@manuscripts/transform 2.0.4 → 2.1.1-LEAN-3094

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

@@ -0,0 +1,45 @@
+"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.supplements = void 0;
+exports.supplements = {
+    content: 'section_title supplement*',
+    attrs: {
+        id: { default: '' },
+        dataTracked: { default: null },
+    },
+    group: 'block',
+    selectable: false,
+    parseDOM: [
+        {
+            tag: 'div.supplements',
+        },
+    ],
+    toDOM: (node) => {
+        const supplements = node;
+        return [
+            'div',
+            {
+                id: supplements.attrs.id,
+                class: 'supplements',
+                spellcheck: 'false',
+                contenteditable: false,
+            },
+            0,
+        ];
+    },
+};

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

@@ -64,6 +64,7 @@ const getSections = (modelMap) => (0, exports.getModelsByType)(modelMap, json_sc
 const getAffiliations = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Affiliation);
 const getContributors = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Contributor);
 const getKeywordElements = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.KeywordsElement);
+const getSupplements = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Supplement);
 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];
@@ -102,6 +103,15 @@ class Decoder {
             ...elements,
         ]);
     }
+    createSupplementsNode() {
+        const elements = getSupplements(this.modelMap)
+            .map((e) => this.decode(e))
+            .filter(Boolean);
+        return schema_1.schema.nodes.supplements.createAndFill({}, [
+            schema_1.schema.nodes.section_title.create({}, schema_1.schema.text('SupplementaryMaterials')),
+            ...elements,
+        ]);
+    }
     createCommentsNode() {
         return schema_1.schema.nodes.comments.createAndFill({}, [
             ...this.comments.values(),
@@ -271,9 +281,8 @@ 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 +301,10 @@ 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;
@@ -618,6 +625,8 @@ class Decoder {
                     addressLine3: model.addressLine3,
                     postCode: model.postCode,
                     country: model.country,
+                    county: model.county,
+                    city: model.city,
                     email: model.email,
                     department: model.department,
                     priority: model.priority,
@@ -629,6 +638,8 @@ class Decoder {
                     id: model._id,
                     role: model.role,
                     affiliations: model.affiliations,
+                    email: model.email,
+                    isJointContributor: model.isJointContributor,
                     bibliographicName: model.bibliographicName,
                     userID: model.userID,
                     invitationID: model.invitationID,
@@ -639,6 +650,17 @@ class Decoder {
                     priority: model.priority,
                 }, schema_1.schema.text('_'));
             },
+            [json_schema_1.ObjectTypes.Supplement]: (data) => {
+                var _a, _b;
+                const model = data;
+                return schema_1.schema.nodes.supplement.create({
+                    id: model._id,
+                    href: model.href,
+                    mimeType: (_a = model.MIME) === null || _a === void 0 ? void 0 : _a.split('/')[0],
+                    mimeSubType: (_b = model.MIME) === null || _b === void 0 ? void 0 : _b.split('/')[1],
+                    title: model.title,
+                });
+            },
         };
         this.decode = (model) => {
             if (!this.creators[model.objectType]) {
@@ -653,6 +675,7 @@ class Decoder {
             const contributors = this.createContributorsNode();
             const affiliations = this.createAffiliationsNode();
             const keywords = this.createKeywordsNode();
+            const suppl = this.createSupplementsNode();
             const { abstracts, body, backmatter } = this.createContentSections();
             const comments = this.createCommentsNode();
             const contents = [
@@ -660,6 +683,7 @@ class Decoder {
                 contributors,
                 affiliations,
                 keywords,
+                suppl,
                 abstracts,
                 body,
                 backmatter,

