@ncukondo/reference-manager 0.23.0 → 0.23.2

package/dist/chunks/{index-eZatWPDi.js → index-7R-uEYOu.js}

@@ -11,7 +11,7 @@ import { z } from "zod";
 import * as path from "node:path";
 import path__default, { extname, join, dirname } from "node:path";
 import "@citation-js/plugin-csl";
-import fs__default, { stat, rename, copyFile, rm, readFile, mkdir, writeFile, mkdtemp, access, unlink, rmdir } from "node:fs/promises";
+import fs__default, { stat, rename, copyFile, unlink, rm, readFile, mkdir, writeFile, mkdtemp, access, rmdir } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import "node:child_process";
 import "node:crypto";
@@ -156,7 +156,16 @@ function findExistingFile(files, filename) {
 async function copyOrMoveFile(sourcePath, destPath, move) {
   try {
     if (move) {
-      await rename(sourcePath, destPath);
+      try {
+        await rename(sourcePath, destPath);
+      } catch (renameError) {
+        if (renameError instanceof Error && "code" in renameError && renameError.code === "EXDEV") {
+          await copyFile(sourcePath, destPath);
+          await unlink(sourcePath);
+        } else {
+          throw renameError;
+        }
+      }
     } else {
       await copyFile(sourcePath, destPath);
     }
@@ -706,7 +715,7 @@ function extractPmcidFromUrl(url) {
   const match = PMC_URL_PATTERN.exec(url);
   return match ? match[1] ?? null : null;
 }
-function extractPmcidFromLocations(locations) {
+function extractPmcidFromLocations$1(locations) {
   for (const loc of locations) {
     if (loc.url_for_pdf) {
       const pmcid = extractPmcidFromUrl(loc.url_for_pdf);
@@ -752,7 +761,7 @@ async function checkUnpaywallDetailed(doi, email) {
   }
   if (locations.length === 0)
     return null;
-  const pmcid = extractPmcidFromLocations(data.oa_locations);
+  const pmcid = extractPmcidFromLocations$1(data.oa_locations);
   const result = { locations };
   if (pmcid)
     result.pmcid = pmcid;
@@ -9510,6 +9519,29 @@ function parseSection(secChildren, level) {
   }
   return { title, level, content, subsections };
 }
+function flushBlockBuffer(buffer, sections) {
+  const content = parseBlockContent(buffer);
+  if (content.length > 0) {
+    sections.push({ title: "", level: 2, content, subsections: [] });
+  }
+}
+function parseMixedBodyChildren(children, sections) {
+  let blockBuffer = [];
+  for (const child of children) {
+    if (getTagName(child) === "sec") {
+      if (blockBuffer.length > 0) {
+        flushBlockBuffer(blockBuffer, sections);
+        blockBuffer = [];
+      }
+      sections.push(parseSection(getChildren(child), 2));
+    } else {
+      blockBuffer.push(child);
+    }
+  }
+  if (blockBuffer.length > 0) {
+    flushBlockBuffer(blockBuffer, sections);
+  }
+}
 function parseJatsBody(xml) {
   const parsed = parser.parse(xml);
   const article = findArticle(parsed);
@@ -9521,14 +9553,9 @@ function parseJatsBody(xml) {
   const sections = [];
   const secs = findChildren(body.children, "sec");
   if (secs.length > 0) {
-    for (const sec of secs) {
-      sections.push(parseSection(sec.children, 2));
-    }
+    parseMixedBodyChildren(body.children, sections);
   } else {
-    const content = parseBlockContent(body.children);
-    if (content.length > 0) {
-      sections.push({ title: "", level: 2, content, subsections: [] });
-    }
+    flushBlockBuffer(body.children, sections);
   }
   return sections;
 }
@@ -10221,6 +10248,16 @@ async function fulltextDiscover(library, options) {
   }
   return discoverResult;
 }
+function extractPmcidFromLocations(locations) {
+  for (const loc of locations) {
+    if (loc.source !== "pmc") continue;
+    const pdfMatch = loc.url.match(/\/pmc\/articles\/(PMC\d+)\//);
+    if (pdfMatch) return pdfMatch[1];
+    const xmlMatch = loc.url.match(/[?&]id=(\d+)/);
+    if (xmlMatch) return `PMC${xmlMatch[1]}`;
+  }
+  return void 0;
+}
 function buildDiscoveryArticle(item) {
   const article = {};
   if (item.DOI) article.doi = item.DOI;
@@ -10239,21 +10276,26 @@ function buildDiscoveryConfig(fulltextConfig) {
   return config;
 }
 async function tryDownloadPdf(locations, tempDir, ctx) {
-  const pdfLocation = locations.find((loc) => loc.urlType === "pdf");
-  if (!pdfLocation) return { attached: false, source: "" };
+  const pdfLocations = locations.filter((loc) => loc.urlType === "pdf");
+  if (pdfLocations.length === 0) return { attached: false, source: "" };
   const pdfPath = join(tempDir, "fulltext.pdf");
-  const pdfResult = await downloadPdf(pdfLocation.url, pdfPath);
-  if (!pdfResult.success) return { attached: false, source: pdfLocation.source };
-  const attachResult = await fulltextAttach(ctx.library, {
-    identifier: ctx.identifier,
-    idType: ctx.idType,
-    filePath: pdfPath,
-    type: "pdf",
-    force: ctx.force,
-    move: true,
-    fulltextDirectory: ctx.fulltextDirectory
-  });
-  return { attached: attachResult.success, source: pdfLocation.source };
+  for (const pdfLocation of pdfLocations) {
+    const pdfResult = await downloadPdf(pdfLocation.url, pdfPath);
+    if (!pdfResult.success) continue;
+    const attachResult = await fulltextAttach(ctx.library, {
+      identifier: ctx.identifier,
+      idType: ctx.idType,
+      filePath: pdfPath,
+      type: "pdf",
+      force: ctx.force,
+      move: true,
+      fulltextDirectory: ctx.fulltextDirectory
+    });
+    if (attachResult.success) {
+      return { attached: true, source: pdfLocation.source };
+    }
+  }
+  return { attached: false, source: pdfLocations[0]?.source ?? "" };
 }
 async function tryDownloadPmcXmlAndConvert(pmcid, tempDir, ctx) {
   const xmlPath = join(tempDir, "fulltext.xml");
@@ -10328,7 +10370,7 @@ async function fulltextFetch(library, options) {
   if (locations.length === 0) {
     return { success: false, error: `No OA sources found for ${identifier}` };
   }
-  const effectivePmcid = item.PMCID ?? discovery.discoveredIds?.pmcid;
+  const effectivePmcid = item.PMCID ?? discovery.discoveredIds?.pmcid ?? extractPmcidFromLocations(locations);
   const tempDir = await mkdtemp(join(tmpdir(), "ref-fulltext-"));
   const ctx = {
     library,
@@ -12522,4 +12564,4 @@ export {
   cite as y,
   list as z
 };
-//# sourceMappingURL=index-eZatWPDi.js.map
+//# sourceMappingURL=index-7R-uEYOu.js.map