@manuscripts/transform 2.3.37 → 2.3.38-LEAN-3911.0

package/dist/es/jats/{jats-versions.js → exporter/jats-versions.js}

@@ -27,7 +27,6 @@ const versions = {
         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}`);

package/dist/es/{transformer → jats/exporter}/labels.js

@@ -13,8 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { schema } from '../schema';
-import { nodeNames } from './node-names';
+import { schema, } from '../../schema';
+import { nodeNames } from '../../transformer/node-names';
 const labelledNodeTypes = [
     schema.nodes.figure_element,
     schema.nodes.table_element,
@@ -25,7 +25,7 @@ const excludedTypes = [schema.nodes.graphical_abstract_section];
 const chooseLabel = (nodeType) => {
     return nodeNames.get(nodeType);
 };
-export const buildTargets = (fragment) => {
+export const buildTargets = (node) => {
     const counters = {};
     for (const nodeType of labelledNodeTypes) {
         counters[nodeType.name] = {
@@ -39,7 +39,7 @@ export const buildTargets = (fragment) => {
         return `${counter.label} ${counter.index}`;
     };
     const targets = new Map();
-    fragment.descendants((node, pos, parent) => {
+    node.descendants((node, pos, parent) => {
         var _a;
         if (node.type.name in counters) {
             if (parent && excludedTypes.includes(parent.type)) {

package/dist/es/{transformer/filename.js → jats/importer/create-article-node.js}

@@ -1,5 +1,5 @@
 /*!
- * © 2019 Atypon Systems LLC
+ * © 2024 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.
@@ -13,11 +13,12 @@
  * 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;
+import { defaultTitle } from '../../lib/deafults';
+import { schema } from '../../schema';
+export const createArticleNode = (attrs) => {
+    const title = schema.nodes.title.createChecked({}, schema.text(defaultTitle));
+    if (!attrs.id) {
+        throw new Error('Manuscript ID is missing');
     }
-    const [, mimeSubType] = contentType.split('/');
-    return `${basename}.${mimeSubType}`;
+    return schema.nodes.manuscript.createAndFill(attrs, title);
 };

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

@@ -299,4 +299,77 @@ export const jatsBodyTransformations = {
             body.prepend(section);
         }
     },
+    moveReferencesToBackmatter(body, references, createElement) {
+        const backmatter = body.querySelector('sec[sec-type="backmatter"]');
+        if (!references || !references.items.size || !backmatter) {
+            return;
+        }
+        const bibliographySection = this.createBibliographySection(createElement);
+        const bibliographyElement = createElement('bibliography-element');
+        references.getBibliographyItems().forEach((item) => {
+            const bibliographyItem = this.createBibliographyItem(item, createElement);
+            bibliographyElement.appendChild(bibliographyItem);
+        });
+        bibliographySection.appendChild(bibliographyElement);
+        backmatter.appendChild(bibliographySection);
+    },
+    createBibliographySection(createElement) {
+        const section = createElement('sec');
+        section.setAttribute('sec-type', 'bibliography_section');
+        const title = createElement('title');
+        title.textContent = 'References';
+        section.appendChild(title);
+        return section;
+    },
+    createBibliographyItem(item, createElement) {
+        var _a, _b, _c;
+        const bibliographyItem = createElement('bibliography-item');
+        bibliographyItem.setAttribute('id', item.id);
+        bibliographyItem.setAttribute('type', item.type);
+        (_a = item.author) === null || _a === void 0 ? void 0 : _a.forEach((author) => {
+            const authorElement = createElement('author');
+            authorElement.setAttribute('id', author._id);
+            authorElement.setAttribute('family', author.family || '');
+            authorElement.setAttribute('given', author.given || '');
+            bibliographyItem.appendChild(authorElement);
+        });
+        if (item.issued) {
+            const issuedEl = createElement('issued');
+            issuedEl.setAttribute('id', ((_b = item.issued) === null || _b === void 0 ? void 0 : _b._id) || '');
+            const dateParts = item.issued['date-parts'];
+            const year = (_c = dateParts === null || dateParts === void 0 ? void 0 : dateParts[0]) === null || _c === void 0 ? void 0 : _c[0];
+            if (year) {
+                issuedEl.setAttribute('year', year.toString());
+            }
+            bibliographyItem.appendChild(issuedEl);
+        }
+        if (item.containerTitle) {
+            bibliographyItem.setAttribute('containerTitle', item.containerTitle);
+        }
+        if (item.volume) {
+            bibliographyItem.setAttribute('volume', item.volume.toString());
+        }
+        if (item.issue) {
+            bibliographyItem.setAttribute('issue', item.issue.toString());
+        }
+        if (item.supplement) {
+            bibliographyItem.setAttribute('supplement', item.supplement);
+        }
+        if (item.page) {
+            bibliographyItem.setAttribute('page', item.page.toString());
+        }
+        if (item.title) {
+            bibliographyItem.setAttribute('title', item.title);
+        }
+        if (item.literal) {
+            bibliographyItem.setAttribute('literal', item.literal);
+        }
+        if (item.doi) {
+            bibliographyItem.setAttribute('DOI', item.doi);
+        }
+        if (item.literal) {
+            bibliographyItem.setAttribute('literal', item.literal);
+        }
+        return bibliographyItem;
+    },
 };

