@ncukondo/reference-manager 0.7.1 → 0.9.0

package/dist/chunks/{index-_7NEUoS7.js → index-DmMZCOno.js}

@@ -1,5 +1,5 @@
 import { Hono } from "hono";
-import { e as CslItemSchema, d as detectDuplicate, h as generateId, q as sortOrderSchema, u as sortFieldSchema, p as pickDefined, t as tokenize, s as search$1, b as sortResults, v as searchSortFieldSchema, L as Library, F as FileWatcher } from "./file-watcher-D7oyc-9z.js";
+import { e as CslItemSchema, d as detectDuplicate, h as generateId, q as sortOrderSchema, u as sortFieldSchema, p as pickDefined, t as tokenize, s as search$1, b as sortResults, v as searchSortFieldSchema, L as Library, F as FileWatcher } from "./file-watcher-DdhXSm1l.js";
 import { existsSync, readFileSync } from "node:fs";
 import { Cite } from "@citation-js/core";
 import "@citation-js/plugin-doi";
@@ -7,8 +7,9 @@ import "@citation-js/plugin-isbn";
 import "@citation-js/plugin-bibtex";
 import "@citation-js/plugin-ris";
 import { z } from "zod";
-import "node:path";
+import { join } from "node:path";
 import "@citation-js/plugin-csl";
+import { unlink } from "node:fs/promises";
 async function updateReference(library, options) {
   const { identifier, idType = "id", updates, onIdCollision = "fail" } = options;
   const updateResult = await library.update(identifier, updates, { idType, onIdCollision });
@@ -120,6 +121,61 @@ const BUILTIN_STYLES = ["apa", "vancouver", "harvard"];
 function isBuiltinStyle(styleName) {
   return BUILTIN_STYLES.includes(styleName);
 }
+function getFulltextAttachmentTypes(item) {
+  const types = [];
+  const fulltext = item.custom?.fulltext;
+  if (fulltext?.pdf) {
+    types.push("pdf");
+  }
+  if (fulltext?.markdown) {
+    types.push("markdown");
+  }
+  return types;
+}
+async function deleteFulltextFiles(item, fulltextDirectory) {
+  const fulltext = item.custom?.fulltext;
+  if (!fulltext) {
+    return;
+  }
+  const filesToDelete = [];
+  if (fulltext.pdf) {
+    filesToDelete.push(join(fulltextDirectory, fulltext.pdf));
+  }
+  if (fulltext.markdown) {
+    filesToDelete.push(join(fulltextDirectory, fulltext.markdown));
+  }
+  for (const filePath of filesToDelete) {
+    try {
+      await unlink(filePath);
+    } catch {
+    }
+  }
+}
+async function removeReference(library, options) {
+  const { identifier, idType = "id", fulltextDirectory, deleteFulltext = false } = options;
+  const result = await library.remove(identifier, { idType });
+  if (!result.removed || !result.removedItem) {
+    return { removed: false };
+  }
+  let deletedFulltextTypes;
+  if (deleteFulltext && fulltextDirectory) {
+    deletedFulltextTypes = getFulltextAttachmentTypes(result.removedItem);
+    if (deletedFulltextTypes.length > 0) {
+      await deleteFulltextFiles(result.removedItem, fulltextDirectory);
+    }
+  }
+  await library.save();
+  return {
+    removed: true,
+    removedItem: result.removedItem,
+    ...deletedFulltextTypes && deletedFulltextTypes.length > 0 && { deletedFulltextTypes }
+  };
+}
+const remove = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  getFulltextAttachmentTypes,
+  removeReference
+}, Symbol.toStringTag, { value: "Module" }));
 const DEFAULT_TTL_MS = 60 * 60 * 1e3;
 const pmidCache = /* @__PURE__ */ new Map();
 const doiCache = /* @__PURE__ */ new Map();
@@ -208,7 +264,8 @@ function normalizeIsbn(isbn) {
 const EXTENSION_MAP = {
   ".json": "json",
   ".bib": "bibtex",
-  ".ris": "ris"
+  ".ris": "ris",
+  ".nbib": "nbib"
 };
 const DOI_URL_PREFIXES = [
   "https://doi.org/",
@@ -237,6 +294,9 @@ function detectByContent(content) {
   if (trimmed.startsWith("TY  -")) {
     return "ris";
   }
+  if (trimmed.startsWith("PMID-")) {
+    return "nbib";
+  }
   return detectIdentifier(trimmed);
 }
 function detectIdentifier(input) {
@@ -440,13 +500,15 @@ function buildPmidResult(pmid, foundItems, validationErrors) {
     return {
       pmid,
       success: false,
-      error: `Invalid CSL-JSON data: ${validationError}`
+      error: `Invalid CSL-JSON data: ${validationError}`,
