@manuscripts/transform 2.6.0 → 2.6.1-LEAN-3966.1

package/dist/es/transformer/filename.js

@@ -1,23 +0,0 @@
-/*!
- * © 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 generateAttachmentFilename = (id, contentType) => {
-    const basename = id.replace(':', '_');
-    if (!contentType) {
-        return basename;
-    }
-    const [, mimeSubType] = contentType.split('/');
-    return `${basename}.${mimeSubType}`;
-};

package/dist/es/transformer/footnotes-order.js

@@ -1,55 +0,0 @@
-/*!
- * © 2022 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 createOrderedFootnotesIDs = (doc) => {
-    const footnotesRefs = [...doc.querySelectorAll('xref[ref-type="fn"][rid]')];
-    const footnotes = [...doc.querySelectorAll('fn:not([fn-type])')];
-    const authorNotesIDs = [...doc.querySelectorAll('author-notes > fn')].map((an) => an.getAttribute('id'));
-    const tableElementFooters = [
-        ...doc.querySelectorAll('table-wrap-foot > fn'),
-    ].map((footer) => footer.getAttribute('id'));
-    const orderedFootnotesIDs = [];
-    footnotesRefs.forEach((ref) => {
-        const refID = ref.getAttribute('rid');
-        if (refID) {
-            orderedFootnotesIDs.push(refID);
-        }
-    });
-    footnotes.forEach((footnote) => {
-        const id = footnote.getAttribute('id');
-        if (id &&
-            !authorNotesIDs.includes(id) &&
-            !orderedFootnotesIDs.includes(id) &&
-            !tableElementFooters.includes(id)) {
-            orderedFootnotesIDs.push(id);
-        }
-    });
-    return orderedFootnotesIDs;
-};
-export const handleFootnotesOrder = (orderedFootnotesIDs, replacements, footnotesOrder) => {
-    const footnotesList = [];
-    let index = 0;
-    orderedFootnotesIDs.forEach((refID) => {
-        const fnID = replacements.get(refID);
-        if (fnID) {
-            footnotesList.push({
-                index,
-                id: fnID,
-            });
-            index++;
-        }
-    });
-    footnotesOrder.footnotesList = footnotesList;
-};

package/dist/es/transformer/highlight-markers.js

@@ -1,132 +0,0 @@
-/*!
- * © 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 highlightableFields = [
-    'caption',
-    'contents',
-    'title',
-];
-export const isHighlightableModel = (model) => {
-    for (const field of highlightableFields) {
-        if (field in model) {
-            return true;
-        }
-    }
-    return false;
-};
-export const extractCommentMarkers = (model) => {
-    if (!isHighlightableModel(model)) {
-        return [];
-    }
-    const comments = new Map();
-    for (const field of highlightableFields) {
-        let html = model[field];
-        if (!html || !html.includes('highlight-marker')) {
-            continue;
-        }
-        const template = document.createElement('template');
-        template.innerHTML = `<div>${html}</div>`;
-        const element = template.content.firstChild;
-        if (!element) {
-            continue;
-        }
-        const markers = element.querySelectorAll('span.highlight-marker');
-        if (!markers.length) {
-            continue;
-        }
-        for (const marker of markers) {
-            const markerHTML = marker.outerHTML;
-            const offset = html.indexOf(markerHTML);
-            if (offset === -1) {
-                continue;
-            }
-            const id = marker.getAttribute('id');
-            const target = marker.getAttribute('data-target-id');
-            if (id && target) {
-                const position = marker.getAttribute('data-position');
-                if (position === 'start') {
-                    const comment = {
-                        _id: id,
-                        from: offset,
-                        to: -1,
-                    };
-                    comments.set(id, comment);
-                }
-                else if (position === 'end') {
-                    const comment = comments.get(id);
-                    if (comment) {
-                        comment.to = offset;
-                    }
-                }
-                else if (position === 'point') {
-                    const comment = {
-                        _id: id,
-                        from: offset,
-                        to: offset,
-                    };
-                    comments.set(id, comment);
-                }
-            }
-            html =
-                html.substring(0, offset) + html.substring(offset + markerHTML.length);
-        }
-        model[field] = html;
-    }
-    return Array.from(comments.values());
-};
-export const insertHighlightMarkers = (contents, commentAnnotations) => {
-    let output = contents;
-    const sortedComments = commentAnnotations.sort((a, b) => {
-        if (a.selector && b.selector) {
-            return b.selector.from - a.selector.from;
-        }
-        else {
-            return 0;
-        }
-    });
-    for (const comment of sortedComments) {
-        let element;
-        if (comment.selector) {
-            if (comment.selector.from === comment.selector.to) {
-                element = createHighlightElement(comment, 'point');
-                output = injectHighlightMarker(element, comment.selector.from, output);
-            }
-            else {
-                element = createHighlightElement(comment, 'start');
-                output = injectHighlightMarker(element, comment.selector.from, output);
-                const updatedEndOffset = element.outerHTML.length + comment.selector.to;
-                element = createHighlightElement(comment, 'end');
-                output = injectHighlightMarker(element, updatedEndOffset, output);
-            }
-        }
-    }
-    return output;
-};
-function injectHighlightMarker(element, offset, contents) {
-    const parts = [
-        contents.substring(0, offset),
-        element.outerHTML,
-        contents.substring(offset),
-    ];
-    return parts.join('');
-}
-const createHighlightElement = (comment, position) => {
-    const element = document.createElement('span');
-    element.className = 'highlight-marker';
-    element.setAttribute('id', comment._id);
-    element.setAttribute('data-target-id', comment.target);
-    element.setAttribute('data-position', position);
-    return element;
-};

