@manuscripts/transform 2.3.35 → 2.3.37-LEAN-3911.0

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

@@ -13,10 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { ObjectTypes, timestamp, } from '@manuscripts/json-schema';
 import mime from 'mime';
 import { DOMParser, Fragment } from 'prosemirror-model';
-import { schema } from '../../schema';
-import { chooseSectionCategory } from '../../transformer';
+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 +33,12 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
+const parsePriority = (priority) => {
+    if (!priority) {
+        return undefined;
+    }
+    return parseInt(priority);
+};
 const getEquationContent = (p) => {
     var _a;
     const element = p;
@@ -95,6 +103,174 @@ const marks = [
     },
 ];
 const nodes = [
+    {
+        tag: 'article',
+        node: 'manuscript',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                doi: element.getAttribute('DOI'),
+                articleType: element.getAttribute('article-type') || '',
+                prototype: element.getAttribute('prototype') || '',
+                primaryLanguageCode: element.getAttribute('primary-language-code') || '',
+            };
+        },
+    },
+    {
+        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-author',
+        node: 'footnote',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                kind: 'footnote',
+            };
+        },
+    },
+    {
+        tag: 'corresp',
+        node: 'corresp',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+                label: element.getAttribute('label'),
+            };
+        },
+    },
+    {
+        tag: 'contributor',
+        node: 'contributor',
+        getAttrs: (node) => {
+            const element = node;
+            const footnote = [];
+            const affiliations = [];
+            const corresp = [];
+            element.querySelectorAll('fn').forEach((fn) => {
+                const noteID = fn.getAttribute('noteID');
+                const noteLabel = fn.getAttribute('noteLabel');
+                if (noteID && noteLabel) {
+                    footnote.push({ noteID, noteLabel });
+                }
+            });
+            element.querySelectorAll('corresp').forEach((correspondence) => {
+                const correspLabel = correspondence.getAttribute('correspLabel');
+                const correspID = correspondence.getAttribute('correspID');
+                if (correspID && correspLabel) {
+                    corresp.push({ correspID, correspLabel });
+                }
+            });
+            element.querySelectorAll('aff').forEach((aff) => {
+                const affID = aff.getAttribute('affiliationID');
+                if (affID) {
+                    affiliations.push(affID);
+                }
+            });
+            const isCorrespondingEl = element.getAttribute('isCorresponding');
+            return {
+                id: element.getAttribute('id'),
+                role: 'author',
+                isCorresponding: isCorrespondingEl
+                    ? isCorrespondingEl === 'true'
+                    : undefined,
+                bibliographicName: {
+                    given: element.getAttribute('given'),
+                    family: element.getAttribute('family'),
+                    ObjectType: 'MPBibliographicName',
+                    _id: generateID(ObjectTypes.BibliographicName),
+                },
+                affiliations,
+                corresp: corresp.length ? corresp : undefined,
+                footnote: footnote.length ? footnote : undefined,
+                ORCIDIdentifier: element.getAttribute('ORCIDIdentifier'),
+                priority: parsePriority(element.getAttribute('priority')),
+            };
+        },
+        getContent: () => {
+            return Fragment.from(schema.text('_'));
+        },
+    },
+    {
+        tag: 'affiliation',
+        node: 'affiliation',
+        getAttrs: (node) => {
+            var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k;
+            const element = node;
+            const emailEl = element.querySelector('email');
+            return {
+                id: element.getAttribute('id'),
+                institution: (_a = element.getAttribute('institution')) !== null && _a !== void 0 ? _a : '',
+                department: (_b = element.getAttribute('department')) !== null && _b !== void 0 ? _b : '',
+                addressLine1: (_c = element.getAttribute('addressLine1')) !== null && _c !== void 0 ? _c : '',
+                addressLine2: (_d = element.getAttribute('addressLine2')) !== null && _d !== void 0 ? _d : '',
+                addressLine3: (_e = element.getAttribute('addressLine3')) !== null && _e !== void 0 ? _e : '',
+                postCode: (_f = element.getAttribute('postCode')) !== null && _f !== void 0 ? _f : '',
+                country: (_g = element.getAttribute('country')) !== null && _g !== void 0 ? _g : '',
+                email: emailEl
+                    ? {
+                        href: (_h = emailEl.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _h !== void 0 ? _h : '',
+                        text: (_k = (_j = emailEl.textContent) === null || _j === void 0 ? void 0 : _j.trim()) !== null && _k !== void 0 ? _k : '',
+                    }
+                    : undefined,
+                priority: parsePriority(element.getAttribute('priority')),
+            };
+        },
+        getContent: () => {
+            return Fragment.from(schema.text('_'));
+        },
+    },
     {
         tag: 'attrib',
         node: 'attribution',
@@ -103,10 +279,6 @@ const nodes = [
         tag: 'back',
         ignore: true,
     },
-    {
-        tag: 'body',
-        node: 'manuscript',
-    },
     {
         tag: 'break',
         node: 'hard_break',
@@ -126,13 +298,13 @@ 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 +495,7 @@ 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 +594,54 @@ 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',
@@ -574,4 +794,4 @@ const nodes = [
         },
     },
 ];
-export const jatsBodyDOMParser = new DOMParser(schema, [...marks, ...nodes]);
+export const jatsDOMParser = new DOMParser(schema, [...marks, ...nodes]);

