@manuscripts/transform 2.6.0 → 2.6.1-LEAN-3911.0

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

@@ -15,116 +15,58 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-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");
+exports.parseJATSArticle = void 0;
 const jats_comments_1 = require("./jats-comments");
-const jats_front_parser_1 = require("./jats-front-parser");
+const jats_dom_parser_1 = require("./jats-dom-parser");
+const jats_journal_meta_parser_1 = require("./jats-journal-meta-parser");
 const jats_parser_utils_1 = require("./jats-parser-utils");
-const jats_reference_parser_1 = require("./jats-reference-parser");
-const parseJATSFront = (doc, front) => {
+const jats_transformations_1 = require("./jats-transformations");
+const processJATS = (doc) => {
     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);
-    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 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');
+    (0, jats_comments_1.markComments)(doc);
     const front = doc.querySelector('front');
-    const body = doc.querySelector('body');
-    const back = doc.querySelector('back');
     if (!front) {
-        throw new errors_1.InvalidInput('Invalid JATS format! Missing front element');
+        return;
     }
-    if (!article) {
-        throw new errors_1.InvalidInput('Invalid JATS format! Missing article element');
-    }
-    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);
-    }
-    models.push(...(0, exports.parseJATSFront)(doc, front));
-    if (body) {
-        models.push(...(0, exports.parseJATSBody)(doc, body, references));
+    (0, jats_transformations_1.moveTitle)(front, createElement);
+    (0, jats_transformations_1.moveContributors)(front, createElement);
+    (0, jats_transformations_1.moveAffiliations)(front, createElement);
+    (0, jats_transformations_1.moveAuthorNotes)(front, createElement);
+    const body = doc.querySelector('body');
+    if (!body) {
+        return;
     }
-    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_transformations_1.ensureSection)(body, createElement);
+    (0, jats_transformations_1.moveCaptionsToEnd)(body);
+    (0, jats_transformations_1.createBoxedElementSection)(body, createElement);
+    (0, jats_transformations_1.createBody)(doc, body, createElement);
+    (0, jats_transformations_1.createAbstracts)(doc, body, createElement);
+    (0, jats_transformations_1.createBackmatter)(doc, body, createElement);
+    (0, jats_transformations_1.createSupplementaryMaterialsSection)(doc, body, createElement);
+    (0, jats_transformations_1.createKeywordsSection)(doc, body, createElement);
+    (0, jats_transformations_1.fixTables)(doc, body, createElement);
+    (0, jats_transformations_1.orderTableFootnote)(doc, body);
+    const back = doc.querySelector('back');
+    if (!back) {
+        return;
     }
-    if (references && references.items.size) {
-        models.push(...createBibliographyModels(references));
+    (0, jats_transformations_1.moveReferencesToBackmatter)(body, back, createElement);
+};
+const createElementFn = (doc) => (tagName) => doc.createElement(tagName);
+const parseJATSArticle = (doc, template) => {
+    const journal = (0, jats_journal_meta_parser_1.parseJournal)(doc);
+    processJATS(doc);
+    const node = jats_dom_parser_1.jatsDOMParser.parse(doc).firstChild;
+    if (!node) {
+        throw new Error('No content was parsed from the JATS article body');
     }
-    if (marks.length) {
-        const comments = (0, jats_comments_1.createComments)(models, marks);
-        models.push(...comments);
+    (0, jats_parser_utils_1.updateDocumentIDs)(node);
+    if (template) {
+        node.attrs.prototype = template;
     }
-    return models;
+    return {
+        node,
+        journal,
+    };
 };
 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 = 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);
+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; } });

package/dist/cjs/{transformer/models.js → lib/deafults.js}

@@ -1,6 +1,6 @@
 "use strict";
 /*!
- * © 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.
@@ -15,3 +15,5 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.defaultTitle = void 0;
+exports.defaultTitle = 'Untitled Manuscript';

