@manuscripts/transform 2.6.0 → 2.6.1-LEAN-3911.0

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

@@ -19,9 +19,7 @@ export const highlightMarker = {
     atom: true,
     attrs: {
         id: { default: '' },
-        tid: { default: '' },
         position: { default: '' },
-        dataTracked: { default: null },
     },
     parseDOM: [
         {
@@ -30,7 +28,6 @@ export const highlightMarker = {
                 const dom = p;
                 return {
                     id: dom.getAttribute('id'),
-                    tid: dom.getAttribute('data-target-id'),
                     position: dom.getAttribute('data-position'),
                 };
             },
@@ -41,7 +38,6 @@ export const 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/es/transformer/id.js

@@ -18,6 +18,3 @@ import { nodeTypesMap } from './node-types';
 export const generateNodeID = (type) => {
     return nodeTypesMap.get(type) + ':' + uuid().toUpperCase();
 };
-export const generateID = (objectType) => {
-    return objectType + ':' + 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 = "2.6.0";
+export const VERSION = "2.6.1-LEAN-3911.0";

package/dist/types/index.d.ts

@@ -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, JSONNode } from './schema/migration/migrate';
+export { JSONNode, migrateFor } from './schema/migration/migrate';
 export { isSectionLabelNode } from './schema/nodes/section_label';
+export * from './transformer';

package/dist/types/jats/{jats-exporter.d.ts → exporter/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 { IDGenerator, MediaPathGenerator } from '../types';
+import { CitationNode, ManuscriptNode } from '../../schema';
+import { IDGenerator } 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 +57,19 @@ 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 +96,3 @@ export declare class JATSExporter {
     private fillEmptyFootnotes;
     private fillEmptyTableFooters;
 }
-export {};

package/dist/types/jats/{jats-versions.d.ts → exporter/jats-versions.d.ts}

@@ -18,6 +18,5 @@ interface VersionIds {
     systemId: string;
 }
 export type Version = '1.1' | '1.2d1' | '1.2';
-export declare const supportedVersions: () => Version[];
 export declare const selectVersionIds: (version: Version) => VersionIds;
 export {};

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

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ManuscriptFragment } from '../schema';
+import { ManuscriptFragment, ManuscriptNode } from '../../schema';
 export interface Target {
     type: string;
     id: string;
     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/{es/transformer/footnote-category.js → types/jats/importer/create-article-node.d.ts}

@@ -1,5 +1,5 @@
 /*!
- * © 2021 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.
@@ -13,4 +13,5 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export const buildFootnoteCategory = (category) => (category && `MPFootnoteCategory:${category}`) || undefined;
+import { ManuscriptAttrs } from '../../schema';
+export declare const createArticleNode: (attrs: Partial<ManuscriptAttrs>) => import("prosemirror-model").Node;

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

@@ -13,18 +13,5 @@
  * 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;
-    text: string;
-};
-export type JATSCommentMark = {
-    token: string;
-    comment: JATSComment;
-};
-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 DEFAULT_PROFILE_ID = "MPUserProfile:0000000000000000000000000000000000000001";
+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-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 +36,11 @@ export declare const parseJournalMeta: (element: Element | null) => {
     publisherName: string | undefined;
     title: string | undefined;
 };
+export declare const parseJournal: (doc: Document) => {
+    objectType: ObjectTypes;
+    abbreviatedTitles: AbbreviatedTitle[];
+    journalIdentifiers: JournalIdentifier[];
+    ISSNs: ISSN[];
+    publisherName: string | undefined;
+    title: string | undefined;
+} | undefined;

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

@@ -14,5 +14,5 @@
  * limitations under the License.
  */
 import { ManuscriptNode } from '../../schema';
-export declare const updateDocumentIDs: (node: ManuscriptNode, replacements: Map<string, string>) => string[];
-export declare const htmlFromJatsNode: (element: Element | undefined | null, createElement: (tagName: string) => HTMLElement) => string | undefined;
+export declare const updateDocumentIDs: (node: ManuscriptNode) => string[];
+export declare const htmlFromJatsNode: (element: Element | undefined | null, createElement?: ((tagName: string) => HTMLElement) | undefined) => string | undefined;

