@manuscripts/transform 1.0.0

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

@@ -0,0 +1,36 @@
+/*!
+ * © 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.
+ */
+const versions = {
+    '1.1': {
+        publicId: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.1 20151215//EN',
+        systemId: 'http://jats.nlm.nih.gov/archiving/1.1/JATS-archive-oasis-article1-mathml3.dtd',
+    },
+    '1.2d1': {
+        publicId: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2d1 20170631//EN',
+        systemId: 'http://jats.nlm.nih.gov/archiving/1.2d1/JATS-archive-oasis-article1-mathml3.dtd',
+    },
+    '1.2': {
+        publicId: '-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with OASIS Tables with MathML3 v1.2 20190208//EN',
+        systemId: 'http://jats.nlm.nih.gov/archiving/1.2/JATS-archive-oasis-article1-mathml3.dtd',
+    },
+};
+export const supportedVersions = () => Object.keys(versions);
+export const selectVersionIds = (version) => {
+    if (!(version in versions)) {
+        throw new Error(`Unknown version ${version}`);
+    }
+    return versions[version];
+};

package/dist/es/lib/attributes.js

@@ -0,0 +1,22 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export const buildElementClass = (attrs) => {
+    const classes = ['MPElement'];
+    if (attrs.paragraphStyle) {
+        classes.push(attrs.paragraphStyle.replace(/:/g, '_'));
+    }
+    return classes.join(' ');
+};

package/dist/es/lib/html.js

@@ -0,0 +1,43 @@
+/*!
+ * © 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.
+ */
+function decodeHTMLEntities(text) {
+    const entities = [
+        ['#x27', "'"],
+        ['#x2F', '/'],
+        ['#39', "'"],
+        ['#47', '/'],
+        ['nbsp', ' '],
+    ];
+    for (let i = 0; i < entities.length; i++) {
+        text = text.replace(new RegExp('&' + entities[i][0] + ';', 'g'), entities[i][1]);
+    }
+    return text;
+}
+export const nodeFromHTML = (html) => {
+    html = html.trim();
+    if (!html.length) {
+        return null;
+    }
+    const template = document.createElement('template');
+    template.innerHTML = html;
+    template.innerHTML = decodeHTMLEntities(template.innerHTML);
+    return template.content.firstChild;
+};
+export const textFromHTML = (html) => {
+    const template = document.createElement('template');
+    template.innerHTML = html;
+    return template.content.textContent;
+};

package/dist/es/lib/styled-content.js

@@ -0,0 +1,23 @@
+/*!
+ * © 2020 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export const normalizeStyleName = (title) => title.replace(/\W+/, '-').toLowerCase();
+export const buildStyledContentClass = (attrs, inlineStyle) => {
+    const classes = ['styled-content'];
+    if (inlineStyle && inlineStyle.title) {
+        classes.push(normalizeStyleName(inlineStyle.title));
+    }
+    return classes.join(' ');
+};

package/dist/es/lib/table-cell-styles.js

@@ -0,0 +1,47 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export const TABLE_CELL_STYLES = [
+    'backgroundColor',
+    'border-top',
+    'border-right',
+    'border-bottom',
+    'border-left',
+    'verticalAlign',
+    'textAlign',
+];
+const dashify = (str) => {
+    return str
+        .trim()
+        .replace(/([a-z])([A-Z])/g, '$1-$2')
+        .replace(/\W/g, (m) => (/[À-ž]/.test(m) ? m : '-'))
+        .replace(/^-+|-+$/g, '')
+        .toLowerCase();
+};
+export const serializeTableCellStyles = (styles) => {
+    return Object.keys(styles)
+        .map((key) => styles[key] && `${dashify(key)}: ${styles[key]}`)
+        .filter(Boolean)
+        .join('; ');
+};
+const isStyleKey = (key) => TABLE_CELL_STYLES.includes(key);
+export const getTableCellStyles = (styles) => {
+    return Object.entries(styles).reduce((acc, [key, value]) => {
+        if (isStyleKey(key)) {
+            acc[key] = value;
+        }
+        return acc;
+    }, {});
+};