+      reason: "validation_error"
     };
   }
   return {
     pmid,
     success: false,
-    error: `PMID ${pmid} not found`
+    error: `PMID ${pmid} not found`,
+    reason: "not_found"
   };
 }
 async function fetchPmids(pmids, config) {
@@ -467,7 +529,8 @@ async function fetchPmids(pmids, config) {
       return pmids.map((pmid) => ({
         pmid,
         success: false,
-        error: errorMsg
+        error: errorMsg,
+        reason: "fetch_error"
       }));
     }
     const data = await response.json();
@@ -479,7 +542,8 @@ async function fetchPmids(pmids, config) {
     return pmids.map((pmid) => ({
       pmid,
       success: false,
-      error: errorMsg
+      error: errorMsg,
+      reason: "fetch_error"
     }));
   }
 }
@@ -487,7 +551,8 @@ async function fetchDoi(doi) {
   if (!DOI_PATTERN.test(doi)) {
     return {
       success: false,
-      error: `Invalid DOI format: ${doi}`
+      error: `Invalid DOI format: ${doi}`,
+      reason: "validation_error"
     };
   }
   const rateLimiter = getRateLimiter("crossref", {});
@@ -498,14 +563,16 @@ async function fetchDoi(doi) {
     if (!rawItems || !Array.isArray(rawItems) || rawItems.length === 0) {
       return {
         success: false,
-        error: `No data returned for DOI ${doi}`
+        error: `No data returned for DOI ${doi}`,
+        reason: "not_found"
       };
     }
     const parseResult = CslItemSchema.safeParse(rawItems[0]);
     if (!parseResult.success) {
       return {
         success: false,
-        error: `Invalid CSL-JSON data for DOI ${doi}: ${parseResult.error.message}`
+        error: `Invalid CSL-JSON data for DOI ${doi}: ${parseResult.error.message}`,
+        reason: "validation_error"
       };
     }
     return { success: true, item: parseResult.data };
@@ -513,7 +580,8 @@ async function fetchDoi(doi) {
     const errorMsg = error instanceof Error ? error.message : String(error);
     return {
       success: false,
-      error: errorMsg
+      error: errorMsg,
+      reason: "fetch_error"
     };
   }
 }
@@ -523,7 +591,8 @@ async function fetchIsbn(isbn) {
   if (!ISBN10_PATTERN.test(isbn) && !ISBN13_PATTERN.test(isbn)) {
     return {
       success: false,
-      error: `Invalid ISBN format: ${isbn}`
+      error: `Invalid ISBN format: ${isbn}`,
+      reason: "validation_error"
     };
   }
   const rateLimiter = getRateLimiter("isbn", {});
@@ -534,14 +603,16 @@ async function fetchIsbn(isbn) {
     if (!rawItems || !Array.isArray(rawItems) || rawItems.length === 0) {
       return {
         success: false,
-        error: `No data returned for ISBN ${isbn}`
+        error: `No data returned for ISBN ${isbn}`,
+        reason: "not_found"
       };
     }
     const parseResult = CslItemSchema.safeParse(rawItems[0]);
     if (!parseResult.success) {
       return {
         success: false,
-        error: `Invalid CSL-JSON data for ISBN ${isbn}: ${parseResult.error.message}`
+        error: `Invalid CSL-JSON data for ISBN ${isbn}: ${parseResult.error.message}`,
+        reason: "validation_error"
       };
     }
     return { success: true, item: parseResult.data };
@@ -549,7 +620,8 @@ async function fetchIsbn(isbn) {
     const errorMsg = error instanceof Error ? error.message : String(error);
     return {
       success: false,
-      error: errorMsg
+      error: errorMsg,
+      reason: "fetch_error"
     };
   }
 }
@@ -559,6 +631,145 @@ function parseBibtex(content) {
 function parseRis(content) {
   return parseWithCitationJs(content, "ris");
 }
+const NBIB_TO_RIS_TAG_MAP = {
+  PMID: "AN",
+  // PubMed ID -> Accession Number
+  TI: "TI",
+  // Title -> Title
+  FAU: "AU",
+  // Full Author -> Author
+  AU: "AU",
+  // Author -> Author (short form, use FAU when available)
+  JT: "JO",
+  // Journal Title -> Journal Name
+  TA: "JA",
+  // Title Abbreviation -> Journal Abbreviation
+  AB: "AB",
+  // Abstract -> Abstract
+  VI: "VL",
+  // Volume -> Volume
+  IP: "IS",
+  // Issue/Part -> Issue Number