package/dist/es/transformer/html.js

@@ -1,393 +0,0 @@
-/*!
- * © 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 { ObjectTypes, } from '@manuscripts/json-schema';
-import { DOMSerializer } from 'prosemirror-model';
-import serializeToXML from 'w3c-xmlserializer';
-import { createCounter } from '../jats/jats-exporter';
-import { buildStyledContentClass } from '../lib/styled-content';
-import { schema, } from '../schema';
-import { generateAttachmentFilename } from './filename';
-import { buildTargets } from './labels';
-import { isNodeType } from './node-types';
-import { hasObjectType } from './object-types';
-import { findJournal, findManuscript, findTitles } from './project-bundle';
-import { chooseSecType } from './section-category';
-const chooseNodeName = (element) => {
-    const nodeName = element.nodeName.toLowerCase();
-    if (nodeName === 'figure') {
-        if (element.classList.contains('table')) {
-            return 'figure-table';
-        }
-        if (element.classList.contains('listing')) {
-            return 'figure-listing';
-        }
-        if (element.classList.contains('equation')) {
-            return 'figure-equation';
-        }
-        return 'figure';
-    }
-    else if (nodeName === 'section') {
-        const sectionCategory = element.getAttribute('data-category');
-        if (sectionCategory) {
-            const secType = chooseSecType(sectionCategory);
-            if (secType) {
-                return secType;
-            }
-        }
-    }
-    else if (element.classList.length === 1) {
-        const className = element.classList.item(0);
-        if (className && !className.startsWith('MP')) {
-            return className;
-        }
-    }
-    return nodeName;
-};
-const createDefaultIdGenerator = () => {
-    const counter = createCounter();
-    return async (element) => {
-        const nodeName = chooseNodeName(element);
-        const index = counter.increment(nodeName);
-        return `${nodeName}-${index}`;
-    };
-};
-export class HTMLTransformer {
-    constructor() {
-        this.serializeToHTML = async (fragment, modelMap, options = {}) => {
-            const { idGenerator, mediaPathGenerator } = options;
-            this.modelMap = modelMap;
-            this.labelTargets = buildTargets(fragment);
-            this.document = document.implementation.createDocument('http://www.w3.org/1999/xhtml', 'html', document.implementation.createDocumentType('html', '', ''));
-            const article = this.document.createElement('article');
-            this.document.documentElement.appendChild(article);
-            article.appendChild(this.buildFront());
-            article.appendChild(this.buildBody(fragment));
-            this.fixBody(fragment);
-            await this.rewriteIDs(idGenerator);
-            if (mediaPathGenerator) {
-                await this.rewriteMediaPaths(mediaPathGenerator);
-            }
-            return serializeToXML(this.document);
-        };
-        this.rewriteMediaPaths = async (mediaPathGenerator) => {
-            for (const image of this.document.querySelectorAll('figure > img')) {
-                const parentFigure = image.parentNode;
-                if (parentFigure) {
-                    const parentID = parentFigure.getAttribute('data-uuid');
-                    if (parentID) {
-                        const newSrc = await mediaPathGenerator(image, parentID);
-                        image.setAttribute('src', newSrc);
-                    }
-                }
-            }
-        };
-        this.rewriteIDs = async (idGenerator = createDefaultIdGenerator()) => {
-            const idMap = new Map();
-            for (const element of this.document.querySelectorAll('[id]')) {
-                const previousID = element.getAttribute('id');
-                if (previousID && !previousID.match(/^MP[a-z]+:[a-z0-9-]+$/i)) {
-                    continue;
-                }
-                const newID = await idGenerator(element);
-                if (newID) {
-                    element.setAttribute('id', newID);
-                    if (previousID) {
-                        const ancores = [
-                            ...this.document.querySelectorAll(`a[href="#${previousID}"]`),
-                        ];
-                        ancores.map((a) => a.setAttribute('href', `#${newID}`));
-                        element.setAttribute('data-uuid', previousID);
-                    }
-                }
-                else {
-                    element.removeAttribute('id');
-                }
-                if (previousID) {
-                    idMap.set(previousID, newID);
-                }
-            }
-            for (const node of this.document.querySelectorAll('[data-reference-ids]')) {
