@manuscripts/transform 1.3.11-LEAN-2745 → 1.3.12

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/',
+        context: 'footnotes_section/|table_element_footer/',
         getAttrs: (node) => {
             const element = node;
             return {
@@ -421,19 +421,18 @@ const nodes = [
     },
     {
         tag: 'table-wrap-foot',
-        node: 'footnotes_element',
+        node: 'table_element_footer',
         getAttrs: (node) => {
             const element = node;
             return {
                 id: element.getAttribute('id'),
-                kind: 'table_footnote',
             };
         },
     },
     {
         tag: 'fn',
         node: 'footnote',
-        context: 'footnotes_element/',
+        context: 'footnotes_element/|table_element_footer/',
         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')];
+        const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot 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

@@ -598,6 +598,7 @@ 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: () => '',
@@ -870,7 +871,7 @@ class JATSExporter {
                 section_title_plain: () => ['title', 0],
                 table: (node) => ['table', { id: normalizeID(node.attrs.id) }, 0],
                 table_element: (node) => {
-                    const element = createFigureElement(node, 'table-wrap', node.type.schema.nodes.table);
+                    const element = createTableElement(node);
                     element.setAttribute('position', 'anchor');
                     return element;
                 },
@@ -909,12 +910,27 @@ class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new prosemirror_model_1.DOMSerializer(nodes, marks);
-            const createFigureElement = (node, nodeName, contentNodeType, figType) => {
+            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 element = this.document.createElement(nodeName);
                 element.setAttribute('id', normalizeID(node.attrs.id));
-                if (figType) {
-                    element.setAttribute('fig-type', figType);
-                }
+                return element;
+            };
+            const appendLabels = (element, node) => {
                 if (node.attrs.label) {
                     const label = this.document.createElement('label');
                     label.textContent = node.attrs.label;
@@ -928,32 +944,42 @@ class JATSExporter {
                         element.appendChild(label);
                     }
                 }
-                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));
-                    }
-                });
+            };
+            const appendAttributions = (element, node) => {
                 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

@@ -82,6 +82,7 @@ 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");
@@ -140,6 +141,7 @@ __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,
@@ -215,5 +217,6 @@ 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/table_element.js

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

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

@@ -0,0 +1,26 @@
+"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/cjs/transformer/decode.js

@@ -123,21 +123,7 @@ class Decoder {
     }
     extractListing(model) {
         if (model.listingID) {
-            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;
+            return this.createListing(model);
         }
     }
     constructor(modelMap, allowMissingElements = false) {
@@ -165,8 +151,6 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.BibliographyItem]: (data) => {
                 const model = data;
-                const commentNodes = this.createCommentsNode(model);
-                commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
                 return schema_1.schema.nodes.bibliography_item.create({
                     id: model._id,
                     type: model.type,
@@ -180,7 +164,6 @@ class Decoder {
                     page: model.page,
                     title: model.title,
                     literal: model.literal,
-                    comments: commentNodes.map((c) => c.attrs.id),
                 });
             },
             [object_types_1.ExtraObjectTypes.PlaceholderElement]: (data) => {
@@ -285,11 +268,13 @@ class Decoder {
                 }, [equation, figcaption]);
             },
             [json_schema_1.ObjectTypes.FootnotesElement]: (data) => {
-                const model = data;
-                const collateByKind = model.collateByKind || 'footnote';
+                const foonotesElementModel = data;
+                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
                 const footnotesOfKind = [];
                 for (const model of this.modelMap.values()) {
-                    if (isFootnote(model) && model.kind === collateByKind) {
+                    if (isFootnote(model) &&
+                        model.kind === collateByKind &&
+                        model.containingObject === foonotesElementModel._id) {
                         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), {
@@ -303,19 +288,21 @@ class Decoder {
                     }
                 }
                 return schema_1.schema.nodes.footnotes_element.create({
-                    id: model._id,
-                    kind: model.collateByKind,
-                    paragraphStyle: model.paragraphStyle,
+                    id: foonotesElementModel._id,
+                    kind: foonotesElementModel.collateByKind,
+                    paragraphStyle: foonotesElementModel.paragraphStyle,
                 }, footnotesOfKind);
             },
             [json_schema_1.ObjectTypes.Footnote]: (data) => {
-                const model = data;
-                const commentNodes = this.createCommentsNode(model);
+                const footnoteModel = data;
+                const commentNodes = this.createCommentsNode(footnoteModel);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                return schema_1.schema.nodes.footnote.create({
-                    id: model._id,
-                    kind: model.kind,
-                    comments: commentNodes.map((c) => c.attrs.id),
+                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),
+                    }),
                 });
             },
             [json_schema_1.ObjectTypes.KeywordsElement]: (data) => {
@@ -439,6 +426,13 @@ 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';
@@ -522,39 +516,16 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.TableElement]: (data) => {
                 const model = data;
-                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 table = this.createTable(model);
+                const tableElementFooter = this.createTableElementFooter(model);
                 const figcaption = this.getFigcaption(model);
                 const commentNodes = this.createCommentsNode(model);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                const content = [table, figcaption];
+                const content = tableElementFooter
+                    ? [table, figcaption, tableElementFooter]
+                    : [table, figcaption];
                 if (model.listingID) {
-                    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);
-                    }
+                    const listing = this.createListing(model);
                     content.push(listing);
                 }
                 else {
@@ -730,6 +701,51 @@ 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.includes(childNode.type)) {
+        if (!nodeTypes || nodeTypes.includes(childNode.type)) {
             ids.push(childNode.attrs.id);
         }
     }
@@ -385,6 +385,9 @@ 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++,
@@ -472,6 +475,7 @@ 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

