@manuscripts/transform 2.3.36 → 2.3.37-LEAN-3911.1

package/dist/es/{transformer → jats}/labels.js

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 import { schema } from '../schema';
-import { nodeNames } from './node-names';
+import { nodeNames } from '../transformer/node-names';
 const labelledNodeTypes = [
     schema.nodes.figure_element,
     schema.nodes.table_element,
@@ -25,7 +25,7 @@ const excludedTypes = [schema.nodes.graphical_abstract_section];
 const chooseLabel = (nodeType) => {
     return nodeNames.get(nodeType);
 };
-export const buildTargets = (fragment) => {
+export const buildTargets = (node) => {
     const counters = {};
     for (const nodeType of labelledNodeTypes) {
         counters[nodeType.name] = {
@@ -39,7 +39,7 @@ export const buildTargets = (fragment) => {
         return `${counter.label} ${counter.index}`;
     };
     const targets = new Map();
-    fragment.descendants((node, pos, parent) => {
+    node.descendants((node, pos, parent) => {
         var _a;
         if (node.type.name in counters) {
             if (parent && excludedTypes.includes(parent.type)) {

package/dist/es/lib/utils.js

@@ -74,3 +74,10 @@ export 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();
 };
+export const setElementAttributes = (element, attributes) => {
+    Object.entries(attributes).forEach(([key, value]) => {
+        if (value) {
+            element.setAttribute(key, value);
+        }
+    });
+};

package/dist/es/transformer/id.js

@@ -15,9 +15,14 @@
  */
 import { v4 as uuid } from 'uuid';
 import { nodeTypesMap } from './node-types';
-export const generateNodeID = (type) => {
-    return nodeTypesMap.get(type) + ':' + uuid().toUpperCase();
-};
+export var ExtraObjectTypes;
+(function (ExtraObjectTypes) {
+    ExtraObjectTypes["PlaceholderElement"] = "MPPlaceholderElement";
+    ExtraObjectTypes["GeneralTableFootnote"] = "MPGeneralTableFootnote";
+})(ExtraObjectTypes || (ExtraObjectTypes = {}));
 export const generateID = (objectType) => {
     return objectType + ':' + uuid().toUpperCase();
 };
+export const generateNodeID = (type) => {
+    return nodeTypesMap.get(type) + ':' + uuid().toUpperCase();
+};

package/dist/es/transformer/index.js

@@ -13,24 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export * from './builders';
-export * from './decode';
-export * from './document-object-types';
-export * from './encode';
-export * from './filename';
-export * from './highlight-markers';
-export * from './html';
 export * from './id';
-export * from './labels';
-export * from './manuscript-dependencies';
-export * from './models';
 export * from './node-names';
 export * from './node-title';
 export * from './node-types';
-export * from './object-types';
-export * from './project-bundle';
 export * from './section-category';
-export * from './serializer';
-export * from './timestamp';
-export * from './update-identifiers';
-export { createTestDoc } from './__tests__/__helpers__/doc';

package/dist/es/version.js

@@ -1 +1 @@
-export const VERSION = "2.3.36";
+export const VERSION = "2.3.37-LEAN-3911.1";

package/dist/{cjs/transformer/models.js → types/jats/importer/create-article-node.d.ts}

@@ -1,6 +1,5 @@
-"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.
@@ -14,4 +13,5 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-Object.defineProperty(exports, "__esModule", { value: true });
+import { Manuscript } from '@manuscripts/json-schema';
+export declare const createArticleNode: (manuscript: Partial<Manuscript>) => import("prosemirror-model").Node;

package/dist/types/jats/importer/index.d.ts

@@ -13,4 +13,5 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export { parseJATSFront, parseJATSBody, parseJATSArticle, } from './parse-jats-article';
+export { createArticleNode } from './create-article-node';
+export { parseJATSArticle } from './parse-jats-article';

