@manuscripts/transform 2.1.1-LEAN-3377-1 → 2.1.1-LEAN-3377-2

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

@@ -265,6 +265,16 @@ exports.jatsBodyTransformations = {
             }
         });
     },
+    orderTableFootnote(doc, body) {
+        const tableInlineFootnotesIds = new Set(Array.from(body.querySelectorAll('tbody > tr > td > xref[ref-type="fn"]').values()).map((inlineFootnote) => inlineFootnote.getAttribute('rid')));
+        const fnGroups = doc.querySelectorAll('table-wrap-foot > fn-group');
+        fnGroups.forEach((fnGroup) => {
+            const orderedFootnotes = Array.from(fnGroup.querySelectorAll('fn')).sort((fn) => tableInlineFootnotesIds.has(fn.getAttribute('id'))
+                ? -1
+                : 0);
+            fnGroup.replaceChildren(...orderedFootnotes);
+        });
+    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

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

package/dist/cjs/transformer/builders.js

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

package/dist/cjs/transformer/decode.js

@@ -68,7 +68,6 @@ const getSupplements = (modelMap) => (0, exports.getModelsByType)(modelMap, json
 const getKeywordGroups = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.KeywordGroup);
 const getKeywords = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Keyword);
 const getTitles = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Titles)[0];
-const isFootnote = (0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Footnote);
 const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
@@ -311,23 +310,25 @@ class Decoder {
             },
             [json_schema_1.ObjectTypes.FootnotesElement]: (data) => {
                 const foonotesElementModel = data;
-                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
                 const footnotesOfKind = [];
-                for (const model of this.modelMap.values()) {
-                    if (isFootnote(model) &&
-                        model.kind === collateByKind &&
-                        model.containingObject === foonotesElementModel._id) {
-                        const comments = this.createCommentNodes(model);
-                        comments.forEach((c) => this.comments.set(c.attrs.id, c));
-                        const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
-                            topNode: schema_1.schema.nodes.footnote.create({
-                                id: model._id,
-                                kind: model.kind,
-                                comments: comments.map((c) => c.attrs.id),
-                            }),
-                        });
-                        footnotesOfKind.push(footnote);
-                    }
+                const footnoteOrder = (0, exports.getModelsByType)(this.modelMap, json_schema_1.ObjectTypes.FootnotesOrder).find((model) => model.containedObjectID === data._id);
+                if (footnoteOrder) {
+                    footnoteOrder.footnotesList.map(({ id }) => {
+                        const model = this.modelMap.get(id);
+                        const collateByKind = foonotesElementModel.collateByKind || 'footnote';
+                        if (model.kind === collateByKind) {
+                            const comments = this.createCommentNodes(model);
+                            comments.forEach((c) => this.comments.set(c.attrs.id, c));
+                            const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
+                                topNode: schema_1.schema.nodes.footnote.create({
+                                    id: model._id,
+                                    kind: model.kind,
+                                    comments: comments.map((c) => c.attrs.id),
+                                }),
+                            });
+                            footnotesOfKind.push(footnote);
+                        }
+                    });
                 }
                 return schema_1.schema.nodes.footnotes_element.create({
                     id: foonotesElementModel._id,
@@ -569,7 +570,7 @@ class Decoder {
             [json_schema_1.ObjectTypes.TableElement]: (data) => {
                 const model = data;
                 const table = this.createTable(model);
-                const tableElementFooter = this.createTableElementFooter(model, table);
+                const tableElementFooter = this.createTableElementFooter(model);
                 const figcaption = this.getFigcaption(model);
                 const comments = this.createCommentNodes(model);
                 comments.forEach((c) => this.comments.set(c.attrs.id, c));
@@ -789,14 +790,14 @@ class Decoder {
         }
         return table;
     }
-    createTableElementFooter(model, table) {
+    createTableElementFooter(model) {
         const tableElementFooterID = model.tableElementFooterID;
         if (!tableElementFooterID) {
             return undefined;
         }
         const tableElementFooterModel = this.getModel(tableElementFooterID);
         return tableElementFooterModel
-            ? this.moveUncitedFootnoteAtEnd(this.decode(tableElementFooterModel), table)
+            ? this.decode(tableElementFooterModel)
             : undefined;
     }
     createListing(id) {
@@ -814,24 +815,5 @@ class Decoder {
             throw new errors_1.MissingElement(id);
         }
     }
-    moveUncitedFootnoteAtEnd(tableElementFooter, table) {
-        const tableInlineFootnoteIds = new Set();
-        table.descendants((node) => {
-            if (node.type === schema_1.schema.nodes.inline_footnote) {
-                ;
-                node.attrs.rids.map((rid) => tableInlineFootnoteIds.add(rid));
-            }
-        });
-        tableElementFooter.forEach((footnoteElement, offset) => {
-            if (footnoteElement.type !== schema_1.schema.nodes.footnotes_element) {
-                return;
-            }
-            const children = [];
-            footnoteElement.content.forEach((node) => children.push(node));
-            children.sort((child) => tableInlineFootnoteIds.has(child.attrs.id) ? -1 : 0);
-            tableElementFooter = tableElementFooter.replace(offset, offset + footnoteElement.nodeSize, new prosemirror_model_1.Slice(prosemirror_model_1.Fragment.from(footnoteElement.copy(prosemirror_model_1.Fragment.from(children))), tableElementFooter.resolve(offset).depth, tableElementFooter.resolve(offset + footnoteElement.nodeSize).depth));
-        });
-        return tableElementFooter;
-    }
 }
 exports.Decoder = Decoder;