-                const rids = node.getAttribute('data-reference-ids');
-                if (rids) {
-                    const newRIDs = rids
-                        .split(/\s+/)
-                        .filter(Boolean)
-                        .map((previousRID) => idMap.get(previousRID))
-                        .filter(Boolean);
-                    if (newRIDs.length) {
-                        node.setAttribute('data-reference-ids', newRIDs.join(' '));
-                    }
-                }
-            }
-            for (const node of this.document.querySelectorAll('[data-reference-id]')) {
-                const rid = node.getAttribute('data-reference-id');
-                if (rid) {
-                    const newRID = idMap.get(rid);
-                    if (newRID) {
-                        node.setAttribute('data-reference-id', newRID);
-                    }
-                }
-            }
-        };
-        this.buildFront = () => {
-            const manuscript = findManuscript(this.modelMap);
-            const journal = findJournal(this.modelMap);
-            const titles = findTitles(this.modelMap);
-            if (!manuscript) {
-                throw new Error('Manuscript not found in project modelMap');
-            }
-            const front = this.document.createElement('header');
-            if (manuscript.headerFigure) {
-                const figure = this.modelMap.get(manuscript.headerFigure);
-                if (figure) {
-                    const headerFigure = document.createElement('figure');
-                    headerFigure.setAttribute('id', figure._id);
-                    front.appendChild(headerFigure);
-                    const filename = generateAttachmentFilename(figure._id, figure.contentType);
-                    const img = this.document.createElement('img');
-                    img.setAttribute('src', filename);
-                    headerFigure.appendChild(img);
-                }
-            }
-            const articleMeta = this.document.createElement('div');
-            front.appendChild(articleMeta);
-            const title = this.document.createElement('h1');
-            if (titles.title) {
-                title.innerHTML = titles.title;
-            }
-            if (journal === null || journal === void 0 ? void 0 : journal.title) {
-                title.setAttribute('data-journal', journal.title);
-            }
-            articleMeta.appendChild(title);
-            if (manuscript.DOI) {
-                const articleID = this.document.createElement('article-id');
-                articleID.setAttribute('pub-id-type', 'doi');
-                articleID.innerHTML = manuscript.DOI;
-                articleMeta.append(articleID);
-            }
-            this.buildContributors(articleMeta);
-            return front;
-        };
-        this.buildBody = (fragment) => {
-            const getModel = (id) => id ? this.modelMap.get(id) : undefined;
-            const nodes = {};
-            for (const [name, node] of Object.entries(schema.nodes)) {
-                if (node.spec.toDOM) {
-                    nodes[name] = node.spec.toDOM;
-                }
-            }
-            nodes.citation = (node) => {
-                const citationNode = node;
-                const element = this.document.createElement('span');
-                element.setAttribute('class', 'citation');
-                const rids = citationNode.attrs.rids;
-                if (rids.length) {
-                    element.setAttribute('data-reference-ids', rids.join(' '));
-                }
-                if (citationNode.attrs.contents) {
-                    element.innerHTML = citationNode.attrs.contents;
-                }
-                return element;
-            };
-            nodes.cross_reference = (node) => {
-                const xref = node;
-                const element = this.document.createElement('a');
-                element.classList.add('cross-reference');
-                element.setAttribute('data-reference-ids', xref.attrs.rids.join(' '));
-                element.textContent = xref.attrs.customLabel || xref.attrs.label;
-                return element;
-            };
-            nodes.listing = (node) => {
-                const listingNode = node;
-                const pre = this.document.createElement('pre');
-                if (listingNode.attrs.id) {
-                    pre.setAttribute('id', listingNode.attrs.id);
-                }
-                pre.classList.add('listing');
-                const code = this.document.createElement('code');
-                if (listingNode.attrs.languageKey) {
-                    code.setAttribute('data-language', listingNode.attrs.languageKey);
-                }
-                code.textContent = listingNode.attrs.contents;