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

@@ -13,6 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { BibliographyItemAttributes } from '../../schema';
+import { References } from './jats-references';
 export declare const jatsBodyTransformations: {
     ensureSection(body: Element, createElement: (tagName: string) => HTMLElement): void;
     createAbstractSection(abstractNode: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
@@ -36,4 +38,7 @@ export declare const jatsBodyTransformations: {
     moveFloatsGroupToBody(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     createKeywords(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     createSuppleMaterials(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
+    moveReferencesToBackmatter(body: Element, references: References | undefined, createElement: (tagName: string) => HTMLElement): void;
+    createBibliographySection(createElement: (tagName: string) => HTMLElement): HTMLElement;
+    createBibliographyItem(item: BibliographyItemAttributes, createElement: (tagName: string) => HTMLElement): HTMLElement;
 };

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

@@ -13,18 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { CommentAnnotation, Model } from '@manuscripts/json-schema';
-import { References } from './jats-references';
 export type JATSComment = {
-    id: string;
+    index: number;
     text: string;
+    id: string;
 };
-export type JATSCommentMark = {
-    token: string;
-    comment: JATSComment;
-};
+export declare const DEFAULT_PROFILE_ID = "MPUserProfile:0000000000000000000000000000000000000001";
 export declare const isJATSComment: (node: Node) => boolean;
 export declare const parseJATSComment: (node: Node) => JATSComment | undefined;
-export declare const markComments: (doc: Document) => JATSCommentMark[];
-export declare const createComments: (models: Model[], marks: JATSCommentMark[]) => CommentAnnotation[];
-export declare const createReferenceComments: (references: References) => CommentAnnotation[];
+export declare const markComments: (doc: Document) => void;

package/dist/types/jats/importer/{jats-body-dom-parser.d.ts → jats-dom-parser.d.ts}

@@ -21,4 +21,4 @@ export type MarkRule = ParseRule & {
 export type NodeRule = ParseRule & {
     node?: Nodes | null;
 };
-export declare const jatsBodyDOMParser: DOMParser;
+export declare const jatsDOMParser: DOMParser;

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

@@ -0,0 +1,38 @@
+/*!
+ * © 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.
+ */
+export declare const defaultTitle = "Untitled Manuscript";
+export declare const jatsFrontTransformations: {
+    setArticleAttrs(doc: Document, template?: string): void;
+    createTitle(front: Element, createElement: (tagName: string) => HTMLElement): Element;
+    createAuthorNotes(document: Document, createElement: (tagName: string) => HTMLElement): HTMLElement | undefined;
+    appendFootnote(node: Element, element: Element, createElement: (tagName: string) => HTMLElement): void;
+    appendParagraph(document: Document, node: Element, element: Element): void;
+    appendCorresp(node: Element, element: Element, createElement: (tagName: string) => HTMLElement): void;
+    createContributors(front: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
+    createContributorElement(priority: number, createElement: (tagName: string) => HTMLElement): HTMLElement;
+    setNameAttrs(node: Element, element: Element): void;
+    setOrcidAttribute(node: Element, element: Element): void;
+    setIsCorrespondingAttribute(node: Element, element: Element): void;
+    setContributorReferences(node: Element, element: Element, createElement: (tagName: string) => HTMLElement): void;
+    appendFootnoteID(xref: Element, footnotes: Element, rid: string, createElement: (tagName: string) => HTMLElement): void;
+    appendCorrespID(xref: Element, corresps: Element, rid: string, createElement: (tagName: string) => HTMLElement): void;
+    appendAffiliationID(affs: Element, rid: string, createElement: (tagName: string) => HTMLElement): void;
+    createAffiliations(front: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
+    createAffiliationElement(element: Element, priority: number, createElement: (tagName: string) => HTMLElement): HTMLElement;
+    appendEmail(element: Element, affiliation: Element): void;
+    setInstitutionAttrs(element: Element, affiliation: Element): void;
+    setAddressAttrs(element: Element, affiliation: Element): void;
+};

package/dist/types/jats/importer/jats-journal-meta-parser.d.ts

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { ObjectTypes } from '@manuscripts/json-schema';
 export type ISSN = {
     ISSN: string;
     publicationType?: string;
@@ -35,3 +36,12 @@ export declare const parseJournalMeta: (element: Element | null) => {
     publisherName: string | undefined;
     title: string | undefined;
 };
+export declare const parseJournal: (element: Element | null) => {
+    _id: string;
+    objectType: ObjectTypes;
+    abbreviatedTitles: AbbreviatedTitle[];
+    journalIdentifiers: JournalIdentifier[];
+    ISSNs: ISSN[];
+    publisherName: string | undefined;
+    title: string | undefined;
+};

