@manuscripts/transform 1.3.11-LEAN-2715-1 → 1.3.11-LEAN-2147

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

@@ -410,7 +410,7 @@ const nodes = [
     {
         tag: 'fn-group',
         node: 'footnotes_element',
-        context: 'footnotes_section/|table_element_footer/',
+        context: 'footnotes_section/',
         getAttrs: (node) => {
             const element = node;
             return {
@@ -421,18 +421,19 @@ const nodes = [
     },
     {
         tag: 'table-wrap-foot',
-        node: 'table_element_footer',
+        node: 'footnotes_element',
         getAttrs: (node) => {
             const element = node;
             return {
                 id: element.getAttribute('id'),
+                kind: 'table_footnote',
             };
         },
     },
     {
         tag: 'fn',
         node: 'footnote',
-        context: 'footnotes_element/|table_element_footer/',
+        context: 'footnotes_element/',
         getAttrs: (node) => {
             const element = node;
             return {

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

@@ -240,7 +240,7 @@ exports.jatsBodyTransformations = {
                 backmatterContainer.append(section);
             }
         }
-        const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot fn)')];
+        const footnotes = [...doc.querySelectorAll('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');

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

@@ -598,7 +598,6 @@ class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
-                table_element_footer: () => ['table-wrap-foot', 0],
                 contributor_list: () => '',
                 contributor: () => '',
                 affiliation_list: () => '',
@@ -690,7 +689,7 @@ class JATSExporter {
                         const rid = getReferencedObjectId(auxiliaryObjectReference.referencedObject);
                         xref.setAttribute('rid', rid);
                     }
-                    xref.textContent = node.attrs.label;
+                    xref.textContent = node.attrs.customLabel || node.attrs.label;
                     return xref;
                 },
                 doc: () => '',
@@ -871,7 +870,7 @@ class JATSExporter {
                 section_title_plain: () => ['title', 0],
                 table: (node) => ['table', { id: normalizeID(node.attrs.id) }, 0],
                 table_element: (node) => {
-                    const element = createTableElement(node);
+                    const element = createFigureElement(node, 'table-wrap', node.type.schema.nodes.table);
                     element.setAttribute('position', 'anchor');
                     return element;
                 },
@@ -910,27 +909,12 @@ class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new prosemirror_model_1.DOMSerializer(nodes, marks);
-            const processChildNodes = (element, node, contentNodeType) => {
-                node.forEach((childNode) => {
-                    if (childNode.type === contentNodeType) {
-                        if (childNode.attrs.id) {
-                            element.appendChild(this.serializeNode(childNode));
-                        }
-                    }
-                    else if (childNode.type === node.type.schema.nodes.paragraph) {
-                        element.appendChild(this.serializeNode(childNode));
-                    }
-                    else if (childNode.type === node.type.schema.nodes.missing_figure) {
-                        element.appendChild(this.serializeNode(childNode));
-                    }
-                });
-            };
-            const createElement = (node, nodeName) => {
+            const createFigureElement = (node, nodeName, contentNodeType, figType) => {
                 const element = this.document.createElement(nodeName);
                 element.setAttribute('id', normalizeID(node.attrs.id));
-                return element;
-            };
-            const appendLabels = (element, node) => {
+                if (figType) {
+                    element.setAttribute('fig-type', figType);
+                }
                 if (node.attrs.label) {
                     const label = this.document.createElement('label');
                     label.textContent = node.attrs.label;
@@ -944,42 +928,32 @@ class JATSExporter {
                         element.appendChild(label);
                     }
                 }
-            };
-            const appendAttributions = (element, node) => {
+                const figcaptionNode = findChildNodeOfType(node, node.type.schema.nodes.figcaption);
+                if (figcaptionNode) {
+                    element.appendChild(this.serializeNode(figcaptionNode));
+                }
+                const footnotesNode = findChildNodeOfType(node, node.type.schema.nodes.footnotes_element);
+                if (footnotesNode) {
+                    element.appendChild(this.serializeNode(footnotesNode));
+                }
+                node.forEach((childNode) => {
+                    if (childNode.type === contentNodeType) {
+                        if (childNode.attrs.id) {
+                            element.appendChild(this.serializeNode(childNode));
+                        }
+                    }
+                    else if (childNode.type === node.type.schema.nodes.paragraph) {
+                        element.appendChild(this.serializeNode(childNode));
+                    }
+                    else if (childNode.type === node.type.schema.nodes.missing_figure) {
+                        element.appendChild(this.serializeNode(childNode));
+                    }
+                });
                 if (node.attrs.attribution) {
                     const attribution = this.document.createElement('attrib');
                     attribution.textContent = node.attrs.attribution.literal;
                     element.appendChild(attribution);
                 }
-            };
-            const appendChildNodeOfType = (element, node, type) => {
-                const childNode = findChildNodeOfType(node, type);
-                if (childNode) {
-                    element.appendChild(this.serializeNode(childNode));
-                }
-            };
-            const createFigureElement = (node, nodeName, contentNodeType, figType) => {
-                const element = createElement(node, nodeName);
-                if (figType) {
-                    element.setAttribute('fig-type', figType);
-                }
-                appendLabels(element, node);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.figcaption);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.footnotes_element);
-                processChildNodes(element, node, contentNodeType);
-                appendAttributions(element, node);
-                if ((0, node_types_1.isExecutableNodeType)(node.type)) {
-                    processExecutableNode(node, element);
-                }
-                return element;
-            };
-            const createTableElement = (node) => {
-                const nodeName = 'table-wrap';
-                const element = createElement(node, nodeName);
-                appendLabels(element, node);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.figcaption);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.table);
-                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

