@manuscripts/transform 1.0.0

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

@@ -0,0 +1,644 @@
+/*!
+ * © 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.
+ */
+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';
+const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
+const chooseContentType = (graphicNode) => {
+    if (graphicNode) {
+        const mimetype = graphicNode.getAttribute('mimetype');
+        const subtype = graphicNode.getAttribute('mime-subtype');
+        if (mimetype && subtype) {
+            return [mimetype, subtype].join('/');
+        }
+        const href = graphicNode.getAttributeNS(XLINK_NAMESPACE, 'href');
+        if (href) {
+            return mime.getType(href) || undefined;
+        }
+    }
+};
+const marks = [
+    {
+        tag: 'bold',
+        mark: 'bold',
+    },
+    {
+        tag: 'code',
+        mark: 'code',
+    },
+    {
+        tag: 'italic',
+        mark: 'italic',
+    },
+    {
+        tag: 'sc',
+        mark: 'smallcaps',
+    },
+    {
+        tag: 'strike',
+        mark: 'strikethrough',
+    },
+    {
+        tag: 'styled-content',
+        mark: 'styled',
+        getAttrs: (node) => ({
+            style: node.getAttribute('style'),
+        }),
+    },
+    {
+        tag: 'sub',
+        mark: 'subscript',
+    },
+    {
+        tag: 'sup',
+        mark: 'superscript',
+    },
+    {
+        tag: 'underline',
+        mark: 'underline',
+    },
+];
+const nodes = [
+    {
+        tag: 'attrib',
+        node: 'attribution',
+    },
+    {
+        tag: 'back',
+        ignore: true,
+    },
+    {
+        tag: 'body',
+        node: 'manuscript',
+    },
+    {
+        tag: 'break',
+        node: 'hard_break',
+    },
+    {
+        tag: 'caption',
+        node: 'figcaption',
+        context: 'figure/',
+    },
+    {
+        tag: 'caption',
+        node: 'figcaption',
+        context: 'figure_element/',
+        getContent: (node, schema) => {
+            const element = node;
+            const content = [];
+            const title = element.querySelector('title');
+            if (title) {
+                const captionTitle = schema.nodes.caption_title.create();
+                content.push(jatsBodyDOMParser.parse(title, { topNode: captionTitle }));
+            }
+            const paragraphs = element.querySelectorAll('p');
+            if (paragraphs.length) {
+                const figcaption = schema.nodes.caption.create();
+                for (const paragraph of paragraphs) {
+                    content.push(jatsBodyDOMParser.parse(paragraph, { topNode: figcaption }));
+                }
+            }
+            return Fragment.from(content);
+        },
+    },
+    {
+        tag: 'caption',
+        node: 'figcaption',
+        context: 'table_element/',
+    },
+    {
+        tag: 'code',
+        node: 'listing',
+        context: 'listing_element/',
+        getAttrs: (node) => {
+            var _a, _b, _c;
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                language: (_a = element.getAttribute('language')) !== null && _a !== void 0 ? _a : '',
+                contents: (_c = (_b = element.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '',
+            };
+        },
+    },
+    {
+        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;
+        },
+    },
+    {
+        tag: 'disp-formula',
+        node: 'equation_element',
+        getAttrs: (node) => {
+            const element = node;
+            const caption = element.querySelector('figcaption');
+            return {
+                id: element.getAttribute('id'),
+                suppressCaption: !caption,
+            };
+        },
+        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();
+            return Fragment.from([
+                schema.nodes.equation.createChecked(attrs),
+                caption
+                    ?