package/dist/es/jats/importer/jats-comments.js

@@ -13,9 +13,9 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { v4 as uuidv4 } from 'uuid';
-import { buildComment, buildContribution, highlightableFields, isHighlightableModel, isKeyword, } from '../../transformer';
-const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
+import { ObjectTypes } from '@manuscripts/json-schema';
+import { generateID } from '../../transformer';
+export const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
 export const isJATSComment = (node) => {
     return (node.nodeType === node.PROCESSING_INSTRUCTION_NODE &&
         node.nodeName === 'AuthorQuery');
@@ -23,34 +23,33 @@ export const isJATSComment = (node) => {
 export const parseJATSComment = (node) => {
     const text = node.textContent;
     if (text) {
-        const id = /id="(.+)"/.exec(text);
         const queryText = /queryText="(.+)"/.exec(text);
-        if (id && queryText) {
+        if (queryText) {
+            const parentNode = node.parentNode;
+            const index = parentNode.outerHTML.indexOf(queryText[1]);
             return {
-                id: id[1],
+                id: generateID(ObjectTypes.CommentAnnotation),
                 text: queryText[1],
+                index,
             };
         }
     }
 };
 export const markComments = (doc) => {
-    const marks = [];
+    var _a;
     const root = doc.getRootNode();
     const queue = [root];
+    const commentsElement = doc.createElement('comments-annotations');
     while (queue.length !== 0) {
         const node = queue.shift();
         if (node) {
             if (isJATSComment(node)) {
                 const comment = parseJATSComment(node);
                 if (comment) {
-                    const token = addMark(doc, node);
-                    if (token) {
-                        const mark = {
-                            token,
-                            comment,
-                        };
-                        marks.push(mark);
-                    }
+                    const highlightMarker = createHighlightMarkerElement(doc, comment.id);
+                    (_a = node.parentNode) === null || _a === void 0 ? void 0 : _a.insertBefore(highlightMarker, node);
+                    const commentElement = createCommentElement(doc, comment);
+                    commentsElement.appendChild(commentElement);
                 }
             }
             node.childNodes.forEach((child) => {
@@ -58,93 +57,19 @@ export const markComments = (doc) => {
             });
         }
     }
-    return marks;
-};
-const addMark = (doc, node) => {
-    const parent = node.parentElement;
-    if (parent) {
-        const token = uuidv4();
-        const tokenNode = doc.createTextNode(token);
-        parent.insertBefore(tokenNode, node);
-        return token;
-    }
-};
-export const createComments = (models, marks) => {
-    const comments = [];
-    for (const model of models) {
-        if (isHighlightableModel(model)) {
-            comments.push(...processModel(model, marks));
-        }
-        else if (isKeyword(model)) {
-            comments.push(...processKeyword(model, marks));
-        }
+    if (commentsElement.hasChildNodes()) {
+        doc.documentElement.appendChild(commentsElement);
     }
-    return comments;
-};
-const getFieldMarks = (content, marks) => {
-    return marks
-        .filter((m) => content.indexOf(m.token) >= 0)
-        .sort((a, b) => content.indexOf(a.token) - content.indexOf(b.token));
 };
-const processModel = (model, marks) => {
-    const comments = [];
-    for (const field of highlightableFields) {
-        const content = model[field];
-        if (!content) {
-            continue;
-        }
-        const results = processContent(model, content, getFieldMarks(content, marks));
-        model[field] = results.content;
-        comments.push(...results.comments);
-    }
-    return comments;
+const createHighlightMarkerElement = (doc, id) => {
+    const highlightMarker = doc.createElement('highlight-marker');
+    highlightMarker.setAttribute('id', id);
+    highlightMarker.setAttribute('position', 'point');
+    return highlightMarker;
 };
-const processKeyword = (model, marks) => {
-    const comments = [];
-    const name = model.name;
-    let content = name;
-    for (const mark of getFieldMarks(name, marks)) {
-        content = name.replace(mark.token, '');
-        const target = model.containedGroup;
-        if (!target) {
-            continue;
-        }
-        const contributions = [buildContribution(DEFAULT_PROFILE_ID)];
-        const comment = buildComment(target, mark.comment.text, undefined, contributions);
-        model.name = content;
-        comments.push(comment);
-    }
-    return comments;
-};
-const processContent = (model, content, marks) => {
-    const comments = [];
-    let result = content;
-    for (const mark of marks) {
-        const token = mark.token;
-        const index = result.indexOf(token);
-        result = result.replace(token, '');
-        const contributions = [buildContribution(DEFAULT_PROFILE_ID)];
-        const selector = {
-            from: index,
-            to: index,
-        };
-        const comment = buildComment(model._id, mark.comment.text, selector, contributions);
-        comments.push(comment);
-    }
-    return {
-        content: result,
-        comments,
-    };
-};
-export const createReferenceComments = (references) => {
-    const comments = [];
-    for (const item of references.getBibliographyItems()) {
-        const id = item._id;
-        for (const comment of references.getComments(id)) {
-            const contributions = [buildContribution(DEFAULT_PROFILE_ID)];
-            const c = buildComment(id, comment.text, undefined, contributions);
-            comments.push(c);
-        }
-    }
-    return comments;
+const createCommentElement = (doc, comment) => {
+    const commentElement = doc.createElement('comment-annotation');
+    commentElement.setAttribute('id', comment.id);
+    commentElement.textContent = comment.text;
+    return commentElement;
 };