@@ -82,7 +82,6 @@ const section_title_1 = require("./nodes/section_title");
 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 toc_element_1 = require("./nodes/toc_element");
@@ -141,7 +140,6 @@ __exportStar(require("./nodes/affiliation_list"), exports);
 __exportStar(require("./nodes/meta_section"), exports);
 __exportStar(require("./nodes/contributor_list"), exports);
 __exportStar(require("./nodes/contributor"), exports);
-__exportStar(require("./nodes/table_element_footer"), exports);
 exports.schema = new prosemirror_model_1.Schema({
     marks: {
         bold: marks_1.bold,
@@ -217,6 +215,5 @@ exports.schema = new prosemirror_model_1.Schema({
         affiliation_list: affiliation_list_1.affiliationList,
         contributor_list: contributor_list_1.contributorList,
         contributor: contributor_1.contributor,
-        table_element_footer: table_element_footer_1.tableElementFooter,
     },
 });

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

@@ -24,6 +24,7 @@ exports.crossReference = {
     attrs: {
         rid: { default: '' },
         label: { default: '' },
+        customLabel: { default: '' },
         dataTracked: { default: null },
     },
     parseDOM: [
@@ -51,7 +52,11 @@ exports.crossReference = {
                 {
                     class: 'kind elementIndex',
                 },
-                ['b', crossReferenceNode.attrs.label],
+                [
+                    'b',
+                    crossReferenceNode.attrs.customLabel ||
+                        crossReferenceNode.attrs.label,
+                ],
             ],
         ];
     },

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) figcaption? table_element_footer? (listing | placeholder)',
+    content: '(table | placeholder) figcaption? footnotes_element? (listing | placeholder)',
     attrs: {
         id: { default: '' },
         paragraphStyle: { default: '' },

