@manuscripts/transform 3.0.21-LEAN-4076.1 → 3.0.21

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

@@ -14,17 +14,12 @@
  * limitations under the License.
  */
 import { defaultTitle } from '../../lib/deafults';
-import { abstractsType, backmatterType, bodyType, } from '../../lib/section-group-type';
-import { chooseSectionCategoryByType, chooseSecType } from '../../transformer';
 import { htmlFromJatsNode } from './jats-parser-utils';
 const removeNodeFromParent = (node) => node.parentNode && node.parentNode.removeChild(node);
 const capitalizeFirstLetter = (str) => str.charAt(0).toUpperCase() + str.slice(1);
 const createSectionGroup = (type, createElement) => {
     const sec = createElement('sec');
-    sec.setAttribute('sec-type', type._id);
-    const title = createElement('title');
-    title.textContent = type.title;
-    sec.appendChild(title);
+    sec.setAttribute('sec-type', type);
     return sec;
 };
 export const moveTitle = (front, createElement) => {
@@ -105,7 +100,7 @@ export const createBoxedElementSection = (body, createElement) => {
     }
 };
 export const createBody = (doc, body, createElement) => {
-    const group = createSectionGroup(bodyType, createElement);
+    const group = createSectionGroup('body', createElement);
     const paragraphs = doc.querySelectorAll('body > p');
     group.append(...paragraphs);
     const sections = doc.querySelectorAll('body > sec:not([sec-type="backmatter"]), body > sec:not([sec-type])');
@@ -117,15 +112,15 @@ export const createBody = (doc, body, createElement) => {
     body.append(group);
 };
 export const createAbstracts = (doc, body, createElement) => {
-    const group = createSectionGroup(abstractsType, createElement);
+    const group = createSectionGroup('abstracts', createElement);
     moveAbstracts(doc, group, createElement);
     body.insertBefore(group, body.lastElementChild);
 };
-export const createBackmatter = (doc, body, createElement) => {
-    const group = createSectionGroup(backmatterType, createElement);
+export const createBackmatter = (doc, body, sectionCategories, createElement) => {
+    const group = createSectionGroup('backmatter', createElement);
     moveBackSections(doc, group);
     moveAppendices(doc, group, createElement);
-    moveSpecialFootnotes(doc, group, createElement);
+    moveSpecialFootnotes(doc, group, sectionCategories, createElement);
     moveFootnotes(doc, group, createElement);
     moveAcknowledgments(doc, group, createElement);
     body.append(group);
@@ -149,12 +144,12 @@ const moveFootnotes = (doc, group, createElement) => {
         group.insertBefore(section, ((_a = group.firstChild) === null || _a === void 0 ? void 0 : _a.nextSibling) || group.firstChild);
     }
 };
-const moveSpecialFootnotes = (doc, group, createElement) => {
+const moveSpecialFootnotes = (doc, group, sectionCategories, createElement) => {
     var _a;
     const fns = [...doc.querySelectorAll('fn[fn-type]')];
     for (const fn of fns) {
         const type = fn.getAttribute('fn-type') || '';
-        const category = chooseSectionCategoryByType(type);
+        const category = sectionCategories.find((category) => category.synonyms.includes(type));
         if (category) {
             const section = createElement('sec');
             const fnTitle = fn.querySelector('p[content-type="fn-title"]');
@@ -169,7 +164,7 @@ const moveSpecialFootnotes = (doc, group, createElement) => {
             }
             section.append(...fn.children);
             removeNodeFromParent(fn);
-            section.setAttribute('sec-type', chooseSecType(category));
+            section.setAttribute('sec-type', category.id);
             group.append(section);
         }
     }

