🌎 Download PMC data from doi/pmid input (#64)

Author: fwkoch

.changeset/strange-snakes-refuse.md

@@ -0,0 +1,5 @@
+---
+'jats-fetch': patch
+---
+
+Download PMC data from doi/pmid input

packages/jats-fetch/src/download.ts

@@ -5,6 +5,8 @@ import type { ISession } from 'myst-cli-utils';
 import { isUrl, tic } from 'myst-cli-utils';
 import {
   constructJatsUrlFromPubMedCentral,
+  convertDOI2PMCID,
+  convertPMID2PMCID,
   getListingsFile,
   getPubMedJatsFromData,
   getPubMedJatsFromS3,
@@ -191,6 +193,21 @@ export async function jatsFetch(
       output = foldername;
     }
   }
+  if (input.match(/^[0-9]+$/)) {
+    // If input is a number, assume it is PMID and try to resolve PMC ID
+    const pmcid = await convertPMID2PMCID(session, input);
+    if (pmcid) {
+      session.log.debug(`Resolved input ${input} to PMC ID: ${pmcid}`);
+      input = pmcid;
+    }
+  }
+  if (doi.validate(input)) {
+    const pmcid = await convertDOI2PMCID(session, input);
+    if (pmcid) {
+      session.log.debug(`Resolved input ${input} to PMC ID: ${pmcid}`);
+      input = pmcid;
+    }
+  }
   if (!output) output = opts.data ? `${input}` : '.';
   if (!path.extname(output)) {
     filename = filename ?? (input.startsWith('PMC') ? `${input}.xml` : 'jats.xml');

packages/jats-fetch/src/pubmed.ts

@@ -140,6 +140,11 @@ export async function convertPMCID2DOI(session: ISession, pmcid: string, opts?:
   return pmDoi;
 }
 
+export async function convertDOI2PMCID(session: ISession, input: string, opts?: ResolutionOptions) {
+  const pmDoi = await convertId(session, input, 'doi', 'pmcid', opts);
+  return pmDoi;
+}
+
 /**
  * Query NIH APIs for single DOI from PubMed ID
  */