🎓 JATS author/affiliation updates (#654)

* 🎓 Separate authors and other contributors into different contrib-groups in JATS * 💵 Institution info is explicitly listed under funding in JATS * 🎓 Add DOI as affiliation identifier in frontmatter and JATS * ✍️ Add affiliation DOI to docs * 🔧 Improve open-funder-registry doi check in JATS * 🔧 Consume doi-utils 2.0.1 with isOpenFunderRegistry
jupyter-book · Oct 11, 2023 · 651dd77 · 651dd77
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diff --git a/.changeset/hungry-deers-tan.md b/.changeset/hungry-deers-tan.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+Institution info is explicitly listed under funding in jats
diff --git a/.changeset/perfect-camels-double.md b/.changeset/perfect-camels-double.md
@@ -0,0 +1,6 @@
+---
+'myst-frontmatter': patch
+'myst-to-jats': patch
+---
+
+Add doi as affiliation identifier in frontmatter and jats
diff --git a/.changeset/twelve-rockets-develop.md b/.changeset/twelve-rockets-develop.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+Separate authors and other contributors into different contrib-groups
diff --git a/docs/frontmatter.md b/docs/frontmatter.md
@@ -390,8 +390,8 @@ affiliations:
     however, at least one of these is required.
 * - `department`
   - a string - the affiliation department (e.g. Chemistry 🧪)
-* - `ror`, `isni`, `ringgold`
-  - Identifiers for the affiliation (ROR, ISNI, and Ringgold).
+* - `doi`, `ror`, `isni`, `ringgold`
+  - Identifiers for the affiliation (DOI, ROR, ISNI, and Ringgold).
 
     We suggest using https://ror.org if possible to search for your institution.
 
@@ -401,6 +401,7 @@ affiliations:
         ringgold: 1846
         isni: 0000 0004 1936 7558
         ror: 05qwgg493
+        doi: 10.13039/100018578
     ```
 * - `email`
   - a string - email of the affiliation, required if `corresponding` is `true`

diff --git a/package-lock.json b/package-lock.json
diff --git a/packages/jtex/docs/document.md b/packages/jtex/docs/document.md
@@ -130,7 +130,7 @@ name (`string`)
 institution, department, address, city, state, postal_code, country (`string`)
 : Individual parts of an affiliation's address information.
 
-isni, ringgold, ror (`string`)
+doi, isni, ringgold, ror (`string`)
 : Institution unique identifiers.
 
 url, email, phone, fax (`string`)
@@ -143,7 +143,7 @@ letter (`string`)
 : The letter of the affiliation, starting at "A". If there are more letters than 26, they will be repeated ("AA").
 
 value (`Affiliation`)
-: This contains most of the same affiliation fields (name, institution, department, address, city, state, postal_code, country, isni, ringgold, ror, url, email, phone, fax).
+: This contains most of the same affiliation fields (name, institution, department, address, city, state, postal_code, country, doi, isni, ringgold, ror, url, email, phone, fax).
 : This field is deprecated and will be removed when all templates are updated. For new templates, please use the values directly on the affiliation (e.g. `affiliation.name`, not `affiliation.value.name`)
 
 The authors and affiliations are often the most complex part of the template, the following statements can give you some ideas of how to use the above properties.

diff --git a/packages/myst-frontmatter/src/frontmatter/types.ts b/packages/myst-frontmatter/src/frontmatter/types.ts
@@ -16,6 +16,7 @@ export interface Affiliation {
   isni?: string;
   ringgold?: number;
   ror?: string;
+  doi?: string;
   url?: string;
   email?: string;
   phone?: string;

diff --git a/packages/myst-frontmatter/src/frontmatter/validators.ts b/packages/myst-frontmatter/src/frontmatter/validators.ts
@@ -122,6 +122,7 @@ const AFFILIATION_KEYS = [
   'isni',
   'ringgold',
   'ror',
+  'doi',
   'url',
   'email',
   'phone',
@@ -288,6 +289,18 @@ function pseudoUniqueId(kind: string, index: number, file?: string) {
   return `${kind}${suffix}-generated-uid-${index}`;
 }
 