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

@@ -1,12 +1,23 @@
-import { BibliographyItem } from '@manuscripts/json-schema';
-import { JATSComment } from './jats-comments';
+/*!
+ * © 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.
+ */
+import { BibliographyItemAttributes } from '../../schema';
 export declare class References {
-    items: Map<string, BibliographyItem>;
+    items: Map<string, BibliographyItemAttributes>;
     IDs: Map<string, string>;
-    comments: Map<string, JATSComment[]>;
     constructor();
-    add(item: BibliographyItem, id: string | null, comments: JATSComment[]): void;
-    getBibliographyItems(): BibliographyItem[];
-    getComments(id: string): JATSComment[];
-    private getValue;
+    add(item: BibliographyItemAttributes, id: string | null): void;
+    getBibliographyItems(): BibliographyItemAttributes[];
 }

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

@@ -13,8 +13,15 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Model } from '@manuscripts/json-schema';
-import { References } from './jats-references';
-export declare const parseJATSFront: (doc: Document, front: Element) => Model[];
-export declare const parseJATSBody: (doc: Document, body: Element, references?: References) => IterableIterator<Model>;
-export declare const parseJATSArticle: (doc: Document) => Model[];
+export declare const parseJATSArticle: (doc: Document, template?: string) => {
+    node: import("prosemirror-model").Node;
+    journal: {
+        _id: string;
+        objectType: import("@manuscripts/json-schema/dist/types").ObjectTypes;
+        abbreviatedTitles: import("./jats-journal-meta-parser").AbbreviatedTitle[];
+        journalIdentifiers: import("./jats-journal-meta-parser").JournalIdentifier[];
+        ISSNs: import("./jats-journal-meta-parser").ISSN[];
+        publisherName: string | undefined;
+        title: string | undefined;
+    };
+};

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

@@ -13,6 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export { parseJATSFront, parseJATSBody, parseJATSArticle } from './importer';
+export { parseJATSArticle, createArticleNode } from './importer';
 export * from './jats-exporter';
 export * from './jats-versions';
+export * from './timestamp';
+export * from './labels';

