@manuscripts/transform 2.1.1 → 2.1.2-LEAN-3092-0

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

@@ -39,7 +39,6 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.footnotes_section, json_schema_1.ObjectTypes.Section],
     [schema_1.schema.nodes.graphical_abstract_section, json_schema_1.ObjectTypes.Section],
     [schema_1.schema.nodes.highlight_marker, json_schema_1.ObjectTypes.HighlightMarker],
-    [schema_1.schema.nodes.inline_equation, json_schema_1.ObjectTypes.InlineMathFragment],
     [schema_1.schema.nodes.keyword, json_schema_1.ObjectTypes.Keyword],
     [schema_1.schema.nodes.keywords_element, json_schema_1.ObjectTypes.KeywordsElement],
     [schema_1.schema.nodes.keywords, json_schema_1.ObjectTypes.Section],

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

@@ -38,7 +38,6 @@ exports.manuscriptObjects = [
     json_schema_1.ObjectTypes.CommentAnnotation,
     json_schema_1.ObjectTypes.Contributor,
     json_schema_1.ObjectTypes.Footnote,
-    json_schema_1.ObjectTypes.InlineMathFragment,
     json_schema_1.ObjectTypes.Section,
 ].concat(exports.elementObjects);
 const isManuscriptModel = (model) => {

package/dist/es/index.js

@@ -1,7 +1,6 @@
 export * from './lib/section-group-type';
 export * from './lib/table-cell-styles';
 export * from './lib/utils';
-export * from './mathjax';
 export * from './schema';
 export * from './transformer';
 export * from './jats';

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

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

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/jats-parser-utils.js

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

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

@@ -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/jats/jats-exporter.js

@@ -88,7 +88,7 @@ const createDefaultIdGenerator = () => {
     const counter = createCounter();
     return async (element) => {
         const value = String(counter.increment(element.nodeName));
-        return `${element.nodeName}-${value}`;
+        return `${element.localName}-${value}`;
     };
 };
 const chooseRefType = (objectType) => {
@@ -156,6 +156,7 @@ export class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
+            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -678,22 +679,20 @@ export class JATSExporter {
                 },
                 doc: () => '',
                 equation: (node) => {
-                    const formula = this.document.createElement('disp-formula');
-                    formula.setAttribute('id', normalizeID(node.attrs.id));
-                    if (node.attrs.TeXRepresentation) {
-                        const math = this.document.createElement('tex-math');
-                        math.textContent = node.attrs.TeXRepresentation;
-                        formula.appendChild(math);
-                    }
-                    else if (node.attrs.MathMLStringRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.MathMLStringRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    return formula;
+                    return this.createEquation(node);
+                },
+                inline_equation: (node) => {
+                    const eqElement = this.document.createElement('inline-formula');
+                    const equation = this.createEquation(node, true);
+                    eqElement.append(equation);
+                    return eqElement;
+                },
+                equation_element: (node) => {
+                    const eqElement = this.document.createElement('disp-formula');
+                    eqElement.setAttribute('id', normalizeID(node.attrs.id));
+                    processChildNodes(eqElement, node, schema.nodes.equation);
+                    return eqElement;
                 },
-                equation_element: (node) => createFigureElement(node, 'fig', node.type.schema.nodes.equation, 'equation'),
                 figcaption: (node) => {
                     if (!node.textContent) {
                         return '';
@@ -743,28 +742,6 @@ export class JATSExporter {
                 },
                 hard_break: () => '',
                 highlight_marker: () => '',
-                inline_equation: (node) => {
-                    const formula = this.document.createElement('inline-formula');
-                    formula.setAttribute('id', normalizeID(node.attrs.id));
-                    if (node.attrs.TeXRepresentation) {
-                        const math = this.document.createElement('tex-math');
-                        math.textContent = node.attrs.TeXRepresentation;
-                        formula.appendChild(math);
-                    }
-                    else if (node.attrs.MathMLRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.MathMLRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    else if (node.attrs.SVGRepresentation) {
-                        const math = this.nodeFromJATS(node.attrs.SVGRepresentation);
-                        if (math) {
-                            formula.appendChild(math);
-                        }
-                    }
-                    return formula;
-                },
                 inline_footnote: (node) => {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'fn');
@@ -1581,6 +1558,21 @@ export class JATSExporter {
             this.citationTexts.set(id, output);
         });
     }
+    createEquation(node, isInline = false) {
+        if (node.attrs.format === 'tex') {
+            const texMath = this.document.createElement('tex-math');
+            texMath.innerHTML = node.attrs.contents;
+            return texMath;
+        }
+        else {
+            const math = this.nodeFromJATS(node.attrs.contents);
+            const mathml = math;
+            if (!isInline) {
+                mathml.setAttribute('id', normalizeID(node.attrs.id));
+            }
+            return mathml;
+        }
+    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === ObjectTypes.Keyword);
         const keywordGroups = new Map();

