🔧 Update jats convert frontmatter default and enable v# suffixed bioRxiv dois (#78)

Author: fwkoch

.changeset/brown-dogs-greet.md

@@ -0,0 +1,5 @@
+---
+'jats-fetch': patch
+---
+
+Enable v# suffixed bioRxiv dois

.changeset/eight-hairs-leave.md

@@ -0,0 +1,6 @@
+---
+'jats-convert': minor
+'jats-cli': minor
+---
+
+Update jats convert frontmatter default

packages/jats-cli/src/convert.ts

@@ -7,11 +7,11 @@ function makeConvertCLI(program: Command) {
     .description('Convert JATS file to MyST mdast json')
     .argument('[input]', 'The JATS file')
     .addOption(
-      new Option(
-        '--frontmatter <frontmatter>',
-        'Treat JATS frontmatter fields as page or project, or ignore if not specified',
-      ).choices(['page', 'project']),
+      new Option('--frontmatter <frontmatter>', 'Treat JATS frontmatter fields as page or project')
+        .choices(['page', 'project'])
+        .default('project'),
     )
+    .addOption(new Option('--no-frontmatter', 'Ignore JATS frontmatter'))
     .addOption(
       new Option(
         '--no-doi, --no-dois',

packages/jats-convert/src/index.ts

@@ -738,7 +738,7 @@ export function jatsConvertTransform(
 export async function jatsConvert(
   session: ISession,
   input?: string,
-  opts?: { frontmatter?: 'page' | 'project'; dois?: boolean; bibtex?: boolean },
+  opts?: { frontmatter?: 'page' | 'project' | false; dois?: boolean; bibtex?: boolean },
 ) {
   const logInfo: Record<string, any> = { jatsVersion: version };
   if (!input) {

packages/jats-fetch/src/biorxiv/data.ts

@@ -17,12 +17,19 @@ export async function getBioRxivS3Metadata(
   if (!resp.ok) {
     throw new Error(`Bad response from ${BIORXIV_LOOKUP_URL}`);
   }
-  const bioRxivMeta = (await resp.json()) as { versions: { s3Bucket: string; s3Key: string }[] };
-  if (!bioRxivMeta.versions?.length) {
-    throw new Error(`Bad response from ${BIORXIV_LOOKUP_URL} - no versions found for ${input}`);
+  const bioRxivMeta = (await resp.json()) as {
+    versions?: { s3Bucket: string; s3Key: string }[];
+    s3Bucket?: string;
+    s3Key?: string;
+  };
+  if (bioRxivMeta.s3Bucket && bioRxivMeta.s3Key) {
+    return { bucketName: bioRxivMeta.s3Bucket, filePath: bioRxivMeta.s3Key };
   }
-  const { s3Bucket, s3Key } = bioRxivMeta.versions[bioRxivMeta.versions.length - 1];
-  return { bucketName: s3Bucket, filePath: s3Key };
+  if (bioRxivMeta.versions?.length) {
+    const { s3Bucket, s3Key } = bioRxivMeta.versions[bioRxivMeta.versions.length - 1];
+    return { bucketName: s3Bucket, filePath: s3Key };
+  }
+  throw new Error(`Bad response from ${BIORXIV_LOOKUP_URL} - no s3 bucket info found for ${input}`);
 }
 
 export async function downloadAndUnzipBioRxiv(