@manuscripts/transform 2.1.1-LEAN-3377-2 → 2.1.1-LEAN-3336-24

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

@@ -525,23 +525,9 @@ 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',
@@ -568,12 +554,12 @@ 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/cjs/jats/importer/jats-body-transformations.js

@@ -239,8 +239,12 @@ exports.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) {
@@ -248,33 +252,10 @@ exports.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);
             }
         });
     },
-    orderTableFootnote(doc, body) {
-        const tableInlineFootnotesIds = new Set(Array.from(body.querySelectorAll('tbody > tr > td > xref[ref-type="fn"]').values()).map((inlineFootnote) => inlineFootnote.getAttribute('rid')));
-        const fnGroups = doc.querySelectorAll('table-wrap-foot > fn-group');
-        fnGroups.forEach((fnGroup) => {
-            const orderedFootnotes = Array.from(fnGroup.querySelectorAll('fn')).sort((fn) => tableInlineFootnotesIds.has(fn.getAttribute('id'))
-                ? -1
-                : 0);
-            fnGroup.replaceChildren(...orderedFootnotes);
-        });
-    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

@@ -67,7 +67,6 @@ const parseJATSBody = (doc, body, references) => {
     jats_body_transformations_1.jatsBodyTransformations.createBackmatter(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createKeywords(doc, body, createElement);
-    jats_body_transformations_1.jatsBodyTransformations.orderTableFootnote(doc, body);
     const node = jats_body_dom_parser_1.jatsBodyDOMParser.parse(body).firstChild;
     if (!node) {
         throw new Error('No content was parsed from the JATS article body');

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

@@ -873,9 +873,13 @@ 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,
                 ],
@@ -956,6 +960,26 @@ 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) {
@@ -976,7 +1000,7 @@ 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 ((0, node_types_1.isExecutableNodeType)(node.type)) {
                     processExecutableNode(node, element);

package/dist/cjs/schema/index.js

@@ -87,7 +87,6 @@ const table_1 = require("./nodes/table");
 const table_col_1 = require("./nodes/table_col");
 const table_element_1 = require("./nodes/table_element");
 const table_element_footer_1 = require("./nodes/table_element_footer");
-const table_row_1 = require("./nodes/table_row");
 const text_1 = require("./nodes/text");
 const title_1 = require("./nodes/title");
 const toc_element_1 = require("./nodes/toc_element");
@@ -137,7 +136,6 @@ __exportStar(require("./nodes/section_title"), exports);
 __exportStar(require("./nodes/table"), exports);
 __exportStar(require("./nodes/table_col"), exports);
 __exportStar(require("./nodes/table_element"), exports);
-__exportStar(require("./nodes/table_row"), exports);
 __exportStar(require("./nodes/text"), exports);
 __exportStar(require("./nodes/toc_element"), exports);
 __exportStar(require("./nodes/toc_section"), exports);
@@ -213,10 +211,9 @@ exports.schema = new prosemirror_model_1.Schema({
         section_title: section_title_1.sectionTitle,
         section_title_plain: section_title_1.sectionTitle,
         table: table_1.table,
-        table_body: table_1.tableBody,
-        table_cell: table_row_1.tableCell,
+        table_cell: table_1.tableCell,
         table_element: table_element_1.tableElement,
-        table_row: table_row_1.tableRow,
+        table_row: table_1.tableRow,
         table_col: table_col_1.tableCol,
         table_colgroup: table_col_1.tableColGroup,
         text: text_1.text,
@@ -230,5 +227,6 @@ exports.schema = new prosemirror_model_1.Schema({
         contributors: contributors_1.contributors,
         supplements: supplements_1.supplements,
         supplement: supplement_1.supplement,
+        table_header: table_1.tableHeader,
     },
 });