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

@@ -13,12 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { schema } from '../../schema';
 import { markComments } from './jats-comments';
-import { jatsDOMParser } from './jats-dom-parser';
+import { JATSDOMParser } from './jats-dom-parser';
 import { parseJournal } from './jats-journal-meta-parser';
 import { updateDocumentIDs } from './jats-parser-utils';
 import { createAbstracts, createBackmatter, createBody, createBoxedElementSection, createKeywordsSection, createSupplementaryMaterialsSection, fixTables, moveAffiliations, moveAuthorNotes, moveAwards, moveCaptionsToEnd, moveContributors, moveReferencesToBackmatter, moveTitle, orderTableFootnote, } from './jats-transformations';
-const processJATS = (doc) => {
+const processJATS = (doc, sectionCategories) => {
     const createElement = createElementFn(doc);
     markComments(doc);
     const front = doc.querySelector('front');
@@ -38,7 +39,7 @@ const processJATS = (doc) => {
     createBoxedElementSection(body, createElement);
     createBody(doc, body, createElement);
     createAbstracts(doc, body, createElement);
-    createBackmatter(doc, body, createElement);
+    createBackmatter(doc, body, sectionCategories, createElement);
     createSupplementaryMaterialsSection(doc, body, createElement);
     createKeywordsSection(doc, body, createElement);
     fixTables(doc, body, createElement);
@@ -50,10 +51,11 @@ const processJATS = (doc) => {
     moveReferencesToBackmatter(body, back, createElement);
 };
 const createElementFn = (doc) => (tagName) => doc.createElement(tagName);
-export const parseJATSArticle = (doc, template) => {
+export const parseJATSArticle = (doc, sectionCategories, template) => {
     const journal = parseJournal(doc);
-    processJATS(doc);
-    const node = jatsDOMParser.parse(doc).firstChild;
+    processJATS(doc, sectionCategories);
+    const node = new JATSDOMParser(sectionCategories, schema).parse(doc)
+        .firstChild;
     if (!node) {
         throw new Error('No content was parsed from the JATS article body');
     }

package/dist/es/lib/{section-group-type.js → section-categories.js}

@@ -1,5 +1,5 @@
 /*!
- * © 2023 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.
@@ -13,15 +13,4 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export const abstractsType = {
-    _id: 'abstracts',
-    title: 'Abstracts',
-};
-export const bodyType = {
-    _id: 'body',
-    title: 'Body',
-};
-export const backmatterType = {
-    _id: 'backmatter',
-    title: 'Backmatter',
-};
+export const getGroupCateogries = (sectionsMap, group) => Array.from(sectionsMap.values()).filter((section) => section.group === group);

package/dist/es/schema/index.js

@@ -137,8 +137,6 @@ export * from './nodes/supplement';
 export * from './nodes/supplements';
 export * from './nodes/corresp';
 export * from './nodes/author_notes';
-export * from './nodes/award';
-export * from './nodes/awards';
 export const schema = new Schema({
     marks: {
         bold,

package/dist/es/schema/migration/migration-scripts/3.0.21.js

@@ -0,0 +1,23 @@
+class Migration3021 {
+    constructor() {
+        this.fromVersion = '3.0.20';
+        this.toVersion = '3.0.21';
+        this.suffixMap = new Map([
+            ['competing-interests', 'coi-statement'],
+            ['acknowledgement', 'acknowledgements'],
+            ['introduction', 'intro'],
+            ['materials-method', 'methods'],
+            ['subsection', ''],
+        ]);
+    }
+    migrateNode(node) {
+        if (node.type === 'section' &&
+            node.attrs.category.startsWith('MPSectionCategory:')) {
+            const [, suffix] = node.attrs.category.split(':', 2);
+            const newCategory = this.suffixMap.get(suffix) || suffix;
+            return Object.assign(Object.assign({}, node), { attrs: Object.assign(Object.assign({}, node.attrs), { category: newCategory }) });
+        }
+        return node;
+    }
+}
+export default Migration3021;

package/dist/es/schema/migration/migration-scripts/index.js

@@ -16,9 +16,11 @@
 import Migration125 from './1.2.5';
 import Migration2322 from './2.3.22';
 import { Migration3012 } from './3.0.12';
+import Migration3021 from './3.0.21';
 const migrations = [
     new Migration125(),
     new Migration2322(),
     new Migration3012(),
+    new Migration3021(),
 ];
 export default migrations;

package/dist/es/transformer/index.js

@@ -17,4 +17,3 @@ export * from './id';
 export * from './node-names';
 export * from './node-title';
 export * from './node-types';
-export * from './section-category';

package/dist/es/version.js

@@ -1 +1 @@
-export const VERSION = "3.0.21-LEAN-4076.1";
+export const VERSION = "3.0.21";

package/dist/types/index.d.ts

@@ -2,10 +2,9 @@ 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/footnotes';
 export * from './lib/utils';
+export * from './lib/section-categories';
 export * from './schema';
 export { JSONNode, migrateFor } from './schema/migration/migrate';
 export { isSectionLabelNode } from './schema/nodes/section_label';

