@manuscripts/transform 2.3.35 → 2.3.37-LEAN-3911.0

package/dist/cjs/jats/importer/create-article-node.js

@@ -0,0 +1,31 @@
+"use strict";
+/*!
+ * © 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.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createArticleNode = void 0;
+const schema_1 = require("../../schema");
+const jats_front_transformations_1 = require("./jats-front-transformations");
+const createArticleNode = (manuscript) => {
+    const title = schema_1.schema.nodes.title.createChecked({}, schema_1.schema.text(jats_front_transformations_1.defaultTitle));
+    return schema_1.schema.nodes.manuscript.createAndFill({
+        id: manuscript._id,
+        doi: manuscript.DOI,
+        articleType: manuscript.articleType,
+        prototype: manuscript.prototype,
+        primaryLanguageCode: manuscript.primaryLanguageCode,
+    }, title);
+};
+exports.createArticleNode = createArticleNode;

package/dist/cjs/jats/importer/index.js

@@ -15,8 +15,8 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseJATSArticle = exports.parseJATSBody = exports.parseJATSFront = void 0;
+exports.parseJATSArticle = exports.createArticleNode = void 0;
+var create_article_node_1 = require("./create-article-node");
+Object.defineProperty(exports, "createArticleNode", { enumerable: true, get: function () { return create_article_node_1.createArticleNode; } });
 var parse_jats_article_1 = require("./parse-jats-article");
-Object.defineProperty(exports, "parseJATSFront", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSFront; } });
-Object.defineProperty(exports, "parseJATSBody", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSBody; } });
 Object.defineProperty(exports, "parseJATSArticle", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSArticle; } });

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

@@ -302,4 +302,74 @@ exports.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);
+        }
+        return bibliographyItem;
+    },
 };

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

@@ -15,10 +15,10 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createReferenceComments = exports.createComments = exports.markComments = exports.parseJATSComment = exports.isJATSComment = void 0;
-const uuid_1 = require("uuid");
+exports.markComments = exports.parseJATSComment = exports.isJATSComment = exports.DEFAULT_PROFILE_ID = void 0;
+const json_schema_1 = require("@manuscripts/json-schema");
 const transformer_1 = require("../../transformer");
-const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
+exports.DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
 const isJATSComment = (node) => {
     return (node.nodeType === node.PROCESSING_INSTRUCTION_NODE &&
         node.nodeName === 'AuthorQuery');
@@ -27,35 +27,34 @@ exports.isJATSComment = isJATSComment;
 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: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.CommentAnnotation),
                 text: queryText[1],
+                index,
             };
         }
     }
 };
 exports.parseJATSComment = parseJATSComment;
 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 ((0, exports.isJATSComment)(node)) {
                 const comment = (0, exports.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) => {
@@ -63,96 +62,20 @@ const markComments = (doc) => {
             });
         }
     }
-    return marks;
-};
-exports.markComments = markComments;
-const addMark = (doc, node) => {
-    const parent = node.parentElement;
-    if (parent) {
-        const token = (0, uuid_1.v4)();
-        const tokenNode = doc.createTextNode(token);
-        parent.insertBefore(tokenNode, node);
-        return token;
+    if (commentsElement.hasChildNodes()) {
+        doc.documentElement.appendChild(commentsElement);
     }
 };
-const createComments = (models, marks) => {
-    const comments = [];
-    for (const model of models) {
-        if ((0, transformer_1.isHighlightableModel)(model)) {
-            comments.push(...processModel(model, marks));
-        }
-        else if ((0, transformer_1.isKeyword)(model)) {
-            comments.push(...processKeyword(model, marks));
-        }
-    }
-    return comments;
-};
-exports.createComments = createComments;
-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 transformer_1.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 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 = [(0, transformer_1.buildContribution)(DEFAULT_PROFILE_ID)];
-        const comment = (0, transformer_1.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 = [(0, transformer_1.buildContribution)(DEFAULT_PROFILE_ID)];
-        const selector = {
-            from: index,
-            to: index,
-        };
-        const comment = (0, transformer_1.buildComment)(model._id, mark.comment.text, selector, contributions);
-        comments.push(comment);
-    }
-    return {
-        content: result,
-        comments,
-    };
+exports.markComments = markComments;
+const createHighlightMarkerElement = (doc, id) => {
+    const highlightMarker = doc.createElement('highlight-marker');
+    highlightMarker.setAttribute('id', id);
+    highlightMarker.setAttribute('position', 'point');
+    return highlightMarker;
 };
-const createReferenceComments = (references) => {
-    const comments = [];
-    for (const item of references.getBibliographyItems()) {
-        const id = item._id;
-        for (const comment of references.getComments(id)) {
-            const contributions = [(0, transformer_1.buildContribution)(DEFAULT_PROFILE_ID)];
-            const c = (0, transformer_1.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;
 };
-exports.createReferenceComments = createReferenceComments;