package/dist/cjs/transformer/decode.js

@@ -123,7 +123,21 @@ class Decoder {
     }
     extractListing(model) {
         if (model.listingID) {
-            return this.createListing(model);
+            const listingModel = this.getModel(model.listingID);
+            let listing;
+            if (listingModel) {
+                listing = this.decode(listingModel);
+            }
+            else if (this.allowMissingElements) {
+                listing = schema_1.schema.nodes.placeholder.create({
+                    id: model.listingID,
+                    label: 'A listing',
+                });
+            }
+            else {
+                throw new errors_1.MissingElement(model.listingID);
+            }
+            return listing;
         }
     }
     constructor(modelMap, allowMissingElements = false) {
@@ -268,13 +282,11 @@ class Decoder {
                 }, [equation, figcaption]);
             },
             [json_schema_1.ObjectTypes.FootnotesElement]: (data) => {
-                const foonotesElementModel = data;
-                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
+                const model = data;
+                const collateByKind = model.collateByKind || 'footnote';
                 const footnotesOfKind = [];
                 for (const model of this.modelMap.values()) {
-                    if (isFootnote(model) &&
-                        model.kind === collateByKind &&
-                        model.containingObject === foonotesElementModel._id) {
+                    if (isFootnote(model) && model.kind === collateByKind) {
                         const commentNodes = this.createCommentsNode(model);
                         commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
                         const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
@@ -288,21 +300,19 @@ class Decoder {
                     }
                 }
                 return schema_1.schema.nodes.footnotes_element.create({
-                    id: foonotesElementModel._id,
-                    kind: foonotesElementModel.collateByKind,
-                    paragraphStyle: foonotesElementModel.paragraphStyle,
+                    id: model._id,
+                    kind: model.collateByKind,
+                    paragraphStyle: model.paragraphStyle,
                 }, footnotesOfKind);
             },
             [json_schema_1.ObjectTypes.Footnote]: (data) => {
-                const footnoteModel = data;
-                const commentNodes = this.createCommentsNode(footnoteModel);
+                const model = data;
+                const commentNodes = this.createCommentsNode(model);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                return this.parseContents(footnoteModel.contents || '<div></div>', undefined, this.getComments(footnoteModel), {
-                    topNode: schema_1.schema.nodes.footnote.create({
-                        id: footnoteModel._id,
-                        kind: footnoteModel.kind,
-                        comments: commentNodes.map((c) => c.attrs.id),
-                    }),
+                return schema_1.schema.nodes.footnote.create({
+                    id: model._id,
+                    kind: model.kind,
+                    comments: commentNodes.map((c) => c.attrs.id),
                 });
             },
             [json_schema_1.ObjectTypes.KeywordsElement]: (data) => {
@@ -426,13 +436,6 @@ class Decoder {
                         throw new Error('Unknown block type');
                 }
             },
-            [json_schema_1.ObjectTypes.TableElementFooter]: (data) => {
-                const model = data;
-                const content = model.containedObjectIDs.map((id) => this.decode(this.modelMap.get(id)));
-                return schema_1.schema.nodes.table_element_footer.create({
-                    id: model._id,
-                }, content);
-            },
             [json_schema_1.ObjectTypes.Section]: (data) => {
                 const model = data;
                 const isKeywordsSection = model.category === 'MPSectionCategory:keywords';
@@ -516,16 +519,39 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.TableElement]: (data) => {
                 const model = data;
-                const table = this.createTable(model);
-                const tableElementFooter = this.createTableElementFooter(model);
+                const tableModel = this.getModel(model.containedObjectID);
+                let table;
+                if (tableModel) {
+                    table = this.decode(tableModel);
+                }
+                else if (this.allowMissingElements) {
+                    table = schema_1.schema.nodes.placeholder.create({
+                        id: model.containedObjectID,
+                        label: 'A table',
+                    });
+                }
+                else {
+                    throw new errors_1.MissingElement(model.containedObjectID);
+                }
                 const figcaption = this.getFigcaption(model);
                 const commentNodes = this.createCommentsNode(model);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                const content = tableElementFooter
-                    ? [table, figcaption, tableElementFooter]
-                    : [table, figcaption];
+                const content = [table, figcaption];
                 if (model.listingID) {
-                    const listing = this.createListing(model);
+                    const listingModel = this.getModel(model.listingID);
+                    let listing;
+                    if (listingModel) {
+                        listing = this.decode(listingModel);
+                    }
+                    else if (this.allowMissingElements) {
+                        listing = schema_1.schema.nodes.placeholder.create({
+                            id: model.listingID,
+                            label: 'A listing',
+                        });
+                    }
+                    else {
+                        throw new errors_1.MissingElement(model.listingID);
+                    }
                     content.push(listing);
                 }
                 else {
@@ -701,51 +727,6 @@ class Decoder {
         this.modelMap = modelMap;
         this.allowMissingElements = allowMissingElements;
     }
-    createTable(model) {
-        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,
-                label: 'A table',
-            });
-        }
-        else {
-            throw new errors_1.MissingElement(tableId);
-        }
-        return table;
-    }
-    createTableElementFooter(model) {
-        const tableElementFooterID = model.tableElementFooterID;
-        if (!tableElementFooterID) {
-            return undefined;
-        }
-        const tableElementFooterModel = this.getModel(tableElementFooterID);
-        return tableElementFooterModel
-            ? this.decode(tableElementFooterModel)
-            : undefined;
-    }
-    createListing(model) {
-        const listingModel = this.getModel(model.listingID);
-        let listing;
-        if (listingModel) {
-            listing = this.decode(listingModel);
-        }
-        else if (this.allowMissingElements) {
-            listing = schema_1.schema.nodes.placeholder.create({
-                id: model.listingID,
-                label: 'A listing',
-            });
-        }
-        else {
-            throw new errors_1.MissingElement(model.listingID);
-        }
-        return listing;
-    }
     getKeywordGroups() {
         const kwdGroupNodes = [];
         const kwdGroupsModels = [

package/dist/cjs/transformer/encode.js

@@ -219,7 +219,7 @@ const containedObjectIDs = (node, nodeTypes) => {
     const ids = [];
     for (let i = 0; i < node.childCount; i++) {
         const childNode = node.child(i);
-        if (!nodeTypes || nodeTypes.includes(childNode.type)) {
+        if (nodeTypes.includes(childNode.type)) {
             ids.push(childNode.attrs.id);
         }
     }
@@ -385,9 +385,6 @@ const encoders = {
         elementType: 'div',
         paragraphStyle: node.attrs.paragraphStyle || undefined,
     }),
-    table_element_footer: (node) => ({
-        containedObjectIDs: containedObjectIDs(node),
-    }),
     footnotes_section: (node, parent, path, priority) => ({
         category: (0, section_category_1.buildSectionCategory)(node),
         priority: priority.value++,
@@ -475,7 +472,6 @@ const encoders = {
     }),
     table_element: (node) => ({
         containedObjectID: attributeOfNodeType(node, 'table', 'id'),
-        tableElementFooterID: attributeOfNodeType(node, 'table_element_footer', 'id'),
         caption: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption),
         title: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption_title, false),
         elementType: 'table',