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

@@ -13,10 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { ObjectTypes } from '@manuscripts/json-schema';
 import mime from 'mime';
 import { DOMParser, Fragment } from 'prosemirror-model';
-import { schema } from '../../schema';
-import { chooseSectionCategory } from '../../transformer';
+import { getTrimmedTextContent, timestamp } from '../../lib/utils';
+import { schema, } from '../../schema';
+import { chooseSectionCategory, generateID } from '../../transformer';
+import { DEFAULT_PROFILE_ID } from './jats-comments';
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const chooseContentType = (graphicNode) => {
     if (graphicNode) {
@@ -31,6 +34,12 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
+const parsePriority = (priority) => {
+    if (!priority) {
+        return undefined;
+    }
+    return parseInt(priority);
+};
 const getEquationContent = (p) => {
     var _a;
     const element = p;
@@ -95,6 +104,224 @@ const marks = [
     },
 ];
 const nodes = [
+    {
+        tag: 'article',
+        node: 'manuscript',
+        getAttrs: (node) => {
+            var _a, _b, _c, _d;
+            const element = node;
+            return {
+                doi: (_a = element.getAttribute('DOI')) !== null && _a !== void 0 ? _a : '',
+                articleType: (_b = element.getAttribute('article-type')) !== null && _b !== void 0 ? _b : '',
+                prototype: (_c = element.getAttribute('prototype')) !== null && _c !== void 0 ? _c : '',
+                primaryLanguageCode: (_d = element.getAttribute('primary-language-code')) !== null && _d !== void 0 ? _d : '',
+            };
+        },
+    },
+    {
+        tag: 'article-title',
+        node: 'title',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'highlight-marker',
+        node: 'highlight_marker',
+        getAttrs: (node) => {
+            var _a;
+            const element = node;
+            const id = element.getAttribute('id');
+            return {
+                id: id,
+                position: (_a = element.getAttribute('position')) !== null && _a !== void 0 ? _a : '',
+            };
+        },
+    },
+    {
+        tag: 'comment-annotation',
+        node: 'comment',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                contents: element.textContent,
+                contributions: [
+                    {
+                        _id: generateID(ObjectTypes.Contribution),
+                        objecType: ObjectTypes.Contribution,
+                        profileID: DEFAULT_PROFILE_ID,
+                        timestamp: timestamp(),
+                    },
+                ],
+            };
+        },
+    },
+    {
+        tag: 'author-notes',
+        node: 'author_notes',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'fn:not([fn-type])',
+        node: 'footnote',
+        context: 'author_notes/',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                kind: 'footnote',
+            };
+        },
+    },
+    {
+        tag: 'corresp',
+        node: 'corresp',
+        getAttrs: (node) => {
+            var _a;
+            const element = node;
+            const label = element.querySelector('label');
+            if (label) {
+                label.remove();
+            }
+            return {
+                id: element.getAttribute('id'),
+                label: (_a = label === null || label === void 0 ? void 0 : label.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
+            };
+        },
+        getContent: (node) => {
+            var _a;
+            const element = node;
+            return Fragment.from(schema.text(((_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || ''));
+        },
+    },
+    {
+        tag: 'contrib[contrib-type="author"]',
+        node: 'contributor',
+        getAttrs: (node) => {
+            var _a, _b;
+            const element = node;
+            const footnote = [];
+            const affiliations = [];
+            const corresp = [];
+            const xrefs = element.querySelectorAll('xref');
+            for (const xref of xrefs) {
