@manuscripts/transform 2.1.3 → 2.1.5-LEAN-3376-0

package/dist/es/jats/importer/jats-body-dom-parser.js

@@ -15,10 +15,8 @@
  */
 import mime from 'mime';
 import { DOMParser, Fragment } from 'prosemirror-model';
-import { convertMathMLToSVG } from '../../mathjax/mathml-to-svg';
-import { convertTeXToSVG } from '../../mathjax/tex-to-svg';
 import { schema } from '../../schema';
-import { chooseSectionCategory, xmlSerializer } from '../../transformer';
+import { chooseSectionCategory } from '../../transformer';
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const chooseContentType = (graphicNode) => {
     if (graphicNode) {
@@ -33,6 +31,28 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
+const getEquationContent = (p) => {
+    var _a;
+    const element = p;
+    const id = element.getAttribute('id');
+    const container = (_a = element.querySelector('alternatives')) !== null && _a !== void 0 ? _a : element;
+    let contents = '';
+    let format = '';
+    for (const child of container.childNodes) {
+        const nodeName = child.nodeName.replace(/^[a-z]:/, '');
+        switch (nodeName) {
+            case 'tex-math':
+                contents = child.innerHTML;
+                format = 'tex';
+                break;
+            case 'mml:math':
+                contents = child.outerHTML;
+                format = 'mathml';
+                break;
+        }
+    }
+    return { id, format, contents };
+};
 const marks = [
     {
         tag: 'bold',
@@ -141,91 +161,26 @@ const nodes = [
         tag: 'inline-formula',
         node: 'inline_equation',
         getAttrs: (node) => {
-            var _a, _b, _c, _d, _e;
             const element = node;
-            const attrs = {
-                id: element.getAttribute('id'),
-                MathMLRepresentation: '',
-                SVGRepresentation: '',
-                TeXRepresentation: '',
-            };
-            const container = (_a = element.querySelector('alternatives')) !== null && _a !== void 0 ? _a : element;
-            for (const child of container.childNodes) {
-                const nodeName = child.nodeName.replace(/^[a-z]:/, '');
-                switch (nodeName) {
-                    case 'tex-math':
-                        attrs.TeXRepresentation = (_c = (_b = child.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
-                        if (attrs.TeXRepresentation) {
-                            attrs.SVGRepresentation =
-                                (_d = convertTeXToSVG(attrs.TeXRepresentation, true)) !== null && _d !== void 0 ? _d : '';
-                        }
-                        break;
-                    case 'mml:math':
-                        ;
-                        child.removeAttribute('id');
-                        attrs.MathMLRepresentation = xmlSerializer.serializeToString(child);
-                        if (attrs.MathMLRepresentation) {
-                            attrs.SVGRepresentation =
-                                (_e = convertMathMLToSVG(attrs.MathMLRepresentation, true)) !== null && _e !== void 0 ? _e : '';
-                        }
-                        break;
-                }
-            }
-            return attrs;
+            return getEquationContent(element);
         },
     },
     {
         tag: 'disp-formula',
         node: 'equation_element',
         getAttrs: (node) => {
+            var _a, _b;
             const element = node;
-            const caption = element.querySelector('figcaption');
             return {
                 id: element.getAttribute('id'),
-                suppressCaption: !caption,
+                label: (_b = (_a = element.querySelector('label')) === null || _a === void 0 ? void 0 : _a.textContent) !== null && _b !== void 0 ? _b : '',
             };
         },
         getContent: (node, schema) => {
-            var _a, _b, _c, _d, _e;
             const element = node;
-            const attrs = {
-                MathMLStringRepresentation: '',
-                SVGStringRepresentation: '',
-                TeXRepresentation: '',
-            };
-            const container = (_a = element.querySelector('alternatives')) !== null && _a !== void 0 ? _a : element;
-            for (const child of container.childNodes) {
-                const nodeName = child.nodeName.replace(/^[a-z]:/, '');
-                switch (nodeName) {
-                    case 'tex-math':
-                        attrs.TeXRepresentation = (_c = (_b = child.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '';
-                        if (attrs.TeXRepresentation) {
-                            attrs.SVGStringRepresentation =
-                                (_d = convertTeXToSVG(attrs.TeXRepresentation, true)) !== null && _d !== void 0 ? _d : '';
-                        }
-                        break;
-                    case 'mml:math':
-                        ;
-                        child.removeAttribute('id');
-                        attrs.MathMLStringRepresentation =
-                            xmlSerializer.serializeToString(child);
-                        if (attrs.MathMLStringRepresentation) {
-                            attrs.SVGStringRepresentation =
-                                (_e = convertMathMLToSVG(attrs.MathMLStringRepresentation, true)) !== null && _e !== void 0 ? _e : '';
-                        }
-                        break;
-                }
-            }
-            const caption = element.querySelector('figcaption');
-            const figcaption = schema.nodes.figcaption.create();
+            const attrs = getEquationContent(element);
             return Fragment.from([
-                schema.nodes.equation.createChecked(attrs),
-                caption
-                    ?
-                        jatsBodyDOMParser.parse(caption, {
-                            topNode: figcaption,
-                        })
-                    : figcaption,
+                schema.nodes.equation.createChecked(Object.assign({}, attrs)),
             ]);
         },
     },
@@ -519,23 +474,9 @@ const nodes = [
             const element = node;
             return {
                 id: element.getAttribute('id'),
-                suppressFooter: !element.querySelector('table > tfoot > tr'),
-                suppressHeader: !element.querySelector('table > thead > tr'),
             };
         },
     },
-    {
-        tag: 'tbody',
-        skip: true,
-    },
-    {
-        tag: 'tfoot',
-        skip: true,
-    },
-    {
-        tag: 'thead',
-        skip: true,
-    },
     {
         tag: 'title',
         node: 'section_title',
@@ -562,12 +503,12 @@ const nodes = [
     },
     {
         tag: 'th',
-        node: 'table_cell',
+        node: 'table_header',
         getAttrs: (node) => {
             const element = node;
             const colspan = element.getAttribute('colspan');
             const rowspan = element.getAttribute('rowspan');
-            return Object.assign(Object.assign(Object.assign({ celltype: 'th' }, (colspan && { colspan })), (rowspan && { rowspan })), { valign: element.getAttribute('valign'), align: element.getAttribute('align'), scope: element.getAttribute('scope'), style: element.getAttribute('style') });
+            return Object.assign(Object.assign(Object.assign({}, (colspan && { colspan })), (rowspan && { rowspan })), { valign: element.getAttribute('valign'), align: element.getAttribute('align'), scope: element.getAttribute('scope'), style: element.getAttribute('style') });
         },
     },
     {