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

@@ -21,9 +21,6 @@ const createOrderedFootnotesIDs = (doc) => {
     const footnotesRefs = [...doc.querySelectorAll('xref[ref-type="fn"][rid]')];
     const footnotes = [...doc.querySelectorAll('fn:not([fn-type])')];
     const authorNotesIDs = [...doc.querySelectorAll('author-notes > fn')].map((an) => an.getAttribute('id'));
-    const tableElementFooters = [
-        ...doc.querySelectorAll('table-wrap-foot > fn'),
-    ].map((footer) => footer.getAttribute('id'));
     const orderedFootnotesIDs = [];
     footnotesRefs.forEach((ref) => {
         const refID = ref.getAttribute('rid');
@@ -35,8 +32,7 @@ const createOrderedFootnotesIDs = (doc) => {
         const id = footnote.getAttribute('id');
         if (id &&
             !authorNotesIDs.includes(id) &&
-            !orderedFootnotesIDs.includes(id) &&
-            !tableElementFooters.includes(id)) {
+            !orderedFootnotesIDs.includes(id)) {
             orderedFootnotesIDs.push(id);
         }
     });

package/dist/cjs/transformer/html.js

@@ -228,7 +228,8 @@ class HTMLTransformer {
                     }
                     element.setAttribute('data-reference-ids', crossReferenceNode.attrs.rid);
                 }
-                element.textContent = crossReferenceNode.attrs.label;
+                element.textContent =
+                    crossReferenceNode.attrs.customLabel || crossReferenceNode.attrs.label;
                 return element;
             };
             nodes.listing = (node) => {

package/dist/cjs/transformer/node-types.js

@@ -56,7 +56,6 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.meta_section, json_schema_1.ObjectTypes.MetaSection],
     [schema_1.schema.nodes.affiliation, json_schema_1.ObjectTypes.Affiliation],
     [schema_1.schema.nodes.contributor, json_schema_1.ObjectTypes.Contributor],
-    [schema_1.schema.nodes.table_element_footer, json_schema_1.ObjectTypes.TableElementFooter],
 ]);
 const isExecutableNodeType = (type) => (0, schema_1.hasGroup)(type, schema_1.GROUP_EXECUTABLE);
 exports.isExecutableNodeType = isExecutableNodeType;

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

@@ -404,7 +404,7 @@ const nodes = [
     {
         tag: 'fn-group',
         node: 'footnotes_element',
-        context: 'footnotes_section/|table_element_footer/',
+        context: 'footnotes_section/',
         getAttrs: (node) => {
             const element = node;
             return {
@@ -415,18 +415,19 @@ const nodes = [
     },
     {
         tag: 'table-wrap-foot',
-        node: 'table_element_footer',
+        node: 'footnotes_element',
         getAttrs: (node) => {
             const element = node;
             return {
                 id: element.getAttribute('id'),
+                kind: 'table_footnote',
             };
         },
     },
     {
         tag: 'fn',
         node: 'footnote',
-        context: 'footnotes_element/|table_element_footer/',
+        context: 'footnotes_element/',
         getAttrs: (node) => {
             const element = node;
             return {

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

@@ -237,7 +237,7 @@ export const jatsBodyTransformations = {
                 backmatterContainer.append(section);
             }
         }
-        const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot fn)')];
+        const footnotes = [...doc.querySelectorAll('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');