+                const rid = xref.getAttribute('rid');
+                const type = xref.getAttribute('ref-type');
+                if (!rid) {
+                    continue;
+                }
+                switch (type) {
+                    case 'fn':
+                        footnote.push({
+                            noteID: rid,
+                            noteLabel: ((_a = xref.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '',
+                        });
+                        break;
+                    case 'corresp':
+                        corresp.push({
+                            correspID: rid,
+                            correspLabel: ((_b = xref.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '',
+                        });
+                        break;
+                    case 'aff':
+                        affiliations.push(rid);
+                        break;
+                }
+            }
+            return {
+                id: element.getAttribute('id'),
+                role: 'author',
+                affiliations,
+                corresp,
+                footnote,
+                isCorresponding: element.getAttribute('corresp')
+                    ? element.getAttribute('corresp') === 'yes'
+                    : undefined,
+                bibliographicName: {
+                    given: getTrimmedTextContent(element, 'name > given-names'),
+                    family: getTrimmedTextContent(element, 'name > surname'),
+                    ObjectType: ObjectTypes.BibliographicName,
+                    _id: generateID(ObjectTypes.BibliographicName),
+                },
+                ORCIDIdentifier: getTrimmedTextContent(element, 'contrib-id[contrib-id-type="orcid"]'),
+                priority: parsePriority(element.getAttribute('priority')),
+            };
+        },
+        getContent: () => {
+            return Fragment.from(schema.text('_'));
+        },
+    },
+    {
+        tag: 'affiliations',
+        node: 'affiliations',
+    },
+    {
+        tag: 'aff',
+        node: 'affiliation',
+        context: 'affiliations/',
+        getAttrs: (node) => {
+            var _a, _b;
+            const element = node;
+            const getEmail = (element) => {
+                var _a, _b, _c;
+                const email = element.querySelector('email');
+                if (email) {
+                    return {
+                        href: (_a = email.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _a !== void 0 ? _a : '',
+                        text: (_c = (_b = email.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '',
+                    };
+                }
+            };
+            const getInstitutionDetails = (element) => {
+                var _a;
+                let department = '';
+                let institution = '';
+                for (const node of element.querySelectorAll('institution')) {
+                    const content = (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim();
+                    if (!content) {
+                        continue;
+                    }
+                    const type = node.getAttribute('content-type');
+                    if (type === 'dept') {
+                        department = content;
+                    }
+                    else {
+                        institution = content;
+                    }
+                }
+                return { department, institution };
+            };
+            const getAddressLine = (element, index) => {
+                return (getTrimmedTextContent(element, `addr-line:nth-of-type(${index})`) ||
+                    '');
+            };
+            const { department, institution } = getInstitutionDetails(element);
+            return {
+                id: element.getAttribute('id'),
+                institution: institution !== null && institution !== void 0 ? institution : '',
+                department: department !== null && department !== void 0 ? department : '',
+                addressLine1: getAddressLine(element, 1),
+                addressLine2: getAddressLine(element, 2),
+                addressLine3: getAddressLine(element, 3),
