@ncukondo/reference-manager 0.5.3 → 0.7.0

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

@@ -1,5 +1,5 @@
 import { Hono } from "hono";
-import { e as CslItemSchema, d as detectDuplicate, t as tokenize, s as search$1, b as sortResults, L as Library, F as FileWatcher } from "./file-watcher-CBAbblss.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-D7oyc-9z.js";
 import { existsSync, readFileSync } from "node:fs";
 import { Cite } from "@citation-js/core";
 import "@citation-js/plugin-doi";
@@ -30,6 +30,92 @@ async function updateReference(library, options) {
   }
   return result;
 }
+function getCreatedAt(item) {
+  const createdAt = item.custom?.created_at;
+  if (!createdAt) return 0;
+  return new Date(createdAt).getTime();
+}
+function getUpdatedAt(item) {
+  const timestamp = item.custom?.timestamp;
+  if (timestamp) return new Date(timestamp).getTime();
+  return getCreatedAt(item);
+}
+function getPublishedDate(item) {
+  const dateParts = item.issued?.["date-parts"]?.[0];
+  if (!dateParts || dateParts.length === 0) return 0;
+  const year = dateParts[0] ?? 0;
+  const month = dateParts[1] ?? 1;
+  const day = dateParts[2] ?? 1;
+  return new Date(year, month - 1, day).getTime();
+}
+function getAuthorName(item) {
+  const firstAuthor = item.author?.[0];
+  if (!firstAuthor) return "Anonymous";
+  return firstAuthor.family ?? firstAuthor.literal ?? "Anonymous";
+}
+function getTitle(item) {
+  return item.title ?? "";
+}
+function getSortValue(item, field) {
+  switch (field) {
+    case "created":
+      return getCreatedAt(item);
+    case "updated":
+      return getUpdatedAt(item);
+    case "published":
+      return getPublishedDate(item);
+    case "author":
+      return getAuthorName(item).toLowerCase();
+    case "title":
+      return getTitle(item).toLowerCase();
+  }
+}
+function compareValues(a, b, order) {
+  const multiplier = order === "desc" ? -1 : 1;
+  if (typeof a === "number" && typeof b === "number") {
+    return (a - b) * multiplier;
+  }
+  const strA = String(a);
+  const strB = String(b);
+  return strA.localeCompare(strB) * multiplier;
+}
+function sortReferences(items, sort, order) {
+  return [...items].sort((a, b) => {
+    const aValue = getSortValue(a, sort);
+    const bValue = getSortValue(b, sort);
+    const primaryCompare = compareValues(aValue, bValue, order);
+    if (primaryCompare !== 0) return primaryCompare;
+    const aCreated = getCreatedAt(a);
+    const bCreated = getCreatedAt(b);
+    const createdCompare = bCreated - aCreated;
+    if (createdCompare !== 0) return createdCompare;
+    return a.id.localeCompare(b.id);
+  });
+}
+function paginate(items, options) {
+  const offset = options.offset ?? 0;
+  const limit = options.limit ?? 0;
+  if (limit < 0) {
+    throw new Error("limit must be non-negative");
+  }
+  if (offset < 0) {
+    throw new Error("offset must be non-negative");
+  }
+  const isUnlimited = limit === 0;
+  const afterOffset = items.slice(offset);
+  const paginatedItems = isUnlimited ? afterOffset : afterOffset.slice(0, limit);
+  let nextOffset = null;
+  if (!isUnlimited && paginatedItems.length > 0) {
+    const nextPosition = offset + paginatedItems.length;
+    if (nextPosition < items.length) {
+      nextOffset = nextPosition;
+    }
+  }
+  return {
+    items: paginatedItems,
+    nextOffset
+  };
+}
 const BUILTIN_STYLES = ["apa", "vancouver", "harvard"];
 function isBuiltinStyle(styleName) {
   return BUILTIN_STYLES.includes(styleName);
@@ -764,13 +850,14 @@ async function processIdentifiers(inputs, options) {
   for (const input of inputs) {
     const isValidPmid = isPmid(input);
     const isValidDoi = isDoi(input);
-    if (isValidPmid || isValidDoi) {
+    const isValidIsbn = isIsbn(input);
+    if (isValidPmid || isValidDoi || isValidIsbn) {
       validIdentifiers.push(input);
     } else {
       const hint = looksLikeFilePath(input) ? " Hint: If this is a file path, check that the file exists." : "";
       results.push({
         success: false,
-        error: `Cannot interpret '${input}' as identifier (not a valid PMID or DOI).${hint}`,
+        error: `Cannot interpret '${input}' as identifier (not a valid PMID, DOI, or ISBN).${hint}`,
         source: input