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

@@ -591,7 +591,6 @@ export class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
-                table_element_footer: () => ['table-wrap-foot', 0],
                 contributor_list: () => '',
                 contributor: () => '',
                 affiliation_list: () => '',
@@ -683,7 +682,7 @@ export class JATSExporter {
                         const rid = getReferencedObjectId(auxiliaryObjectReference.referencedObject);
                         xref.setAttribute('rid', rid);
                     }
-                    xref.textContent = node.attrs.label;
+                    xref.textContent = node.attrs.customLabel || node.attrs.label;
                     return xref;
                 },
                 doc: () => '',
@@ -864,7 +863,7 @@ export class JATSExporter {
                 section_title_plain: () => ['title', 0],
                 table: (node) => ['table', { id: normalizeID(node.attrs.id) }, 0],
                 table_element: (node) => {
-                    const element = createTableElement(node);
+                    const element = createFigureElement(node, 'table-wrap', node.type.schema.nodes.table);
                     element.setAttribute('position', 'anchor');
                     return element;
                 },
@@ -903,27 +902,12 @@ export class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new DOMSerializer(nodes, marks);
-            const processChildNodes = (element, node, contentNodeType) => {
-                node.forEach((childNode) => {
-                    if (childNode.type === contentNodeType) {
-                        if (childNode.attrs.id) {
-                            element.appendChild(this.serializeNode(childNode));
-                        }
-                    }
-                    else if (childNode.type === node.type.schema.nodes.paragraph) {
-                        element.appendChild(this.serializeNode(childNode));
-                    }
-                    else if (childNode.type === node.type.schema.nodes.missing_figure) {
-                        element.appendChild(this.serializeNode(childNode));
-                    }
-                });
-            };
-            const createElement = (node, nodeName) => {
+            const createFigureElement = (node, nodeName, contentNodeType, figType) => {
                 const element = this.document.createElement(nodeName);
                 element.setAttribute('id', normalizeID(node.attrs.id));
-                return element;
-            };
-            const appendLabels = (element, node) => {
+                if (figType) {
+                    element.setAttribute('fig-type', figType);
+                }
                 if (node.attrs.label) {
                     const label = this.document.createElement('label');
                     label.textContent = node.attrs.label;
@@ -937,42 +921,32 @@ export class JATSExporter {
                         element.appendChild(label);
                     }
                 }
-            };
-            const appendAttributions = (element, node) => {
+                const figcaptionNode = findChildNodeOfType(node, node.type.schema.nodes.figcaption);
+                if (figcaptionNode) {
+                    element.appendChild(this.serializeNode(figcaptionNode));
+                }
+                const footnotesNode = findChildNodeOfType(node, node.type.schema.nodes.footnotes_element);
+                if (footnotesNode) {
+                    element.appendChild(this.serializeNode(footnotesNode));
+                }
+                node.forEach((childNode) => {
+                    if (childNode.type === contentNodeType) {
+                        if (childNode.attrs.id) {
+                            element.appendChild(this.serializeNode(childNode));
+                        }
+                    }
+                    else if (childNode.type === node.type.schema.nodes.paragraph) {
+                        element.appendChild(this.serializeNode(childNode));
+                    }
+                    else if (childNode.type === node.type.schema.nodes.missing_figure) {
+                        element.appendChild(this.serializeNode(childNode));
+                    }
+                });
                 if (node.attrs.attribution) {
                     const attribution = this.document.createElement('attrib');
                     attribution.textContent = node.attrs.attribution.literal;
                     element.appendChild(attribution);
                 }
-            };
-            const appendChildNodeOfType = (element, node, type) => {
-                const childNode = findChildNodeOfType(node, type);
-                if (childNode) {
-                    element.appendChild(this.serializeNode(childNode));
-                }
-            };
-            const createFigureElement = (node, nodeName, contentNodeType, figType) => {
-                const element = createElement(node, nodeName);
-                if (figType) {
-                    element.setAttribute('fig-type', figType);
-                }
-                appendLabels(element, node);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.figcaption);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.footnotes_element);
-                processChildNodes(element, node, contentNodeType);
-                appendAttributions(element, node);
-                if (isExecutableNodeType(node.type)) {
-                    processExecutableNode(node, element);
-                }
-                return element;
-            };
-            const createTableElement = (node) => {
-                const nodeName = 'table-wrap';
-                const element = createElement(node, nodeName);
-                appendLabels(element, node);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.figcaption);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.table);
-                appendChildNodeOfType(element, node, node.type.schema.nodes.table_element_footer);
                 if (isExecutableNodeType(node.type)) {
                     processExecutableNode(node, element);
                 }

package/dist/es/schema/index.js

@@ -65,7 +65,6 @@ import { sectionTitle } from './nodes/section_title';
 import { table, tableBody } from './nodes/table';
 import { tableCol, tableColGroup } from './nodes/table_col';
 import { tableElement } from './nodes/table_element';
-import { tableElementFooter } from './nodes/table_element_footer';
 import { tableCell, tableRow } from './nodes/table_row';
 import { text } from './nodes/text';
 import { tocElement } from './nodes/toc_element';
@@ -124,7 +123,6 @@ export * from './nodes/affiliation_list';
 export * from './nodes/meta_section';
 export * from './nodes/contributor_list';
 export * from './nodes/contributor';
-export * from './nodes/table_element_footer';
 export const schema = new Schema({
     marks: {
         bold,
@@ -200,6 +198,5 @@ export const schema = new Schema({
         affiliation_list: affiliationList,
         contributor_list: contributorList,
         contributor: contributor,
-        table_element_footer: tableElementFooter,
     },
 });

package/dist/es/schema/nodes/cross_reference.js

@@ -21,6 +21,7 @@ export const crossReference = {
     attrs: {
         rid: { default: '' },
         label: { default: '' },
+        customLabel: { default: '' },
         dataTracked: { default: null },
     },
     parseDOM: [
@@ -48,7 +49,11 @@ export const crossReference = {
                 {
                     class: 'kind elementIndex',
                 },
-                ['b', crossReferenceNode.attrs.label],
+                [
+                    'b',
+                    crossReferenceNode.attrs.customLabel ||
+                        crossReferenceNode.attrs.label,
+                ],
             ],
         ];
     },