package/dist/types/jats/jats-exporter.d.ts

@@ -13,18 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Model } from '@manuscripts/json-schema';
+import { BibliographyItem, Journal } from '@manuscripts/json-schema';
 import { CitationProvider } from '@manuscripts/library';
 import { DOMSerializer } from 'prosemirror-model';
-import { CitationNode, ManuscriptFragment, ManuscriptNode } from '../schema';
-import { Target } from '../transformer/labels';
+import { CitationNode, ManuscriptNode } from '../schema';
 import { IDGenerator, MediaPathGenerator } from '../types';
 import { Version } from './jats-versions';
-interface Links {
-    self?: {
-        [key: string]: string;
-    };
-}
+import { Target } from './labels';
 export declare const createCounter: () => {
     increment: (field: string) => number;
 };
@@ -32,17 +27,11 @@ export type CSLOptions = {
     style: string;
     locale: string;
 };
-export interface JATSExporterOptions {
-    csl: CSLOptions;
+export type ExportOptions = {
     version?: Version;
-    doi?: string;
-    id?: string;
-    frontMatterOnly?: boolean;
-    links?: Links;
-    citationType?: 'element' | 'mixed';
-    idGenerator?: IDGenerator;
-    mediaPathGenerator?: MediaPathGenerator;
-}
+    journal?: Journal;
+    csl: CSLOptions;
+};
 export declare const buildCitations: (citations: CitationNode[]) => {
     citationID: string;
     citationItems: {
@@ -54,13 +43,12 @@ export declare const buildCitations: (citations: CitationNode[]) => {
 }[];
 export declare class JATSExporter {
     protected document: Document;
-    protected modelMap: Map<string, Model>;
-    protected models: Model[];
     protected serializer: DOMSerializer;
     protected labelTargets?: Map<string, Target>;
     protected citationTexts: Map<string, string>;
     protected citationProvider: CitationProvider;
-    protected generateCitations(fragment: ManuscriptFragment): {
+    protected manuscriptNode: ManuscriptNode;
+    protected generateCitations(): {
         citationID: string;
         citationItems: {
             id: string;
@@ -69,20 +57,20 @@ export declare class JATSExporter {
             noteIndex: number;
         };
     }[];
-    protected generateCitationTexts(fragment: ManuscriptFragment, csl: CSLOptions): void;
-    serializeToJATS: (fragment: ManuscriptFragment, modelMap: Map<string, Model>, manuscriptID: string, options: JATSExporterOptions) => Promise<string>;
+    protected getLibraryItem: (manuscriptID: string) => (id: string) => BibliographyItem | undefined;
+    protected generateCitationTexts(csl: CSLOptions, manuscriptID: string): void;
+    serializeToJATS: (manuscriptNode: ManuscriptNode, options: ExportOptions) => Promise<string>;
     private nodeFromJATS;
     protected rewriteMediaPaths: (generator: MediaPathGenerator) => Promise<void>;
     protected rewriteIDs: (generator?: IDGenerator) => Promise<void>;
     protected setTitleContent: (element: HTMLElement, title: string) => void;
-    protected buildFront: (doi?: string, id?: string, links?: Links) => HTMLElement;
+    protected buildFront: (journal?: Journal) => HTMLElement;
     protected buildDateElement: (timestamp: number, type: string) => HTMLElement;
     protected buildCountingElement: (tagName: string, count: number | undefined) => HTMLElement | undefined;
-    protected buildBody: (fragment: ManuscriptFragment) => HTMLBodyElement;
+    protected buildBody: () => HTMLBodyElement;
     protected buildBack: (body: HTMLElement) => HTMLElement;
     protected createSerializer: () => void;
     private createEquation;
-    protected serializeFragment: (fragment: ManuscriptFragment) => HTMLElement | DocumentFragment;
     protected serializeNode: (node: ManuscriptNode) => Node;
     private validateContributor;
     private buildContributors;
@@ -109,4 +97,3 @@ export declare class JATSExporter {
     private fillEmptyFootnotes;
     private fillEmptyTableFooters;
 }
-export {};

package/dist/types/{transformer → jats}/labels.d.ts

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { ManuscriptNode } from 'migration-base';
 import { ManuscriptFragment } from '../schema';
 export interface Target {
     type: string;
@@ -20,4 +21,4 @@ export interface Target {
     label: string;
     caption: string;
 }
-export declare const buildTargets: (fragment: ManuscriptFragment) => Map<string, Target>;
+export declare const buildTargets: (node: ManuscriptNode | ManuscriptFragment) => Map<string, Target>;

package/dist/types/lib/utils.d.ts

@@ -26,3 +26,6 @@ export declare const findParentNodeClosestToPos: ($pos: ResolvedPos, predicate:
     node: ProsemirrorNode;
 } | undefined;
 export declare const getTrimmedTextContent: (node: Element | Document | null, querySelector: string) => string | null | undefined;
+export declare const setElementAttributes: (element: Element, attributes: {
+    [key: string]: string | undefined;
+}) => void;