+  PG: "SP",
+  // Pagination -> Start Page (includes range)
+  DP: "PY",
+  // Date of Publication -> Publication Year
+  LA: "LA",
+  // Language -> Language
+  MH: "KW",
+  // MeSH Headings -> Keywords
+  OT: "KW",
+  // Other Terms -> Keywords
+  AD: "AD",
+  // Affiliation/Address -> Author Address
+  IS: "SN",
+  // ISSN -> Serial Number
+  PT: "TY"
+  // Publication Type -> Type of Reference
+};
+const NBIB_PUBLICATION_TYPE_MAP = {
+  "Journal Article": "JOUR",
+  Review: "JOUR",
+  Book: "BOOK",
+  "Book Chapter": "CHAP",
+  "Conference Paper": "CPAPER",
+  Thesis: "THES",
+  Report: "RPRT"
+};
+function parseNbibEntry(entry) {
+  const result = [];
+  const lines = entry.split("\n");
+  let currentTag = "";
+  let currentValue = "";
+  for (const line of lines) {
+    const tagMatch = line.match(/^([A-Z]{2,4})\s*-\s*(.*)$/);
+    if (tagMatch) {
+      if (currentTag) {
+        result.push({ tag: currentTag, value: currentValue.trim() });
+      }
+      currentTag = tagMatch[1] ?? "";
+      currentValue = tagMatch[2] ?? "";
+    } else if (currentTag && line.match(/^\s+/)) {
+      currentValue += ` ${line.trim()}`;
+    }
+  }
+  if (currentTag) {
+    result.push({ tag: currentTag, value: currentValue.trim() });
+  }
+  return result;
+}
+function convertNbibTagToRisLine(tag, value) {
+  if (tag === "AID" && value.includes("[doi]")) {
+    const doi = value.replace(/\s*\[doi\].*$/, "").trim();
+    return { line: `DO  - ${doi}` };
+  }
+  if (tag === "AID" && value.includes("[pii]")) {
+    const pii = value.replace(/\s*\[pii\].*$/, "").trim();
+    return { line: `C1  - ${pii}` };
+  }
+  const risTag = NBIB_TO_RIS_TAG_MAP[tag];
+  if (!risTag) {
+    return null;
+  }
+  if (risTag === "PY") {
+    const yearMatch = value.match(/^(\d{4})/);
+    return yearMatch ? { line: `PY  - ${yearMatch[1]}` } : null;
+  }
+  if (risTag === "TY") {
+    const risType = NBIB_PUBLICATION_TYPE_MAP[value] || "JOUR";
+    return { line: `TY  - ${risType}`, isType: true };
+  }
+  return { line: `${risTag}  - ${value}` };
+}
+function convertSingleNbibEntryToRis(entry) {
+  const parsed = parseNbibEntry(entry);
+  if (parsed.length === 0) {
+    return "";
+  }
+  const risLines = [];
+  let hasType = false;
+  for (const { tag, value } of parsed) {
+    const converted = convertNbibTagToRisLine(tag, value);
+    if (!converted) {
+      continue;
+    }
+    if (converted.isType) {
+      risLines.unshift(converted.line);
+      hasType = true;
+    } else {
+      risLines.push(converted.line);
+    }
+  }
+  if (!hasType) {
+    risLines.unshift("TY  - JOUR");
+  }
+  risLines.push("ER  -");
+  return risLines.join("\n");
+}
+function convertNbibToRis(content) {
+  const trimmed = content.trim();
+  if (!trimmed) {
+    return "";
+  }
+  const entries = trimmed.split(/\n\s*\n/).filter((e) => e.trim());
+  const risEntries = entries.map((entry) => convertSingleNbibEntryToRis(entry)).filter(Boolean);
+  return risEntries.join("\n\n");
+}
+function parseNbib(content) {
+  const trimmed = content.trim();
+  if (!trimmed) {
+    return { success: true, items: [] };
+  }
+  const risContent = convertNbibToRis(trimmed);
+  if (!risContent) {
+    return {
+      success: false,
+      items: [],
+      error: "Failed to convert NBIB to RIS: No valid entries found"
+    };
+  }
+  return parseRis(risContent);
+}
 function parseWithCitationJs(content, format) {
   const trimmed = content.trim();
   if (!trimmed) {
@@ -622,7 +833,8 @@ function buildUnknownResults(unknowns) {
   return unknowns.map((unknown) => ({
     success: false,
     error: `Cannot interpret '${unknown}' as identifier (not a valid PMID or DOI)`,
-    source: unknown
+    source: unknown,
+    reason: "validation_error"
   }));
 }
 async function fetchPmidsWithCache(pmids, pubmedConfig) {
@@ -650,7 +862,8 @@ async function fetchPmidsWithCache(pmids, pubmedConfig) {
         results.push({
           success: false,
           error: fetchResult.error,
-          source: fetchResult.pmid
