@manuscripts/transform 2.3.38-LEAN-3911.0 → 2.6.0

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

@@ -1,34 +1,34 @@
 "use strict";
-/*!
- * © 2023 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.References = void 0;
 class References {
     constructor() {
         this.items = new Map();
         this.IDs = new Map();
+        this.comments = new Map();
     }
-    add(item, id) {
-        this.items.set(item.id, item);
+    add(item, id, comments) {
+        this.items.set(item._id, item);
+        this.comments.set(item._id, comments);
         if (id) {
-            this.IDs.set(id, item.id);
+            this.IDs.set(id, item._id);
         }
     }
     getBibliographyItems() {
         return [...this.items.values()];
     }
+    getComments(id) {
+        return this.getValue(id, this.comments) || [];
+    }
+    getValue(id, map) {
+        const value = map.get(id);
+        if (value) {
+            return value;
+        }
+        const id2 = this.IDs.get(id);
+        if (id2) {
+            return map.get(id2);
+        }
+    }
 }
 exports.References = References;

package/dist/cjs/jats/importer/parse-jats-article.js

@@ -15,77 +15,116 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseJATSArticle = void 0;
+exports.parseJATSArticle = exports.parseJATSBody = exports.parseJATSFront = void 0;
 const errors_1 = require("../../errors");
+const transformer_1 = require("../../transformer");
+const builders_1 = require("../../transformer/builders");
+const id_1 = require("../../transformer/id");
+const project_bundle_1 = require("../../transformer/project-bundle");
+const jats_body_dom_parser_1 = require("./jats-body-dom-parser");
 const jats_body_transformations_1 = require("./jats-body-transformations");
 const jats_comments_1 = require("./jats-comments");
-const jats_dom_parser_1 = require("./jats-dom-parser");
-const jats_front_transformations_1 = require("./jats-front-transformations");
-const jats_journal_meta_parser_1 = require("./jats-journal-meta-parser");
+const jats_front_parser_1 = require("./jats-front-parser");
 const jats_parser_utils_1 = require("./jats-parser-utils");
 const jats_reference_parser_1 = require("./jats-reference-parser");
+const parseJATSFront = (doc, front) => {
+    const createElement = createElementFn(doc);
+    const journal = jats_front_parser_1.jatsFrontParser.parseJournal(front.querySelector('journal-meta'));
+    const titles = jats_front_parser_1.jatsFrontParser.parseTitles(front.querySelector('article-meta > title-group'), createElement);
+    const DOI = jats_front_parser_1.jatsFrontParser.parseDOI(front);
+    const { affiliations, affiliationIDs } = jats_front_parser_1.jatsFrontParser.parseAffiliations([
+        ...front.querySelectorAll('article-meta > contrib-group > aff'),
+    ]);
+    const { footnotes, footnoteIDs, authorNotes, authorNotesParagraphs, correspondingIDs, correspondingList, } = jats_front_parser_1.jatsFrontParser.parseAuthorNotes(front.querySelector('article-meta > author-notes'));
+    const authors = jats_front_parser_1.jatsFrontParser.parseContributors([
+        ...front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]'),
+    ], affiliationIDs, footnoteIDs, correspondingIDs);
+    const history = jats_front_parser_1.jatsFrontParser.parseDates(front.querySelector('article-meta > history'));
+    const counts = jats_front_parser_1.jatsFrontParser.parseCounts(front.querySelector('article-meta counts'));
+    const manuscript = Object.assign(Object.assign(Object.assign(Object.assign({}, (0, builders_1.buildManuscript)()), counts), history), { DOI });
+    return generateIDs([
+        manuscript,
+        titles,
+        journal,
+        ...authorNotesParagraphs,
+        ...authorNotes,
+        ...footnotes,
+        ...authors,
+        ...affiliations,
+        ...correspondingList,
+    ]);
+};
+exports.parseJATSFront = parseJATSFront;
 const parseJATSBody = (doc, body, references) => {
     const createElement = createElementFn(doc);
     jats_body_transformations_1.jatsBodyTransformations.ensureSection(body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.moveCaptionsToEnd(body);
     jats_body_transformations_1.jatsBodyTransformations.fixTables(body, createElement);
+    jats_body_transformations_1.jatsBodyTransformations.createBoxedElementSection(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createBody(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createAbstracts(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createBackmatter(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createKeywords(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.orderTableFootnote(doc, body);
-    jats_body_transformations_1.jatsBodyTransformations.moveReferencesToBackmatter(body, references, createElement);
-};
-const parseJATSFront = (doc, front, template) => {
-    const createElement = createElementFn(doc);
-    jats_front_transformations_1.jatsFrontTransformations.setArticleAttrs(doc, template);
-    const authorNotes = jats_front_transformations_1.jatsFrontTransformations.createAuthorNotes(doc, createElement);
-    if (authorNotes) {
-        doc.documentElement.prepend(authorNotes);
-    }
-    const affiliations = jats_front_transformations_1.jatsFrontTransformations.createAffiliations(front, createElement);
-    if (affiliations) {