package/dist/es/jats/importer/jats-body-transformations.js

@@ -199,7 +199,9 @@ export const jatsBodyTransformations = {
         }
     },
     moveFootnotes(doc, group, createElement) {
-        const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot fn)')];
+        const footnotes = [
+            ...doc.querySelectorAll('fn:not(table-wrap-foot fn, author-notes fn)'),
+        ];
         const footnotesSection = doc.querySelector('sec[sec-type="endnotes"]');
         const footnotesSectionGroup = footnotesSection === null || footnotesSection === void 0 ? void 0 : footnotesSection.querySelector('fn-group');
         const containingGroup = footnotesSectionGroup || createElement('fn-group');
@@ -236,8 +238,12 @@ export const jatsBodyTransformations = {
         }
     },
     fixTables(body, createElement) {
-        const tables = body.querySelectorAll('table-wrap > table');
-        tables.forEach((table) => {
+        const tableWraps = body.querySelectorAll('table-wrap');
+        tableWraps.forEach((tableWrap) => {
+            const table = tableWrap.querySelector('table');
+            if (!table) {
+                return;
+            }
             const colgroup = table.querySelector('colgroup');
             const cols = table.querySelectorAll('col');
             if (!colgroup && table.firstChild && cols.length > 0) {
@@ -245,20 +251,7 @@ export const jatsBodyTransformations = {
                 for (const col of cols) {
                     colgroup.appendChild(col);
                 }
-                table.insertBefore(colgroup, table.firstChild);
-            }
-            const tbody = table.querySelector('tbody');
-            if (tbody) {
-                const headerRow = table.querySelector('thead > tr');
-                if (!headerRow) {
-                    const tr = createElement('tr');
-                    tbody.insertBefore(tr, tbody.firstElementChild);
-                }
-                const footerRow = table.querySelector('tfoot > tr');
-                if (!footerRow) {
-                    const tr = createElement('tr');
-                    tbody.appendChild(tr);
-                }
+                tableWrap.insertBefore(colgroup, table.nextSibling);
             }
         });
     },