       });
     }
@@ -889,7 +976,8 @@ async function processImportResult(result, existingItems, addedIds, force, libra
     }
   }
   const allExistingIds = /* @__PURE__ */ new Set([...existingItems.map((i) => i.id), ...addedIds]);
-  const { id, changed } = resolveIdCollision(item.id, allExistingIds);
+  const generatedId = generateId(item);
+  const { id, changed } = resolveIdCollision(generatedId, allExistingIds);
   const finalItem = { ...item, id };
   await library.add(finalItem);
   addedIds.add(id);
@@ -899,7 +987,7 @@ async function processImportResult(result, existingItems, addedIds, force, libra
   };
   if (changed) {
     addedItem.idChanged = true;
-    addedItem.originalId = item.id;
+    addedItem.originalId = generatedId;
   }
   return { type: "added", item: addedItem };
 }
@@ -930,6 +1018,47 @@ const add = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty(
   __proto__: null,
   addReferences
 }, Symbol.toStringTag, { value: "Module" }));
+function buildPubmedConfig(config) {
+  const pubmedConfig = {};
+  if (config.pubmed.email !== void 0) {
+    pubmedConfig.email = config.pubmed.email;
+  }
+  if (config.pubmed.apiKey !== void 0) {
+    pubmedConfig.apiKey = config.pubmed.apiKey;
+  }
+  return pubmedConfig;
+}
+function createAddRoute(library, config) {
+  const route = new Hono();
+  route.post("/", async (c) => {
+    let body;
+    try {
+      body = await c.req.json();
+    } catch {
+      return c.json({ error: "Invalid JSON" }, 400);
+    }
+    if (!body || typeof body !== "object") {
+      return c.json({ error: "Request body must be an object" }, 400);
+    }
+    const { inputs, options } = body;
+    if (!inputs || !Array.isArray(inputs) || inputs.length === 0) {
+      return c.json({ error: "inputs must be a non-empty array of strings" }, 400);
+    }
+    if (!inputs.every((input) => typeof input === "string")) {
+      return c.json({ error: "All inputs must be strings" }, 400);
+    }
+    const addOptions = {
+      force: options?.force ?? false,
+      pubmedConfig: buildPubmedConfig(config)
+    };
+    if (options?.format) {
+      addOptions.format = options.format;
+    }
+    const result = await addReferences(inputs, library, addOptions);
+    return c.json(result);
+  });
+  return route;
+}
 function formatAuthor(author) {
   const family = author.family || "";
   const givenInitial = author.given ? `${author.given.charAt(0)}.` : "";
@@ -1281,113 +1410,6 @@ const cite = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty
   __proto__: null,
   citeReferences
 }, Symbol.toStringTag, { value: "Module" }));
-async function listReferences(library, options) {
-  const format = options.format ?? "pretty";
-  const items = await library.getAll();
-  switch (format) {
-    case "json":
-      return { items: items.map((item) => JSON.stringify(item)) };
-    case "bibtex":
-      return { items: items.map((item) => formatBibtex([item])) };
-    case "ids-only":
-      return { items: items.map((item) => item.id) };
-    case "uuid":
-      return {
-        items: items.filter(
-          (item) => Boolean(item.custom?.uuid)
-        ).map((item) => item.custom.uuid)
-      };
-    default:
-      return { items: items.map((item) => formatPretty([item])) };
-  }
-}
-const list = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
-  __proto__: null,
-  listReferences
-}, Symbol.toStringTag, { value: "Module" }));
-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;
-}
-async function searchReferences(library, options) {
-  const format = options.format ?? "pretty";
-  const query = options.query;
-  const allItems = await library.getAll();
-  let matchedItems;
-  if (!query.trim()) {
-    matchedItems = allItems;
-  } else {
-    const tokens = tokenize(query).tokens;
-    const results = search$1(allItems, tokens);
-    const sorted = sortResults(results);
-    matchedItems = sorted.map((result) => result.reference);
-  }
-  switch (format) {
-    case "json":
-      return { items: matchedItems.map((item) => JSON.stringify(item)) };
-    case "bibtex":
-      return { items: matchedItems.map((item) => formatBibtex([item])) };
-    case "ids-only":
-      return { items: matchedItems.map((item) => item.id) };