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),
@@ -508,8 +488,11 @@ const encoders = {
         addressLine1: node.attrs.addressLine1,
         addressLine2: node.attrs.addressLine2,
         addressLine3: node.attrs.addressLine3,
+        department: node.attrs.department,
         postCode: node.attrs.postCode,
         country: node.attrs.country,
+        county: node.attrs.county,
+        city: node.attrs.city,
         email: node.attrs.email,
         priority: node.attrs.priority,
     }),
@@ -520,11 +503,19 @@ const encoders = {
         userID: node.attrs.userID,
         invitationID: node.attrs.invitationID,
         isCorresponding: node.attrs.isCorresponding,
+        isJointContributor: node.attrs.isJointContributor,
         ORCIDIdentifier: node.attrs.ORCIDIdentifier,
         footnote: node.attrs.footnote,
         corresp: node.attrs.corresp,
         priority: node.attrs.priority,
     }),
+    supplement: (node) => ({
+        href: node.attrs.href,
+        title: node.attrs.title,
+        MIME: node.attrs.mimeType && node.attrs.mimeSubType
+            ? [node.attrs.mimeType, node.attrs.mimeSubType].join('/')
+            : '',
+    }),
 };
 const modelData = (node, parent, path, priority) => {
     const encoder = encoders[node.type.name];
@@ -553,6 +544,7 @@ const containerTypes = [
     schema_1.schema.nodes.contributors,
     schema_1.schema.nodes.affiliations,
     schema_1.schema.nodes.keywords,
+    schema_1.schema.nodes.supplements,
     schema_1.schema.nodes.abstracts,
     schema_1.schema.nodes.body,
     schema_1.schema.nodes.backmatter,
@@ -580,8 +572,7 @@ 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],
@@ -61,6 +60,7 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.contributors, json_schema_1.ObjectTypes.Section],
     [schema_1.schema.nodes.affiliations, json_schema_1.ObjectTypes.Section],
     [schema_1.schema.nodes.title, json_schema_1.ObjectTypes.Titles],
+    [schema_1.schema.nodes.supplement, json_schema_1.ObjectTypes.Supplement],
 ]);
 const isExecutableNodeType = (type) => (0, schema_1.hasGroup)(type, schema_1.GROUP_EXECUTABLE);
 exports.isExecutableNodeType = isExecutableNodeType;

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 +31,24 @@ 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',
@@ -141,91 +157,27 @@ 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 = 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);
+            const id = element.getAttribute('id');
             return Fragment.from([
-                schema.nodes.equation.createChecked(attrs),
-                caption
-                    ?
-                        jatsBodyDOMParser.parse(caption, {
-                            topNode: figcaption,
-                        })
-                    : figcaption,
+                schema.nodes.equation.createChecked(Object.assign({ id }, attrs)),
             ]);
         },
     },
@@ -424,6 +376,25 @@ const nodes = [
         tag: 'sec[sec-type="keywords"]',
         node: 'keywords',
     },
+    {
+        tag: 'sec[sec-type="supplementary-material"]',
+        node: 'supplements',
+    },
+    {
+        tag: 'supplementary-material',
+        node: 'supplement',
+        getAttrs: (node) => {
+            var _a;
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                href: element.getAttributeNS(XLINK_NAMESPACE, 'href'),
+                mimeType: element.getAttribute('mimetype'),
+                mimeSubType: element.getAttribute('mime-subtype'),
+                title: (_a = element.querySelector('title')) === null || _a === void 0 ? void 0 : _a.textContent,
+            };
+        },
+    },
     {
         tag: 'sec[sec-type="abstracts"]',
         node: 'abstracts',
@@ -520,7 +491,7 @@ const nodes = [
     {
         tag: 'title',
         node: 'section_title',
-        context: 'section/|footnotes_section/|bibliography_section/|keywords/',
+        context: 'section/|footnotes_section/|bibliography_section/|keywords/|supplements/',
     },
     {
         tag: 'title',

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

@@ -284,4 +284,18 @@ export const jatsBodyTransformations = {
             body.prepend(section);
         }
     },
+    createSuppleMaterials(document, body, createElement) {
+        const suppleMaterials = [
+            ...document.querySelectorAll('article-meta > supplementary-material'),
+        ];
+        if (suppleMaterials.length > 0) {
+            const section = createElement('sec');
+            section.setAttribute('sec-type', 'supplementary-material');
+            const title = createElement('title');
+            title.textContent = 'supplementary-material';
+            section.append(title);
+            section.append(...suppleMaterials);
+            body.prepend(section);
+        }
+    },
 };

