 ? \"warning\" : \"ok\";\n  return { id, uuid, status, findings, checkedAt, checkedSources };\n}\n\n/**\n * Query Crossref and return findings.\n */\nasync function checkCrossref(doi: string, config?: CheckConfig): Promise<CheckFinding[]> {\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 [];\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 findings;\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 version available: ${update.doi}`\n          : \"Published version available\",\n        details: newDoiDetail,\n      };\n    default:\n      return null;\n  }\n}\n"],"names":[],"mappings":"AAgBA,eAAsB,eAAe,MAAe,QAA4C;AAC9F,QAAM,KAAK,KAAK;AAChB,QAAM,OAAQ,KAAK,QAAQ,QAAmB;AAC9C,QAAM,aAAY,oBAAI,KAAA,GAAO,YAAA;AAC7B,QAAM,WAA2B,CAAA;AACjC,QAAM,iBAA2B,CAAA;AAEjC,QAAM,SAAS,CAAC,CAAC,KAAK;AACtB,QAAM,UAAU,CAAC,CAAC,KAAK;AAGvB,MAAI,CAAC,UAAU,CAAC,SAAS;AACvB,WAAO,EAAE,IAAI,MAAM,QAAQ,WAAW,UAAU,IAAI,WAAW,gBAAgB,GAAC;AAAA,EAClF;AAGA,MAAI,QAAQ;AACV,mBAAe,KAAK,UAAU;AAC9B,UAAM,mBAAmB,MAAM,cAAc,KAAK,KAAe,MAAM;AACvE,aAAS,KAAK,GAAG,gBAAgB;AAAA,EACnC;AAGA,MAAI,SAAS;AACX,mBAAe,KAAK,QAAQ;AAC5B,UAAM,iBAAiB,MAAM,YAAY,KAAK,MAAgB,MAAM;AAEpE,eAAW,MAAM,gBAAgB;AAC/B,UAAI,CAAC,SAAS,KAAK,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,GAAG;AAC7C,iBAAS,KAAK,EAAE;AAAA,MAClB;AAAA,IACF;AAAA,EACF;AAEA,QAAM,SAAS,SAAS,SAAS,IAAI,YAAY;AACjD,SAAO,EAAE,IAAI,MAAM,QAAQ,UAAU,WAAW,eAAA;AAClD;AAKA,eAAe,cAAc,KAAa,QAA+C;AACvF,QAAM,EAAE,cAAA,IAAkB,MAAM,OAAO,+BAAsB;AAC7D,QAAM,iBAAiB,QAAQ,QAAQ,EAAE,OAAO,OAAO,UAAU;AACjE,QAAM,SAAS,MAAM,cAAc,KAAK,cAAc;AACtD,MAAI,CAAC,OAAO,QAAS,QAAO,CAAA;AAE5B,QAAM,WAA2B,CAAA;AACjC,aAAW,UAAU,OAAO,SAAS;AACnC,UAAM,UAAU,kBAAkB,MAAM;AACxC,QAAI,SAAS;AACX,eAAS,KAAK,OAAO;AAAA,IACvB;AAAA,EACF;AACA,SAAO;AACT;AAKA,eAAe,YAAY,MAAc,QAA+C;AACtF,QAAM,EAAE,YAAA,IAAgB,MAAM,OAAO,6BAAoB;AACzD,QAAM,SAAS,MAAM,YAAY,MAAM,QAAQ,MAAM;AACrD,MAAI,CAAC,OAAO,QAAS,QAAO,CAAA;AAE5B,QAAM,WAA2B,CAAA;AACjC,MAAI,OAAO,aAAa;AACtB,aAAS,KAAK;AAAA,MACZ,MAAM;AAAA,MACN,SAAS;AAAA,IAAA,CACV;AAAA,EACH;AACA,MAAI,OAAO,YAAY;AACrB,aAAS,KAAK;AAAA,MACZ,MAAM;AAAA,MACN,SAAS;AAAA,IAAA,CACV;AAAA,EACH;AACA,SAAO;AACT;AAKA,SAAS,kBAAkB,QAAiD;AAC1E,QAAM,YAAY,OAAO,MAAM,EAAE,eAAe,OAAO,IAAA,IAAQ,CAAA;AAC/D,QAAM,aAAa,OAAO,OAAO,EAAE,gBAAgB,OAAO,KAAA,IAAS,CAAA;AACnE,QAAM,eAAe,OAAO,MAAM,EAAE,QAAQ,OAAO,IAAA,IAAQ,CAAA;AAE3D,UAAQ,OAAO,MAAA;AAAA,IACb,KAAK;AACH,aAAO;AAAA,QACL,MAAM;AAAA,QACN,SAAS,OAAO,OACZ,iCAAiC,OAAO,IAAI,KAC5C;AAAA,QACJ,SAAS,EAAE,GAAG,WAAW,GAAG,WAAA;AAAA,MAAW;AAAA,IAE3C,KAAK;AACH,aAAO;AAAA,QACL,MAAM;AAAA,QACN,SAAS,OAAO,OACZ,mCAAmC,OAAO,IAAI,KAC9C;AAAA,QACJ,SAAS,EAAE,GAAG,WAAW,GAAG,WAAA;AAAA,MAAW;AAAA,IAE3C,KAAK;AACH,aAAO;AAAA,QACL,MAAM;AAAA,QACN,SAAS,OAAO,MACZ,gCAAgC,OAAO,GAAG,KAC1C;AAAA,QACJ,SAAS;AAAA,MAAA;AAAA,IAEb;AACE,aAAO;AAAA,EAAA;AAEb;"}

package/dist/chunks/crossref-client-DGNz4PNW.js

@@ -1,52 +0,0 @@
-import { g as getRateLimiter } from "./index-D2HsxXnK.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}-${d}` };
-}
-async function queryCrossref(doi, config) {
-  const rateLimiter = getRateLimiter("crossref", {});
-  await rateLimiter.acquire();
-  try {
-    const url = new URL(`${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 updates = updateTo.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 } : {}
-      };
-    });
-    return { success: true, updates };
-  } catch (error) {
-    return {
-      success: false,
-      error: error instanceof Error ? error.message : String(error)
-    };
-  }
-}
-export {
-  queryCrossref
-};
-//# sourceMappingURL=crossref-client-DGNz4PNW.js.map

package/dist/chunks/crossref-client-DGNz4PNW.js.map

@@ -1 +0,0 @@
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package/dist/chunks/fix-interaction-BpfMLRNY.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"fix-interaction-BpfMLRNY.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  | \"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    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\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      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      // Update with fetched metadata, preserving id and custom fields\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\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, 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