package/dist/es/jats/importer/jats-front-parser.js

@@ -15,7 +15,7 @@
  */
 import debug from 'debug';
 import { getTrimmedTextContent } from '../../lib/utils';
-import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildJournal, buildTitles, } from '../../transformer';
+import { buildAffiliation, buildAuthorNotes, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildJournal, buildParagraph, buildTitles, } from '../../transformer';
 import { parseJournalMeta } from './jats-journal-meta-parser';
 import { htmlFromJatsNode } from './jats-parser-utils';
 const warn = debug('manuscripts-transform');
@@ -173,7 +173,45 @@ export const jatsFrontParser = {
             affiliationIDs,
         };
     },
-    parseAuthorNotes(elements) {
+    parseAuthorNotes(element) {
+        if (!element) {
+            return {
+                footnotes: [],
+                footnoteIDs: new Map(),
+                authorNotes: [],
+                authorNotesParagraphs: [],
+                correspondingIDs: new Map(),
+                correspondingList: [],
+            };
+        }
+        const { footnotes, footnoteIDs } = this.parseFootnotes([
+            ...element.querySelectorAll('fn:not([fn-type])'),
+        ]);
+        const authorNotesParagraphs = this.parseParagraphs([
+            ...element.querySelectorAll(':scope > p'),
+        ]);
+        const { correspondingList, correspondingIDs } = this.parseCorresp([
+            ...element.querySelectorAll('corresp'),
+        ]);
+        const authorNotes = [
+            buildAuthorNotes([
+                ...footnoteIDs.values(),
+                ...authorNotesParagraphs.map((p) => p._id),
+            ]),
+        ];
+        return {
+            footnotes,
+            footnoteIDs,
+            authorNotesParagraphs,
+            authorNotes,
+            correspondingIDs,
+            correspondingList,
+        };
+    },
+    parseParagraphs(elements) {
+        return elements.map((p) => buildParagraph(p.innerHTML));
+    },
+    parseFootnotes(elements) {
         const footnoteIDs = new Map();
         const footnotes = elements.map((element) => {
             const fn = buildFootnote('', element.innerHTML);

package/dist/es/jats/importer/jats-parser-utils.js

@@ -13,6 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { v4 as uuidv4 } from 'uuid';
+import { schema } from '../../schema';
 import { generateID, nodeTypesMap } from '../../transformer';
 export const updateDocumentIDs = (node, replacements) => {
     const warnings = [];
@@ -26,6 +28,10 @@ function recurseDoc(node, fn) {
     node.descendants((n) => fn(n));
 }
 const updateNodeID = (node, replacements, warnings) => {
+    if (node.type === schema.nodes.inline_equation) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `InlineMathFragment:${uuidv4()}` });
+        return;
+    }
     if (!('id' in node.attrs)) {
         return;
     }

package/dist/es/jats/importer/parse-jats-article.js

@@ -32,12 +32,7 @@ export const parseJATSFront = (doc, front) => {
     const { affiliations, affiliationIDs } = jatsFrontParser.parseAffiliations([
         ...front.querySelectorAll('article-meta > contrib-group > aff'),
     ]);
-    const { footnotes, footnoteIDs } = jatsFrontParser.parseAuthorNotes([
-        ...front.querySelectorAll('article-meta > author-notes > fn:not([fn-type])'),
-    ]);
-    const { correspondingList, correspondingIDs } = jatsFrontParser.parseCorresp([
-        ...front.querySelectorAll('article-meta > author-notes > corresp'),
-    ]);
+    const { footnotes, footnoteIDs, authorNotes, authorNotesParagraphs, correspondingIDs, correspondingList, } = jatsFrontParser.parseAuthorNotes(front.querySelector('article-meta > author-notes'));
     const authors = jatsFrontParser.parseContributors([
         ...front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]'),
     ], affiliationIDs, footnoteIDs, correspondingIDs);
@@ -48,6 +43,8 @@ export const parseJATSFront = (doc, front) => {
         manuscript,
         titles,
         journal,
+        ...authorNotesParagraphs,
+        ...authorNotes,
         ...footnotes,
         ...authors,
         ...affiliations,

