@manuscripts/transform 2.0.1-LEAN-3083-3 → 2.0.1-LEAN-3092

package/dist/cjs/index.js

@@ -18,7 +18,6 @@ exports.isSectionLabelNode = void 0;
 __exportStar(require("./lib/section-group-type"), exports);
 __exportStar(require("./lib/table-cell-styles"), exports);
 __exportStar(require("./lib/utils"), exports);
-__exportStar(require("./mathjax"), exports);
 __exportStar(require("./schema"), exports);
 __exportStar(require("./transformer"), exports);
 __exportStar(require("./jats"), exports);

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

@@ -21,8 +21,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.jatsBodyDOMParser = void 0;
 const mime_1 = __importDefault(require("mime"));
 const prosemirror_model_1 = require("prosemirror-model");
-const mathml_to_svg_1 = require("../../mathjax/mathml-to-svg");
-const tex_to_svg_1 = require("../../mathjax/tex-to-svg");
 const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
@@ -39,6 +37,24 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
+const getEquationContent = (p) => {
+    var _a;
+    const element = p;
+    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':
+            case 'mml:math':
+                contents = child.outerHTML;
+                format = nodeName === 'tex-math' ? 'tex' : 'mathml';
+                break;
+        }
+    }
+    return { format, contents };
+};
 const marks = [
     {
         tag: 'bold',
@@ -147,91 +163,27 @@ 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 = (0, tex_to_svg_1.convertTeXToSVG)(attrs.TeXRepresentation, true)) !== null && _d !== void 0 ? _d : '';
-                        }
-                        break;
-                    case 'mml:math':
-                        ;
-                        child.removeAttribute('id');
-                        attrs.MathMLRepresentation = transformer_1.xmlSerializer.serializeToString(child);
-                        if (attrs.MathMLRepresentation) {
-                            attrs.SVGRepresentation =
-                                (_e = (0, mathml_to_svg_1.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 = (0, tex_to_svg_1.convertTeXToSVG)(attrs.TeXRepresentation, true)) !== null && _d !== void 0 ? _d : '';
-                        }
-                        break;
-                    case 'mml:math':
-                        ;
-                        child.removeAttribute('id');
-                        attrs.MathMLStringRepresentation =
-                            transformer_1.xmlSerializer.serializeToString(child);
-                        if (attrs.MathMLStringRepresentation) {
-                            attrs.SVGStringRepresentation =
-                                (_e = (0, mathml_to_svg_1.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);
+            const id = element.getAttribute('id');
             return prosemirror_model_1.Fragment.from([
-                schema.nodes.equation.createChecked(attrs),
-                caption
-                    ?
-                        exports.jatsBodyDOMParser.parse(caption, {
-                            topNode: figcaption,
-                        })
-                    : figcaption,
+                schema.nodes.equation.createChecked(Object.assign({ id }, attrs)),
             ]);
         },
     },

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

@@ -152,6 +152,7 @@ class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
+            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -672,22 +673,23 @@ 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;
+                    const math = this.nodeFromJATS(node.attrs.contents);
+                    const mathEl = math;
+                    mathEl.setAttribute('id', normalizeID(node.attrs.id));
+                    return mathEl;
+                },
+                inline_equation: (node) => {
+                    const eqElement = this.document.createElement('inline-formula');
+                    const math = this.nodeFromJATS(node.attrs.contents);
+                    eqElement.append(math);
+                    return eqElement;
+                },
+                equation_element: (node) => {
+                    const eqElement = this.document.createElement('disp-formula');
+                    eqElement.setAttribute('id', normalizeID(node.attrs.id));
+                    processChildNodes(eqElement, node, schema_1.schema.nodes.equation);
+                    return eqElement;
                 },
-                equation_element: (node) => createFigureElement(node, 'fig', node.type.schema.nodes.equation, 'equation'),
                 figcaption: (node) => {
                     if (!node.textContent) {
                         return '';
@@ -737,28 +739,6 @@ 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');

package/dist/cjs/schema/index.js

@@ -115,7 +115,6 @@ __exportStar(require("./nodes/footnotes_section"), exports);
 __exportStar(require("./nodes/graphical_abstract_section"), exports);
 __exportStar(require("./nodes/hard_break"), exports);
 __exportStar(require("./nodes/highlight_marker"), exports);
-__exportStar(require("./nodes/inline_equation"), exports);
 __exportStar(require("./nodes/inline_footnote"), exports);
 __exportStar(require("./nodes/keyword"), exports);
 __exportStar(require("./nodes/keywords_element"), exports);