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const tableElement = {
-    content: '(table | placeholder) figcaption? table_element_footer? (listing | placeholder)',
+    content: '(table | placeholder) figcaption? footnotes_element? (listing | placeholder)',
     attrs: {
         id: { default: '' },
         paragraphStyle: { default: '' },

package/dist/es/transformer/decode.js

@@ -113,7 +113,21 @@ export class Decoder {
     }
     extractListing(model) {
         if (model.listingID) {
-            return this.createListing(model);
+            const listingModel = this.getModel(model.listingID);
+            let listing;
+            if (listingModel) {
+                listing = this.decode(listingModel);
+            }
+            else if (this.allowMissingElements) {
+                listing = schema.nodes.placeholder.create({
+                    id: model.listingID,
+                    label: 'A listing',
+                });
+            }
+            else {
+                throw new MissingElement(model.listingID);
+            }
+            return listing;
         }
     }
     constructor(modelMap, allowMissingElements = false) {
@@ -258,13 +272,11 @@ export class Decoder {
                 }, [equation, figcaption]);
             },
             [ObjectTypes.FootnotesElement]: (data) => {
-                const foonotesElementModel = data;
-                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
+                const model = data;
+                const collateByKind = model.collateByKind || 'footnote';
                 const footnotesOfKind = [];
                 for (const model of this.modelMap.values()) {
-                    if (isFootnote(model) &&
-                        model.kind === collateByKind &&
-                        model.containingObject === foonotesElementModel._id) {
+                    if (isFootnote(model) && model.kind === collateByKind) {
                         const commentNodes = this.createCommentsNode(model);
                         commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
                         const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
@@ -278,21 +290,19 @@ export class Decoder {
                     }
                 }
                 return schema.nodes.footnotes_element.create({
-                    id: foonotesElementModel._id,
-                    kind: foonotesElementModel.collateByKind,
-                    paragraphStyle: foonotesElementModel.paragraphStyle,
+                    id: model._id,
+                    kind: model.collateByKind,
+                    paragraphStyle: model.paragraphStyle,
                 }, footnotesOfKind);
             },
             [ObjectTypes.Footnote]: (data) => {
-                const footnoteModel = data;
-                const commentNodes = this.createCommentsNode(footnoteModel);
+                const model = data;
+                const commentNodes = this.createCommentsNode(model);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                return this.parseContents(footnoteModel.contents || '<div></div>', undefined, this.getComments(footnoteModel), {
-                    topNode: schema.nodes.footnote.create({
-                        id: footnoteModel._id,
-                        kind: footnoteModel.kind,
-                        comments: commentNodes.map((c) => c.attrs.id),
-                    }),
+                return schema.nodes.footnote.create({
+                    id: model._id,
+                    kind: model.kind,
+                    comments: commentNodes.map((c) => c.attrs.id),
                 });
             },
             [ObjectTypes.KeywordsElement]: (data) => {
@@ -416,13 +426,6 @@ export class Decoder {
                         throw new Error('Unknown block type');
                 }
             },
-            [ObjectTypes.TableElementFooter]: (data) => {
-                const model = data;
-                const content = model.containedObjectIDs.map((id) => this.decode(this.modelMap.get(id)));
-                return schema.nodes.table_element_footer.create({
-                    id: model._id,
-                }, content);
-            },
             [ObjectTypes.Section]: (data) => {
                 const model = data;
                 const isKeywordsSection = model.category === 'MPSectionCategory:keywords';
@@ -506,16 +509,39 @@ export class Decoder {
             },
             [ObjectTypes.TableElement]: (data) => {
                 const model = data;
-                const table = this.createTable(model);
-                const tableElementFooter = this.createTableElementFooter(model);
+                const tableModel = this.getModel(model.containedObjectID);
+                let table;
+                if (tableModel) {
+                    table = this.decode(tableModel);
+                }
+                else if (this.allowMissingElements) {
+                    table = schema.nodes.placeholder.create({
+                        id: model.containedObjectID,
+                        label: 'A table',
+                    });
+                }
+                else {
+                    throw new MissingElement(model.containedObjectID);
+                }
                 const figcaption = this.getFigcaption(model);
                 const commentNodes = this.createCommentsNode(model);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                const content = tableElementFooter
-                    ? [table, figcaption, tableElementFooter]
-                    : [table, figcaption];
+                const content = [table, figcaption];
                 if (model.listingID) {
-                    const listing = this.createListing(model);
+                    const listingModel = this.getModel(model.listingID);
+                    let listing;
+                    if (listingModel) {
+                        listing = this.decode(listingModel);
+                    }
+                    else if (this.allowMissingElements) {
+                        listing = schema.nodes.placeholder.create({
+                            id: model.listingID,
+                            label: 'A listing',
+                        });
+                    }
+                    else {
+                        throw new MissingElement(model.listingID);
+                    }
                     content.push(listing);
                 }
                 else {
@@ -691,51 +717,6 @@ export class Decoder {
         this.modelMap = modelMap;
         this.allowMissingElements = allowMissingElements;
     }
-    createTable(model) {
-        const tableId = model.containedObjectID;
-        const tableModel = this.getModel(tableId);
-        let table;
-        if (tableModel) {
-            table = this.decode(tableModel);
-        }
-        else if (this.allowMissingElements) {
-            table = schema.nodes.placeholder.create({
-                id: tableId,
-                label: 'A table',
-            });
-        }
-        else {
-            throw new MissingElement(tableId);
-        }
-        return table;
-    }
-    createTableElementFooter(model) {
-        const tableElementFooterID = model.tableElementFooterID;
-        if (!tableElementFooterID) {
-            return undefined;
-        }
-        const tableElementFooterModel = this.getModel(tableElementFooterID);
-        return tableElementFooterModel
-            ? this.decode(tableElementFooterModel)
-            : undefined;
-    }
-    createListing(model) {
-        const listingModel = this.getModel(model.listingID);
-        let listing;
-        if (listingModel) {
-            listing = this.decode(listingModel);
-        }
-        else if (this.allowMissingElements) {
-            listing = schema.nodes.placeholder.create({
-                id: model.listingID,
-                label: 'A listing',
-            });
-        }
-        else {
-            throw new MissingElement(model.listingID);
-        }
-        return listing;
-    }
     getKeywordGroups() {
         const kwdGroupNodes = [];
         const kwdGroupsModels = [