@@ -21,6 +21,9 @@ 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');
@@ -32,7 +35,8 @@ const createOrderedFootnotesIDs = (doc) => {
         const id = footnote.getAttribute('id');
         if (id &&
             !authorNotesIDs.includes(id) &&
-            !orderedFootnotesIDs.includes(id)) {
+            !orderedFootnotesIDs.includes(id) &&
+            !tableElementFooters.includes(id)) {
             orderedFootnotesIDs.push(id);
         }
     });

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

@@ -56,6 +56,7 @@ 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/',
+        context: 'footnotes_section/|table_element_footer/',
         getAttrs: (node) => {
             const element = node;
             return {
@@ -415,19 +415,18 @@ const nodes = [
     },
     {
         tag: 'table-wrap-foot',
-        node: 'footnotes_element',
+        node: 'table_element_footer',
         getAttrs: (node) => {
             const element = node;
             return {
                 id: element.getAttribute('id'),
-                kind: 'table_footnote',
             };
         },
     },
     {
         tag: 'fn',
         node: 'footnote',
-        context: 'footnotes_element/',
+        context: 'footnotes_element/|table_element_footer/',
         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')];
+        const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot 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

@@ -591,6 +591,7 @@ 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: () => '',
@@ -863,7 +864,7 @@ export class JATSExporter {
                 section_title_plain: () => ['title', 0],
                 table: (node) => ['table', { id: normalizeID(node.attrs.id) }, 0],
                 table_element: (node) => {
-                    const element = createFigureElement(node, 'table-wrap', node.type.schema.nodes.table);
+                    const element = createTableElement(node);
                     element.setAttribute('position', 'anchor');
                     return element;
                 },
@@ -902,12 +903,27 @@ export class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new DOMSerializer(nodes, marks);
-            const createFigureElement = (node, nodeName, contentNodeType, figType) => {
+            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 element = this.document.createElement(nodeName);
                 element.setAttribute('id', normalizeID(node.attrs.id));
-                if (figType) {
-                    element.setAttribute('fig-type', figType);
-                }
+                return element;
+            };
+            const appendLabels = (element, node) => {
                 if (node.attrs.label) {
                     const label = this.document.createElement('label');
                     label.textContent = node.attrs.label;
@@ -921,32 +937,42 @@ export class JATSExporter {
                         element.appendChild(label);
                     }
                 }
-                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));
-                    }
-                });
+            };
+            const appendAttributions = (element, node) => {
                 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

@@ -65,6 +65,7 @@ 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';
@@ -123,6 +124,7 @@ 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,
@@ -198,5 +200,6 @@ export const schema = new Schema({
         affiliation_list: affiliationList,
         contributor_list: contributorList,
         contributor: contributor,
+        table_element_footer: tableElementFooter,
     },
 });

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

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

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

@@ -0,0 +1,23 @@
+/*!
+ * © 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/es/transformer/decode.js

