👩‍🔬 Only add affiliations associated with authors to JATS and myst-te…

…mplates (#662) * 🎓 JATS only includes authors as contrib and author affiliations as aff * 🎓 Only add author affiliations/contrib to template doc * 👩‍🔬 Remove author contrib id --------- Co-authored-by: Rowan Cockett <[email protected]>
jupyter-book · Oct 13, 2023 · d25debf · d25debf
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diff --git a/.changeset/cyan-coins-guess.md b/.changeset/cyan-coins-guess.md
@@ -0,0 +1,5 @@
+---
+'myst-templates': patch
+---
+
+Only add author affiliations/contrib to template doc
diff --git a/.changeset/light-shirts-tease.md b/.changeset/light-shirts-tease.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+JATS only includes authors as top-level contribs
diff --git a/.changeset/metal-pans-remember.md b/.changeset/metal-pans-remember.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+Remove contrib id, authors cannot be referenced.
diff --git a/.changeset/purple-dancers-report.md b/.changeset/purple-dancers-report.md
@@ -0,0 +1,5 @@
+---
+'myst-to-jats': patch
+---
+
+JATS only includes author affiliations in aff list
diff --git a/packages/myst-templates/src/frontmatter.spec.ts b/packages/myst-templates/src/frontmatter.spec.ts
@@ -164,4 +164,119 @@ describe('extendFrontmatter', () => {
       },
     ]);
   });
+  it('affiliations are only used from authors', async () => {
+    const frontmatter: PageFrontmatter = {
+      authors: [
+        {
+          name: 'John Doe',
+          affiliations: ['aff1'],
+        },
+        {
+          name: 'Jane Doe',
+          affiliations: ['aff1', 'col2'],
+        },
+      ],
+      affiliations: [
+        {
+          id: 'aff1',
+          name: 'univ 1',
+        },
+        {
+          id: 'aff2',
+          name: 'univ 2',
+        },
+        {
+          id: 'col1',
+          name: 'group 1',
+          collaboration: true,
+        },
+        {
+          id: 'col2',
+          name: 'group 2',
+          collaboration: true,
+        },
+      ],
+    };
+    const doc = extendFrontmatter(frontmatter);
+    expect(doc.authors).toEqual([
+      {
+        name: 'John Doe',
+        given_name: 'John',
+        surname: 'Doe',
+        index: 1,
+        letter: 'A',
+        affiliations: [
+          {
+            id: 'aff1',
+            name: 'univ 1',
+            value: {
+              id: 'aff1',
+              name: 'univ 1',
+            },
+            index: 1,
+            letter: 'A',
+          },
+        ],
+      },
+      {
+        name: 'Jane Doe',
+        given_name: 'Jane',
+        surname: 'Doe',
+        index: 2,
+        letter: 'B',
+        affiliations: [
+          {
+            id: 'aff1',
+            name: 'univ 1',
+            value: {
+              id: 'aff1',
+              name: 'univ 1',
+            },
+            index: 1,
+            letter: 'A',
+          },
+        ],
+        collaborations: [
+          {
+            id: 'col2',
+            name: 'group 2',
+            collaboration: true,
+            value: {
+              id: 'col2',
+              name: 'group 2',
+              collaboration: true,
+            },
+            index: 1,
+            letter: 'A',
+          },
+        ],
+      },
+    ]);
+    expect(doc.affiliations).toEqual([
+      {
+        id: 'aff1',
+        name: 'univ 1',
+        value: {
+          id: 'aff1',
+          name: 'univ 1',
+        },
+        index: 1,
+        letter: 'A',
+      },
+    ]);
+    expect(doc.collaborations).toEqual([
+      {
+        id: 'col2',
+        name: 'group 2',
+        collaboration: true,
+        value: {
+          id: 'col2',
+          name: 'group 2',
+          collaboration: true,
+        },
+        index: 1,
+        letter: 'A',
+      },
+    ]);
+  });
 });
diff --git a/packages/myst-templates/src/frontmatter.ts b/packages/myst-templates/src/frontmatter.ts
@@ -1,4 +1,4 @@
-import type { Contributor, PageFrontmatter } from 'myst-frontmatter';
+import type { Affiliation, Contributor, PageFrontmatter } from 'myst-frontmatter';
 import type { RendererAuthor, RendererDoc, ValueAndIndex } from './types.js';
 