package/dist/cjs/schema/nodes/table.js

@@ -15,20 +15,57 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.tableBody = exports.table = void 0;
+exports.tableHeader = exports.tableCell = exports.tableRow = exports.table = void 0;
+const prosemirror_tables_1 = require("prosemirror-tables");
+function createCellAttribute(attributeName, defaultValue = null, customGetFromDOM, customSetDOMAttr) {
+    return {
+        default: defaultValue,
+        getFromDOM(dom) {
+            if (customGetFromDOM) {
+                return customGetFromDOM(dom);
+            }
+            return dom.getAttribute(attributeName);
+        },
+        setDOMAttr(value, attrs) {
+            if (customSetDOMAttr) {
+                customSetDOMAttr(value, attrs);
+            }
+            else if (value) {
+                attrs[attributeName] = value;
+            }
+        },
+    };
+}
+const tableOptions = {
+    cellContent: 'inline*',
+    cellAttributes: {
+        placeholder: createCellAttribute('data-placeholder-text', 'Data', (dom) => dom.getAttribute('data-placeholder-text') || ''),
+        valign: createCellAttribute('valign'),
+        align: createCellAttribute('align'),
+        scope: createCellAttribute('scope'),
+        style: createCellAttribute('style'),
+        colspan: createCellAttribute('colspan', 1, (dom) => Number(dom.getAttribute('colspan') || 1), (value, attrs) => {
+            if (value && value !== 1) {
+                attrs['colspan'] = String(value);
+            }
+        }),
+        rowspan: createCellAttribute('rowspan', 1, (dom) => Number(dom.getAttribute('rowspan') || 1), (value, attrs) => {
+            if (value && value !== 1) {
+                attrs['rowspan'] = String(value);
+            }
+        }),
+    },
+};
+const tableNodes = (0, prosemirror_tables_1.tableNodes)(tableOptions);
 exports.table = {
-    content: 'table_colgroup? table_body',
-    tableRole: 'table',
-    isolating: true,
-    group: 'block',
-    selectable: false,
     attrs: {
         id: { default: '' },
-        headerRows: { default: 1 },
-        footerRows: { default: 1 },
         dataTracked: { default: null },
-        comments: { default: null },
     },
+    content: 'table_row+',
+    tableRole: 'table',
+    isolating: true,
+    group: 'block',
     parseDOM: [
         {
             tag: 'table',
@@ -36,35 +73,20 @@ exports.table = {
                 const dom = p;
                 return {
                     id: dom.getAttribute('id'),
-                    headerRows: dom.dataset && dom.dataset['header-rows'],
-                    footerRows: dom.dataset && dom.dataset['footer-rows'],
                 };
             },
         },
     ],
-    toDOM: (node) => {
-        const tableNode = node;
+    toDOM(node) {
         return [
             'table',
             {
-                id: tableNode.attrs.id,
-                'data-header-rows': String(node.attrs.headerRows),
-                'data-footer-rows': String(node.attrs.footerRows),
+                id: node.attrs.id,
             },
-            0,
+            ['tbody', 0],
         ];
     },
 };
-exports.tableBody = {
-    content: 'table_row+',
-    group: 'block',
-    tableRole: 'table',
-    parseDOM: [
-        {
-            tag: 'tbody',
-        },
-    ],
-    toDOM() {
-        return ['tbody', 0];
-    },
-};
+exports.tableRow = Object.assign(Object.assign({}, tableNodes.table_row), { attrs: Object.assign(Object.assign({}, tableNodes.table_row.attrs), { dataTracked: { default: null } }) });
+exports.tableCell = Object.assign(Object.assign({}, tableNodes.table_cell), { attrs: Object.assign(Object.assign({}, tableNodes.table_cell.attrs), { dataTracked: { default: null } }) });
+exports.tableHeader = Object.assign(Object.assign({}, tableNodes.table_header), { attrs: Object.assign(Object.assign({}, tableNodes.table_header.attrs), { dataTracked: { default: null } }) });

package/dist/cjs/schema/nodes/table_element.js

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.tableElement = void 0;
 exports.tableElement = {
-    content: '(table | placeholder) table_element_footer? figcaption? (listing | placeholder)',
+    content: '(table | placeholder) table_colgroup? table_element_footer? figcaption? (listing | placeholder)',
     attrs: {
         id: { default: '' },
         paragraphStyle: { default: '' },

package/dist/cjs/transformer/builders.js

@@ -130,11 +130,10 @@ const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     kind,
 });
 exports.buildFootnote = buildFootnote;
-const buildFootnotesOrder = (footnotesList, containedObjectID) => ({
+const buildFootnotesOrder = (footnotesList) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.FootnotesOrder),
     objectType: json_schema_1.ObjectTypes.FootnotesOrder,
     footnotesList,
-    containedObjectID,
 });
 exports.buildFootnotesOrder = buildFootnotesOrder;
 const buildCorresp = (contents) => ({