+function validateDoi(value: any, opts: ValidationOptions) {
+  const doiString = validateString(value, opts);
+  if (doiString !== undefined) {
+    if (doi.validate(doiString, { strict: true })) {
+      return doiString;
+    } else {
+      validationError('must be valid DOI', opts);
+    }
+  }
+  return undefined;
+}
+
 /**
  * Update stash of authors/affiliations based on input value
  *
@@ -428,6 +441,9 @@ export function validateAffiliation(input: any, opts: ValidationOptions) {
       ...incrementOptions('ringgold', opts),
     });
   }
+  if (defined(value.doi)) {
+    output.doi = validateDoi(value.doi, incrementOptions('doi', opts));
+  }
   if (defined(value.collaboration)) {
     output.collaboration = validateBoolean(
       value.collaboration,
@@ -1161,15 +1177,7 @@ export function validateSharedProjectFrontmatterKeys(
     output.name = validateString(value.name, incrementOptions('name', opts));
   }
   if (defined(value.doi)) {
-    const doiOpts = incrementOptions('doi', opts);
-    const doiString = validateString(value.doi, doiOpts);
-    if (doiString !== undefined) {
-      if (doi.validate(doiString, { strict: true })) {
-        output.doi = doiString;
-      } else {
-        validationError('must be valid DOI', doiOpts);
-      }
-    }
+    output.doi = validateDoi(value.doi, incrementOptions('doi', opts));
   }
   if (defined(value.arxiv)) {
     output.arxiv = validateUrl(value.arxiv, {

diff --git a/packages/myst-frontmatter/tests/affiliations.yml b/packages/myst-frontmatter/tests/affiliations.yml
@@ -307,3 +307,25 @@ cases:
       affiliations:
         - id: univa
           name: University A
+  - title: Affiliation with doi passes
+    raw:
+      affiliations:
+        - id: univa
+          name: University A
+          doi: 10.13039/100000879
+    normalized:
+      affiliations:
+        - id: univa
+          name: University A
+          doi: 10.13039/100000879
+  - title: Affiliation with invalid doi fails
+    raw:
+      affiliations:
+        - id: univa
+          name: University A
+          doi: invalid doi
+    normalized:
+      affiliations:
+        - id: univa
+          name: University A
+    errors: 1
diff --git a/packages/myst-to-jats/package.json b/packages/myst-to-jats/package.json
@@ -37,6 +37,7 @@
   "dependencies": {
     "citation-js-utils": "^1.0.2",
     "credit-roles": "^2.1.0",
+    "doi-utils": "^2.0.1",
     "jats-tags": "^1.0.1",
     "katex": "^0.15.2",
     "myst-common": "^1.1.7",

diff --git a/packages/myst-to-jats/src/frontmatter.ts b/packages/myst-to-jats/src/frontmatter.ts
@@ -1,5 +1,6 @@
-import type { Contributor, ProjectFrontmatter } from 'myst-frontmatter';
+import type { Contributor, ProjectFrontmatter, Affiliation } from 'myst-frontmatter';
 import * as credit from 'credit-roles';
+import { doi } from 'doi-utils';
 import type { Element, IJatsSerializer } from './types.js';
 
 export function getJournalIds(): Element[] {
@@ -213,16 +214,86 @@ export function getArticleAuthors(frontmatter: ProjectFrontmatter): Element[] {
     }
     return { type: 'element', name: 'contrib', attributes, elements };
   };
-  const contribs = [
-    ...(frontmatter.authors ?? []).map((author): Element => {
-      return generateContrib(author, 'author');
-    }),
-    ...(frontmatter.contributors ?? []).map((contributor): Element => {
-      return generateContrib(contributor);
-    }),
-  ];
+  const authorContribs = (frontmatter.authors ?? []).map((author): Element => {
+    return generateContrib(author, 'author');
+  });
+  const otherContribs = (frontmatter.contributors ?? []).map((contributor): Element => {
+    return generateContrib(contributor);
+  });
+  const contribGroups: Element[] = [];
+  if (authorContribs.length) {
+    contribGroups.push({ type: 'element', name: 'contrib-group', elements: authorContribs });
+  }
+  if (otherContribs.length) {
+    contribGroups.push({ type: 'element', name: 'contrib-group', elements: otherContribs });
+  }
+  return contribGroups;
+}
 