 const ALPHA = 'ABCDEFGHIJKLMNOPQURSUVWXYZ';
@@ -71,18 +71,22 @@ function addIndicesToAuthors(
 
 export function extendFrontmatter(frontmatter: PageFrontmatter): RendererDoc {
   const datetime = frontmatter.date ? new Date(frontmatter.date) : new Date();
-  const affiliations =
-    frontmatter.affiliations
-      ?.filter((aff) => aff.id && !aff.collaboration)
-      .map((aff, index) => {
-        return { ...aff, value: aff, ...indexAndLetter(index) };
-      }) ?? [];
-  const collaborations =
-    frontmatter.affiliations
-      ?.filter((aff) => aff.id && aff.collaboration)
-      .map((aff, index) => {
-        return { ...aff, value: aff, ...indexAndLetter(index) };
-      }) ?? [];
+  // Only add affiliations from authors, not contributors
+  const affIds = [
+    ...new Set(frontmatter.authors?.map((auth) => auth.affiliations ?? []).flat() ?? []),
+  ];
+  const affiliations = affIds
+    .map((id) => frontmatter.affiliations?.find((aff) => aff.id === id))
+    .filter((aff): aff is Affiliation => !!aff?.id && !aff.collaboration)
+    .map((aff, index) => {
+      return { ...aff, value: aff, ...indexAndLetter(index) };
+    });
+  const collaborations = affIds
+    .map((id) => frontmatter.affiliations?.find((aff) => aff.id === id))
+    .filter((aff): aff is Affiliation => !!aff?.id && !!aff.collaboration)
+    .map((aff, index) => {
+      return { ...aff, value: aff, ...indexAndLetter(index) };
+    });
   const doc: RendererDoc = {
     ...frontmatter,
     date: {

diff --git a/packages/myst-to-jats/src/frontmatter.ts b/packages/myst-to-jats/src/frontmatter.ts
@@ -160,7 +160,6 @@ export function getArticleAuthors(frontmatter: ProjectFrontmatter): Element[] {
     const attributes: Record<string, any> = {};
     const elements: Element[] = [];
     if (type) attributes['contrib-type'] = type;
-    if (author.id) attributes.id = author.id;
     if (author.corresponding) attributes.corresp = 'yes';
     if (author.deceased) attributes['deceased'] = 'yes';
     if (author.equal_contributor != null) {
@@ -228,16 +227,10 @@ export function getArticleAuthors(frontmatter: ProjectFrontmatter): Element[] {
   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;
 }
 
@@ -309,84 +302,93 @@ function instWrapElementsFromAffiliation(affiliation: Affiliation, includeDept =
 }
 