-    case "uuid":
-      return {
-        items: matchedItems.filter(
-          (item) => Boolean(item.custom?.uuid)
-        ).map((item) => item.custom.uuid)
-      };
-    default:
-      return { items: matchedItems.map((item) => formatPretty([item])) };
-  }
-}
-const search = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
-  __proto__: null,
-  searchReferences
-}, Symbol.toStringTag, { value: "Module" }));
-function buildPubmedConfig(config) {
-  const pubmedConfig = {};
-  if (config.pubmed.email !== void 0) {
-    pubmedConfig.email = config.pubmed.email;
-  }
-  if (config.pubmed.apiKey !== void 0) {
-    pubmedConfig.apiKey = config.pubmed.apiKey;
-  }
-  return pubmedConfig;
-}
-function createAddRoute(library, config) {
-  const route = new Hono();
-  route.post("/", async (c) => {
-    let body;
-    try {
-      body = await c.req.json();
-    } catch {
-      return c.json({ error: "Invalid JSON" }, 400);
-    }
-    if (!body || typeof body !== "object") {
-      return c.json({ error: "Request body must be an object" }, 400);
-    }
-    const { inputs, options } = body;
-    if (!inputs || !Array.isArray(inputs) || inputs.length === 0) {
-      return c.json({ error: "inputs must be a non-empty array of strings" }, 400);
-    }
-    if (!inputs.every((input) => typeof input === "string")) {
-      return c.json({ error: "All inputs must be strings" }, 400);
-    }
-    const addOptions = {
-      force: options?.force ?? false,
-      pubmedConfig: buildPubmedConfig(config)
-    };
-    if (options?.format) {
-      addOptions.format = options.format;
-    }
-    const result = await addReferences(inputs, library, addOptions);
-    return c.json(result);
-  });
-  return route;
-}
 const CiteRequestSchema = z.object({
   identifiers: z.array(z.string()).min(1, "identifiers must be a non-empty array"),
   idType: z.enum(["id", "uuid", "doi", "pmid", "isbn"]).optional(),
@@ -1431,8 +1453,51 @@ const healthRoute = new Hono();
 healthRoute.get("/", (c) => {
   return c.json({ status: "ok" });
 });
+function formatItems$1(items, format) {
+  switch (format) {
+    case "json":
+      return items.map((item) => JSON.stringify(item));
+    case "bibtex":
+      return items.map((item) => formatBibtex([item]));
+    case "ids-only":
+      return items.map((item) => item.id);
+    case "uuid":
+      return items.filter(
+        (item) => Boolean(item.custom?.uuid)
+      ).map((item) => item.custom.uuid);
+    default:
+      return items.map((item) => formatPretty([item]));
+  }
+}
+async function listReferences(library, options) {
+  const format = options.format ?? "pretty";
+  const sort = options.sort ?? "updated";
+  const order = options.order ?? "desc";
+  const limit = options.limit ?? 0;
+  const offset = options.offset ?? 0;
+  const allItems = await library.getAll();
+  const total = allItems.length;
+  const sorted = sortReferences(allItems, sort, order);
+  const { items: paginatedItems, nextOffset } = paginate(sorted, { limit, offset });
+  const formattedItems = formatItems$1(paginatedItems, format);
+  return {
+    items: formattedItems,
+    total,
+    limit,
+    offset,
+    nextOffset
+  };
+}
+const list = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  listReferences
+}, Symbol.toStringTag, { value: "Module" }));
 const listRequestBodySchema = z.object({
-  format: z.enum(["pretty", "json", "bibtex", "ids-only", "uuid"]).optional()
+  format: z.enum(["pretty", "json", "bibtex", "ids-only", "uuid"]).optional(),
+  sort: sortFieldSchema.optional(),
+  order: sortOrderSchema.optional(),
+  limit: z.number().int().min(0).optional(),
+  offset: z.number().int().min(0).optional()
 });
 function createListRoute(library) {
   const route = new Hono();
@@ -1445,18 +1510,30 @@ function createListRoute(library) {
     }
     const parseResult = listRequestBodySchema.safeParse(body);
     if (!parseResult.success) {
-      return c.json({ error: "Request body must be an object" }, 400);
+      const errorMessage = parseResult.error.issues[0]?.message ?? "Invalid request body";
+      return c.json({ error: errorMessage }, 400);
     }
     const requestBody = parseResult.data;
-    const options = {};