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

@@ -6,7 +6,6 @@ exports.contributor = {
     attrs: {
         id: { default: '' },
         role: { default: '' },
-        email: { default: '' },
         affiliations: { default: [] },
         footnote: { default: undefined },
         corresp: { default: undefined },
@@ -14,7 +13,6 @@ exports.contributor = {
         userID: { default: undefined },
         invitationID: { default: undefined },
         isCorresponding: { default: undefined },
-        isJointContributor: { default: undefined },
         ORCIDIdentifier: { default: undefined },
         priority: { default: undefined },
         dataTracked: { default: null },

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

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 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.
@@ -20,9 +20,8 @@ const json_schema_1 = require("@manuscripts/json-schema");
 exports.equation = {
     attrs: {
         id: { default: '' },
-        MathMLStringRepresentation: { default: '' },
-        SVGStringRepresentation: { default: '' },
-        TeXRepresentation: { default: '' },
+        contents: { default: '' },
+        format: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block',
@@ -30,26 +29,25 @@ exports.equation = {
         {
             tag: `div.${json_schema_1.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(json_schema_1.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/cjs/schema/nodes/equation_element.js

@@ -17,11 +17,10 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.equationElement = void 0;
 exports.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 },
     },
@@ -29,7 +28,7 @@ exports.equationElement = {
     group: 'block element',
     parseDOM: [
         {
-            tag: 'figure.equation',
+            tag: 'div.equation',
             getAttrs: (p) => {
                 const dom = p;
                 return {
@@ -41,7 +40,7 @@ exports.equationElement = {
     toDOM: (node) => {
         const equationElementNode = node;
         return [
-            'figure',
+            'div',
             {
                 class: 'equation',
                 id: equationElementNode.attrs.id,

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

@@ -16,43 +16,39 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.inlineEquation = void 0;
-const json_schema_1 = require("@manuscripts/json-schema");
 exports.inlineEquation = {
     attrs: {
-        id: { default: '' },
-        MathMLRepresentation: { default: '' },
-        SVGRepresentation: { default: '' },
-        TeXRepresentation: { default: '' },
         dataTracked: { default: null },
+        comments: { default: null },
+        contents: { default: '' },
+        format: { default: '' },
     },
+    selectable: false,
     atom: true,
     inline: true,
     draggable: true,
     group: 'inline',
     parseDOM: [
         {
-            tag: `span.${json_schema_1.ObjectTypes.InlineMathFragment}`,
+            tag: `span.MPInlineMathFragment`,
             getAttrs: (p) => {
                 const dom = p;
                 return {
-                    id: dom.getAttribute('id'),
-                    MathMLRepresentation: dom.getAttribute('data-mathml-representation') || '',
-                    SVGRepresentation: dom.innerHTML || '',
-                    TeXRepresentation: dom.getAttribute('data-tex-representation') || '',
+                    format: dom.getAttribute('data-equation-format'),
+                    contents: dom.innerHTML,
                 };
             },
         },
     ],
     toDOM: (node) => {
         const inlineEquationNode = node;
+        const { contents, format } = inlineEquationNode.attrs;
         const dom = document.createElement('span');
-        dom.classList.add(json_schema_1.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.classList.add('MPInlineMathFragment');
+        if (format) {
+            dom.setAttribute('data-equation-format', format);
         }
-        dom.innerHTML = inlineEquationNode.attrs.SVGRepresentation;
+        dom.innerHTML = contents;
         return dom;
     },
 };