package/dist/es/transformer/encode.js

@@ -211,7 +211,7 @@ const containedObjectIDs = (node, nodeTypes) => {
     const ids = [];
     for (let i = 0; i < node.childCount; i++) {
         const childNode = node.child(i);
-        if (!nodeTypes || nodeTypes.includes(childNode.type)) {
+        if (nodeTypes.includes(childNode.type)) {
             ids.push(childNode.attrs.id);
         }
     }
@@ -377,9 +377,6 @@ const encoders = {
         elementType: 'div',
         paragraphStyle: node.attrs.paragraphStyle || undefined,
     }),
-    table_element_footer: (node) => ({
-        containedObjectIDs: containedObjectIDs(node),
-    }),
     footnotes_section: (node, parent, path, priority) => ({
         category: buildSectionCategory(node),
         priority: priority.value++,
@@ -467,7 +464,6 @@ const encoders = {
     }),
     table_element: (node) => ({
         containedObjectID: attributeOfNodeType(node, 'table', 'id'),
-        tableElementFooterID: attributeOfNodeType(node, 'table_element_footer', 'id'),
         caption: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption),
         title: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption_title, false),
         elementType: 'table',

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

@@ -18,9 +18,6 @@ export const createOrderedFootnotesIDs = (doc) => {
     const footnotesRefs = [...doc.querySelectorAll('xref[ref-type="fn"][rid]')];
     const footnotes = [...doc.querySelectorAll('fn:not([fn-type])')];
     const authorNotesIDs = [...doc.querySelectorAll('author-notes > fn')].map((an) => an.getAttribute('id'));
-    const tableElementFooters = [
-        ...doc.querySelectorAll('table-wrap-foot > fn'),
-    ].map((footer) => footer.getAttribute('id'));
     const orderedFootnotesIDs = [];
     footnotesRefs.forEach((ref) => {
         const refID = ref.getAttribute('rid');
@@ -32,8 +29,7 @@ export const createOrderedFootnotesIDs = (doc) => {
         const id = footnote.getAttribute('id');
         if (id &&
             !authorNotesIDs.includes(id) &&
-            !orderedFootnotesIDs.includes(id) &&
-            !tableElementFooters.includes(id)) {
+            !orderedFootnotesIDs.includes(id)) {
             orderedFootnotesIDs.push(id);
         }
     });

package/dist/es/transformer/html.js

@@ -222,7 +222,8 @@ export class HTMLTransformer {
                     }
                     element.setAttribute('data-reference-ids', crossReferenceNode.attrs.rid);
                 }
-                element.textContent = crossReferenceNode.attrs.label;
+                element.textContent =
+                    crossReferenceNode.attrs.customLabel || crossReferenceNode.attrs.label;
                 return element;
             };
             nodes.listing = (node) => {