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

@@ -0,0 +1,259 @@
+/*!
+ * © 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.
+ * 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 { getTrimmedTextContent } from '../../lib/utils';
+import { generateID } from '../../transformer';
+import { htmlFromJatsNode } from './jats-parser-utils';
+export const defaultTitle = 'Untitled Manuscript';
+export const jatsFrontTransformations = {
+    setArticleAttrs(doc, template) {
+        var _a;
+        const doi = (_a = doc.querySelector('article-meta > article-id[pub-id-type="doi"]')) === null || _a === void 0 ? void 0 : _a.textContent;
+        const Attrs = {
+            DOI: doi !== null && doi !== void 0 ? doi : '',
+            prototype: template !== null && template !== void 0 ? template : '',
+            id: generateID(ObjectTypes.Manuscript),
+        };
+        Object.entries(Attrs).forEach(([key, value]) => {
+            var _a;
+            if (value) {
+                (_a = doc.querySelector('article')) === null || _a === void 0 ? void 0 : _a.setAttribute(key, value);
+            }
+        });
+    },
+    createTitle(front, createElement) {
+        var _a;
+        let title = front.querySelector('article-meta > title-group > article-title');
+        if (title) {
+            title.innerHTML = (_a = htmlFromJatsNode(title, createElement)) !== null && _a !== void 0 ? _a : defaultTitle;
+        }
+        else {
+            title = createElement('article-title');
+            title.textContent = defaultTitle;
+        }
+        return title;
+    },
+    createAuthorNotes(document, createElement) {
+        const authornotes = document.querySelector('article-meta > author-notes');
+        if (!authornotes) {
+            return;
+        }
+        const authorNotesEl = createElement('author-notes');
+        authornotes
+            .querySelectorAll('fn:not([fn-type]), :scope > p, corresp')
+            .forEach((node) => {
+            switch (node.nodeName) {
+                case 'fn': {
+                    this.appendFootnote(node, authorNotesEl, createElement);
+                    break;
+                }
+                case 'p': {
+                    this.appendParagraph(document, node, authorNotesEl);
+                    break;
+                }
+                case 'corresp': {
+                    this.appendCorresp(node, authorNotesEl, createElement);
+                    break;
+                }
+            }
+        });
+        return authorNotesEl;
+    },
+    appendFootnote(node, element, createElement) {
+        const fnEl = createElement('fn-author');
+        fnEl.innerHTML = node.innerHTML;
+        fnEl.setAttribute('kind', 'footnote');
+        const id = node.getAttribute('id');
+        if (id) {
+            fnEl.setAttribute('id', id);
+        }
+        element.append(fnEl);
+    },
+    appendParagraph(document, node, element) {
+        const pEl = document.createElementNS(null, 'p');
+        pEl.innerHTML = node.innerHTML;
+        element.append(pEl);
+    },
+    appendCorresp(node, element, createElement) {
+        var _a, _b;
+        const correspEl = createElement('corresp');
+        const label = node.querySelector('label');
+        if (label) {
+            label.remove();
+        }
+        correspEl.textContent = ((_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '';
+        correspEl.setAttribute('label', ((_b = label === null || label === void 0 ? void 0 : label.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '');
+        const id = node.getAttribute('id');
+        if (id) {
+            correspEl.setAttribute('id', id);
+        }
+        element.append(correspEl);
+    },
+    createContributors(front, createElement) {
+        const contribs = front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]');
+        const contributors = createElement('contributors');
+        contribs.forEach((element, priority) => {
+            const contributor = this.createContributorElement(priority, createElement);
+            this.setNameAttrs(element, contributor);
+            this.setOrcidAttribute(element, contributor);
+            this.setIsCorrespondingAttribute(element, contributor);
+            this.setContributorReferences(element, contributor, createElement);
+            contributors.append(contributor);
+        });
+        return contributors;
+    },
+    createContributorElement(priority, createElement) {
+        const contributor = createElement('contributor');
+        contributor.setAttribute('priority', priority.toString());
+        contributor.setAttribute('role', 'author');
+        return contributor;
+    },
+    setNameAttrs(node, element) {
+        const given = getTrimmedTextContent(node, 'name > given-names');
+        if (given) {
+            element.setAttribute('given', given);
+        }
+        const surname = getTrimmedTextContent(node, 'name > surname');
+        if (surname) {
+            element.setAttribute('family', surname);