package/dist/types/jats/importer/jats-dom-parser.d.ts

@@ -13,12 +13,27 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { DOMParser, ParseRule } from 'prosemirror-model';
-import { Marks, Nodes } from '../../schema';
-export type MarkRule = ParseRule & {
-    mark: Marks | null;
-};
-export type NodeRule = ParseRule & {
-    node?: Nodes | null;
-};
-export declare const jatsDOMParser: DOMParser;
+import { ParseOptions, Schema } from 'prosemirror-model';
+import { SectionCategory } from '../../schema';
+export declare class JATSDOMParser {
+    private sectionCategories;
+    private schema;
+    private XLINK_NAMESPACE;
+    private parser;
+    constructor(sectionCategories: SectionCategory[], schema: Schema);
+    parse(doc: Node, options?: ParseOptions): import("prosemirror-model").Node;
+    private isMatchingCategory;
+    private chooseSectionCategory;
+    private chooseContentType;
+    private parsePriority;
+    private getEquationContent;
+    private parseDates;
+    private getEmail;
+    private getInstitutionDetails;
+    private getAddressLine;
+    private getHTMLContent;
+    private chooseBibliographyItemType;
+    private parseRef;
+    private nodes;
+    private marks;
+}

package/dist/types/jats/importer/jats-transformations.d.ts

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { SectionCategory } from '../../schema';
 export type CreateElement = (tagName: string) => HTMLElement;
 export declare const moveTitle: (front: Element, createElement: CreateElement) => void;
 export declare const moveAuthorNotes: (front: Element, createElement: CreateElement) => void;
@@ -23,7 +24,7 @@ export declare const moveAbstracts: (doc: Document, group: Element, createElemen
 export declare const createBoxedElementSection: (body: Element, createElement: (tagName: string) => HTMLElement) => void;
 export declare const createBody: (doc: Document, body: Element, createElement: CreateElement) => void;
 export declare const createAbstracts: (doc: Document, body: Element, createElement: CreateElement) => void;
-export declare const createBackmatter: (doc: Document, body: Element, createElement: CreateElement) => void;
+export declare const createBackmatter: (doc: Document, body: Element, sectionCategories: SectionCategory[], createElement: CreateElement) => void;
 export declare const moveCaptionsToEnd: (body: Element) => void;
 export declare const createKeywordsSection: (document: Document, body: Element, createElement: CreateElement) => void;
 export declare const createSupplementaryMaterialsSection: (document: Document, body: Element, createElement: CreateElement) => void;

package/dist/types/jats/importer/parse-jats-article.d.ts

@@ -13,8 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ActualManuscriptNode } from '../../schema';
-export declare const parseJATSArticle: (doc: Document, template?: string) => {
+import { ActualManuscriptNode, SectionCategory } from '../../schema';
+export declare const parseJATSArticle: (doc: Document, sectionCategories: SectionCategory[], template?: string) => {
     node: ActualManuscriptNode;
     journal: {
         objectType: import("@manuscripts/json-schema/dist/types").ObjectTypes;

package/dist/types/lib/{section-group-type.d.ts → section-categories.d.ts}

@@ -1,5 +1,5 @@
 /*!
- * © 2023 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.
@@ -13,11 +13,5 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export type SectionGroupTypeID = 'abstracts' | 'body' | 'backmatter';
-export type SectionGroupType = {
-    _id: SectionGroupTypeID;
-    title: string;
-};
-export declare const abstractsType: SectionGroupType;
-export declare const bodyType: SectionGroupType;
-export declare const backmatterType: SectionGroupType;
+import { SectionCategory, SectionGroup } from '../schema';
+export declare const getGroupCateogries: (sectionsMap: Map<string, SectionCategory>, group: SectionGroup) => SectionCategory[];

package/dist/types/schema/index.d.ts

@@ -74,6 +74,4 @@ export * from './nodes/supplement';
 export * from './nodes/supplements';
 export * from './nodes/corresp';
 export * from './nodes/author_notes';
-export * from './nodes/award';
-export * from './nodes/awards';
 export declare const schema: Schema<Nodes, Marks>;