-    if (requestBody.format !== void 0) {
-      options.format = requestBody.format;
-    }
+    const options = pickDefined(requestBody, [
+      "format",
+      "sort",
+      "order",
+      "limit",
+      "offset"
+    ]);
     const result = await listReferences(library, options);
     return c.json(result);
   });
   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) => {
@@ -1570,9 +1647,71 @@ function createReferencesRoute(library) {
   });
   return route;
 }
+function formatItems(items, format) {
+  switch (format) {
+    case "json":
+      return items.map((item) => JSON.stringify(item));
+    case "bibtex":
+      return items.map((item) => formatBibtex([item]));
+    case "ids-only":
+      return items.map((item) => item.id);
+    case "uuid":
+      return items.filter(
+        (item) => Boolean(item.custom?.uuid)
+      ).map((item) => item.custom.uuid);
+    default:
+      return items.map((item) => formatPretty([item]));
+  }
+}
+async function searchReferences(library, options) {
+  const format = options.format ?? "pretty";
+  const query = options.query;
+  const sort = options.sort ?? "updated";
+  const order = options.order ?? "desc";
+  const limit = options.limit ?? 0;
+  const offset = options.offset ?? 0;
+  const allItems = await library.getAll();
+  let matchedItems;
+  if (!query.trim()) {
+    matchedItems = allItems;
+  } else {
+    const tokens = tokenize(query).tokens;
+    const results = search$1(allItems, tokens);
+    if (sort === "relevance") {
+      const sorted2 = sortResults(results);
+      matchedItems = order === "desc" ? sorted2.map((r) => r.reference) : sorted2.map((r) => r.reference).reverse();
+    } else {
+      matchedItems = results.map((r) => r.reference);
+    }
+  }
+  const total = matchedItems.length;
+  let sorted;
+  if (sort === "relevance") {
+    sorted = matchedItems;
+  } else {
+    sorted = sortReferences(matchedItems, sort, order);
+  }
+  const { items: paginatedItems, nextOffset } = paginate(sorted, { limit, offset });
+  const formattedItems = formatItems(paginatedItems, format);
+  return {
+    items: formattedItems,
+    total,
+    limit,
+    offset,
+    nextOffset
+  };
+}
+const search = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
+  __proto__: null,
+  searchReferences
+}, Symbol.toStringTag, { value: "Module" }));
 const searchRequestBodySchema = z.object({
   query: z.string(),
-  format: z.enum(["pretty", "json", "bibtex", "ids-only", "uuid"]).optional()
+  format: z.enum(["pretty", "json", "bibtex", "ids-only", "uuid"]).optional(),
+  sort: searchSortFieldSchema.optional(),
+  order: sortOrderSchema.optional(),
+  limit: z.number().int().min(0).optional(),
+  offset: z.number().int().min(0).optional()
 });
 function createSearchRoute(library) {
   const route = new Hono();
@@ -1585,15 +1724,14 @@ function createSearchRoute(library) {
     }
     const parseResult = searchRequestBodySchema.safeParse(body);
     if (!parseResult.success) {
-      return c.json({ error: "Invalid request body" }, 400);
+      const errorMessage = parseResult.error.issues[0]?.message ?? "Invalid request body";
+      return c.json({ error: errorMessage }, 400);
     }
     const requestBody = parseResult.data;
     const options = {
-      query: requestBody.query
+      query: requestBody.query,
+      ...pickDefined(requestBody, ["format", "sort", "order", "limit", "offset"])
     };
-    if (requestBody.format !== void 0) {
-      options.format = requestBody.format;
-    }
     const result = await searchReferences(library, options);
     return c.json(result);
   });
@@ -1641,17 +1779,14 @@ async function startServerWithFileWatcher(libraryPath, config) {
 }
 export {
   BUILTIN_STYLES as B,
-  addReferences as a,
-  startServerWithFileWatcher as b,
-  citeReferences as c,
-  createServer as d,
-  add as e,
-  cite as f,
-  list as g,
-  search as h,
-  listReferences as l,
-  removeReference as r,
-  searchReferences as s,
+  formatBibtex as a,
+  add as b,
+  createServer as c,
+  cite as d,
+  search as e,
+  formatBibliographyCSL as f,
+  list as l,
+  startServerWithFileWatcher as s,
   updateReference as u
 };
-//# sourceMappingURL=index-Bl_mOQRe.js.map
+//# sourceMappingURL=index-_7NEUoS7.js.map