+        }
+    },
+    setOrcidAttribute(node, element) {
+        const orcid = getTrimmedTextContent(node, 'contrib-id[contrib-id-type="orcid"]');
+        if (orcid) {
+            element.setAttribute('ORCIDIdentifier', orcid);
+        }
+    },
+    setIsCorrespondingAttribute(node, element) {
+        const isCorresponding = node.getAttribute('corresp') === 'yes';
+        if (isCorresponding) {
+            element.setAttribute('isCorresponding', isCorresponding.toString());
+        }
+    },
+    setContributorReferences(node, element, createElement) {
+        const xrefs = node.querySelectorAll('xref');
+        const footnotes = createElement('fns');
+        const corresps = createElement('corresps');
+        const affs = createElement('affs');
+        xrefs.forEach((xref) => {
+            const rid = xref.getAttribute('rid');
+            const type = xref.getAttribute('ref-type');
+            if (rid) {
+                switch (type) {
+                    case 'fn':
+                        this.appendFootnoteID(xref, footnotes, rid, createElement);
+                        break;
+                    case 'corresp':
+                        this.appendCorrespID(xref, corresps, rid, createElement);
+                        break;
+                    case 'aff':
+                        this.appendAffiliationID(affs, rid, createElement);
+                        break;
+                }
+            }
+        });
+        element.append(footnotes, corresps, affs);
+    },
+    appendFootnoteID(xref, footnotes, rid, createElement) {
+        var _a;
+        const fn = createElement('fn');
+        fn.setAttribute('noteID', rid);
+        fn.setAttribute('noteLabel', ((_a = xref.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '');
+        footnotes.append(fn);
+    },
+    appendCorrespID(xref, corresps, rid, createElement) {
+        var _a;
+        const corresp = createElement('corresp');
+        corresp.setAttribute('correspID', rid);
+        corresp.setAttribute('correspLabel', ((_a = xref.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '');
+        corresps.append(corresp);
+    },
+    appendAffiliationID(affs, rid, createElement) {
+        const rids = rid.split(/\s+/).filter(Boolean);
+        if (rids.length) {
+            rids.forEach((affID) => {
+                const aff = createElement('aff');
+                aff.setAttribute('affiliationID', affID);
+                affs.append(aff);
+            });
+        }
+    },
+    createAffiliations(front, createElement) {
+        const affiliations = front.querySelectorAll('article-meta > contrib-group > aff');
+        const affiliationGroup = createElement('affiliations');
+        affiliations.forEach((element, priority) => {
+            const affiliation = this.createAffiliationElement(element, priority, createElement);
+            this.setInstitutionAttrs(element, affiliation);
+            this.setAddressAttrs(element, affiliation);
+            this.appendEmail(element, affiliation);
+            affiliationGroup.append(affiliation);
+        });
+        return affiliationGroup;
+    },
+    createAffiliationElement(element, priority, createElement) {
+        const affiliation = createElement('affiliation');
+        affiliation.setAttribute('priority', priority.toString());
+        const id = element.getAttribute('id');
+        if (id) {
+            affiliation.setAttribute('id', id);
+        }
+        return affiliation;
+    },
+    appendEmail(element, affiliation) {
+        const emailEl = element.querySelector('email');
+        if (emailEl) {
+            affiliation.appendChild(emailEl);
+        }
+    },
+    setInstitutionAttrs(element, affiliation) {
+        var _a;
+        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') {
+                affiliation.setAttribute('department', content);
+            }
+            else {
+                affiliation.setAttribute('institution', content);
+            }
+        }
+    },
+    setAddressAttrs(element, affiliation) {
+        const addressLine1 = getTrimmedTextContent(element, 'addr-line:nth-of-type(1)');
+        const addressLine2 = getTrimmedTextContent(element, 'addr-line:nth-of-type(2)');
+        const addressLine3 = getTrimmedTextContent(element, 'addr-line:nth-of-type(3)');
+        const postCode = getTrimmedTextContent(element, 'postal-code');
+        const country = getTrimmedTextContent(element, 'country');
+        if (addressLine1) {
+            affiliation.setAttribute('addressLine1', addressLine1);
+        }
+        if (addressLine2) {
+            affiliation.setAttribute('addressLine2', addressLine2);
+        }
+        if (addressLine3) {
+            affiliation.setAttribute('addressLine3', addressLine3);
+        }
+        if (postCode) {
+            affiliation.setAttribute('postCode', postCode);
+        }
+        if (country) {
+            affiliation.setAttribute('country', country);
+        }
+    },
+};