@@ -113,21 +113,7 @@ export class Decoder {
     }
     extractListing(model) {
         if (model.listingID) {
-            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;
+            return this.createListing(model);
         }
     }
     constructor(modelMap, allowMissingElements = false) {
@@ -155,8 +141,6 @@ export class Decoder {
             },
             [ObjectTypes.BibliographyItem]: (data) => {
                 const model = data;
-                const commentNodes = this.createCommentsNode(model);
-                commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
                 return schema.nodes.bibliography_item.create({
                     id: model._id,
                     type: model.type,
@@ -170,7 +154,6 @@ export class Decoder {
                     page: model.page,
                     title: model.title,
                     literal: model.literal,
-                    comments: commentNodes.map((c) => c.attrs.id),
                 });
             },
             [ExtraObjectTypes.PlaceholderElement]: (data) => {
@@ -275,11 +258,13 @@ export class Decoder {
                 }, [equation, figcaption]);
             },
             [ObjectTypes.FootnotesElement]: (data) => {
-                const model = data;
-                const collateByKind = model.collateByKind || 'footnote';
+                const foonotesElementModel = data;
+                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
                 const footnotesOfKind = [];
                 for (const model of this.modelMap.values()) {
-                    if (isFootnote(model) && model.kind === collateByKind) {
+                    if (isFootnote(model) &&
+                        model.kind === collateByKind &&
+                        model.containingObject === foonotesElementModel._id) {
                         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), {
@@ -293,19 +278,21 @@ export class Decoder {
                     }
                 }
                 return schema.nodes.footnotes_element.create({
-                    id: model._id,
-                    kind: model.collateByKind,
-                    paragraphStyle: model.paragraphStyle,
+                    id: foonotesElementModel._id,
+                    kind: foonotesElementModel.collateByKind,
+                    paragraphStyle: foonotesElementModel.paragraphStyle,
                 }, footnotesOfKind);
             },
             [ObjectTypes.Footnote]: (data) => {
-                const model = data;
-                const commentNodes = this.createCommentsNode(model);
+                const footnoteModel = data;
+                const commentNodes = this.createCommentsNode(footnoteModel);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                return schema.nodes.footnote.create({
-                    id: model._id,
-                    kind: model.kind,
-                    comments: commentNodes.map((c) => c.attrs.id),
+                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),
+                    }),
                 });
             },
             [ObjectTypes.KeywordsElement]: (data) => {
@@ -429,6 +416,13 @@ 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';
@@ -512,39 +506,16 @@ export class Decoder {
             },
             [ObjectTypes.TableElement]: (data) => {
                 const model = data;
-                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 table = this.createTable(model);
+                const tableElementFooter = this.createTableElementFooter(model);
                 const figcaption = this.getFigcaption(model);
                 const commentNodes = this.createCommentsNode(model);
                 commentNodes.forEach((c) => this.comments.set(c.attrs.id, c));
-                const content = [table, figcaption];
+                const content = tableElementFooter
+                    ? [table, figcaption, tableElementFooter]
+                    : [table, figcaption];
                 if (model.listingID) {
-                    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);
-                    }
+                    const listing = this.createListing(model);
                     content.push(listing);
                 }
                 else {
@@ -720,6 +691,51 @@ 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.includes(childNode.type)) {
+        if (!nodeTypes || nodeTypes.includes(childNode.type)) {
             ids.push(childNode.attrs.id);
         }
     }
@@ -377,6 +377,9 @@ 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++,
@@ -464,6 +467,7 @@ 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

@@ -18,6 +18,9 @@ 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');
@@ -29,7 +32,8 @@ export const createOrderedFootnotesIDs = (doc) => {
         const id = footnote.getAttribute('id');
         if (id &&
             !authorNotesIDs.includes(id) &&
-            !orderedFootnotesIDs.includes(id)) {
+            !orderedFootnotesIDs.includes(id) &&
+            !tableElementFooters.includes(id)) {
             orderedFootnotesIDs.push(id);
         }
     });

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

@@ -53,6 +53,7 @@ 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

@@ -69,4 +69,5 @@ 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/table_element_footer.d.ts

@@ -0,0 +1,25 @@
+/*!
+ * © 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 {};

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';
+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 ManuscriptSchema = Schema<Nodes, Marks>;
 export type ManuscriptEditorState = EditorState;
 export type ManuscriptEditorView = EditorView;

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

@@ -42,5 +42,8 @@ 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-2745",
+  "version": "1.3.12",
   "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",
+    "@manuscripts/json-schema": "^2.1.2",
     "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"
   }
-}
+}