package/dist/es/lib/utils.js

@@ -0,0 +1,59 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import { isGraphicalAbstractSectionNode } from '../schema/nodes/graphical_abstract_section';
+export function* iterateChildren(node, recurse = false) {
+    for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        yield child;
+        if (recurse) {
+            for (const grandchild of iterateChildren(child, true)) {
+                yield grandchild;
+            }
+        }
+    }
+}
+export const findNodePositions = (state, predicate) => {
+    const found = [];
+    state.doc.descendants((node, nodePos) => {
+        if (predicate(node)) {
+            found.push(nodePos);
+        }
+        return true;
+    });
+    return found;
+};
+export const isInGraphicalAbstractSection = ($pos) => {
+    for (let i = $pos.depth; i > 0; i--) {
+        const node = $pos.node(i);
+        if (isGraphicalAbstractSectionNode(node)) {
+            return true;
+        }
+    }
+    return false;
+};
+export const findParentNodeClosestToPos = ($pos, predicate) => {
+    for (let i = $pos.depth; i > 0; i--) {
+        const node = $pos.node(i);
+        if (predicate(node)) {
+            return {
+                pos: i > 0 ? $pos.before(i) : 0,
+                start: $pos.start(i),
+                depth: i,
+                node,
+            };
+        }
+    }
+};

package/dist/es/mathjax/index.js

@@ -0,0 +1,12 @@
+export const convertMathMLToSVG = async (mathml, display) => {
+    const { convertMathMLToSVG } = await import('./mathml-to-svg');
+    return convertMathMLToSVG(mathml, display);
+};
+export const convertTeXToMathML = async (tex, display) => {
+    const { convertTeXToMathML } = await import('./tex-to-mathml');
+    return convertTeXToMathML(tex, display);
+};
+export const convertTeXToSVG = async (tex, display) => {
+    const { convertTeXToSVG } = await import('./tex-to-svg');
+    return convertTeXToSVG(tex, display);
+};

package/dist/es/mathjax/mathjax-packages.js

@@ -0,0 +1,17 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import { AllPackages } from 'mathjax-full/js/input/tex/AllPackages';
+export const packages = AllPackages.filter((name) => name !== 'html' && name !== 'bussproofs');

package/dist/es/mathjax/mathml-to-svg.js

@@ -0,0 +1,52 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import 'mathjax-full/js/util/entities/all';
+import { HTMLAdaptor } from 'mathjax-full/js/adaptors/HTMLAdaptor';
+import { HTMLDocument } from 'mathjax-full/js/handlers/html/HTMLDocument';
+import { MathML } from 'mathjax-full/js/input/mathml';
+import { SVG } from 'mathjax-full/js/output/svg';
+import { xmlSerializer } from '../transformer';
+class ManuscriptsHTMLAdaptor extends HTMLAdaptor {
+    setAttribute(node, name, value, ns) {
+        if (name !== 'xmlns') {
+            ns ? node.setAttributeNS(ns, name, value) : node.setAttribute(name, value);
+        }
+    }
+}
+const InputJax = new MathML();
+const OutputJax = new SVG({
+    fontCache: 'none',
+});
+const adaptor = new ManuscriptsHTMLAdaptor(window);
+const doc = new HTMLDocument(document, adaptor, {
+    InputJax,
+    OutputJax,
+});
+doc.addStyleSheet();
+export const convertMathMLToSVG = (mathml, display) => {
+    const item = doc.convert(mathml, {
+        display,
+        em: 16,
+        ex: 8,
+        containerWidth: 1000000,
+        lineWidth: 1000000,
+        scale: 1,
+    });
+    if (!item || !item.firstChild) {
+        return null;
+    }
+    return xmlSerializer.serializeToString(item.firstChild);
+};

package/dist/es/mathjax/tex-to-mathml.js

@@ -0,0 +1,45 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import 'mathjax-full/js/util/entities/all';
+import { HTMLAdaptor } from 'mathjax-full/js/adaptors/HTMLAdaptor';
+import { STATE } from 'mathjax-full/js/core/MathItem.js';
+import { SerializedMmlVisitor } from 'mathjax-full/js/core/MmlTree/SerializedMmlVisitor';
+import { HTMLDocument } from 'mathjax-full/js/handlers/html/HTMLDocument';
+import { TeX } from 'mathjax-full/js/input/tex';
+import { packages } from './mathjax-packages';
+const InputJax = new TeX({
+    packages,
+});
+const adaptor = new HTMLAdaptor(window);
+const doc = new HTMLDocument(document, adaptor, {
+    InputJax,
+});
+const visitor = new SerializedMmlVisitor();
+export const convertTeXToMathML = (tex, display) => {
+    const item = doc.convert(tex, {
+        display,
+        em: 16,
+        ex: 8,
+        containerWidth: 1000000,
+        lineWidth: 1000000,
+        scale: 1,
+        end: STATE.CONVERT,
+    });
+    if (!item) {
+        return null;
+    }
+    return visitor.visitTree(item);
+};