package/dist/cjs/transformer/encode.js

@@ -596,6 +596,9 @@ const encode = (node) => {
             child.type !== schema_1.schema.nodes.inline_equation) {
             return;
         }
+        if (child.type === schema_1.schema.nodes.footnotes_element) {
+            addFootnotesOrderModel(child, models);
+        }
         const { model, markers } = (0, exports.modelFromNode)(child, parent, path, priority);
         markers.forEach((marker) => {
             const comment = models.get(marker._id);
@@ -647,3 +650,9 @@ const generateElementOrder = (node, nodeType) => {
     order.elements = ids;
     return order;
 };
+const addFootnotesOrderModel = (child, models) => {
+    const footnoteList = [];
+    child.forEach((footnote, _, index) => footnoteList.push({ id: footnote.attrs.id, index }));
+    const footnotesOrder = (0, builders_1.buildFootnotesOrder)(footnoteList, child.attrs.id);
+    models.set(footnotesOrder._id, footnotesOrder);
+};

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

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

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

@@ -262,6 +262,16 @@ export const jatsBodyTransformations = {
             }
         });
     },
+    orderTableFootnote(doc, body) {
+        const tableInlineFootnotesIds = new Set(Array.from(body.querySelectorAll('tbody > tr > td > xref[ref-type="fn"]').values()).map((inlineFootnote) => inlineFootnote.getAttribute('rid')));
+        const fnGroups = doc.querySelectorAll('table-wrap-foot > fn-group');
+        fnGroups.forEach((fnGroup) => {
+            const orderedFootnotes = Array.from(fnGroup.querySelectorAll('fn')).sort((fn) => tableInlineFootnotesIds.has(fn.getAttribute('id'))
+                ? -1
+                : 0);
+            fnGroup.replaceChildren(...orderedFootnotes);
+        });
+    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

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

package/dist/es/transformer/builders.js

@@ -108,10 +108,11 @@ export const buildFootnote = (containingObject, contents, kind = 'footnote') =>
     contents,
     kind,
 });
-export const buildFootnotesOrder = (footnotesList) => ({
+export const buildFootnotesOrder = (footnotesList, containedObjectID) => ({
     _id: generateID(ObjectTypes.FootnotesOrder),
     objectType: ObjectTypes.FootnotesOrder,
     footnotesList,
+    containedObjectID,
 });
 export const buildCorresp = (contents) => ({
     _id: generateID(ObjectTypes.Corresponding),

