🔧 Allow conference chairs; remove jats refs in abstracts

.changeset/perfect-numbers-beg.md

@@ -0,0 +1,5 @@
+---
+"crossref-utils": patch
+---
+
+Add chair contributor_type option

.changeset/pretty-otters-fix.md

@@ -0,0 +1,5 @@
+---
+"crossref-utils": patch
+---
+
+Remove xrefs from abstract tree

README.md

@@ -29,6 +29,7 @@ This will prompt the user to select new DOIs, if they are not present in MyST me
 - `--name`, `--email`: Depositor name and email. Default Depositor is Curvenote.
 - `--registrant`: Registrant organization. Default is `Crossref` - likely this should not be changed.
 - `--id`: Unique ID for the deposit. By default, a random ID will be autogenerated - likely this should not be changed.
+- `--contributor-type`: For **conference** deposits only, sets the `contributor_role` for people listed under MyST `editors` in the proceedings metadata. Values are `editor` (default) or `chair`. Other deposit types ignore this flag.
 
 ### Deposit types
 
@@ -85,7 +86,8 @@ You may also specify in the frontmatter:
 - `venue.issn` - series issn
 - `venue.doi` - series doi
 - `volume.subject` - proceedings subject
-- `editors` - proceedings editors
+- `volume.doi` - proceedings doi
+- `editors` - proceedings editors (or "chairs" if `--contributor-type chair` is specified)
 
 #### Dataset
 

src/cli/deposit.ts

@@ -33,6 +33,7 @@ import {
   transformCiteToText,
   transformNewlineToSpace,
   transformXrefToLink,
+  unwrapJatsXrefElements,
 } from './utils.js';
 import type { ProjectFrontmatter } from 'myst-frontmatter';
 import { selectNewDois } from './generate.js';
@@ -57,6 +58,7 @@ type DepositOptions = {
   journalAbbr?: string;
   journalDoi?: string;
   prefix?: string;
+  contributorType?: 'editor' | 'chair';
 };
 
 type DepositSource = {
@@ -130,11 +132,13 @@ export async function depositArticleFromSource(session: ISession, depositSource:
     transformNewlineToSpace(abstractPart);
     const serializer = new JatsSerializer(new VFile(), abstractPart as any);
     const jats = serializer.render(true).elements();
-    abstract = u(
-      'element',
-      { name: 'jats:abstract' },
-      jats.map((e) => element2JatsUnist(e)),
-    ) as Element;
+    abstract = unwrapJatsXrefElements(
+      u(
+        'element',
+        { name: 'jats:abstract' },
+        jats.map((e) => element2JatsUnist(e)),
+      ) as Element,
+    );
   } else if (description) {
     // Use the project description as the fallback for the abstract
     abstractPart = {
@@ -144,11 +148,13 @@ export async function depositArticleFromSource(session: ISession, depositSource:
     transformNewlineToSpace(abstractPart);
     const serializer = new JatsSerializer(new VFile(), abstractPart as any);
     const jats = serializer.render(true).elements();
-    abstract = u(
-      'element',
-      { name: 'jats:abstract' },
-      jats.map((e) => element2JatsUnist(e)),
-    ) as Element;
+    abstract = unwrapJatsXrefElements(
+      u(
+        'element',
+        { name: 'jats:abstract' },
+        jats.map((e) => element2JatsUnist(e)),
+      ) as Element,
+    );
   }
   return { frontmatter: frontmatter ?? {}, dois, abstract, configFile };
 }
@@ -369,7 +375,11 @@ function issueDataFromArticles(
       }
     }
     if (editors?.length && !proceedingsEditors) {
-      proceedingsEditors = contributorsXmlFromMystEditors(frontmatter);
+      const proceedingsEditorRole =
+        opts.type === 'conference' && opts.contributorType === 'chair' ? 'chair' : 'editor';
+      proceedingsEditors = contributorsXmlFromMystEditors(frontmatter, {
+        contributor_role: proceedingsEditorRole,
+      });
     }
   });
   if (!publicationDate && (volumeNumber || volumeDoi || issueNumber || issueDoi)) {
@@ -419,6 +429,11 @@ export async function deposit(session: ISession, opts: DepositOptions) {
   if (!depositType) {
     throw new Error('No deposit type specified');
   }
+  if (depositType !== 'conference' && opts.contributorType === 'chair') {
+    session.log.warn(
+      '`--contributor-type chair` only applies to conference deposits; using editor role for this deposit type.',
+    );
+  }
   if (!name) {
     const resp = await inquirer.prompt([
       {
@@ -661,6 +676,14 @@ function makeDepositCLI(program: Command) {
     .addOption(new Option('--registrant <value>', 'Registrant organization').default('Crossref'))
     .addOption(new Option('-o, --output <value>', 'Output file'))
     .addOption(new Option('--prefix <value>', 'Prefix for new DOIs'))
+    .addOption(
+      new Option(
+        '--contributor-type <value>',
+        'Contributor role for myst `editors` in conference proceedings',
+      )
+        .choices(['editor', 'chair'])
+        .default('editor'),
+    )
     .action(clirun(deposit, { program, getSession: (logger) => new Session({ logger }) }));
   return command;
 }

src/cli/utils.ts

@@ -2,6 +2,7 @@ import fs from 'node:fs';
 import { u } from 'unist-builder';
 import { selectAll } from 'unist-util-select';
 import { liftChildren, type GenericNode, type GenericParent } from 'myst-common';
+import type { Element, ElementContent } from 'xast';
 
 type JatsAttributes = Record<string, string | undefined>;
 
