jats-cli 1.0.11 → 1.0.12

package/dist/jats.cjs

@@ -48999,7 +48999,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.0.11";
+var version = "1.0.12";
 var version_default = version;
 
 // src/parse.ts
@@ -57911,6 +57911,7 @@ async function getPubMedJatsFromS3(session, pmcid) {
     session.log.debug(`Not available from open-access S3 bucket: ${pmcid}`);
     return { success: false, source: pmcid };
   } else {
+    session.log.debug(`Fetching PMC JATS from S3 bucket: ${pmcid}`);
     const result = await downloadFileFromS3(client, found.path, OA_CONFIG);
     return result;
   }
@@ -58071,6 +58072,9 @@ async function downloadFromUrl(session, jatsUrl, opts) {
     session.log.warn(`Expected content-type "application/xml" instead we got "${contentType}" for ${jatsUrl}`);
   }
   const data = await resp.text();
+  if (!data.match(/<article/)) {
+    throw new Error(`XML downloaded from ${jatsUrl} does not look like a JATS article`);
+  }
   session.log.debug(toc(`Fetched document with content-type "${contentType}" in %s`));
   return data;
 }
@@ -58126,17 +58130,23 @@ async function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
     }
     return { success: false, source: expectedUrls[0] };
   }
-  if (doi.validate(urlOrDoi)) {
-    const jatsUrl = await customResolveJatsUrlFromDoi(session, urlOrDoi, opts);
-    const data = await downloadFromUrl(session, jatsUrl, opts);
-    return { success: true, source: jatsUrl, data };
-  }
-  if (isUrl(urlOrDoi)) {
-    session.log.debug("No resolver matched, and the URL doesn't look like a DOI. We will attempt to download it directly.");
-    const data = await downloadFromUrl(session, urlOrDoi, opts);
-    return { success: true, source: urlOrDoi, data };
+  try {
+    if (doi.validate(urlOrDoi)) {
+      const jatsUrl = await customResolveJatsUrlFromDoi(session, urlOrDoi, opts);
+      const data = await downloadFromUrl(session, jatsUrl, opts);
+      return { success: true, source: jatsUrl, data };
+    }
+    if (isUrl(urlOrDoi)) {
+      session.log.debug("No resolver matched, and the URL doesn't look like a DOI. We will attempt to download it directly.");
+      const data = await downloadFromUrl(session, urlOrDoi, opts);
+      return { success: true, source: urlOrDoi, data };
+    }
+  } catch (error) {
+    session.log.debug(error.message);
+    return { success: false, source: urlOrDoi };
   }
-  throw new Error(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
+  session.log.debug(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
+  return { success: false, source: urlOrDoi };
 }
 async function jatsFetch(session, input, opts) {
   var _a, _b;
@@ -58154,15 +58164,14 @@ async function jatsFetch(session, input, opts) {
     throw new Error(`Output must be an XML file or a directory`);
   }
   let result;
-  try {
+  if (input.startsWith("PMC")) {
+    result = await getPubMedJatsFromS3(session, input);
+  }
+  if (!(result === null || result === void 0 ? void 0 : result.data)) {
     result = await downloadJatsFromUrl(session, input);
-  } catch {
   }
   if (!(result === null || result === void 0 ? void 0 : result.data) && input.startsWith("PMC")) {
-    result = await getPubMedJatsFromS3(session, input);
-    if (!(result === null || result === void 0 ? void 0 : result.data)) {
-      result = await getPubMedJatsFromData(session, input, import_node_path4.default.dirname(output), opts.listing);
-    }
+    result = await getPubMedJatsFromData(session, input, import_node_path4.default.dirname(output), opts.listing);
   }
   if (!(result === null || result === void 0 ? void 0 : result.data)) {
     throw new Error(`Unable to resolve JATS XML content from ${input}`);
@@ -64977,7 +64986,9 @@ function recurseSections(tree, depth = 1, titleType) {
       firstChild3 = (_b = sec.children) === null || _b === void 0 ? void 0 : _b[1];
     }
     if ((firstChild3 === null || firstChild3 === void 0 ? void 0 : firstChild3.type) === "title") {
-      if (titleType === "strong") {
+      if (sec.type === "ack" && toText(firstChild3).toLowerCase().startsWith("ack")) {
+        firstChild3.type = "__delete__";
+      } else if (titleType === "strong") {
         firstChild3.type = "p";
         firstChild3.children = [{ type: "bold", children: firstChild3.children }];
       } else {
@@ -64986,6 +64997,8 @@ function recurseSections(tree, depth = 1, titleType) {
         firstChild3.depth = depth;
       }
     }
+    if (sec.type === "ack")
+      sec.part = "acknowledgments";
     recurseSections(sec, depth + 1, titleType);
   });
 }
@@ -64995,8 +65008,6 @@ function sectionTransform(tree, titleType) {
   remove(tree, "__delete__");
   const topSections = (_a = tree.children) === null || _a === void 0 ? void 0 : _a.filter((n) => isSection(n));
   topSections.forEach((sec) => {
-    if (sec.type === "ack")
-      sec.part = "acknowledgments";
     sec.type = "block";
   });
   while (select3("sec", tree))
@@ -65462,7 +65473,7 @@ function journalTransforms(tree) {
 }
 
 // ../jats-convert/dist/version.js
-var version3 = "1.0.11";
+var version3 = "1.0.12";
 var version_default3 = version3;
 
 // ../jats-convert/dist/myst/inlineCitations.js
@@ -65980,7 +65991,7 @@ var handlers = {
       }
       case RefType.fn:
       case RefType.tableFn: {
-        state2.renderInline(node, "footnoteReference", { label, identifier });
+        state2.addLeaf("footnoteReference", { label, identifier });
         return;
       }
       default: {

package/dist/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "1.0.11";
+declare const version = "1.0.12";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.11';
+const version = '1.0.12';
 export default version;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-cli",
-  "version": "1.0.11",
+  "version": "1.0.12",
   "description": "Typescript CLI for with JATS",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "homepage": "https://github.com/curvenote/jats",
@@ -45,11 +45,11 @@
   "dependencies": {
     "doi-utils": "^2.0.0",
     "fair-principles": "^2.0.0",
-    "jats-convert": "^1.0.11",
-    "jats-fetch": "^1.0.11",
-    "jats-tags": "^1.0.11",
-    "jats-utils": "^1.0.11",
-    "jats-xml": "^1.0.11",
+    "jats-convert": "^1.0.12",
+    "jats-fetch": "^1.0.12",
+    "jats-tags": "^1.0.12",
+    "jats-utils": "^1.0.12",
+    "jats-xml": "^1.0.12",
     "js-yaml": "^4.1.0",
     "unist-util-is": "^5.2.1",
     "unist-util-select": "^4.0.0"