package/dist/es/jats/jats-exporter.js

@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ObjectTypes, } from '@manuscripts/json-schema';
+import { getModelsByType, ObjectTypes, } from '@manuscripts/json-schema';
 import { CitationProvider } from '@manuscripts/library';
 import debug from 'debug';
-import { DOMParser, DOMSerializer } from 'prosemirror-model';
+import { DOMParser as ProseMirrorDOMParser, DOMSerializer, } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
 import { nodeFromHTML, textFromHTML } from '../lib/html';
 import { normalizeStyleName } from '../lib/styled-content';
@@ -32,7 +32,7 @@ import { selectVersionIds } from './jats-versions';
 const warn = debug('manuscripts-transform');
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const normalizeID = (id) => id.replace(/:/g, '_');
-const parser = DOMParser.fromSchema(schema);
+const parser = ProseMirrorDOMParser.fromSchema(schema);
 const findChildNodeOfType = (node, nodeType) => {
     for (const child of iterateChildren(node)) {
         if (child.type === nodeType) {
@@ -88,7 +88,7 @@ const createDefaultIdGenerator = () => {
     const counter = createCounter();
     return async (element) => {
         const value = String(counter.increment(element.nodeName));
-        return `${element.nodeName}-${value}`;
+        return `${element.localName}-${value}`;
     };
 };
 const chooseRefType = (objectType) => {
@@ -156,6 +156,7 @@ export class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
+            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -606,6 +607,7 @@ export class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
+                author_notes: () => ['author-notes', 0],
                 title: () => '',
                 affiliations: () => '',
                 contributors: () => '',
@@ -678,22 +680,20 @@ export class JATSExporter {
                 },
                 doc: () => '',
                 equation: (node) => {
-                    const formula = this.document.createElement('disp-formula');
-                    formula.setAttribute('id', normalizeID(node.attrs.id));
-                    if (node.attrs.TeXRepresentation) {
-                        const math = this.document.createElement('tex-math');
-                        math.textContent = node.attrs.TeXRepresentation;
-                        formula.appendChild(math);
-                    }
-                    else if (node.attrs.MathMLStringRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.MathMLStringRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    return formula;
+                    return this.createEquation(node);
+                },
+                inline_equation: (node) => {
+                    const eqElement = this.document.createElement('inline-formula');
+                    const equation = this.createEquation(node, true);
+                    eqElement.append(equation);
+                    return eqElement;
+                },
+                equation_element: (node) => {
+                    const eqElement = this.document.createElement('disp-formula');
+                    eqElement.setAttribute('id', normalizeID(node.attrs.id));
+                    processChildNodes(eqElement, node, schema.nodes.equation);
+                    return eqElement;
                 },
-                equation_element: (node) => createFigureElement(node, 'fig', node.type.schema.nodes.equation, 'equation'),
                 figcaption: (node) => {
                     if (!node.textContent) {
                         return '';
@@ -743,28 +743,6 @@ export class JATSExporter {
                 },
                 hard_break: () => '',
                 highlight_marker: () => '',
-                inline_equation: (node) => {
-                    const formula = this.document.createElement('inline-formula');
-                    formula.setAttribute('id', normalizeID(node.attrs.id));
-                    if (node.attrs.TeXRepresentation) {
-                        const math = this.document.createElement('tex-math');
-                        math.textContent = node.attrs.TeXRepresentation;
-                        formula.appendChild(math);
-                    }
-                    else if (node.attrs.MathMLRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.MathMLRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    else if (node.attrs.SVGRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.SVGRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    return formula;
-                },
                 inline_footnote: (node) => {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'fn');
@@ -865,9 +843,13 @@ export class JATSExporter {
                     element.setAttribute('position', 'anchor');
                     return element;
                 },
-                table_body: () => ['tbody', 0],
                 table_cell: (node) => [
-                    node.attrs.celltype,