package/dist/es/jats/importer/jats-front-parser.js

@@ -15,7 +15,7 @@
  */
 import debug from 'debug';
 import { getTrimmedTextContent } from '../../lib/utils';
-import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildJournal, buildSupplementaryMaterial, buildTitles, } from '../../transformer';
+import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildJournal, buildTitles, } from '../../transformer';
 import { parseJournalMeta } from './jats-journal-meta-parser';
 import { htmlFromJatsNode } from './jats-parser-utils';
 const warn = debug('manuscripts-transform');
@@ -122,25 +122,6 @@ export const jatsFrontParser = {
         }
         return history;
     },
-    parseSupplements(elements) {
-        var _a, _b, _c, _d;
-        if (!(elements === null || elements === void 0 ? void 0 : elements.length)) {
-            return [];
-        }
-        const supplements = [];
-        for (const element of elements) {
-            const title = (_a = getTrimmedTextContent(element, 'caption > title')) !== null && _a !== void 0 ? _a : '';
-            const href = (_b = element.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _b !== void 0 ? _b : '';
-            const supplement = buildSupplementaryMaterial(title, href);
-            const mimeType = (_c = element.getAttribute('mimetype')) !== null && _c !== void 0 ? _c : '';
-            const mimeSubtype = (_d = element.getAttribute('mime-subtype')) !== null && _d !== void 0 ? _d : '';
-            if (mimeType && mimeSubtype) {
-                supplement.MIME = [mimeType, mimeSubtype].join('/');
-            }
-            supplements.push(supplement);
-        }
-        return supplements;
-    },
     parseAffiliations(elements) {
         const affiliationIDs = new Map();
         const affiliations = elements.map((element, priority) => {

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

@@ -40,9 +40,6 @@ export const parseJATSFront = (doc, front) => {
     const authors = jatsFrontParser.parseContributors([
         ...front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]'),
     ], affiliationIDs, footnoteIDs, correspondingIDs);
-    const supplements = jatsFrontParser.parseSupplements([
-        ...front.querySelectorAll('article-meta > supplementary-material'),
-    ]);
     const history = jatsFrontParser.parseDates(front.querySelector('article-meta > history'));
     const counts = jatsFrontParser.parseCounts(front.querySelector('article-meta counts'));
     const manuscript = Object.assign(Object.assign(Object.assign({}, buildManuscript()), counts), history);
@@ -54,7 +51,6 @@ export const parseJATSFront = (doc, front) => {
         ...authors,
         ...affiliations,
         ...correspondingList,
-        ...supplements,
     ]);
 };
 export const parseJATSBody = (doc, body, references) => {
@@ -65,6 +61,7 @@ export const parseJATSBody = (doc, body, references) => {
     jatsBodyTransformations.createBody(doc, body, createElement);
     jatsBodyTransformations.createAbstracts(doc, body, createElement);
     jatsBodyTransformations.createBackmatter(doc, body, createElement);
+    jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jatsBodyTransformations.createKeywords(doc, body, createElement);
     const node = jatsBodyDOMParser.parse(body).firstChild;
     if (!node) {

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

@@ -156,6 +156,7 @@ export class JATSExporter {
         };
         this.nodeFromJATS = (JATSFragment) => {
             JATSFragment = JATSFragment.trim();
+            JATSFragment = JATSFragment.replace(' ', ' ');
             if (!JATSFragment.length) {
                 return null;
             }
@@ -620,6 +621,8 @@ export class JATSExporter {
                 body: () => ['body', 0],
                 abstracts: () => ['abstract', 0],
                 backmatter: () => ['backmatter', 0],
+                supplement: () => '',
+                supplements: () => '',
                 bibliography_section: (node) => [
                     'ref-list',
                     { id: normalizeID(node.attrs.id) },
@@ -676,22 +679,23 @@ 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;
+                    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.nodes.equation);
+                    return eqElement;
                 },
-                equation_element: (node) => createFigureElement(node, 'fig', node.type.schema.nodes.equation, 'equation'),
                 figcaption: (node) => {
                     if (!node.textContent) {
                         return '';
@@ -741,28 +745,6 @@ 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');