+                        jatsBodyDOMParser.parse(caption, {
+                            topNode: figcaption,
+                        })
+                    : figcaption,
+            ]);
+        },
+    },
+    {
+        tag: 'disp-quote[content-type=quote]',
+        node: 'blockquote_element',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'disp-quote[content-type=pullquote]',
+        node: 'pullquote_element',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'ext-link',
+        node: 'link',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                href: element.getAttributeNS(XLINK_NAMESPACE, 'href') || '',
+                title: element.getAttributeNS(XLINK_NAMESPACE, 'title') || '',
+            };
+        },
+    },
+    {
+        tag: 'fig[fig-type=equation]',
+        node: 'equation_element',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'fig[fig-type=listing]',
+        node: 'listing_element',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'graphic[specific-use=MISSING]',
+        node: 'missing_figure',
+        context: 'figure_element/',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'graphic',
+        node: 'figure',
+        context: 'figure_element/',
+        getAttrs: (node) => {
+            const element = node;
+            const position = element.getAttribute('position');
+            const src = element.getAttributeNS(XLINK_NAMESPACE, 'href');
+            return {
+                id: element.getAttribute('id'),
+                contentType: chooseContentType(element || undefined) || '',
+                src,
+                position,
+            };
+        },
+    },
+    {
+        tag: 'fig',
+        node: 'figure_element',
+        getAttrs: (node) => {
+            var _a, _b, _c, _d;
+            const element = node;
+            const labelNode = element.querySelector('label');
+            if (labelNode) {
+                element.removeChild(labelNode);
+            }
+            const attrib = element.querySelector('attrib');
+            const position = element.getAttribute('position');
+            const attribution = attrib
+                ? {
+                    literal: (_b = (_a = attrib.textContent) === null || _a === void 0 ? void 0 : _a.trim()) !== null && _b !== void 0 ? _b : '',
+                }
+                : undefined;
+            return {
+                id: element.getAttribute('id'),
+                label: (_d = (_c = labelNode === null || labelNode === void 0 ? void 0 : labelNode.textContent) === null || _c === void 0 ? void 0 : _c.trim()) !== null && _d !== void 0 ? _d : '',
+                attribution: attribution,
+                position,
+            };
+        },
+    },
+    {
+        tag: 'ref',
+        node: 'bibliography_item',
+        context: 'bibliography_element/',
+        getAttrs: (node) => {
+            const element = node;
+            const ref = {
+                id: element.getAttribute('id'),
+                type: element.getAttribute('type'),
+            };
+            const author = element.getAttribute('author');
+            if (author) {
+                ref.author = author;
+            }
+            const issued = element.getAttribute('issued');
+            if (issued) {
+                ref.issued = issued;
+            }
+            const containerTitle = element.getAttribute('container-title');
+            if (containerTitle) {
+                ref.containerTitle = containerTitle;
+            }
+            const doi = element.getAttribute('doi');
+            if (doi) {
+                ref.doi = doi;
+            }
+            const volume = element.getAttribute('volume');
+            if (volume) {
+                ref.volume = volume;
+            }
+            const issue = element.getAttribute('issue');
+            if (issue) {
+                ref.issue = issue;
+            }
+            const supplement = element.getAttribute('supplement');
+            if (supplement) {
+                ref.supplement = supplement;
+            }
+            const page = element.getAttribute('page');
+            if (page) {
+                ref.page = page;
+            }
+            const title = element.getAttribute('title');
+            if (title) {
+                ref.title = title;
+            }
+            const literal = element.getAttribute('literal');
+            if (literal) {
+                ref.literal = literal;
+            }
+            return ref;
+        },
+    },
+    {
+        tag: 'ref-list',
+        node: 'bibliography_element',
+        context: 'bibliography_section/',
+        getAttrs: (node) => {
+            const element = node;
+            const titleNode = element.querySelector('title');
+            if (titleNode) {
+                element.removeChild(titleNode);
+            }
+            return {
+                id: element.getAttribute('id'),
+                contents: '',
+            };
+        },
+    },