+                    'td',
+                    Object.assign(Object.assign({ valign: node.attrs.valign, align: node.attrs.align, scope: node.attrs.scope, style: node.attrs.style }, (node.attrs.rowspan > 1 && { rowspan: node.attrs.rowspan })), (node.attrs.colspan > 1 && { colspan: node.attrs.colspan })),
+                    0,
+                ],
+                table_header: (node) => [
+                    'th',
                     Object.assign(Object.assign({ valign: node.attrs.valign, align: node.attrs.align, scope: node.attrs.scope, style: node.attrs.style }, (node.attrs.rowspan > 1 && { rowspan: node.attrs.rowspan })), (node.attrs.colspan > 1 && { colspan: node.attrs.colspan })),
                     0,
                 ],
@@ -948,6 +930,26 @@ export class JATSExporter {
                     element.appendChild(this.serializeNode(childNode));
                 }
             };
+            const appendTable = (element, node) => {
+                const tableNode = findChildNodeOfType(node, node.type.schema.nodes.table);
+                const colGroupNode = findChildNodeOfType(node, node.type.schema.nodes.table_colgroup);
+                if (!tableNode) {
+                    return;
+                }
+                const table = this.serializeNode(tableNode);
+                const tbodyElement = this.document.createElement('tbody');
+                while (table.firstChild) {
+                    const child = table.firstChild;
+                    table.removeChild(child);
+                    tbodyElement.appendChild(child);
+                }
+                table.appendChild(tbodyElement);
+                if (colGroupNode) {
+                    const colGroup = this.serializeNode(colGroupNode);
+                    table.insertBefore(colGroup, table.firstChild);
+                }
+                element.appendChild(table);
+            };
             const createFigureElement = (node, nodeName, contentNodeType, figType) => {
                 const element = createElement(node, nodeName);
                 if (figType) {
@@ -968,7 +970,7 @@ export class JATSExporter {
                 const element = createElement(node, nodeName);
                 appendLabels(element, node);
                 appendChildNodeOfType(element, node, node.type.schema.nodes.figcaption);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.table);
+                appendTable(element, node);
                 appendChildNodeOfType(element, node, node.type.schema.nodes.table_element_footer);
                 if (isExecutableNodeType(node.type)) {
                     processExecutableNode(node, element);
@@ -1026,6 +1028,7 @@ export class JATSExporter {
             }
         };
         this.buildContributors = (articleMeta) => {
+            var _a;
             const contributors = this.models.filter(isContributor);
             const authorContributors = contributors
                 .filter((contributor) => contributor.role === 'author')
@@ -1244,56 +1247,59 @@ export class JATSExporter {
                         }
                     });
                 }
-                const noteIDs = [];
-                for (const contributor of [...authorContributors, ...otherContributors]) {
-                    if (contributor.footnote) {
-                        const ids = contributor.footnote.map((note) => {
-                            return note.noteID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                    if (contributor.corresp) {
-                        const ids = contributor.corresp.map((corresp) => {
-                            return corresp.correspID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                }
-                const footnotes = [];
-                footnotes.push(...this.models.filter(hasObjectType(ObjectTypes.Footnote)));
-                const correspodings = [];
-                correspodings.push(...this.models.filter(hasObjectType(ObjectTypes.Corresponding)));
-                if (footnotes || correspodings) {
-                    const authorNotesEl = this.document.createElement('author-notes');
-                    const usedFootnotes = footnotes.filter((footnote) => {
-                        return noteIDs.includes(footnote._id);
-                    });
-                    const usedCorrespodings = correspodings.filter((corresp) => {
-                        return noteIDs.includes(corresp._id);
-                    });
-                    usedFootnotes.forEach((footnote) => {
-                        const authorFootNote = this.document.createElement('fn');
-                        authorFootNote.setAttribute('id', normalizeID(footnote._id));
-                        authorFootNote.innerHTML = footnote.contents;
-                        authorNotesEl.appendChild(authorFootNote);
-                    });
-                    usedCorrespodings.forEach((corresponding) => {