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

@@ -13,14 +13,36 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { BibliographicDate, BibliographicName } from '@manuscripts/json-schema';
 import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
-interface Attrs {
+type LooseNumber = string | number;
+export interface BibliographyItemAuthor {
+    given?: string;
+    family?: string;
+    _id: string;
+    objectType: 'MPBibliographicName';
+}
+export interface BibliographyItemDate {
+    'date-parts'?: [
+        [
+            LooseNumber,
+            LooseNumber?,
+            LooseNumber?
+        ],
+        [
+            LooseNumber,
+            LooseNumber?,
+            LooseNumber?
+        ]?
+    ];
+    _id: string;
+    objectType: 'MPBibliographicDate';
+}
+export interface BibliographyItemAttributes {
     id: string;
     type: string;
-    author?: BibliographicName[];
-    issued?: BibliographicDate;
+    author?: BibliographyItemAuthor[];
+    issued?: BibliographyItemDate;
     containerTitle?: string;
     doi?: string;
     volume?: string;
@@ -29,9 +51,10 @@ interface Attrs {
     page?: string;
     title?: string;
     literal?: string;
+    paragraphStyle?: string;
 }
 export interface BibliographyItemNode extends ManuscriptNode {
-    attrs: Attrs;
+    attrs: BibliographyItemAttributes;
 }
 export declare const bibliographyItem: NodeSpec;
 export {};

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

@@ -1,9 +1,18 @@
 import { BibliographicName } from '@manuscripts/json-schema';
 import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
+export type ContributorCorresp = {
+    correspID: string;
+    correspLabel: string;
+};
+export type ContributorFootnote = {
+    noteID: string;
+    noteLabel: string;
+};
 interface Attrs {
     id: string;
     role: string;
+    corresp: ContributorCorresp[];
     affiliations: string[];
     bibliographicName: BibliographicName;
     userID: string;
@@ -13,6 +22,7 @@ interface Attrs {
     ORCIDIdentifier: string;
     priority: number;
     isJointContributor: boolean;
+    footnote: ContributorFootnote[];
 }
 export interface ContributorNode extends ManuscriptNode {
     attrs: Attrs;

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

@@ -17,6 +17,7 @@ import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
 interface Attrs {
     id: string;
+    type: string;
 }
 export interface KeywordGroupNode extends ManuscriptNode {
     attrs: Attrs;

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

@@ -15,6 +15,9 @@
  */
 import { ObjectTypes } from '@manuscripts/json-schema';
 import { ManuscriptNodeType } from '../schema';
-import { ExtraObjectTypes } from './object-types';
-export declare const generateNodeID: (type: ManuscriptNodeType) => string;
+export declare enum ExtraObjectTypes {
+    PlaceholderElement = "MPPlaceholderElement",
+    GeneralTableFootnote = "MPGeneralTableFootnote"
+}
 export declare const generateID: (objectType: ObjectTypes | ExtraObjectTypes) => string;
+export declare const generateNodeID: (type: ManuscriptNodeType) => string;

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

@@ -13,24 +13,8 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export * from './builders';
-export * from './decode';
-export * from './document-object-types';
-export * from './encode';
-export * from './filename';
-export * from './highlight-markers';
-export * from './html';
 export * from './id';
-export * from './labels';
-export * from './manuscript-dependencies';
-export * from './models';
 export * from './node-names';
 export * from './node-title';
 export * from './node-types';
-export * from './object-types';
-export * from './project-bundle';
 export * from './section-category';
-export * from './serializer';
-export * from './timestamp';
-export * from './update-identifiers';
-export { createTestDoc } from './__tests__/__helpers__/doc';

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const VERSION = "2.3.36";
+export declare const VERSION = "2.3.37-LEAN-3911.1";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.3.36",
+  "version": "2.3.37-LEAN-3911.1",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -38,6 +38,7 @@
     "mime": "^3.0.0",
     "prosemirror-model": "^1.18.3",
     "prosemirror-tables": "^1.3.5",
+    "prosemirror-utils": "^1.2.2",
     "semver": "^7.6.2",
     "uuid": "^9.0.0",
     "w3c-xmlserializer": "^4.0.0"
@@ -82,4 +83,4 @@
     "rimraf": "^3.0.2",
     "typescript": "^4.0.5"
   }
-}
+}