package/dist/cjs/lib/utils.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
+exports.timestamp = exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
 const bibliography_section_1 = require("../schema/nodes/bibliography_section");
 const graphical_abstract_section_1 = require("../schema/nodes/graphical_abstract_section");
 function* iterateChildren(node, recurse = false) {
@@ -83,3 +83,5 @@ const getTrimmedTextContent = (node, querySelector) => {
     return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
 };
 exports.getTrimmedTextContent = getTrimmedTextContent;
+const timestamp = () => Math.floor(Date.now() / 1000);
+exports.timestamp = timestamp;

package/dist/cjs/schema/nodes/highlight_marker.js

@@ -22,9 +22,7 @@ exports.highlightMarker = {
     atom: true,
     attrs: {
         id: { default: '' },
-        tid: { default: '' },
         position: { default: '' },
-        dataTracked: { default: null },
     },
     parseDOM: [
         {
@@ -33,7 +31,6 @@ exports.highlightMarker = {
                 const dom = p;
                 return {
                     id: dom.getAttribute('id'),
-                    tid: dom.getAttribute('data-target-id'),
                     position: dom.getAttribute('data-position'),
                 };
             },
@@ -44,7 +41,6 @@ exports.highlightMarker = {
         const dom = document.createElement('span');
         dom.className = 'highlight-marker';
         dom.setAttribute('id', highlightMarkerNode.attrs.id);
-        dom.setAttribute('data-target-id', highlightMarkerNode.attrs.tid);
         dom.setAttribute('data-position', highlightMarkerNode.attrs.position);
         return dom;
     },

package/dist/cjs/transformer/id.js

@@ -15,14 +15,10 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateID = exports.generateNodeID = void 0;
+exports.generateNodeID = void 0;
 const uuid_1 = require("uuid");
 const node_types_1 = require("./node-types");
 const generateNodeID = (type) => {
     return node_types_1.nodeTypesMap.get(type) + ':' + (0, uuid_1.v4)().toUpperCase();
 };
 exports.generateNodeID = generateNodeID;
-const generateID = (objectType) => {
-    return objectType + ':' + (0, uuid_1.v4)().toUpperCase();
-};
-exports.generateID = generateID;

package/dist/cjs/transformer/index.js

@@ -29,26 +29,8 @@ 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.createTestDoc = void 0;
-__exportStar(require("./builders"), exports);
-__exportStar(require("./decode"), exports);
-__exportStar(require("./document-object-types"), exports);
-__exportStar(require("./encode"), exports);
-__exportStar(require("./filename"), exports);
-__exportStar(require("./highlight-markers"), exports);
-__exportStar(require("./html"), exports);
 __exportStar(require("./id"), exports);
-__exportStar(require("./labels"), exports);
-__exportStar(require("./manuscript-dependencies"), exports);
-__exportStar(require("./models"), exports);
 __exportStar(require("./node-names"), exports);
 __exportStar(require("./node-title"), exports);
 __exportStar(require("./node-types"), exports);
-__exportStar(require("./object-types"), exports);
-__exportStar(require("./project-bundle"), exports);
 __exportStar(require("./section-category"), exports);
-__exportStar(require("./serializer"), exports);
-__exportStar(require("./timestamp"), exports);
-__exportStar(require("./update-identifiers"), exports);
-var doc_1 = require("./__tests__/__helpers__/doc");
-Object.defineProperty(exports, "createTestDoc", { enumerable: true, get: function () { return doc_1.createTestDoc; } });

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "2.6.0";
+exports.VERSION = "2.6.1-LEAN-3911.0";

package/dist/es/index.js

@@ -1,11 +1,11 @@
+export * from './errors';
+export { getVersion } from './getVersion';
+export * from './jats';
+export * from './jats/types';
 export * from './lib/section-group-type';
 export * from './lib/table-cell-styles';
 export * from './lib/utils';
 export * from './schema';
-export * from './transformer';
-export * from './jats';
-export * from './types';
-export * from './errors';
-export { getVersion } from './getVersion';
 export { migrateFor } from './schema/migration/migrate';
 export { isSectionLabelNode } from './schema/nodes/section_label';
+export * from './transformer';