package/dist/cjs/transformer/decode.js

@@ -68,6 +68,7 @@ const getSupplements = (modelMap) => (0, exports.getModelsByType)(modelMap, json
 const getKeywordGroups = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.KeywordGroup);
 const getKeywords = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Keyword);
 const getTitles = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Titles)[0];
+const isFootnote = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Footnote);
 const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
@@ -310,25 +311,23 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.FootnotesElement]: (data) => {
                 const foonotesElementModel = data;
+                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
                 const footnotesOfKind = [];
-                const footnoteOrder = (0, exports.getModelsByType)(this.modelMap, json_schema_1.ObjectTypes.FootnotesOrder).find((model) => model.containedObjectID === data._id);
-                if (footnoteOrder) {
-                    footnoteOrder.footnotesList.map(({ id }) => {
-                        const model = this.modelMap.get(id);
-                        const collateByKind = foonotesElementModel.collateByKind || 'footnote';
-                        if (model.kind === collateByKind) {
-                            const comments = this.createCommentNodes(model);
-                            comments.forEach((c) => this.comments.set(c.attrs.id, c));
-                            const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
-                                topNode: schema_1.schema.nodes.footnote.create({
-                                    id: model._id,
-                                    kind: model.kind,
-                                    comments: comments.map((c) => c.attrs.id),
-                                }),
-                            });
-                            footnotesOfKind.push(footnote);
-                        }
-                    });
+                for (const model of this.modelMap.values()) {
+                    if (isFootnote(model) &&
+                        model.kind === collateByKind &&
+                        model.containingObject === foonotesElementModel._id) {
+                        const comments = this.createCommentNodes(model);
+                        comments.forEach((c) => this.comments.set(c.attrs.id, c));
+                        const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
+                            topNode: schema_1.schema.nodes.footnote.create({
+                                id: model._id,
+                                kind: model.kind,
+                                comments: comments.map((c) => c.attrs.id),
+                            }),
+                        });
+                        footnotesOfKind.push(footnote);
+                    }
                 }
                 return schema_1.schema.nodes.footnotes_element.create({
                     id: foonotesElementModel._id,
@@ -558,33 +557,32 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.Table]: (data) => {
                 const model = data;
-                const comments = this.createCommentNodes(model);
-                comments.forEach((c) => this.comments.set(c.attrs.id, c));
-                return this.parseContents(model.contents, undefined, this.getComments(model), {
+                return this.parseContents(model.contents, undefined, [], {
                     topNode: schema_1.schema.nodes.table.create({
                         id: model._id,
-                        comments: comments.map((c) => c.attrs.id),
                     }),
                 });
             },
             [json_schema_1.ObjectTypes.TableElement]: (data) => {
                 const model = data;
                 const table = this.createTable(model);
+                const tableColGroup = this.createTableColGroup(model);
                 const tableElementFooter = this.createTableElementFooter(model);
                 const figcaption = this.getFigcaption(model);
                 const comments = this.createCommentNodes(model);
                 comments.forEach((c) => this.comments.set(c.attrs.id, c));
-                const content = tableElementFooter
-                    ? [table, tableElementFooter, figcaption]
-                    : [table, figcaption];
-                if (model.listingID) {
-                    const listing = this.createListing(model.listingID);
-                    content.push(listing);
+                const content = [table];
+                if (tableColGroup) {
+                    content.push(tableColGroup);
                 }
-                else {
-                    const listing = schema_1.schema.nodes.listing.create();
-                    content.push(listing);
+                if (tableElementFooter) {
+                    content.push(tableElementFooter);
                 }
+                content.push(figcaption);
+                const listing = model.listingID
+                    ? this.createListing(model.listingID)
+                    : schema_1.schema.nodes.listing.create();
+                content.push(listing);
                 return schema_1.schema.nodes.table_element.createChecked({
                     id: model._id,
                     table: model.containedObjectID,
@@ -773,23 +771,33 @@ class Decoder {
         this.allowMissingElements = allowMissingElements;
     }
     createTable(model) {
-        const tableId = model.containedObjectID;
-        const tableModel = this.getModel(tableId);
+        const tableID = model.containedObjectID;
+        const tableModel = this.getModel(tableID);
         let table;
         if (tableModel) {
             table = this.decode(tableModel);
         }
         else if (this.allowMissingElements) {
             table = schema_1.schema.nodes.placeholder.create({
-                id: tableId,
+                id: tableID,
                 label: 'A table',
             });
         }
         else {
-            throw new errors_1.MissingElement(tableId);
+            throw new errors_1.MissingElement(tableID);
         }
         return table;
     }
+    createTableColGroup(model) {
+        const tableID = model.containedObjectID;
+        const tableModel = this.getModel(tableID);
+        if (!tableModel || !tableModel.contents.includes('<colgroup>')) {
+            return undefined;
+        }
+        return this.parseContents(tableModel.contents, undefined, [], {
+            topNode: schema_1.schema.nodes.table_colgroup.create(),
+        });
+    }
     createTableElementFooter(model) {
         const tableElementFooterID = model.tableElementFooterID;
         if (!tableElementFooterID) {