-                pre.appendChild(code);
-                return pre;
-            };
-            nodes.text = (node) => node.text;
-            const marks = {};
-            for (const [name, mark] of Object.entries(schema.marks)) {
-                if (mark.spec.toDOM) {
-                    marks[name] = mark.spec.toDOM;
-                }
-            }
-            marks.styled = (mark) => {
-                const inlineStyle = getModel(mark.attrs.rid);
-                const attrs = {
-                    class: buildStyledContentClass(mark.attrs, inlineStyle),
-                };
-                return ['span', attrs];
-            };
-            nodes.comments = () => '';
-            const serializer = new DOMSerializer(nodes, marks);
-            return serializer.serializeFragment(fragment, { document });
-        };
-        this.idSelector = (id) => '#' + id.replace(/:/g, '\\:');
-        this.fixFigure = (node) => {
-            const figure = this.document.querySelector(`[id="${node.attrs.id}"]`);
-            if (figure) {
-                const filename = generateAttachmentFilename(node.attrs.id, node.attrs.contentType);
-                const img = this.document.createElement('img');
-                img.setAttribute('src', filename);
-                figure.insertBefore(img, figure.firstChild);
-            }
-        };
-        this.fixBody = (fragment) => {
-            fragment.descendants((node) => {
-                if (node.attrs.id) {
-                    const selector = this.idSelector(node.attrs.id);
-                    const element = this.document.querySelector(`${selector}`);
-                    if (element && this.labelTargets) {
-                        const target = this.labelTargets.get(node.attrs.id);
-                        if (target) {
-                            const label = this.document.createElement('label');
-                            label.textContent = target.label;
-                            element.appendChild(label);
-                        }
-                    }
-                    if (node.attrs.titleSuppressed) {
-                        const title = this.document.querySelector(`${selector} > h1`);
-                        if (title && title.parentNode) {
-                            title.parentNode.removeChild(title);
-                        }
-                    }
-                    if (node.attrs.suppressCaption) {
-                        const caption = this.document.querySelector(`${selector} > figcaption`);
-                        if (caption && caption.parentNode) {
-                            caption.parentNode.removeChild(caption);
-                        }
-                    }
-                    if (isNodeType(node, 'figure')) {
-                        this.fixFigure(node);
-                    }
-                    if (isNodeType(node, 'figure_element')) {
-                        const figureGroup = this.document.querySelector(`${selector}`);
-                        if (figureGroup) {
-                            const figures = this.document.querySelectorAll(`${selector} > figure`);
-                            const caption = this.document.querySelector(`${selector} > figcaption`);
-                            const listing = this.document.querySelector(`${selector} > pre.listing`);
-                            if (listing && !listing.textContent) {
-                                listing.remove();
-                            }
-                            if (figures.length === 1) {
-                                const [figure] = figures;
-                                figure.setAttribute('data-fig-type', 'figure');
-                                if (caption) {
-                                    figure.insertBefore(caption, figure.firstChild);
-                                }
-                                const label = this.document.querySelector(`${selector} > label`);
-                                if (label) {
-                                    figure.insertBefore(label, figure.firstChild);
-                                }
-                                if (figureGroup.parentElement) {
-                                    figureGroup.parentElement.replaceChild(figure, figureGroup);
-                                }
-                            }
-                            if (figures.length === 0 && !caption) {
-                                figureGroup.remove();
-                            }
-                        }
-                    }
-                }
-            });
-        };
-    }
-    buildContributors(articleMeta) {
-        const contributors = Array.from(this.modelMap.values()).filter(hasObjectType(ObjectTypes.Contributor));
-        const affiliationIDs = [];