+          source: fetchResult.pmid,
+          reason: fetchResult.reason
         });
       }
     }
@@ -670,7 +883,12 @@ async function fetchDoisWithCache(dois) {
       cacheDoiResult(doi, fetchResult.item);
       results.push({ success: true, item: fetchResult.item, source: doi });
     } else {
-      results.push({ success: false, error: fetchResult.error, source: doi });
+      results.push({
+        success: false,
+        error: fetchResult.error,
+        source: doi,
+        reason: fetchResult.reason
+      });
     }
   }
   return results;
@@ -688,7 +906,12 @@ async function fetchIsbnsWithCache(isbns) {
       cacheIsbnResult(isbn, fetchResult.item);
       results.push({ success: true, item: fetchResult.item, source: isbn });
     } else {
-      results.push({ success: false, error: fetchResult.error, source: isbn });
+      results.push({
+        success: false,
+        error: fetchResult.error,
+        source: isbn,
+        reason: fetchResult.reason
+      });
     }
   }
   return results;
@@ -709,7 +932,8 @@ function parseJsonContent(content) {
         results.push({
           success: false,
           error: `Invalid CSL-JSON: ${parseResult.error.message}`,
-          source: "json"
+          source: "json",
+          reason: "validation_error"
         });
       }
     }
@@ -717,7 +941,14 @@ function parseJsonContent(content) {
   } catch (error) {
     const message = error instanceof Error ? error.message : String(error);
     return {
-      results: [{ success: false, error: `Failed to parse JSON: ${message}`, source: "json" }]
+      results: [
+        {
+          success: false,
+          error: `Failed to parse JSON: ${message}`,
+          source: "json",
+          reason: "parse_error"
+        }
+      ]
     };
   }
 }
@@ -726,7 +957,12 @@ function parseBibtexContent(content) {
   if (!parseResult.success) {
     return {
       results: [
-        { success: false, error: parseResult.error ?? "Failed to parse BibTeX", source: "bibtex" }
+        {
+          success: false,
+          error: parseResult.error ?? "Failed to parse BibTeX",
+          source: "bibtex",
+          reason: "parse_error"
+        }
       ]
     };
   }
@@ -746,7 +982,12 @@ function parseRisContent(content) {
   if (!parseResult.success) {
     return {
       results: [
-        { success: false, error: parseResult.error ?? "Failed to parse RIS", source: "ris" }
+        {
+          success: false,
+          error: parseResult.error ?? "Failed to parse RIS",
+          source: "ris",
+          reason: "parse_error"
+        }
       ]
     };
   }
@@ -761,6 +1002,31 @@ function parseRisContent(content) {
     }))
   };
 }
+function parseNbibContent(content) {
+  const parseResult = parseNbib(content);
+  if (!parseResult.success) {
+    return {
+      results: [
+        {
+          success: false,
+          error: parseResult.error ?? "Failed to parse NBIB",
+          source: "nbib",
+          reason: "parse_error"
+        }
+      ]
+    };
+  }
+  if (parseResult.items.length === 0) {
+    return { results: [] };
+  }
+  return {
+    results: parseResult.items.map((item) => ({
+      success: true,
+      item,
+      source: "nbib"
+    }))
+  };
+}
 async function importFromContent(content, format, _options) {
   let actualFormat;
   if (format === "auto") {
@@ -771,7 +1037,8 @@ async function importFromContent(content, format, _options) {
           {
             success: false,
             error: "Cannot detect input format. Use --format to specify explicitly.",
-            source: "content"
+            source: "content",
+            reason: "validation_error"
           }
         ]
       };
@@ -786,13 +1053,16 @@ async function importFromContent(content, format, _options) {
       return parseBibtexContent(content);
     case "ris":
       return parseRisContent(content);
+    case "nbib":
+      return parseNbibContent(content);
     default:
       return {
         results: [