 export function getArticleAffiliations(frontmatter: ProjectFrontmatter): Element[] {
-  const affs = frontmatter.affiliations?.map((affiliation): Element => {
-    const elements: Element[] = [];
-    const attributes: Record<string, any> = {};
-    if (affiliation.id) {
-      attributes.id = affiliation.id;
-    }
-    elements.push(...instWrapElementsFromAffiliation(affiliation));
-    if (affiliation.address) {
-      elements.push({
-        type: 'element',
-        name: 'addr-line',
-        elements: [{ type: 'text', text: affiliation.address }],
-      });
-    }
-    if (affiliation.city) {
-      elements.push({
-        type: 'element',
-        name: 'city',
-        elements: [{ type: 'text', text: affiliation.city }],
-      });
-    }
-    if (affiliation.state) {
-      elements.push({
-        type: 'element',
-        name: 'state',
-        elements: [{ type: 'text', text: affiliation.state }],
-      });
-    }
-    if (affiliation.postal_code) {
-      elements.push({
-        type: 'element',
-        name: 'postal-code',
-        elements: [{ type: 'text', text: affiliation.postal_code }],
-      });
-    }
-    if (affiliation.country) {
-      elements.push({
-        type: 'element',
-        name: 'country',
-        elements: [{ type: 'text', text: affiliation.country }],
-      });
-    }
-    if (affiliation.phone) {
-      elements.push({
-        type: 'element',
-        name: 'phone',
-        elements: [{ type: 'text', text: affiliation.phone }],
-      });
-    }
-    if (affiliation.fax) {
-      elements.push({
-        type: 'element',
-        name: 'fax',
-        elements: [{ type: 'text', text: affiliation.fax }],
-      });
-    }
-    if (affiliation.email) {
-      elements.push({
-        type: 'element',
-        name: 'email',
-        elements: [{ type: 'text', text: affiliation.email }],
-      });
-    }
-    if (affiliation.url) {
-      elements.push({
+  if (!frontmatter.affiliations?.length) return [];
+  // Only add affiliations from authors, not contributors
+  const affIds = [
+    ...new Set(frontmatter.authors?.map((auth) => auth.affiliations ?? []).flat() ?? []),
+  ];
+  if (!affIds?.length) return [];
+  const affs = affIds
+    .map((id) => frontmatter.affiliations?.find((aff) => aff.id === id))
+    .filter((aff): aff is Affiliation => !!aff)
+    .map((affiliation): Element => {
+      const elements: Element[] = [];
+      const attributes: Record<string, any> = {};
+      if (affiliation.id) {
+        attributes.id = affiliation.id;
+      }
+      elements.push(...instWrapElementsFromAffiliation(affiliation));
+      if (affiliation.address) {
+        elements.push({
+          type: 'element',
+          name: 'addr-line',
+          elements: [{ type: 'text', text: affiliation.address }],
+        });
+      }
+      if (affiliation.city) {
+        elements.push({
+          type: 'element',
+          name: 'city',
+          elements: [{ type: 'text', text: affiliation.city }],
+        });
+      }
+      if (affiliation.state) {
+        elements.push({
+          type: 'element',
+          name: 'state',
+          elements: [{ type: 'text', text: affiliation.state }],
+        });
+      }
+      if (affiliation.postal_code) {
+        elements.push({
+          type: 'element',
+          name: 'postal-code',
+          elements: [{ type: 'text', text: affiliation.postal_code }],
+        });
+      }
+      if (affiliation.country) {
+        elements.push({
+          type: 'element',
+          name: 'country',
+          elements: [{ type: 'text', text: affiliation.country }],
+        });
+      }
+      if (affiliation.phone) {
+        elements.push({
+          type: 'element',
+          name: 'phone',
+          elements: [{ type: 'text', text: affiliation.phone }],
+        });
+      }
+      if (affiliation.fax) {
+        elements.push({
+          type: 'element',
+          name: 'fax',
+          elements: [{ type: 'text', text: affiliation.fax }],
+        });
+      }
+      if (affiliation.email) {
+        elements.push({
+          type: 'element',
+          name: 'email',
+          elements: [{ type: 'text', text: affiliation.email }],
+        });
+      }
+      if (affiliation.url) {
+        elements.push({
+          type: 'element',
+          name: 'ext-link',
+          attributes: { 'ext-link-type': 'uri', 'xlink:href': affiliation.url },
+          elements: [{ type: 'text', text: affiliation.url }],
+        });
+      }
+      return {
         type: 'element',
-        name: 'ext-link',
-        attributes: { 'ext-link-type': 'uri', 'xlink:href': affiliation.url },
-        elements: [{ type: 'text', text: affiliation.url }],
-      });
-    }
-    return {
-      type: 'element',
-      name: 'aff',
-      attributes,
-      elements,
-    };
-  });
+        name: 'aff',
+        attributes,
+        elements,
+      };
+    });
   return affs ? affs : [];
 }