package/dist/es/mathjax/tex-to-svg.js

@@ -0,0 +1,55 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import 'mathjax-full/js/util/entities/all';
+import { HTMLAdaptor } from 'mathjax-full/js/adaptors/HTMLAdaptor';
+import { HTMLDocument } from 'mathjax-full/js/handlers/html/HTMLDocument';
+import { TeX } from 'mathjax-full/js/input/tex';
+import { SVG } from 'mathjax-full/js/output/svg';
+import { xmlSerializer } from '../transformer';
+import { packages } from './mathjax-packages';
+class ManuscriptsHTMLAdaptor extends HTMLAdaptor {
+    setAttribute(node, name, value, ns) {
+        if (name !== 'xmlns') {
+            ns ? node.setAttributeNS(ns, name, value) : node.setAttribute(name, value);
+        }
+    }
+}
+const InputJax = new TeX({
+    packages,
+});
+const OutputJax = new SVG({
+    fontCache: 'none',
+});
+const adaptor = new ManuscriptsHTMLAdaptor(window);
+const doc = new HTMLDocument(document, adaptor, {
+    InputJax,
+    OutputJax,
+});
+doc.addStyleSheet();
+export const convertTeXToSVG = (tex, display) => {
+    const item = doc.convert(tex, {
+        display,
+        em: 16,
+        ex: 8,
+        containerWidth: 1000000,
+        lineWidth: 1000000,
+        scale: 1,
+    });
+    if (!item || !item.firstChild) {
+        return null;
+    }
+    return xmlSerializer.serializeToString(item.firstChild);
+};

package/dist/es/schema/groups.js

@@ -0,0 +1,27 @@
+/*!
+ * © 2020 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export const GROUP_BLOCK = 'block';
+export const GROUP_ELEMENT = 'element';
+export const GROUP_EXECUTABLE = 'executable';
+export const GROUP_LIST = 'list';
+export const GROUP_SECTION = 'sections';
+export const hasGroup = (nodeType, groupName) => {
+    const { group } = nodeType.spec;
+    if (!group) {
+        return false;
+    }
+    return group.split(/\s+/).includes(groupName);
+};