package/dist/es/schema/index.js

@@ -100,7 +100,6 @@ export * from './nodes/footnotes_section';
 export * from './nodes/graphical_abstract_section';
 export * from './nodes/hard_break';
 export * from './nodes/highlight_marker';
-export * from './nodes/inline_equation';
 export * from './nodes/inline_footnote';
 export * from './nodes/keyword';
 export * from './nodes/keywords_element';

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

@@ -1,5 +1,5 @@
 /*!
- * © 2019 Atypon Systems LLC
+ * © 2023 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.
@@ -17,9 +17,8 @@ import { ObjectTypes } from '@manuscripts/json-schema';
 export const equation = {
     attrs: {
         id: { default: '' },
-        MathMLStringRepresentation: { default: '' },
-        SVGStringRepresentation: { default: '' },
-        TeXRepresentation: { default: '' },
+        contents: { default: '' },
+        format: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block',
@@ -27,26 +26,25 @@ export const equation = {
         {
             tag: `div.${ObjectTypes.Equation}`,
             getAttrs: (p) => {
-                const dom = p;
+                const htmlEl = p;
                 return {
-                    id: dom.getAttribute('id'),
-                    MathMLStringRepresentation: dom.getAttribute('data-mathml-string-representation'),
-                    SVGStringRepresentation: dom.innerHTML,
-                    TeXRepresentation: dom.getAttribute('data-tex-representation'),
+                    id: htmlEl.getAttribute('id'),
+                    format: htmlEl.getAttribute('data-equation-format'),
+                    contents: htmlEl.innerHTML,
                 };
             },
         },
     ],
     toDOM: (node) => {
         const equationNode = node;
+        const { id, contents, format } = equationNode.attrs;
         const dom = document.createElement('div');
-        dom.setAttribute('id', equationNode.attrs.id);
         dom.classList.add(ObjectTypes.Equation);
-        if (equationNode.attrs.MathMLStringRepresentation) {
-            dom.setAttribute('data-mathml-string-representation', equationNode.attrs.MathMLStringRepresentation);
+        dom.setAttribute('id', id);
+        if (format) {
+            dom.setAttribute('data-equation-format', format);
         }
-        dom.setAttribute('data-tex-representation', equationNode.attrs.TeXRepresentation);
-        dom.innerHTML = equationNode.attrs.SVGStringRepresentation;
+        dom.innerHTML = contents;
         return dom;
     },
 };

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

@@ -14,11 +14,10 @@
  * limitations under the License.
  */
 export const equationElement = {
-    content: '(equation | placeholder) figcaption',
+    content: '(equation | placeholder)',
     attrs: {
         id: { default: '' },
-        suppressCaption: { default: true },
-        suppressTitle: { default: undefined },
+        label: { default: '' },
         dataTracked: { default: null },
         comments: { default: null },
     },
@@ -26,7 +25,7 @@ export const equationElement = {
     group: 'block element',
     parseDOM: [
         {
-            tag: 'figure.equation',
+            tag: 'div.equation',
             getAttrs: (p) => {
                 const dom = p;
                 return {
@@ -38,7 +37,7 @@ export const equationElement = {
     toDOM: (node) => {
         const equationElementNode = node;
         return [
-            'figure',
+            'div',
             {
                 class: 'equation',
                 id: equationElementNode.attrs.id,