+    {
+        tag: 'fn-group',
+        node: 'footnotes_element',
+        context: 'footnotes_section/',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                kind: 'footnote',
+            };
+        },
+    },
+    {
+        tag: 'table-wrap-foot',
+        node: 'footnotes_element',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                kind: 'table_footnote',
+            };
+        },
+    },
+    {
+        tag: 'fn',
+        node: 'footnote',
+        context: 'footnotes_element/',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                kind: 'footnote',
+            };
+        },
+    },
+    {
+        tag: 'front',
+        ignore: true,
+    },
+    {
+        tag: 'list[list-type=bullet]',
+        node: 'bullet_list',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'list[list-type=order]',
+        node: 'ordered_list',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'list-item',
+        node: 'list_item',
+    },
+    {
+        tag: 'p',
+        node: 'paragraph',
+        context: 'section/',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'p',
+        node: 'paragraph',
+    },
+    {
+        tag: 'sec[sec-type="endnotes"]',
+        node: 'footnotes_section',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'sec[sec-type="bibliography"]',
+        node: 'bibliography_section',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'sec',
+        node: 'section',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                category: chooseSectionCategory(element),
+            };
+        },
+    },
+    {
+        tag: 'label',
+        context: 'section/',
+        node: 'section_label',
+    },
+    {
+        tag: 'label',
+        context: 'table_element/',
+        ignore: true,
+    },
+    {
+        tag: 'label',
+        context: 'figure/',
+        ignore: true,
+    },
+    {
+        tag: 'table',
+        node: 'table',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'table-wrap',
+        node: 'table_element',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                suppressFooter: !element.querySelector('table > tfoot > tr'),
+                suppressHeader: !element.querySelector('table > thead > tr'),
+            };
+        },
+    },
+    {
+        tag: 'tbody',
+        skip: true,
+    },
+    {
+        tag: 'tfoot',
+        skip: true,
+    },
+    {
+        tag: 'thead',
+        skip: true,
+    },
+    {
+        tag: 'title',
+        node: 'section_title',
+        context: 'section/|footnotes_section/|bibliography_section/',
+    },
+    {
+        tag: 'title',
+        node: 'caption_title',
+        context: 'figcaption/',
+    },
+    {
+        tag: 'tr',
+        node: 'table_row',
+    },
+    {
+        tag: 'td',
+        node: 'table_cell',
+        getAttrs: (node) => {
+            const element = node;
+            const colspan = element.getAttribute('colspan');
+            const rowspan = element.getAttribute('rowspan');
+            return Object.assign(Object.assign(Object.assign({}, (colspan && { colspan })), (rowspan && { rowspan })), { valign: element.getAttribute('valign'), align: element.getAttribute('align'), scope: element.getAttribute('scope'), style: element.getAttribute('style') });
+        },
+    },
+    {
+        tag: 'th',
+        node: 'table_cell',
+        getAttrs: (node) => {
+            const element = node;
+            const colspan = element.getAttribute('colspan');
+            const rowspan = element.getAttribute('rowspan');
+            return Object.assign(Object.assign(Object.assign({ celltype: 'th' }, (colspan && { colspan })), (rowspan && { rowspan })), { valign: element.getAttribute('valign'), align: element.getAttribute('align'), scope: element.getAttribute('scope'), style: element.getAttribute('style') });
+        },
+    },
+    {
+        tag: 'col',
+        node: 'table_col',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                width: element.getAttribute('width'),
+            };
+        },
+    },
+    {
+        tag: 'colgroup',
+        node: 'table_colgroup',
+    },
+    {
+        tag: 'xref[ref-type="bibr"]',
+        node: 'citation',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                rid: element.getAttribute('rid'),
+                contents: element.textContent,
+            };
+        },
+    },
+    {
+        tag: 'xref[ref-type="fn"]',
+        node: 'inline_footnote',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                rid: element.getAttribute('rid'),
+                contents: element.textContent,
+            };
+        },
+    },
+    {
+        tag: 'xref',
+        node: 'cross_reference',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                rid: element.getAttribute('rid'),
+                label: element.textContent,
+            };
+        },
+    },
+];
+export const jatsBodyDOMParser = new DOMParser(schema, [...marks, ...nodes]);