package/dist/cjs/transformer/builders.js

@@ -18,7 +18,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildJournal = exports.buildAttribution = exports.buildContributorRole = exports.buildContribution = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildInlineMathFragment = exports.buildNote = exports.buildComment = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildKeywordGroup = exports.buildKeyword = exports.buildBibliographyElement = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = void 0;
+exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildJournal = exports.buildAttribution = exports.buildContributorRole = exports.buildContribution = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildNote = exports.buildComment = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildKeywordGroup = exports.buildKeyword = exports.buildBibliographyElement = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const schema_1 = require("../schema");
@@ -115,13 +115,6 @@ const buildNote = (target, source, contents = '') => ({
     contents,
 });
 exports.buildNote = buildNote;
-const buildInlineMathFragment = (containingObject, TeXRepresentation) => ({
-    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.InlineMathFragment),
-    objectType: json_schema_1.ObjectTypes.InlineMathFragment,
-    containingObject: containingObject || undefined,
-    TeXRepresentation,
-});
-exports.buildInlineMathFragment = buildInlineMathFragment;
 const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.Footnote),
     objectType: json_schema_1.ObjectTypes.Footnote,

package/dist/cjs/transformer/decode.js

@@ -271,9 +271,8 @@ class Decoder {
                 const model = data;
                 return schema_1.schema.nodes.equation.createChecked({
                     id: model._id,
-                    MathMLStringRepresentation: model.MathMLStringRepresentation,
-                    SVGStringRepresentation: model.SVGStringRepresentation,
-                    TeXRepresentation: model.TeXRepresentation,
+                    contents: model.contents,
+                    format: model.format,
                 });
             },
             [json_schema_1.ObjectTypes.EquationElement]: (data) => {
@@ -292,12 +291,10 @@ class Decoder {
                 else {
                     throw new errors_1.MissingElement(model.containedObjectID);
                 }
-                const figcaption = this.getFigcaption(model);
                 return schema_1.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]);
             },
             [json_schema_1.ObjectTypes.FootnotesElement]: (data) => {
                 const foonotesElementModel = data;
@@ -629,7 +626,6 @@ class Decoder {
                     id: model._id,
                     role: model.role,
                     affiliations: model.affiliations,
-                    email: model.email,
                     bibliographicName: model.bibliographicName,
                     userID: model.userID,
                     invitationID: model.invitationID,

package/dist/cjs/transformer/encode.js

@@ -62,12 +62,6 @@ const listContents = (node) => {
     }
     return (0, w3c_xmlserializer_1.default)(output);
 };
-const svgDefs = (svg) => {
-    const template = document.createElement('template');
-    template.innerHTML = svg.trim();
-    const defs = template.content.querySelector('defs');
-    return defs ? (0, w3c_xmlserializer_1.default)(defs) : undefined;
-};
 const tableRowDisplayStyle = (tagName, parent) => {
     switch (tagName) {
         case 'thead':
@@ -353,20 +347,12 @@ const encoders = {
             : false,
     }),
     equation: (node) => ({
-        MathMLStringRepresentation: node.attrs.MathMLStringRepresentation || undefined,
-        TeXRepresentation: node.attrs.TeXRepresentation,
-        SVGStringRepresentation: node.attrs.SVGStringRepresentation,
+        contents: node.attrs.contents,
+        format: node.attrs.format,
     }),
     equation_element: (node) => ({
         containedObjectID: attributeOfNodeType(node, 'equation', '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: 'p',
-        suppressCaption: Boolean(node.attrs.suppressCaption) || undefined,
-        suppressTitle: node.attrs.suppressTitle === undefined ||
-            node.attrs.suppressTitle === true
-            ? undefined
-            : false,
+        label: node.attrs.label,
     }),
     figure: (node) => ({
         contentType: node.attrs.contentType || undefined,
@@ -413,12 +399,6 @@ const encoders = {
             .map((childNode) => childNode.attrs.id)
             .filter((id) => id),
     }),
-    inline_equation: (node, parent) => ({
-        containingObject: parent.attrs.id,
-        TeXRepresentation: node.attrs.TeXRepresentation,
-        SVGRepresentation: node.attrs.SVGRepresentation,
-        SVGGlyphs: svgDefs(node.attrs.SVGRepresentation),
-    }),
     keyword: (node, parent) => ({
         containedGroup: parent.attrs.id,
         name: keywordContents(node),
@@ -580,8 +560,7 @@ const encode = (node) => {
         if (placeholderTypes.includes(child.type)) {
             return;
         }
-        if (parent.type === schema_1.schema.nodes.paragraph &&
-            child.type !== schema_1.schema.nodes.inline_equation) {
+        if (parent.type === schema_1.schema.nodes.paragraph) {
             return;
         }
         const { model, markers } = (0, exports.modelFromNode)(child, parent, path, priority);

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';