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

@@ -13,14 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ObjectTypes } from '@manuscripts/json-schema';
 export const inlineEquation = {
     attrs: {
-        id: { default: '' },
-        MathMLRepresentation: { default: '' },
-        SVGRepresentation: { default: '' },
-        TeXRepresentation: { default: '' },
         dataTracked: { default: null },
+        comments: { default: null },
+        id: { default: '' },
+        contents: { default: '' },
+        format: { default: '' },
     },
     atom: true,
     inline: true,
@@ -28,28 +27,27 @@ export const inlineEquation = {
     group: 'inline',
     parseDOM: [
         {
-            tag: `span.${ObjectTypes.InlineMathFragment}`,
+            tag: `span.MPInlineMathFragment`,
             getAttrs: (p) => {
                 const dom = p;
                 return {
+                    format: dom.getAttribute('data-equation-format'),
                     id: dom.getAttribute('id'),
-                    MathMLRepresentation: dom.getAttribute('data-mathml-representation') || '',
-                    SVGRepresentation: dom.innerHTML || '',
-                    TeXRepresentation: dom.getAttribute('data-tex-representation') || '',
+                    contents: dom.innerHTML,
                 };
             },
         },
     ],
     toDOM: (node) => {
         const inlineEquationNode = node;
+        const { id, contents, format } = inlineEquationNode.attrs;
         const dom = document.createElement('span');
-        dom.classList.add(ObjectTypes.InlineMathFragment);
-        dom.setAttribute('id', inlineEquationNode.attrs.id);
-        dom.setAttribute('data-tex-representation', inlineEquationNode.attrs.TeXRepresentation);
-        if (inlineEquationNode.attrs.MathMLRepresentation) {
-            dom.setAttribute('data-mathml-representation', inlineEquationNode.attrs.MathMLRepresentation);
+        dom.setAttribute('id', id);
+        dom.classList.add('MPInlineMathFragment');
+        if (format) {
+            dom.setAttribute('data-equation-format', format);
         }
-        dom.innerHTML = inlineEquationNode.attrs.SVGRepresentation;
+        dom.innerHTML = contents;
         return dom;
     },
 };

package/dist/es/transformer/builders.js

@@ -95,12 +95,6 @@ export const buildNote = (target, source, contents = '') => ({
     source,
     contents,
 });
-export const buildInlineMathFragment = (containingObject, TeXRepresentation) => ({
-    _id: generateID(ObjectTypes.InlineMathFragment),
-    objectType: ObjectTypes.InlineMathFragment,
-    containingObject: containingObject || undefined,
-    TeXRepresentation,
-});
 export const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     _id: generateID(ObjectTypes.Footnote),
     objectType: ObjectTypes.Footnote,
@@ -108,10 +102,11 @@ 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

@@ -32,7 +32,7 @@ import { abstractsType, backmatterType, bodyType, } from '../lib/section-group-t
 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;
@@ -272,9 +271,8 @@ export class Decoder {
                 const model = data;
                 return schema.nodes.equation.createChecked({
                     id: model._id,
-                    MathMLStringRepresentation: model.MathMLStringRepresentation,
-                    SVGStringRepresentation: model.SVGStringRepresentation,
-                    TeXRepresentation: model.TeXRepresentation,
+                    contents: model.contents,
+                    format: model.format,
                 });
             },
             [ObjectTypes.EquationElement]: (data) => {
@@ -293,32 +291,32 @@ export class Decoder {
                 else {
                     throw new MissingElement(model.containedObjectID);
                 }
-                const figcaption = this.getFigcaption(model);
                 return schema.nodes.equation_element.createChecked({
                     id: model._id,
-                    suppressCaption: Boolean(model.suppressCaption),
-                    suppressTitle: Boolean(model.suppressTitle === undefined ? true : model.suppressTitle),
-                }, [equation, figcaption]);
+                    label: model.label,
+                }, [equation]);
             },
             [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,