@manuscripts/transform 2.3.34-LEAN-3911.2 → 2.3.35

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

@@ -15,8 +15,8 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-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; } });
+exports.parseJATSArticle = exports.parseJATSBody = exports.parseJATSFront = void 0;
 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-dom-parser.js → jats-body-dom-parser.js}

@@ -18,13 +18,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.jatsDOMParser = void 0;
-const json_schema_1 = require("@manuscripts/json-schema");
+exports.jatsBodyDOMParser = void 0;
 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) {
@@ -39,12 +37,6 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
-const parsePriority = (priority) => {
-    if (!priority) {
-        return undefined;
-    }
-    return parseInt(priority);
-};
 const getEquationContent = (p) => {
     var _a;
     const element = p;
@@ -109,174 +101,6 @@ 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',
@@ -285,6 +109,10 @@ const nodes = [
         tag: 'back',
         ignore: true,
     },
+    {
+        tag: 'body',
+        node: 'manuscript',
+    },
     {
         tag: 'break',
         node: 'hard_break',
@@ -304,13 +132,13 @@ const nodes = [
             const title = element.querySelector('title');
             if (title) {
                 const captionTitle = schema.nodes.caption_title.create();
-                content.push(exports.jatsDOMParser.parse(title, { topNode: captionTitle }));
+                content.push(exports.jatsBodyDOMParser.parse(title, { topNode: captionTitle }));
             }
             const paragraphs = element.querySelectorAll('p');
             if (paragraphs.length) {
                 const figcaption = schema.nodes.caption.create();
                 for (const paragraph of paragraphs) {
-                    content.push(exports.jatsDOMParser.parse(paragraph, { topNode: figcaption }));
+                    content.push(exports.jatsBodyDOMParser.parse(paragraph, { topNode: figcaption }));
                 }
             }
             return prosemirror_model_1.Fragment.from(content);
@@ -501,7 +329,7 @@ const nodes = [
             const paragraphs = [];
             node.childNodes.forEach((p) => {
                 const paragraph = schema_1.schema.nodes.paragraph.create();
-                const content = exports.jatsDOMParser.parse(p, {
+                const content = exports.jatsBodyDOMParser.parse(p, {
                     topNode: paragraph,
                 });
                 paragraphs.push(content);
@@ -600,54 +428,6 @@ 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',
@@ -800,4 +580,4 @@ const nodes = [
         },
     },
 ];
-exports.jatsDOMParser = new prosemirror_model_1.DOMParser(schema_1.schema, [...marks, ...nodes]);
+exports.jatsBodyDOMParser = new prosemirror_model_1.DOMParser(schema_1.schema, [...marks, ...nodes]);

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

@@ -302,74 +302,4 @@ 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.markComments = exports.parseJATSComment = exports.isJATSComment = exports.DEFAULT_PROFILE_ID = void 0;
-const json_schema_1 = require("@manuscripts/json-schema");
+exports.createReferenceComments = exports.createComments = exports.markComments = exports.parseJATSComment = exports.isJATSComment = void 0;
+const uuid_1 = require("uuid");
 const transformer_1 = require("../../transformer");
-exports.DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
+const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
 const isJATSComment = (node) => {
     return (node.nodeType === node.PROCESSING_INSTRUCTION_NODE &&
         node.nodeName === 'AuthorQuery');
@@ -27,34 +27,35 @@ exports.isJATSComment = isJATSComment;
 const parseJATSComment = (node) => {
     const text = node.textContent;
     if (text) {
+        const id = /id="(.+)"/.exec(text);
         const queryText = /queryText="(.+)"/.exec(text);
-        if (queryText) {
-            const parentNode = node.parentNode;
-            const index = parentNode.outerHTML.indexOf(queryText[1]);
+        if (id && queryText) {
             return {
-                id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.CommentAnnotation),
+                id: id[1],
                 text: queryText[1],
-                index,
             };
         }
     }
 };
 exports.parseJATSComment = parseJATSComment;
 const markComments = (doc) => {
-    var _a;
+    const marks = [];
     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 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);
+                    const token = addMark(doc, node);
+                    if (token) {
+                        const mark = {
+                            token,
+                            comment,
+                        };
+                        marks.push(mark);
+                    }
                 }
             }
             node.childNodes.forEach((child) => {
@@ -62,20 +63,96 @@ const markComments = (doc) => {
             });
         }
     }
-    if (commentsElement.hasChildNodes()) {
-        doc.documentElement.appendChild(commentsElement);
-    }
+    return marks;
 };
 exports.markComments = markComments;
-const createHighlightMarkerElement = (doc, id) => {
-    const highlightMarker = doc.createElement('highlight-marker');
-    highlightMarker.setAttribute('id', id);
-    highlightMarker.setAttribute('position', 'point');
-    return highlightMarker;
+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;
+    }
 };
-const createCommentElement = (doc, comment) => {
-    const commentElement = doc.createElement('comment-annotation');
-    commentElement.setAttribute('id', comment.id);
-    commentElement.textContent = comment.text;
-    return commentElement;
+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,
+    };
+};
+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;
 };
+exports.createReferenceComments = createReferenceComments;