package/dist/es/transformer/decode.js

@@ -26,13 +26,13 @@ var __rest = (this && this.__rest) || function (s, e) {
 };
 import { ObjectTypes, } from '@manuscripts/json-schema';
 import debug from 'debug';
-import { DOMParser, Fragment, Slice } from 'prosemirror-model';
+import { DOMParser } from 'prosemirror-model';
 import { MissingElement } from '../errors';
 import { abstractsType, backmatterType, bodyType, } from '../lib/section-group-type';
 import { schema, } from '../schema';
 import { buildTitles } from './builders';
 import { insertHighlightMarkers } from './highlight-markers';
-import { ExtraObjectTypes, hasObjectType, isCommentAnnotation, isManuscript, } from './object-types';
+import { ExtraObjectTypes, isCommentAnnotation, isManuscript, } from './object-types';
 import { chooseSectionLableName, chooseSectionNodeType, chooseSecType, getSectionGroupType, guessSectionCategory, } from './section-category';
 import { timestamp } from './timestamp';
 const warn = debug('manuscripts-transform');
@@ -59,7 +59,6 @@ const getSupplements = (modelMap) => getModelsByType(modelMap, ObjectTypes.Suppl
 const getKeywordGroups = (modelMap) => getModelsByType(modelMap, ObjectTypes.KeywordGroup);
 const getKeywords = (modelMap) => getModelsByType(modelMap, ObjectTypes.Keyword);
 const getTitles = (modelMap) => getModelsByType(modelMap, ObjectTypes.Titles)[0];
-const isFootnote = hasObjectType(ObjectTypes.Footnote);
 const hasParentSection = (id) => (section) => section.path &&
     section.path.length > 1 &&
     section.path[section.path.length - 2] === id;
@@ -302,23 +301,25 @@ export class Decoder {
             },
             [ObjectTypes.FootnotesElement]: (data) => {
                 const foonotesElementModel = data;
-                const collateByKind = foonotesElementModel.collateByKind || 'footnote';
                 const footnotesOfKind = [];
-                for (const model of this.modelMap.values()) {
-                    if (isFootnote(model) &&
-                        model.kind === collateByKind &&
-                        model.containingObject === foonotesElementModel._id) {
-                        const comments = this.createCommentNodes(model);
-                        comments.forEach((c) => this.comments.set(c.attrs.id, c));
-                        const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
-                            topNode: schema.nodes.footnote.create({
-                                id: model._id,
-                                kind: model.kind,
-                                comments: comments.map((c) => c.attrs.id),
-                            }),
-                        });
-                        footnotesOfKind.push(footnote);
-                    }
+                const footnoteOrder = getModelsByType(this.modelMap, ObjectTypes.FootnotesOrder).find((model) => model.containedObjectID === data._id);
+                if (footnoteOrder) {
+                    footnoteOrder.footnotesList.map(({ id }) => {
+                        const model = this.modelMap.get(id);
+                        const collateByKind = foonotesElementModel.collateByKind || 'footnote';
+                        if (model.kind === collateByKind) {
+                            const comments = this.createCommentNodes(model);
+                            comments.forEach((c) => this.comments.set(c.attrs.id, c));
+                            const footnote = this.parseContents(model.contents || '<div></div>', undefined, this.getComments(model), {
+                                topNode: schema.nodes.footnote.create({
+                                    id: model._id,
+                                    kind: model.kind,
+                                    comments: comments.map((c) => c.attrs.id),
+                                }),
+                            });
+                            footnotesOfKind.push(footnote);
+                        }
+                    });
                 }
                 return schema.nodes.footnotes_element.create({
                     id: foonotesElementModel._id,
@@ -560,7 +561,7 @@ export class Decoder {
             [ObjectTypes.TableElement]: (data) => {
                 const model = data;
                 const table = this.createTable(model);
-                const tableElementFooter = this.createTableElementFooter(model, table);
+                const tableElementFooter = this.createTableElementFooter(model);
                 const figcaption = this.getFigcaption(model);
                 const comments = this.createCommentNodes(model);
                 comments.forEach((c) => this.comments.set(c.attrs.id, c));
@@ -780,14 +781,14 @@ export class Decoder {
         }
         return table;
     }
-    createTableElementFooter(model, table) {
+    createTableElementFooter(model) {
         const tableElementFooterID = model.tableElementFooterID;
         if (!tableElementFooterID) {
             return undefined;
         }
         const tableElementFooterModel = this.getModel(tableElementFooterID);
         return tableElementFooterModel
-            ? this.moveUncitedFootnoteAtEnd(this.decode(tableElementFooterModel), table)
+            ? this.decode(tableElementFooterModel)
             : undefined;
     }
     createListing(id) {
@@ -805,23 +806,4 @@ export class Decoder {
             throw new MissingElement(id);
         }
     }
-    moveUncitedFootnoteAtEnd(tableElementFooter, table) {
-        const tableInlineFootnoteIds = new Set();
-        table.descendants((node) => {
-            if (node.type === schema.nodes.inline_footnote) {
-                ;
-                node.attrs.rids.map((rid) => tableInlineFootnoteIds.add(rid));
-            }
-        });
-        tableElementFooter.forEach((footnoteElement, offset) => {
-            if (footnoteElement.type !== schema.nodes.footnotes_element) {
-                return;
-            }
-            const children = [];
-            footnoteElement.content.forEach((node) => children.push(node));
-            children.sort((child) => tableInlineFootnoteIds.has(child.attrs.id) ? -1 : 0);
-            tableElementFooter = tableElementFooter.replace(offset, offset + footnoteElement.nodeSize, new Slice(Fragment.from(footnoteElement.copy(Fragment.from(children))), tableElementFooter.resolve(offset).depth, tableElementFooter.resolve(offset + footnoteElement.nodeSize).depth));
-        });
-        return tableElementFooter;
-    }
 }

