jats-cli 1.0.16 → 1.0.18

package/dist/jats.cjs

@@ -48999,7 +48999,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.0.16";
+var version = "1.0.18";
 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) {
@@ -58125,7 +58125,7 @@ async function customResolveJatsUrlFromDoi(session, doiString, opts) {
 }
 
 // ../jats-fetch/dist/download.js
-async function downloadFromUrl(session, jatsUrl, opts) {
+async function downloadFromUrlOrThrow(session, jatsUrl, opts) {
   var _a, _b;
   const toc = tic();
   session.log.debug(`Fetching JATS from ${jatsUrl}`);
@@ -58145,6 +58145,16 @@ async function downloadFromUrl(session, jatsUrl, opts) {
   session.log.debug(toc(`Fetched document with content-type "${contentType}" in %s`));
   return data;
 }
+async function downloadFromUrl(session, jatsUrl, opts) {
+  try {
+    const data = await downloadFromUrlOrThrow(session, jatsUrl, opts);
+    if (data)
+      return { success: true, source: jatsUrl, data };
+  } catch (error) {
+    session.log.debug(error.message);
+  }
+  return { success: false, source: jatsUrl };
+}
 async function getJatsUrlFromDoi(session, urlOrDoi, opts) {
   var _a, _b, _c, _d, _e;
   if (!doi.validate(urlOrDoi))
@@ -58172,48 +58182,50 @@ async function getJatsUrlFromDoi(session, urlOrDoi, opts) {
   session.log.debug(`Could not find XML in DOI record ${doiUrl}`);
   return void 0;
 }
-async function downloadJatsFromUrl(session, urlOrDoi, opts = {}) {
-  if (import_node_fs5.default.existsSync(urlOrDoi)) {
-    session.log.debug(`JATS returned from local file ${urlOrDoi}`);
-    const data = import_node_fs5.default.readFileSync(urlOrDoi).toString();
-    return { success: true, source: urlOrDoi, data };
-  }
-  const expectedUrls = (await Promise.all([
-    constructJatsUrlFromPubMedCentral(session, urlOrDoi, opts),
-    getJatsUrlFromDoi(session, urlOrDoi, opts)
-  ])).filter((u2) => !!u2);
-  if (expectedUrls.length > 0) {
-    session.log.debug(["Trying URLs:\n", ...expectedUrls.map((url) => ` ${url}
-`)].join("  - "));
-    for (let index2 = 0; index2 < expectedUrls.length; index2++) {
-      const url = expectedUrls[index2];
-      try {
-        const data = await downloadFromUrl(session, url, opts);
-        if (data)
-          return { success: true, source: url, data };
-      } catch (error) {
-        session.log.debug(error.message);
-      }
-    }
-    return { success: false, source: expectedUrls[0] };
+async function downloadJatsFromUrl(session, urlOrId, opts = {}) {
+  let result = { success: false, source: urlOrId };
+  if (import_node_fs5.default.existsSync(urlOrId)) {
+    session.log.debug(`JATS returned from local file ${urlOrId}`);
+    const data = import_node_fs5.default.readFileSync(urlOrId).toString();
+    return { success: true, source: urlOrId, 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 (doi.validate(urlOrId)) {
+    let url;
+    try {
+      url = await customResolveJatsUrlFromDoi(session, urlOrId, opts);
+    } catch (error) {
+      session.log.debug(error.message);
     }
-    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 };
+    if (url) {
+      result = await downloadFromUrl(session, url, opts);
+      if (result.success && result.data)
+        return result;
+    }
+    url = await getJatsUrlFromDoi(session, urlOrId, opts);
+    if (url) {
+      result = await downloadFromUrl(session, url, opts);
+      if (result.success && result.data)
+        return result;
     }
-  } 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`);
-  return { success: false, source: urlOrDoi };
+  if (urlOrId.startsWith("PMC")) {
+    result = await getPubMedJatsFromS3(session, urlOrId);
+    if (result.success && result.data)
+      return result;
+  }
+  if (urlOrId.startsWith("PMC") || doi.validate(urlOrId)) {
+    const url = await constructJatsUrlFromPubMedCentral(session, urlOrId, opts);
+    if (url) {
+      result = await downloadFromUrl(session, url, opts);
+    }
+    return result;
+  }
+  if (isUrl(urlOrId)) {
+    result = await downloadFromUrl(session, urlOrId, opts);
+    return result;
+  }
+  session.log.debug(`Could not find ${urlOrId} locally or resolve it to a valid JATS url`);
+  return result;
 }
 async function jatsFetch(session, input, opts) {
   var _a;
@@ -58228,6 +58240,7 @@ async function jatsFetch(session, input, opts) {
   }
   let output = opts.output;
   let filename;
+  let altInput;
   if (input.endsWith(".tar.gz")) {
     opts.data = true;
     const foldername = input.split("/").slice(-1)[0].slice(0, -".tar.gz".length);
@@ -58247,7 +58260,7 @@ async function jatsFetch(session, input, opts) {
     const pmcid = await convertDOI2PMCID(session, input);
     if (pmcid) {
       session.log.debug(`Resolved input ${input} to PMC ID: ${pmcid}`);
-      input = pmcid;
+      altInput = pmcid;
     }
   }
   if (!output)
@@ -58263,12 +58276,12 @@ async function jatsFetch(session, input, opts) {
   if (opts.data) {
     result = await getPubMedJatsFromData(session, input, import_node_path4.default.dirname(output), opts.listing);
   }
-  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 downloadJatsFromUrl(session, input);
   }
+  if (!(result === null || result === void 0 ? void 0 : result.data) && altInput) {
+    result = await downloadJatsFromUrl(session, altInput);
+  }
   if (!(result === null || result === void 0 ? void 0 : result.data) && input.startsWith("PMC")) {
     result = await getPubMedJatsFromData(session, input, import_node_path4.default.dirname(output), opts.listing);
   }
@@ -65610,7 +65623,7 @@ function journalTransforms(fullTree, body) {
 }
 
 // ../jats-convert/dist/version.js
-var version3 = "1.0.16";
+var version3 = "1.0.18";
 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 = "1.0.18";
 export default version;
 //# sourceMappingURL=version.d.ts.map

package/dist/version.js

@@ -1,2 +1,2 @@
-const version = '1.0.16';
+const version = '1.0.18';
 export default version;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "jats-cli",
-  "version": "1.0.16",
+  "version": "1.0.18",
   "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": "^1.0.18",
+    "jats-fetch": "^1.0.18",
+    "jats-tags": "^1.0.18",
+    "jats-utils": "^1.0.18",
+    "jats-xml": "^1.0.18",
     "js-yaml": "^4.1.0",
     "unist-util-is": "^5.2.1",
     "unist-util-select": "^4.0.0"