           {
             success: false,
             error: `Unsupported format for content parsing: ${actualFormat}`,
-            source: "content"
+            source: "content",
+            reason: "validation_error"
           }
         ]
       };
@@ -839,7 +1109,8 @@ async function processFile(filePath, options) {
       {
         success: false,
         error: `Failed to read file: ${message}`,
-        source: filePath
+        source: filePath,
+        reason: "fetch_error"
       }
     ];
   }
@@ -858,7 +1129,8 @@ async function processIdentifiers(inputs, options) {
       results.push({
         success: false,
         error: `Cannot interpret '${input}' as identifier (not a valid PMID, DOI, or ISBN).${hint}`,
-        source: input
+        source: input,
+        reason: "validation_error"
       });
     }
   }
@@ -893,7 +1165,7 @@ async function importFromInputs(inputs, options) {
 }
 async function processStdinContent(content, options) {
   const format = options.format || "auto";
-  if (format === "json" || format === "bibtex" || format === "ris") {
+  if (format === "json" || format === "bibtex" || format === "ris" || format === "nbib") {
     const result = await importFromContent(content, format);
     return result.results.map((r) => ({
       ...r,
@@ -905,7 +1177,7 @@ async function processStdinContent(content, options) {
     return processIdentifiers(identifiers2, options);
   }
   const detectedFormat = detectByContent(content);
-  if (detectedFormat === "json" || detectedFormat === "bibtex" || detectedFormat === "ris") {
+  if (detectedFormat === "json" || detectedFormat === "bibtex" || detectedFormat === "ris" || detectedFormat === "nbib") {
     const result = await importFromContent(content, detectedFormat);
     return result.results.map((r) => ({
       ...r,
@@ -962,7 +1234,10 @@ function buildImportOptions(options) {
 }
 async function processImportResult(result, existingItems, addedIds, force, library) {
   if (!result.success) {
-    return { type: "failed", item: { source: result.source, error: result.error } };
+    return {
+      type: "failed",
+      item: { source: result.source, error: result.error, reason: result.reason }
+    };
   }
   const item = result.item;
   if (!force) {
@@ -971,7 +1246,11 @@ async function processImportResult(result, existingItems, addedIds, force, libra
     if (existingMatch) {
       return {
         type: "skipped",
-        item: { source: result.source, existingId: existingMatch.existing.id ?? "" }
+        item: {
+          source: result.source,
+          existingId: existingMatch.existing.id ?? "",
+          duplicateType: existingMatch.type
+        }
       };
     }
   }
@@ -979,10 +1258,12 @@ async function processImportResult(result, existingItems, addedIds, force, libra
   const generatedId = generateId(item);
   const { id, changed } = resolveIdCollision(generatedId, allExistingIds);
   const finalItem = { ...item, id };
-  await library.add(finalItem);
+  const addedToLibrary = await library.add(finalItem);
   addedIds.add(id);
+  const uuid = addedToLibrary.custom?.uuid ?? "";
   const addedItem = {
     id,
+    uuid,
     title: typeof finalItem.title === "string" ? finalItem.title : ""
   };
   if (changed) {
@@ -1526,14 +1807,6 @@ function createListRoute(library) {
   });
   return route;
 }
-async function removeReference(library, options) {
-  const { identifier, idType = "id" } = options;
-  const result = await library.remove(identifier, { idType });
-  if (result.removed) {
-    await library.save();
-  }
-  return result;
-}
 function createReferencesRoute(library) {
   const route = new Hono();
   route.get("/", async (c) => {
@@ -1785,8 +2058,10 @@ export {
   cite as d,
   search as e,
   formatBibliographyCSL as f,
+  getFulltextAttachmentTypes as g,
   list as l,
+  remove as r,
   startServerWithFileWatcher as s,
   updateReference as u
 };
-//# sourceMappingURL=index-_7NEUoS7.js.map
+//# sourceMappingURL=index-DmMZCOno.js.map