package/dist/es/schema/index.js

@@ -0,0 +1,178 @@
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import { Schema } from 'prosemirror-model';
+import { bold, code, italic, smallcaps, strikethrough, styled, subscript, superscript, tracked_delete, tracked_insert, underline, } from './marks';
+import { attribution } from './nodes/attribution';
+import { bibliographyElement } from './nodes/bibliography_element';
+import { bibliographyItem } from './nodes/bibliography_item';
+import { bibliographySection } from './nodes/bibliography_section';
+import { blockquoteElement } from './nodes/blockquote_element';
+import { caption } from './nodes/caption';
+import { captionTitle } from './nodes/caption_title';
+import { citation } from './nodes/citation';
+import { comment } from './nodes/comment';
+import { crossReference } from './nodes/cross_reference';
+import { doc } from './nodes/doc';
+import { equation } from './nodes/equation';
+import { equationElement } from './nodes/equation_element';
+import { figcaption } from './nodes/figcaption';
+import { figure } from './nodes/figure';
+import { figureElement } from './nodes/figure_element';
+import { footnote } from './nodes/footnote';
+import { footnotesElement } from './nodes/footnotes_element';
+import { footnotesSection } from './nodes/footnotes_section';
+import { graphicalAbstractSection } from './nodes/graphical_abstract_section';
+import { hardBreak } from './nodes/hard_break';
+import { highlightMarker } from './nodes/highlight_marker';
+import { inlineEquation } from './nodes/inline_equation';
+import { inlineFootnote } from './nodes/inline_footnote';
+import { keywordsElement } from './nodes/keywords_element';
+import { keywordsSection } from './nodes/keywords_section';
+import { link } from './nodes/link';
+import { bulletList, listItem, orderedList } from './nodes/list';
+import { listing } from './nodes/listing';
+import { listingElement } from './nodes/listing_element';
+import { manuscript } from './nodes/manuscript';
+import { missingFigure } from './nodes/missing_figure';
+import { paragraph } from './nodes/paragraph';
+import { placeholder } from './nodes/placeholder';
+import { placeholderElement } from './nodes/placeholder_element';
+import { pullquoteElement } from './nodes/pullquote_element';
+import { section } from './nodes/section';
+import { sectionLabel } from './nodes/section_label';
+import { sectionTitle } from './nodes/section_title';
+import { table, tableBody } from './nodes/table';
+import { tableCol, tableColGroup } from './nodes/table_col';
+import { tableElement } from './nodes/table_element';
+import { tableCell, tableRow } from './nodes/table_row';
+import { text } from './nodes/text';
+import { tocElement } from './nodes/toc_element';
+import { tocSection } from './nodes/toc_section';
+export * from './groups';
+export * from './types';
+export * from './nodes/comment';
+export * from './nodes/attribution';
+export * from './nodes/bibliography_item';
+export * from './nodes/bibliography_element';
+export * from './nodes/bibliography_section';
+export * from './nodes/blockquote_element';
+export * from './nodes/caption';
+export * from './nodes/caption_title';
+export * from './nodes/citation';
+export * from './nodes/cross_reference';
+export * from './nodes/doc';
+export * from './nodes/equation';
+export * from './nodes/equation_element';
+export * from './nodes/figcaption';
+export * from './nodes/figure';
+export * from './nodes/figure_element';
+export * from './nodes/footnote';
+export * from './nodes/footnotes_element';
+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/keywords_element';
+export * from './nodes/keywords_section';
+export * from './nodes/link';
+export * from './nodes/list';
+export * from './nodes/listing';
+export * from './nodes/listing_element';
+export * from './nodes/manuscript';
+export * from './nodes/missing_figure';
+export * from './nodes/paragraph';
+export * from './nodes/placeholder';
+export * from './nodes/placeholder_element';
+export * from './nodes/pullquote_element';
+export * from './nodes/section';
+export * from './nodes/section_title';
+export * from './nodes/table';
+export * from './nodes/table_col';
+export * from './nodes/table_element';
+export * from './nodes/table_row';
+export * from './nodes/text';
+export * from './nodes/toc_element';
+export * from './nodes/toc_section';
+export const schema = new Schema({
+    marks: {
+        bold,
+        code,
+        italic,
+        smallcaps,
+        strikethrough,
+        styled,
+        subscript,
+        superscript,
+        underline,
+        tracked_insert,
+        tracked_delete,
+    },
+    nodes: {
+        comment,
+        attribution,
+        bibliography_item: bibliographyItem,
+        bibliography_element: bibliographyElement,
+        bibliography_section: bibliographySection,
+        blockquote_element: blockquoteElement,
+        bullet_list: bulletList,
+        caption,
+        caption_title: captionTitle,
+        citation,
+        cross_reference: crossReference,
+        doc,
+        equation,
+        equation_element: equationElement,
+        figcaption,
+        figure,
+        figure_element: figureElement,
+        footnote,
+        footnotes_element: footnotesElement,
+        footnotes_section: footnotesSection,
+        graphical_abstract_section: graphicalAbstractSection,
+        hard_break: hardBreak,
+        highlight_marker: highlightMarker,
+        inline_equation: inlineEquation,
+        inline_footnote: inlineFootnote,
+        keywords_element: keywordsElement,
+        keywords_section: keywordsSection,
+        link,
+        list_item: listItem,
+        listing,
+        listing_element: listingElement,
+        manuscript,
+        missing_figure: missingFigure,
+        ordered_list: orderedList,
+        paragraph,
+        placeholder,
+        placeholder_element: placeholderElement,
+        pullquote_element: pullquoteElement,
+        section,
+        section_label: sectionLabel,
+        section_title: sectionTitle,
+        table,
+        table_body: tableBody,
+        table_cell: tableCell,
+        table_element: tableElement,
+        table_row: tableRow,
+        table_col: tableCol,
+        table_colgroup: tableColGroup,
+        text,
+        toc_element: tocElement,
+        toc_section: tocSection,
+    },
+});