package/dist/es/transformer/node-types.js

@@ -53,7 +53,6 @@ export const nodeTypesMap = new Map([
     [schema.nodes.meta_section, ObjectTypes.MetaSection],
     [schema.nodes.affiliation, ObjectTypes.Affiliation],
     [schema.nodes.contributor, ObjectTypes.Contributor],
-    [schema.nodes.table_element_footer, ObjectTypes.TableElementFooter],
 ]);
 export const isExecutableNodeType = (type) => hasGroup(type, GROUP_EXECUTABLE);
 export const isElementNodeType = (type) => hasGroup(type, GROUP_ELEMENT);

package/dist/types/schema/index.d.ts

@@ -69,5 +69,4 @@ export * from './nodes/affiliation_list';
 export * from './nodes/meta_section';
 export * from './nodes/contributor_list';
 export * from './nodes/contributor';
-export * from './nodes/table_element_footer';
 export declare const schema: Schema<Nodes, Marks>;

package/dist/types/schema/nodes/cross_reference.d.ts

@@ -18,6 +18,7 @@ import { ManuscriptNode } from '../types';
 interface Attrs {
     rid: string;
     label: string;
+    customLabel: string;
 }
 export interface CrossReferenceNode extends ManuscriptNode {
     attrs: Attrs;

package/dist/types/schema/types.d.ts

@@ -17,7 +17,7 @@ import { Fragment, Mark as ProsemirrorMark, MarkType, Node as ProsemirrorNode, N
 import { EditorState, NodeSelection, Plugin, TextSelection, Transaction } from 'prosemirror-state';
 import { EditorView, NodeView } from 'prosemirror-view';
 export type Marks = 'bold' | 'code' | 'italic' | 'smallcaps' | 'strikethrough' | 'styled' | 'subscript' | 'superscript' | 'underline' | 'tracked_insert' | 'tracked_delete';
-export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'bullet_list' | 'caption' | 'caption_title' | 'comment' | 'comment_list' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figcaption' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keywords_group' | 'keywords_section' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'missing_figure' | 'ordered_list' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_body' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'text' | 'toc_element' | 'toc_section' | 'affiliation' | 'meta_section' | 'affiliation_list' | 'contributor_list' | 'contributor' | 'table_element_footer';
+export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'bullet_list' | 'caption' | 'caption_title' | 'comment' | 'comment_list' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figcaption' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keywords_group' | 'keywords_section' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'missing_figure' | 'ordered_list' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_body' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'text' | 'toc_element' | 'toc_section' | 'affiliation' | 'meta_section' | 'affiliation_list' | 'contributor_list' | 'contributor';
 export type ManuscriptSchema = Schema<Nodes, Marks>;
 export type ManuscriptEditorState = EditorState;
 export type ManuscriptEditorView = EditorView;

package/dist/types/transformer/decode.d.ts

@@ -42,8 +42,5 @@ export declare class Decoder {
     private getKeywords;
     private getManuscriptID;
     private getFigcaption;
-    private createTable;
-    private createTableElementFooter;
-    private createListing;
     private getKeywordGroups;
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "1.3.11-LEAN-2715-1",
+  "version": "1.3.11-LEAN-2147",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,7 +29,7 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "2.1.1-LEAN-2715-4",
+    "@manuscripts/json-schema": "^2.1.1",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
     "mathjax-full": "^3.2.2",
@@ -82,4 +82,4 @@
     "prosemirror-state": "^1.4.2",
     "prosemirror-view": "^1.29.1"
   }
-}
+}

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

@@ -1,26 +0,0 @@
-"use strict";
-/*!
- * © 2019 Atypon Systems LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.tableElementFooter = void 0;
-exports.tableElementFooter = {
-    attrs: {
-        id: { default: '' },
-    },
-    content: '(paragraph | footnotes_element)+',
-    group: 'block element',
-    toDOM: () => ['table-wrap-foot', 0],
-};

package/dist/es/schema/nodes/table_element_footer.js

@@ -1,23 +0,0 @@
-/*!
- * © 2019 Atypon Systems LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-export const tableElementFooter = {
-    attrs: {
-        id: { default: '' },
-    },
-    content: '(paragraph | footnotes_element)+',
-    group: 'block element',
-    toDOM: () => ['table-wrap-foot', 0],
-};

package/dist/types/schema/nodes/table_element_footer.d.ts

@@ -1,25 +0,0 @@
-/*!
- * © 2019 Atypon Systems LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *    http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-import { NodeSpec } from 'prosemirror-model';
-import { ManuscriptNode } from '../types';
-interface Attrs {
-    id: string;
-}
-export interface TableElementFooterNode extends ManuscriptNode {
-    attrs: Attrs;
-}
-export declare const tableElementFooter: NodeSpec;
-export {};