+                postCode: (_a = getTrimmedTextContent(element, 'postal-code')) !== null && _a !== void 0 ? _a : '',
+                country: (_b = getTrimmedTextContent(element, 'country')) !== null && _b !== void 0 ? _b : '',
+                email: getEmail(element),
+                priority: parsePriority(element.getAttribute('priority')),
+            };
+        },
+        getContent: () => {
+            return Fragment.from(schema.text('_'));
+        },
+    },
     {
         tag: 'attrib',
         node: 'attribution',
@@ -103,10 +330,6 @@ const nodes = [
         tag: 'back',
         ignore: true,
     },
-    {
-        tag: 'body',
-        node: 'manuscript',
-    },
     {
         tag: 'break',
         node: 'hard_break',
@@ -126,13 +349,13 @@ const nodes = [
             const title = element.querySelector('title');
             if (title) {
                 const captionTitle = schema.nodes.caption_title.create();
-                content.push(jatsBodyDOMParser.parse(title, { topNode: captionTitle }));
+                content.push(jatsDOMParser.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 }));
+                    content.push(jatsDOMParser.parse(paragraph, { topNode: figcaption }));
                 }
             }
             return Fragment.from(content);
@@ -323,7 +546,7 @@ const nodes = [
             const paragraphs = [];
             node.childNodes.forEach((p) => {
                 const paragraph = schema.nodes.paragraph.create();
-                const content = jatsBodyDOMParser.parse(p, {
+                const content = jatsDOMParser.parse(p, {
                     topNode: paragraph,
                 });
                 paragraphs.push(content);
@@ -422,6 +645,54 @@ const nodes = [
         tag: 'sec[sec-type="backmatter"]',
         node: 'backmatter',
     },
+    {
+        tag: 'bibliography-element',
+        node: 'bibliography_element',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
+    {
+        tag: 'bibliography-item',
+        node: 'bibliography_item',
+        getAttrs: (node) => {
+            const element = node;
+            const authors = [];
+            element.querySelectorAll('author').forEach((author) => {
+                authors.push({
+                    _id: author.getAttribute('id') || '',
+                    given: author.getAttribute('given') || '',
+                    family: author.getAttribute('family') || '',
+                    objectType: 'MPBibliographicName',
+                });
+            });
+            const issuedEl = element.querySelector('issued');
+            const issued = issuedEl
+                ? {
+                    objectType: 'MPBibliographicDate',
+                    _id: issuedEl.getAttribute('id'),
+                    'date-parts': [[issuedEl.getAttribute('year')]],
+                }
+                : undefined;
+            return {
+                id: element.getAttribute('id'),
+                type: element.getAttribute('type'),
+                containerTitle: element.getAttribute('container-title'),
+                volume: element.getAttribute('volume'),
+                issue: element.getAttribute('issue'),
+                supplement: element.getAttribute('supplement'),
+                page: element.getAttribute('page'),
+                title: element.getAttribute('title'),
+                literal: element.getAttribute('literal'),
+                author: authors,
+                issued,
+                DOI: element.getAttribute('DOI'),
+            };
+        },
+    },
     {
         tag: 'sec',
         node: 'section',
@@ -492,7 +763,7 @@ const nodes = [
     {
         tag: 'title',
         node: 'section_title',
-        context: 'section/|footnotes_section/|bibliography_section/|keywords/|supplements/',
+        context: 'section/|footnotes_section/|bibliography_section/|keywords/|supplements/|author_notes/',
     },
     {
         tag: 'title',
@@ -574,4 +845,4 @@ const nodes = [
         },
     },
 ];
-export const jatsBodyDOMParser = new DOMParser(schema, [...marks, ...nodes]);
+export const jatsDOMParser = new DOMParser(schema, [...marks, ...nodes]);