jats-cli 1.0.16 → 1.0.17

package/dist/jats.cjs

@@ -48999,7 +48999,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.0.16";
+var version = "1.0.17";
 var version_default = version;
 
 // src/parse.ts
@@ -49645,7 +49645,7 @@ function writeFileToFolder(filename, data, opts) {
 }
 
 // ../../node_modules/doi-utils/dist/validatePart.js
-var DOI_VALIDATION_PATTERN = /^10.\d{4,9}\/[-._;()/:A-Z0-9]+$/i;
+var DOI_VALIDATION_PATTERN = /^10\.\d{4,9}\/[-._;()/:A-Z0-9]+$/i;
 function validatePart(possibleDOI) {
   if (!possibleDOI)
     return false;
@@ -49663,10 +49663,10 @@ var doiOrg = {
 };
 var elife = {
   test(url) {
-    return url.hostname.endsWith("elifesciences.org") && url.pathname.startsWith("/articles/");
+    return url.hostname.endsWith("elifesciences.org") && /^\/(?:articles|reviewed-preprints)\/\d+$/.test(url.pathname);
   },
   parse(url) {
-    return `10.7554/eLife.${url.pathname.replace("/articles/", "")}`;
+    return `10.7554/eLife.${url.pathname.replace(/^\/(?:articles|reviewed-preprints)\//, "")}`;
   }
 };
 var zenodo = {
@@ -49683,7 +49683,7 @@ var biorxiv = {
   },
   parse(url) {
     var _a;
-    return (_a = clumpParts(url).find(validatePart)) === null || _a === void 0 ? void 0 : _a.replace(/v([\d]*)$/, "");
+    return (_a = clumpParts(url).find(validatePart)) === null || _a === void 0 ? void 0 : _a.replace(/v\d+(\.[a-zA-Z-]+)?$/, "");
   }
 };
 function clumpParts(url) {
@@ -58178,10 +58178,19 @@ async function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
     const data = import_node_fs5.default.readFileSync(urlOrDoi).toString();
     return { success: true, source: urlOrDoi, data };
   }
-  const expectedUrls = (await Promise.all([
+  const expectedUrls = [];
+  try {
+    expectedUrls.push(await customResolveJatsUrlFromDoi(session, urlOrDoi, opts));
+  } catch {
+    session.log.debug(`No custom resolvers match ${urlOrDoi}`);
+  }
+  expectedUrls.push(...(await Promise.all([
     constructJatsUrlFromPubMedCentral(session, urlOrDoi, opts),
     getJatsUrlFromDoi(session, urlOrDoi, opts)
-  ])).filter((u2) => !!u2);
+  ])).filter((u2) => !!u2));
+  if (isUrl(urlOrDoi)) {
+    expectedUrls.push(urlOrDoi);
+  }
   if (expectedUrls.length > 0) {
     session.log.debug(["Trying URLs:\n", ...expectedUrls.map((url) => ` ${url}
 `)].join("  - "));
@@ -58197,22 +58206,7 @@ async function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
     }
     return { success: false, source: expectedUrls[0] };
   }
-  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 };
-  }
-  session.log.debug(`Could not find ${urlOrDoi} locally, and it doesn't look like a URL or DOI`);
+  session.log.debug(`Could not find ${urlOrDoi} locally or resolve it to a valid JATS url`);
   return { success: false, source: urlOrDoi };
 }
 async function jatsFetch(session, input, opts) {
@@ -65610,7 +65604,7 @@ function journalTransforms(fullTree, body) {
 }
 
 // ../jats-convert/dist/version.js
-var version3 = "1.0.16";
+var version3 = "1.0.17";
 var version_default3 = version3;
 
 // ../jats-convert/dist/myst/inlineCitations.js

package/dist/version.d.ts

@@ -1,3 +1,3 @@
-declare const version = "1.0.16";
+declare const version = "1.0.17";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.16';
+const version = '1.0.17';
 export default version;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-cli",
-  "version": "1.0.16",
+  "version": "1.0.17",
   "description": "Typescript CLI for with JATS",
   "author": "Rowan Cockett <rowan@continuous.foundation>",
   "homepage": "https://github.com/continuous-foundation/jats",
@@ -43,13 +43,13 @@
     "url": "https://github.com/continuous-foundation/jats/issues"
   },
   "dependencies": {
-    "doi-utils": "^2.0.0",
+    "doi-utils": "^2.0.6",
     "fair-principles": "^2.0.0",
-    "jats-convert": "^1.0.16",
-    "jats-fetch": "^1.0.16",
-    "jats-tags": "^1.0.16",
-    "jats-utils": "^1.0.16",
-    "jats-xml": "^1.0.16",
+    "jats-convert": "^1.0.17",
+    "jats-fetch": "^1.0.17",
+    "jats-tags": "^1.0.17",
+    "jats-utils": "^1.0.17",
+    "jats-xml": "^1.0.17",
     "js-yaml": "^4.1.0",
     "unist-util-is": "^5.2.1",
     "unist-util-select": "^4.0.0"