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

@@ -18,11 +18,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.jatsBodyDOMParser = void 0;
+exports.jatsDOMParser = void 0;
+const json_schema_1 = require("@manuscripts/json-schema");
 const mime_1 = __importDefault(require("mime"));
 const prosemirror_model_1 = require("prosemirror-model");
 const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
+const jats_comments_1 = require("./jats-comments");
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const chooseContentType = (graphicNode) => {
     if (graphicNode) {
@@ -37,6 +39,12 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
+const parsePriority = (priority) => {
+    if (!priority) {
+        return undefined;
+    }
+    return parseInt(priority);
+};
 const getEquationContent = (p) => {
     var _a;
     const element = p;
@@ -101,6 +109,174 @@ 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: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.Contribution),
+                        objecType: json_schema_1.ObjectTypes.Contribution,
+                        profileID: jats_comments_1.DEFAULT_PROFILE_ID,
+                        timestamp: (0, json_schema_1.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: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.BibliographicName),
+                },
+                affiliations,
+                corresp: corresp.length ? corresp : undefined,
+                footnote: footnote.length ? footnote : undefined,
+                ORCIDIdentifier: element.getAttribute('ORCIDIdentifier'),
+                priority: parsePriority(element.getAttribute('priority')),
+            };
+        },
+        getContent: () => {
+            return prosemirror_model_1.Fragment.from(schema_1.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 prosemirror_model_1.Fragment.from(schema_1.schema.text('_'));
+        },
+    },
     {
         tag: 'attrib',
         node: 'attribution',
@@ -109,10 +285,6 @@ const nodes = [
         tag: 'back',
         ignore: true,
     },
-    {
-        tag: 'body',
-        node: 'manuscript',
-    },
     {
         tag: 'break',
         node: 'hard_break',
@@ -132,13 +304,13 @@ const nodes = [
             const title = element.querySelector('title');
             if (title) {
                 const captionTitle = schema.nodes.caption_title.create();
-                content.push(exports.jatsBodyDOMParser.parse(title, { topNode: captionTitle }));
+                content.push(exports.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(exports.jatsBodyDOMParser.parse(paragraph, { topNode: figcaption }));
+                    content.push(exports.jatsDOMParser.parse(paragraph, { topNode: figcaption }));
                 }
             }
             return prosemirror_model_1.Fragment.from(content);
@@ -329,7 +501,7 @@ const nodes = [
             const paragraphs = [];
             node.childNodes.forEach((p) => {
                 const paragraph = schema_1.schema.nodes.paragraph.create();
-                const content = exports.jatsBodyDOMParser.parse(p, {
+                const content = exports.jatsDOMParser.parse(p, {
                     topNode: paragraph,
                 });
                 paragraphs.push(content);
@@ -428,6 +600,54 @@ 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',
@@ -580,4 +800,4 @@ const nodes = [
         },
     },
 ];
-exports.jatsBodyDOMParser = new prosemirror_model_1.DOMParser(schema_1.schema, [...marks, ...nodes]);
+exports.jatsDOMParser = new prosemirror_model_1.DOMParser(schema_1.schema, [...marks, ...nodes]);