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

@@ -0,0 +1,32 @@
+/*!
+ * © 2020 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 type CreateElement = (tagName: string) => HTMLElement;
+export declare const ensureSection: (body: Element, createElement: CreateElement) => void;
+export declare const moveTitle: (front: Element, createElement: CreateElement) => void;
+export declare const moveAuthorNotes: (front: Element, createElement: CreateElement) => void;
+export declare const moveContributors: (front: Element, createElement: CreateElement) => void;
+export declare const moveAffiliations: (front: Element, createElement: CreateElement) => void;
+export declare const moveAbstracts: (doc: Document, group: Element, createElement: CreateElement) => void;
+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 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;
+export declare const moveReferencesToBackmatter: (body: Element, back: Element, createElement: CreateElement) => void;
+export declare const orderTableFootnote: (doc: Document, body: Element) => void;
+export declare const fixTables: (doc: Document, body: Element, createElement: CreateElement) => void;

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[];
+import { ActualManuscriptNode } from '../../schema';
+export declare const parseJATSArticle: (doc: Document, template?: string) => {
+    node: ActualManuscriptNode;
+    journal: {
+        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;
+    } | 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 * from './jats-exporter';
-export * from './jats-versions';
+export * from './exporter/jats-exporter';
+export * from './exporter/jats-versions';
+export * from './exporter/labels';
+export * from './importer/create-article-node';
+export { parseJATSArticle } from './importer/parse-jats-article';

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

@@ -0,0 +1 @@
+export type IDGenerator = (element: Element) => Promise<string | null>;

package/dist/{es/transformer/models.js → types/lib/deafults.d.ts}

@@ -1,5 +1,5 @@
 /*!
- * © 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.
@@ -13,4 +13,4 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export {};
+export declare const defaultTitle = "Untitled Manuscript";

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

@@ -26,3 +26,4 @@ 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 timestamp: () => number;

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

@@ -16,7 +16,7 @@
 import { BibliographicDate, BibliographicName } from '@manuscripts/json-schema';
 import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
-interface Attrs {
+export interface BibliographyItemAttrs {
     id: string;
     type: string;
     author?: BibliographicName[];
@@ -29,9 +29,9 @@ interface Attrs {
     page?: string;
     title?: string;
     literal?: string;
+    paragraphStyle?: string;
 }
 export interface BibliographyItemNode extends ManuscriptNode {
-    attrs: Attrs;
+    attrs: BibliographyItemAttrs;
 }
 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/highlight_marker.d.ts

@@ -17,9 +17,7 @@ import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
 interface Attrs {
     id: string;
-    tid: string;
     position: string;
-    text: string;
 }
 export interface HighlightMarkerNode 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/schema/nodes/manuscript.d.ts

@@ -16,13 +16,14 @@
 import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
 export interface ActualManuscriptNode extends ManuscriptNode {
-    attrs: {
-        id: string;
-        doi: string;
-        articleType: string;
-        prototype: string;
-        primaryLanguageCode: string;
-    };
+    attrs: ManuscriptAttrs;
+}
+export interface ManuscriptAttrs {
+    id: string;
+    doi: string;
+    articleType: string;
+    prototype: string;
+    primaryLanguageCode: string;
 }
 export declare const manuscript: NodeSpec;
 export declare const isManuscriptNode: (node: ManuscriptNode) => node is import("prosemirror-model").Node;

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

@@ -17,9 +17,6 @@ import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
 interface Attrs {
     id: string;
-    title: string;
-    subtitle: string;
-    runningTitle: string;
     placeholder: string;
 }
 export interface TitleNode extends ManuscriptNode {

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

@@ -13,8 +13,5 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ObjectTypes } from '@manuscripts/json-schema';
 import { ManuscriptNodeType } from '../schema';
-import { ExtraObjectTypes } from './object-types';
 export declare const generateNodeID: (type: ManuscriptNodeType) => string;
-export declare const generateID: (objectType: ObjectTypes | ExtraObjectTypes) => 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 = "2.6.0";
+export declare const VERSION = "2.6.1-LEAN-3911.0";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.6.0",
+  "version": "2.6.1-LEAN-3911.0",
   "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"