package/dist/es/transformer/encode.js

@@ -17,7 +17,7 @@ import { DOMSerializer } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
 import { iterateChildren } from '../lib/utils';
 import { hasGroup, isHighlightMarkerNode, isManuscriptNode, isSectionNode, schema, } from '../schema';
-import { auxiliaryObjectTypes, buildAttribution, buildElementsOrder, } from './builders';
+import { auxiliaryObjectTypes, buildAttribution, buildElementsOrder, buildFootnotesOrder, } from './builders';
 import { extractCommentMarkers } from './highlight-markers';
 import { nodeTypesMap } from './node-types';
 import { buildSectionCategory } from './section-category';
@@ -587,6 +587,9 @@ export const encode = (node) => {
             child.type !== schema.nodes.inline_equation) {
             return;
         }
+        if (child.type === schema.nodes.footnotes_element) {
+            addFootnotesOrderModel(child, models);
+        }
         const { model, markers } = modelFromNode(child, parent, path, priority);
         markers.forEach((marker) => {
             const comment = models.get(marker._id);
@@ -637,3 +640,9 @@ const generateElementOrder = (node, nodeType) => {
     order.elements = ids;
     return order;
 };
+const addFootnotesOrderModel = (child, models) => {
+    const footnoteList = [];
+    child.forEach((footnote, _, index) => footnoteList.push({ id: footnote.attrs.id, index }));
+    const footnotesOrder = buildFootnotesOrder(footnoteList, child.attrs.id);
+    models.set(footnotesOrder._id, footnotesOrder);
+};

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

@@ -13,7 +13,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { buildFootnotesOrder } from './builders';
 export const createOrderedFootnotesIDs = (doc) => {
     const footnotesRefs = [...doc.querySelectorAll('xref[ref-type="fn"][rid]')];
     const footnotes = [...doc.querySelectorAll('fn:not([fn-type])')];
@@ -54,4 +53,3 @@ export const handleFootnotesOrder = (orderedFootnotesIDs, replacements, footnote
     });
     footnotesOrder.footnotesList = footnotesList;
 };
-export const createEmptyFootnotesOrder = () => buildFootnotesOrder([]);

package/dist/types/jats/importer/jats-body-transformations.d.ts

@@ -32,6 +32,7 @@ export declare const jatsBodyTransformations: {
     moveFootnotes(doc: Document, group: Element, createElement: (tagName: string) => HTMLElement): void;
     moveCaptionsToEnd(body: Element): void;
     fixTables(body: Element, createElement: (tagName: string) => HTMLElement): void;
+    orderTableFootnote(doc: Document, body: Element): void;
     moveFloatsGroupToBody(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     createKeywords(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     createSuppleMaterials(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;

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

@@ -46,7 +46,7 @@ export declare const buildComment: (target: string, contents?: string, selector?
 export declare const buildNote: (target: string, source: 'EMAIL' | 'EDITOR' | 'DASHBOARD', contents?: string) => Build<ManuscriptNote>;
 export declare const buildInlineMathFragment: (containingObject: string, TeXRepresentation: string) => Build<InlineMathFragment>;
 export declare const buildFootnote: (containingObject: string, contents: string, kind?: 'footnote' | 'endnote') => Build<Footnote>;
-export declare const buildFootnotesOrder: (footnotesList: FootnotesOrderIndexList) => Build<FootnotesOrder>;
+export declare const buildFootnotesOrder: (footnotesList: FootnotesOrderIndexList, containedObjectID: string) => Build<FootnotesOrder>;
 export declare const buildCorresp: (contents: string) => Build<Corresponding>;
 export declare const buildSection: (priority?: number, path?: string[]) => Build<Section>;
 export declare const buildParagraph: (placeholderInnerHTML: string) => Build<ParagraphElement>;

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

@@ -45,5 +45,4 @@ export declare class Decoder {
     private createTable;
     private createTableElementFooter;
     private createListing;
-    private moveUncitedFootnoteAtEnd;
 }

package/dist/types/transformer/footnotes-order.d.ts

@@ -20,4 +20,3 @@ export type FootnotesOrderIndexList = {
 }[];
 export declare const createOrderedFootnotesIDs: (doc: Document) => string[];
 export declare const handleFootnotesOrder: (orderedFootnotesIDs: Array<string>, replacements: Map<string, string>, footnotesOrder: FootnotesOrder) => void;
-export declare const createEmptyFootnotesOrder: () => import("./builders").Build<FootnotesOrder>;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.1.1-LEAN-3377-1",
+  "version": "2.1.1-LEAN-3377-2",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,8 +29,8 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "^2.2.2",
-    "@manuscripts/library": "1.3.2",
+    "@manuscripts/json-schema": "2.2.3-LEAN-3377-0",
+    "@manuscripts/library": "1.3.2-LEAN-3377-0",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
     "mathjax-full": "^3.2.2",