package/dist/es/jats/importer/jats-journal-meta-parser.js

@@ -13,7 +13,9 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { ObjectTypes } from '@manuscripts/json-schema';
 import { getTrimmedTextContent } from '../../lib/utils';
+import { generateID } from '../../transformer';
 export const parseJournalIdentifiers = (element) => {
     var _a;
     if (!element) {
@@ -84,3 +86,7 @@ export const parseJournalMeta = (element) => {
         title: (_b = getTrimmedTextContent(element, 'journal-title-group > journal-title')) !== null && _b !== void 0 ? _b : undefined,
     };
 };
+export const parseJournal = (element) => {
+    const meta = parseJournalMeta(element);
+    return Object.assign(Object.assign({}, meta), { _id: generateID(ObjectTypes.Journal), objectType: ObjectTypes.Journal });
+};

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

@@ -14,24 +14,38 @@
  * limitations under the License.
  */
 import { v4 as uuidv4 } from 'uuid';
-import { schema } from '../../schema';
+import { schema, } from '../../schema';
 import { generateID, nodeTypesMap } from '../../transformer';
 export const updateDocumentIDs = (node, replacements) => {
     const warnings = [];
-    recurseDoc(node, (n) => updateNodeID(n, replacements, warnings));
+    const highlightNodes = [];
+    recurseDoc(node, (n, parent) => updateNodeID(n, parent, replacements, warnings, highlightNodes));
     recurseDoc(node, (n) => updateNodeRID(n, replacements, warnings));
     recurseDoc(node, (n) => updateNodeRIDS(n, replacements, warnings));
+    recurseDoc(node, (n) => updateContributorNodesIDS(n, replacements, warnings));
     return warnings;
 };
-function recurseDoc(node, fn) {
-    fn(node);
-    node.descendants((n) => fn(n));
+function recurseDoc(node, fn, parent = null) {
+    fn(node, parent);
+    node.descendants((n, pos, parent) => fn(n, parent));
 }
-const updateNodeID = (node, replacements, warnings) => {
+const updateNodeID = (node, parent, replacements, warnings, highlightNodes) => {
     if (node.type === schema.nodes.inline_equation) {
         node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `InlineMathFragment:${uuidv4()}` });
         return;
     }
+    if (node.type === schema.nodes.highlight_marker) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { tid: parent === null || parent === void 0 ? void 0 : parent.attrs.id });
+        highlightNodes.push(node);
+        return;
+    }
+    if (node.type === schema.nodes.comment) {
+        const highlightNode = highlightNodes.find((n) => n.attrs.id === node.attrs.id);
+        if (highlightNode) {
+            node.attrs = Object.assign(Object.assign({}, node.attrs), { target: highlightNode.attrs.tid });
+        }
+        return;
+    }
     if (node.type === schema.nodes.general_table_footnote) {
         node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `GeneralTableFootnote:${uuidv4()}` });
         return;
@@ -74,6 +88,26 @@ const updateNodeRIDS = (node, replacements, warnings) => {
     }
     node.attrs = Object.assign(Object.assign({}, node.attrs), { rids: previousRIDs.map((r) => replacements.get(r) || r) });
 };
+const updateContributorNodesIDS = (node, replacements, warnings) => {
+    var _a, _b;
+    if (node.type === schema.nodes.contributor) {
+        const footnote = (_a = node.attrs.footnote) === null || _a === void 0 ? void 0 : _a.map((fn) => {
+            return Object.assign(Object.assign({}, fn), { noteID: replacements.get(fn.noteID) });
+        });
+        const corresp = (_b = node.attrs.corresp) === null || _b === void 0 ? void 0 : _b.map((corresp) => {
+            return Object.assign(Object.assign({}, corresp), { correspID: replacements.get(corresp.correspID) });
+        });
+        const affiliations = node.attrs.affiliations.map((affiliation) => {
+            return replacements.get(affiliation);
+        });
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { footnote,
+            corresp,
+            affiliations });
+    }
+    if (node.type !== schema.nodes.contributors) {
+        return false;
+    }
+};
 const JATS_TO_HTML_MAPPING = new Map([
     ['bold', 'b'],
     ['italic', 'i'],