package/dist/types/schema/migration/migration-scripts/3.0.21.d.ts

@@ -0,0 +1,9 @@
+import { JSONNode } from '../migrate';
+import { MigrationScript } from '../migration-script';
+declare class Migration3021 implements MigrationScript {
+    fromVersion: string;
+    toVersion: string;
+    private suffixMap;
+    migrateNode(node: JSONNode): JSONNode;
+}
+export default Migration3021;

package/dist/types/schema/migration/migration-scripts/index.d.ts

@@ -16,5 +16,6 @@
 import Migration125 from './1.2.5';
 import Migration2322 from './2.3.22';
 import { Migration3012 } from './3.0.12';
-declare const migrations: (Migration125 | Migration2322 | Migration3012)[];
+import Migration3021 from './3.0.21';
+declare const migrations: (Migration125 | Migration2322 | Migration3012 | Migration3021)[];
 export default migrations;

package/dist/types/schema/types.d.ts

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Fragment, Mark as ProsemirrorMark, MarkType, Node as ProsemirrorNode, NodeSpec, NodeType, ResolvedPos, Schema, Slice } from 'prosemirror-model';
+import { Fragment, Mark as ProsemirrorMark, MarkType, Node as ProsemirrorNode, NodeSpec, NodeType, ParseRule, ResolvedPos, Schema, Slice } from 'prosemirror-model';
 import { EditorState, NodeSelection, Plugin, TextSelection, Transaction } from 'prosemirror-state';
 import { EditorView, NodeView } from 'prosemirror-view';
 export type Marks = 'bold' | 'code' | 'italic' | 'smallcaps' | 'strikethrough' | 'styled' | 'subscript' | 'superscript' | 'underline' | 'tracked_insert' | 'tracked_delete';
@@ -43,3 +43,23 @@ export type DataTrackedAttrs = {
     userID: string;
     createdAt: number;
 };
+export type SectionGroup = 'abstracts' | 'body' | 'backmatter';
+export type SectionCategory = {
+    id: string;
+    synonyms: string[];
+    titles: [string, ...string[]];
+    group?: SectionGroup;
+    isUnique: boolean;
+};
+export type ManuscriptTemplate = {
+    _id: string;
+    bundle: string;
+    title: string;
+    sectionCategories: SectionCategory[];
+};
+export type MarkRule = ParseRule & {
+    mark: Marks | null;
+};
+export type NodeRule = ParseRule & {
+    node?: Nodes | null;
+};

package/dist/types/transformer/index.d.ts

@@ -17,4 +17,3 @@ export * from './id';
 export * from './node-names';
 export * from './node-title';
 export * from './node-types';
-export * from './section-category';

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const VERSION = "3.0.21-LEAN-4076.1";
+export declare const VERSION = "3.0.21";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "3.0.21-LEAN-4076.1",
+  "version": "3.0.21",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",

package/dist/cjs/lib/table-cell-styles.js

@@ -1,52 +0,0 @@
-"use strict";
-/*!
- * © 2019 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.getTableCellStyles = exports.serializeTableCellStyles = exports.TABLE_CELL_STYLES = void 0;
-exports.TABLE_CELL_STYLES = [
-    'backgroundColor',
-    'border-top',
-    'border-right',
-    'border-bottom',
-    'border-left',
-    'verticalAlign',
-    'textAlign',
-];
-const dashify = (str) => {
-    return str
-        .trim()
-        .replace(/([a-z])([A-Z])/g, '$1-$2')
-        .replace(/\W/g, (m) => (/[À-ž]/.test(m) ? m : '-'))
-        .replace(/^-+|-+$/g, '')
-        .toLowerCase();
-};
-const serializeTableCellStyles = (styles) => {
-    return Object.keys(styles)
-        .map((key) => styles[key] && `${dashify(key)}: ${styles[key]}`)
-        .filter(Boolean)
-        .join('; ');
-};
-exports.serializeTableCellStyles = serializeTableCellStyles;
-const isStyleKey = (key) => exports.TABLE_CELL_STYLES.includes(key);
-const getTableCellStyles = (styles) => {
-    return Object.entries(styles).reduce((acc, [key, value]) => {
-        if (isStyleKey(key)) {
-            acc[key] = value;
-        }
-        return acc;
-    }, {});
-};
-exports.getTableCellStyles = getTableCellStyles;