-        if (contributors && contributors.length) {
-            const contribGroup = this.document.createElement('div');
-            contribGroup.classList.add('contrib-group');
-            articleMeta.appendChild(contribGroup);
-            contributors.sort((a, b) => Number(a.priority) - Number(b.priority));
-            contributors.forEach((contributor) => {
-                const contrib = this.document.createElement('span');
-                contrib.classList.add('contrib');
-                contrib.setAttribute('id', contributor._id);
-                if (contributor.isCorresponding) {
-                    contrib.setAttribute('data-corresp', 'yes');
-                }
-                const name = this.document.createElement('span');
-                name.classList.add('contrib-name');
-                contrib.appendChild(name);
-                const { given, family } = contributor.bibliographicName;
-                if (given) {
-                    const givenNames = this.document.createElement('span');
-                    givenNames.classList.add('contrib-given-names');
-                    givenNames.textContent = given;
-                    name.appendChild(givenNames);
-                }
-                if (family) {
-                    if (given) {
-                        const separator = document.createTextNode(' ');
-                        name.appendChild(separator);
-                    }
-                    const surname = this.document.createElement('span');
-                    surname.classList.add('contrib-surname');
-                    surname.textContent = family;
-                    name.appendChild(surname);
-                }
-                if (contributor.email) {
-                    const link = this.document.createElement('a');
-                    link.href = `mailto:${contributor.email}`;
-                    contrib.appendChild(link);
-                }
-                if (contributor.affiliations) {
-                    contributor.affiliations.forEach((rid) => {
-                        const link = this.document.createElement('a');
-                        link.setAttribute('data-ref-type', 'aff');
-                        link.setAttribute('href', '#' + rid);
-                        const affiliationIndex = affiliationIDs.indexOf(rid);
-                        if (affiliationIndex > -1) {
-                            link.textContent = String(affiliationIndex + 1);
-                        }
-                        else {
-                            affiliationIDs.push(rid);
-                            link.textContent = String(affiliationIDs.length);
-                        }
-                        contrib.appendChild(link);
-                    });
-                }
-                contribGroup.appendChild(contrib);
-            });
-        }
-        if (affiliationIDs.length) {
-            const affiliationList = this.document.createElement('ol');
-            affiliationList.classList.add('affiliations-list');
-            articleMeta.appendChild(affiliationList);
-            for (const affiliationID of affiliationIDs) {
-                const affiliation = this.modelMap.get(affiliationID);
-                if (affiliation) {
-                    const affiliationItem = this.document.createElement('li');
-                    affiliationItem.classList.add('affiliation');
-                    affiliationItem.setAttribute('id', affiliation._id);
-                    if (affiliation.institution) {
-                        affiliationItem.textContent = affiliation.institution;
-                    }
-                    affiliationList.appendChild(affiliationItem);
-                }
-            }
-        }
-    }
-}

package/dist/es/transformer/manuscript-dependencies.js

@@ -1,17 +0,0 @@
-var __rest = (this && this.__rest) || function (s, e) {
-    var t = {};
-    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
-        t[p] = s[p];
-    if (s != null && typeof Object.getOwnPropertySymbols === "function")
-        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
-            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
-                t[p[i]] = s[p[i]];
-        }
-    return t;
-};
-import { generateID } from './id';
-export const fromPrototype = (model) => {
-    const { _id } = model, data = __rest(model, ["_id"]);
-    const output = Object.assign(Object.assign({}, data), { prototype: _id, _id: generateID(model.objectType) });
-    return output;
-};

package/dist/es/transformer/model-map.js

@@ -1,22 +0,0 @@
-/*!
- * © 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 { generateID } from './id';
-export const addModelToMap = (modelMap) => (data) => {
-    if (!data._id) {
-        data._id = generateID(data.objectType);
-    }
-    modelMap.set(data._id, data);
-};