@@ -30,6 +31,29 @@ export function element2JatsUnist(element: JatsElement): Node {
   throw new Error(`Invalid Jats element: ${element}`);
 }
 
+/**
+ * Remove `jats:xref` wrappers from a JATS xast subtree, keeping only their children.
+ */
+export function unwrapJatsXrefElements(node: Element): Element {
+  const children = node.children ?? [];
+  const newChildren: ElementContent[] = [];
+  for (const child of children) {
+    if (child.type === 'element') {
+      const processed = unwrapJatsXrefElements(child);
+      if (processed.name === 'jats:xref') {
+        for (const inner of processed.children) {
+          newChildren.push(inner.type === 'element' ? unwrapJatsXrefElements(inner) : inner);
+        }
+      } else {
+        newChildren.push(processed);
+      }
+    } else {
+      newChildren.push(child);
+    }
+  }
+  return { ...node, children: newChildren };
+}
+
 /**
  * Transform to handle xrefs that resolve to external sites
  *

src/contributors.ts

@@ -70,7 +70,11 @@ export function contributorsXmlFromMystAuthors(
   );
 }
 
-export function contributorsXmlFromMystEditors(myst: PageFrontmatter): Element | undefined {
+export function contributorsXmlFromMystEditors(
+  myst: PageFrontmatter,
+  opts?: { contributor_role?: ContributorOptions['contributor_role'] },
+): Element | undefined {
+  const contributor_role = opts?.contributor_role ?? 'editor';
   const editors =
     myst.editors
       ?.map((editor) => myst.contributors?.find(({ id }) => editor === id))
@@ -88,7 +92,7 @@ export function contributorsXmlFromMystEditors(myst: PageFrontmatter): Element |
       contributorXml({
         ...(editor as ContributorOptions),
         sequence: index === 0 ? 'first' : 'additional',
-        contributor_role: 'editor',
+        contributor_role,
       }),
     ),
   );

tests/contributors.spec.ts

@@ -0,0 +1,26 @@
+import { describe, test, expect } from 'vitest';
+import { toXml } from 'xast-util-to-xml';
+import type { PageFrontmatter } from 'myst-frontmatter';
+import { contributorsXmlFromMystEditors } from '../src/contributors.js';
+
+describe('contributorsXmlFromMystEditors', () => {
+  const baseMyst = {
+    editors: ['ed1'],
+    contributors: [
+      {
+        id: 'ed1',
+        nameParsed: { given: 'Pat', family: 'Organizer', literal: 'Pat Organizer' },
+      },
+    ],
+  } as unknown as PageFrontmatter;
+
+  test('defaults myst editors to Crossref contributor_role editor', () => {
+    const el = contributorsXmlFromMystEditors(baseMyst);
+    expect(toXml(el!)).toContain('contributor_role="editor"');
+  });
+
+  test('supports chair role for proceedings editors', () => {
+    const el = contributorsXmlFromMystEditors(baseMyst, { contributor_role: 'chair' });
+    expect(toXml(el!)).toContain('contributor_role="chair"');
+  });
+});

tests/utils.spec.ts

@@ -1,6 +1,8 @@
 import { describe, test, expect } from 'vitest';
+import { u } from 'unist-builder';
 import { toXml } from 'xast-util-to-xml';
 import { publicationDateXml } from '../src';
+import { unwrapJatsXrefElements } from '../src/cli/utils.js';
 import type { Element } from 'xast';
 
 describe('CrossRef Utilities', () => {
@@ -29,3 +31,31 @@ describe('CrossRef Utilities', () => {
     }
   });
 });
+
+describe('unwrapJatsXrefElements', () => {
+  test('removes jats:xref wrapper, keeps children', () => {
+    const tree = u('element', { name: 'jats:p', attributes: {} }, [
+      u('text', 'See '),
+      u('element', { name: 'jats:xref', attributes: { 'ref-type': 'fig', rid: 'f1' } }, [
+        u('element', { name: 'jats:bold', attributes: {} }, [u('text', 'Figure 1')]),
+      ]),
+      u('text', ' for details.'),
+    ]) as Element;
+    const out = unwrapJatsXrefElements(tree);
+    const xml = toXml(out);
+    expect(xml).not.toContain('xref');
+    expect(xml).toContain('Figure 1');
+    expect(xml).toContain('See ');
+    expect(xml).toContain('for details.');
+  });
+
+  test('unwraps nested jats:xref', () => {
+    const tree = u('element', { name: 'jats:p', attributes: {} }, [
+      u('element', { name: 'jats:xref', attributes: {} }, [
+        u('element', { name: 'jats:xref', attributes: {} }, [u('text', 'inner')]),
+      ]),
+    ]) as Element;
+    const out = unwrapJatsXrefElements(tree);
+    expect(toXml(out)).toBe('<jats:p>inner</jats:p>');
+  });
+});