-                        const correspondingEl = this.document.createElement('corresp');
-                        correspondingEl.setAttribute('id', normalizeID(corresponding._id));
-                        if (corresponding.label) {
-                            const labelEl = this.document.createElement('label');
-                            labelEl.textContent = corresponding.label;
-                            correspondingEl.appendChild(labelEl);
+                const authorNotesEl = this.document.createElement('author-notes');
+                const usedCorrespodings = this.getUsedCorrespondings([
+                    ...authorContributors,
+                    ...otherContributors,
+                ]);
+                usedCorrespodings.forEach((corresp) => {
+                    this.appendCorrespondingToElement(corresp, authorNotesEl);
+                });
+                const authorNotes = (_a = getModelsByType(this.modelMap, ObjectTypes.AuthorNotes)) === null || _a === void 0 ? void 0 : _a[0];
+                if (authorNotes) {
+                    authorNotes.containedObjectIDs.forEach((id) => {
+                        const model = this.modelMap.get(id);
+                        if (!model) {
+                            return;
+                        }
+                        if (id.startsWith('MPParagraphElement')) {
+                            this.appendParagraphToElement(model, authorNotesEl);
+                        }
+                        else if (id.startsWith('MPFootnote')) {
+                            this.appendFootnoteToElement(model, authorNotesEl);
                         }
-                        correspondingEl.append(corresponding.contents);
-                        authorNotesEl.appendChild(correspondingEl);
                     });
-                    if (authorNotesEl.childNodes.length > 0) {
-                        articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
-                    }
                 }
+                if (authorNotesEl.childNodes.length > 0) {
+                    articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
+                }
+            }
+        };
+        this.appendCorrespondingToElement = (corresponding, element) => {
+            const correspondingEl = this.document.createElement('corresp');
+            correspondingEl.setAttribute('id', normalizeID(corresponding._id));
+            if (corresponding.label) {
+                const labelEl = this.document.createElement('label');
+                labelEl.textContent = corresponding.label;
+                correspondingEl.appendChild(labelEl);
+            }
+            correspondingEl.append(corresponding.contents);
+            element.appendChild(correspondingEl);
+        };
+        this.appendParagraphToElement = (paragraph, element) => {
+            const parser = new DOMParser();
+            const xmlDoc = parser.parseFromString(paragraph.contents, 'text/xml');
+            const paragraphEl = xmlDoc.firstChild;
+            if (paragraphEl && paragraphEl.nodeName === 'p') {
+                element.appendChild(paragraphEl);
             }
         };
+        this.appendFootnoteToElement = (footnote, element) => {
+            const footnoteEl = this.document.createElement('fn');
+            footnoteEl.setAttribute('id', normalizeID(footnote._id));
+            footnoteEl.innerHTML = footnote.contents;
+            element.appendChild(footnoteEl);
+        };
         this.fixBody = (body, fragment) => {
             fragment.descendants((node) => {
                 if (node.attrs.id) {
@@ -1581,6 +1587,27 @@ export class JATSExporter {
             this.citationTexts.set(id, output);
         });
     }
+    createEquation(node, isInline = false) {
+        if (node.attrs.format === 'tex') {
+            const texMath = this.document.createElement('tex-math');
+            texMath.innerHTML = node.attrs.contents;
+            return texMath;
+        }
+        else {
+            const math = this.nodeFromJATS(node.attrs.contents);
+            const mathml = math;
+            if (!isInline) {
+                mathml.setAttribute('id', normalizeID(node.attrs.id));
+            }
+            return mathml;
+        }
+    }
+    getUsedCorrespondings(contributors) {
+        return contributors
+            .flatMap((c) => { var _a; return (_a = c.corresp) !== null && _a !== void 0 ? _a : []; })
+            .map((corresp) => this.modelMap.get(corresp.correspID))
+            .filter((corresp) => !!corresp);
+    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === ObjectTypes.Keyword);
         const keywordGroups = new Map();
@@ -1652,6 +1679,9 @@ export class JATSExporter {
                             }
                         }
                     }
+                    if (!fnGroup.hasChildNodes()) {
+                        fnGroup.remove();
+                    }
                 }
             }
         });