package/dist/cjs/transformer/encode.js

@@ -115,8 +115,9 @@ function buildTableColGroup(cols) {
 }
 const tableContents = (node, parent) => {
     const input = serializer.serializeNode(node);
+    const parentInput = serializer.serializeNode(parent);
     const output = document.createElement('table');
-    const colgroup = buildTableColGroup(Array.from(input.querySelectorAll('col')));
+    const colgroup = buildTableColGroup(Array.from(parentInput.querySelectorAll('col')));
     if (colgroup) {
         output.appendChild(colgroup);
     }
@@ -596,9 +597,6 @@ const encode = (node) => {
             child.type !== schema_1.schema.nodes.inline_equation) {
             return;
         }
-        if (child.type === schema_1.schema.nodes.footnotes_element) {
-            addFootnotesOrderModel(child, models);
-        }
         const { model, markers } = (0, exports.modelFromNode)(child, parent, path, priority);
         markers.forEach((marker) => {
             const comment = models.get(marker._id);
@@ -650,9 +648,3 @@ const generateElementOrder = (node, nodeType) => {
     order.elements = ids;
     return order;
 };
-const addFootnotesOrderModel = (child, models) => {
-    const footnoteList = [];
-    child.forEach((footnote, _, index) => footnoteList.push({ id: footnote.attrs.id, index }));
-    const footnotesOrder = (0, builders_1.buildFootnotesOrder)(footnoteList, child.attrs.id);
-    models.set(footnotesOrder._id, footnotesOrder);
-};

package/dist/cjs/transformer/footnotes-order.js

@@ -15,7 +15,8 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.handleFootnotesOrder = exports.createOrderedFootnotesIDs = void 0;
+exports.createEmptyFootnotesOrder = exports.handleFootnotesOrder = exports.createOrderedFootnotesIDs = void 0;
+const builders_1 = require("./builders");
 const createOrderedFootnotesIDs = (doc) => {
     const footnotesRefs = [...doc.querySelectorAll('xref[ref-type="fn"][rid]')];
     const footnotes = [...doc.querySelectorAll('fn:not([fn-type])')];
@@ -58,3 +59,5 @@ const handleFootnotesOrder = (orderedFootnotesIDs, replacements, footnotesOrder)
     footnotesOrder.footnotesList = footnotesList;
 };
 exports.handleFootnotesOrder = handleFootnotesOrder;
+const createEmptyFootnotesOrder = () => (0, builders_1.buildFootnotesOrder)([]);
+exports.createEmptyFootnotesOrder = createEmptyFootnotesOrder;

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

@@ -519,23 +519,9 @@ 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 +548,12 @@ 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

@@ -236,8 +236,12 @@ 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) {
@@ -245,33 +249,10 @@ 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);
             }
         });
     },
-    orderTableFootnote(doc, body) {
-        const tableInlineFootnotesIds = new Set(Array.from(body.querySelectorAll('tbody > tr > td > xref[ref-type="fn"]').values()).map((inlineFootnote) => inlineFootnote.getAttribute('rid')));
-        const fnGroups = doc.querySelectorAll('table-wrap-foot > fn-group');
-        fnGroups.forEach((fnGroup) => {
-            const orderedFootnotes = Array.from(fnGroup.querySelectorAll('fn')).sort((fn) => tableInlineFootnotesIds.has(fn.getAttribute('id'))
-                ? -1
-                : 0);
-            fnGroup.replaceChildren(...orderedFootnotes);
-        });
-    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

@@ -63,7 +63,6 @@ export const parseJATSBody = (doc, body, references) => {
     jatsBodyTransformations.createBackmatter(doc, body, createElement);
     jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jatsBodyTransformations.createKeywords(doc, body, createElement);
-    jatsBodyTransformations.orderTableFootnote(doc, body);
     const node = jatsBodyDOMParser.parse(body).firstChild;
     if (!node) {
         throw new Error('No content was parsed from the JATS article body');

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

@@ -865,9 +865,13 @@ 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 +952,26 @@ 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 +992,7 @@ 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);