-        doc.documentElement.prepend(affiliations);
-    }
-    const contributors = jats_front_transformations_1.jatsFrontTransformations.createContributors(front, createElement);
-    if (contributors) {
-        doc.documentElement.prepend(contributors);
-    }
-    const title = jats_front_transformations_1.jatsFrontTransformations.createTitle(front, createElement);
-    if (title) {
-        doc.documentElement.prepend(title);
+    const node = jats_body_dom_parser_1.jatsBodyDOMParser.parse(body).firstChild;
+    if (!node) {
+        throw new Error('No content was parsed from the JATS article body');
     }
+    const replacements = new Map(references === null || references === void 0 ? void 0 : references.IDs);
+    (0, jats_parser_utils_1.updateDocumentIDs)(node, replacements);
+    return (0, transformer_1.encode)(node).values();
+};
+exports.parseJATSBody = parseJATSBody;
+const createBibliographyModels = (references) => {
+    const models = [];
+    const bibliographyItems = references.getBibliographyItems();
+    const bibliographyElement = (0, transformer_1.buildBibliographyElement)(bibliographyItems);
+    const bibliographySection = Object.assign(Object.assign({}, (0, transformer_1.buildSection)(99)), { category: 'MPSectionCategory:bibliography', elementIDs: [bibliographyElement._id], title: 'References' });
+    const comments = (0, jats_comments_1.createReferenceComments)(references);
+    models.push(bibliographySection);
+    models.push(bibliographyElement);
+    models.push(...bibliographyItems);
+    models.push(...comments);
+    return models;
 };
 const createElementFn = (doc) => (tagName) => doc.createElement(tagName);
-const parseJATSArticle = (doc, template) => {
+const generateIDs = (models) => models.map((m) => m._id ? m : Object.assign(Object.assign({}, m), { _id: (0, id_1.generateID)(m.objectType) }));
+const parseJATSArticle = (doc) => {
     const article = doc.querySelector('article');
     const front = doc.querySelector('front');
     const body = doc.querySelector('body');
     const back = doc.querySelector('back');
-    if (!article || !front) {
-        throw new errors_1.InvalidInput('invalid JATS format');
+    if (!front) {
+        throw new errors_1.InvalidInput('Invalid JATS format! Missing front element');
+    }
+    if (!article) {
+        throw new errors_1.InvalidInput('Invalid JATS format! Missing article element');
     }
-    (0, jats_comments_1.markComments)(doc);
-    const journal = (0, jats_journal_meta_parser_1.parseJournal)(front.querySelector('journal-meta'));
+    const marks = (0, jats_comments_1.markComments)(doc);
     const createElement = createElementFn(doc);
+    const models = [];
     let references;
     if (back) {
         references = jats_reference_parser_1.jatsReferenceParser.parseReferences([...back.querySelectorAll('ref-list > ref')], createElement);
     }
-    const replacements = new Map(references === null || references === void 0 ? void 0 : references.IDs);
-    parseJATSFront(doc, front, template);
+    models.push(...(0, exports.parseJATSFront)(doc, front));
     if (body) {
-        parseJATSBody(doc, body, references);
+        models.push(...(0, exports.parseJATSBody)(doc, body, references));
     }
-    const node = jats_dom_parser_1.jatsDOMParser.parse(doc).firstChild;
-    if (!node) {
-        throw new Error('No content was parsed from the JATS article body');
+    const modelMap = new Map(models.map((model) => [model._id, model]));
+    const manuscript = (0, project_bundle_1.findManuscript)(modelMap);
+    if (manuscript) {
+        const type = article.getAttribute('article-type');
+        manuscript.articleType = type || 'other';
     }
-    (0, jats_parser_utils_1.updateDocumentIDs)(node, replacements);
-    return {
-        node: node,
-        journal,
-    };
+    if (references && references.items.size) {
+        models.push(...createBibliographyModels(references));
+    }
+    if (marks.length) {
+        const comments = (0, jats_comments_1.createComments)(models, marks);
+        models.push(...comments);
+    }
+    return models;
 };
 exports.parseJATSArticle = parseJATSArticle;

package/dist/cjs/jats/index.js

@@ -29,10 +29,10 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseJATSArticle = void 0;
-__exportStar(require("./exporter/jats-exporter"), exports);
-__exportStar(require("./exporter/jats-versions"), exports);
-__exportStar(require("./exporter/labels"), exports);
-__exportStar(require("./importer/create-article-node"), exports);
-var parse_jats_article_1 = require("./importer/parse-jats-article");
-Object.defineProperty(exports, "parseJATSArticle", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSArticle; } });
+exports.parseJATSArticle = exports.parseJATSBody = exports.parseJATSFront = void 0;
+var importer_1 = require("./importer");
+Object.defineProperty(exports, "parseJATSFront", { enumerable: true, get: function () { return importer_1.parseJATSFront; } });
+Object.defineProperty(exports, "parseJATSBody", { enumerable: true, get: function () { return importer_1.parseJATSBody; } });
+Object.defineProperty(exports, "parseJATSArticle", { enumerable: true, get: function () { return importer_1.parseJATSArticle; } });
+__exportStar(require("./jats-exporter"), exports);
+__exportStar(require("./jats-versions"), exports);