-  return contribs?.length ? [{ type: 'element', name: 'contrib-group', elements: contribs }] : [];
+function instWrapElementsFromAffiliation(affiliation: Affiliation): Element[] {
+  const elements: Element[] = [];
+  const instWrapElements: Element[] = [];
+  if (affiliation.name) {
+    instWrapElements.push({
+      type: 'element',
+      name: 'institution',
+      elements: [{ type: 'text', text: affiliation.name }],
+    });
+  }
+  if (affiliation.isni) {
+    instWrapElements.push({
+      type: 'element',
+      name: 'institution-id',
+      attributes: { 'institution-id-type': 'isni' },
+      elements: [{ type: 'text', text: affiliation.isni }],
+    });
+  }
+  if (affiliation.ringgold) {
+    instWrapElements.push({
+      type: 'element',
+      name: 'institution-id',
+      attributes: { 'institution-id-type': 'ringgold' },
+      elements: [{ type: 'text', text: `${affiliation.ringgold}` }],
+    });
+  }
+  if (affiliation.ror) {
+    instWrapElements.push({
+      type: 'element',
+      name: 'institution-id',
+      attributes: { 'institution-id-type': 'ror' },
+      elements: [{ type: 'text', text: affiliation.ror }],
+    });
+  }
+  if (affiliation.doi) {
+    const doiAttrs: Record<string, string> = { 'institution-id-type': 'doi' };
+    if (doi.isOpenFunderRegistry(affiliation.doi)) {
+      doiAttrs.vocab = 'open-funder-registry';
+    }
+    instWrapElements.push({
+      type: 'element',
+      name: 'institution-id',
+      attributes: doiAttrs,
+      elements: [{ type: 'text', text: affiliation.doi }],
+    });
+  }
+  if (instWrapElements.length) {
+    elements.push({ type: 'element', name: 'institution-wrap', elements: instWrapElements });
+  }
+  if (affiliation.department) {
+    elements.push({
+      type: 'element',
+      name: 'institution-wrap',
+      elements: [
+        {
+          type: 'element',
+          name: 'institution',
+          attributes: { 'content-type': 'dept' },
+          elements: [{ type: 'text', text: affiliation.department }],
+        },
+      ],
+    });
+  }
+  return elements;
 }
 
 export function getArticleAffiliations(frontmatter: ProjectFrontmatter): Element[] {
@@ -232,55 +303,7 @@ export function getArticleAffiliations(frontmatter: ProjectFrontmatter): Element
     if (affiliation.id) {
       attributes.id = affiliation.id;
     }
-    const instWrapElements: Element[] = [];
-    if (affiliation.name) {
-      instWrapElements.push({
-        type: 'element',
-        name: 'institution',
-        elements: [{ type: 'text', text: affiliation.name }],
-      });
-    }
-    if (affiliation.isni) {
-      instWrapElements.push({
-        type: 'element',
-        name: 'institution-id',
-        attributes: { 'institution-id-type': 'isni' },
-        elements: [{ type: 'text', text: affiliation.isni }],
-      });
-    }
-    if (affiliation.ringgold) {
-      instWrapElements.push({
-        type: 'element',
-        name: 'institution-id',
-        attributes: { 'institution-id-type': 'ringgold' },
-        elements: [{ type: 'text', text: `${affiliation.ringgold}` }],
-      });
-    }
-    if (affiliation.ror) {
-      instWrapElements.push({
-        type: 'element',
-        name: 'institution-id',
-        attributes: { 'institution-id-type': 'ror' },
-        elements: [{ type: 'text', text: affiliation.ror }],
-      });
-    }
-    if (instWrapElements.length) {
-      elements.push({ type: 'element', name: 'institution-wrap', elements: instWrapElements });
-    }
-    if (affiliation.department) {
-      elements.push({
-        type: 'element',
-        name: 'institution-wrap',
-        elements: [
-          {
-            type: 'element',
-            name: 'institution',
-            attributes: { 'content-type': 'dept' },
-            elements: [{ type: 'text', text: affiliation.department }],
-          },
-        ],
-      });
-    }
+    elements.push(...instWrapElementsFromAffiliation(affiliation));
     if (affiliation.address) {
       elements.push({
         type: 'element',
@@ -400,19 +423,18 @@ export function getFundingGroup(frontmatter: ProjectFrontmatter): Element[] {
       elements.push(
         ...fund.awards.map((award): Element => {
           const awardElements: Element[] = [];
-          if (award.sources?.length) {
+          const resolvedSources = award.sources
+            ?.map((source) => {
+              return frontmatter.affiliations?.find((aff) => aff.id === source);
+            })
+            .filter((source): source is Affiliation => !!source);
+          if (resolvedSources?.length) {
             awardElements.push(
-              ...award.sources.map((source): Element => {
+              ...resolvedSources.map((source): Element => {
                 return {
                   type: 'element',
                   name: 'funding-source',
-                  elements: [
-                    {
-                      type: 'element',
-                      name: 'xref',
-                      attributes: { 'ref-type': 'aff', rid: source },
-                    },
-                  ],
+                  elements: instWrapElementsFromAffiliation(source),
                 };
               }),
             );