@manuscripts/transform 3.0.38 → 3.0.40

package/dist/cjs/jats/exporter/jats-exporter.js

@@ -343,6 +343,16 @@ class JATSExporter {
             if (!journalMeta.hasChildNodes()) {
                 journalMeta.remove();
             }
+            const selfUri = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.attachment).find((result) => result.node.attrs.type === 'document');
+            if (selfUri) {
+                const selfUriElement = this.document.createElement('self-uri');
+                selfUriElement.setAttribute('content-type', selfUri.node.attrs.type);
+                selfUriElement.setAttributeNS(XLINK_NAMESPACE, 'href', selfUri.node.attrs.href);
+                const insertBeforeElements = articleMeta.querySelector('related-article, related-object, abstract, trans-abstract, kwd-group, funding-group, support-group, conference, counts, custom-meta-group');
+                insertBeforeElements
+                    ? articleMeta.insertBefore(selfUriElement, insertBeforeElements)
+                    : articleMeta.appendChild(selfUriElement);
+            }
             return front;
         };
         this.buildDateElement = (timestamp, type) => {
@@ -543,6 +553,8 @@ class JATSExporter {
         };
         this.createSerializer = () => {
             const nodes = {
+                attachment: () => '',
+                attachments: () => '',
                 image_element: (node) => node.content.firstChild
                     ? createGraphic(node.content.firstChild, false)
                     : '',

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

@@ -74,9 +74,7 @@ const markComments = (doc) => {
             });
         }
     }
-    if (comments.hasChildNodes()) {
-        doc.documentElement.appendChild(comments);
-    }
+    doc.documentElement.appendChild(comments);
 };
 exports.markComments = markComments;
 const createHighlightMarkerElement = (doc, id) => {

package/dist/cjs/jats/importer/jats-dom-parser.js

@@ -222,6 +222,18 @@ class JATSDOMParser {
             return attrs;
         };
         this.nodes = [
+            {
+                tag: 'attachments > self-uri',
+                node: 'attachment',
+                getAttrs: (node) => {
+                    const element = node;
+                    return {
+                        id: element.getAttribute('id'),
+                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href') || '',
+                        type: element.getAttribute('content-type') || '',
+                    };
+                },
+            },
             {
                 tag: 'article',
                 node: 'manuscript',
@@ -255,6 +267,10 @@ class JATSDOMParser {
                     };
                 },
             },
+            {
+                tag: 'comments',
+                node: 'comments',
+            },
             {
                 tag: 'comment',
                 node: 'comment',

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

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fixTables = exports.orderTableFootnote = exports.moveReferencesToBackmatter = exports.createSupplementaryMaterialsSection = exports.createKeywordsSection = exports.moveCaptionsToEnd = exports.createBackmatter = exports.createAbstracts = exports.createBody = exports.createBoxedElementSection = exports.moveAbstracts = exports.moveAffiliations = exports.moveContributors = exports.moveAwards = exports.moveAuthorNotes = exports.moveTitle = exports.addMissingCaptions = void 0;
+exports.fixTables = exports.createAttachments = exports.orderTableFootnote = exports.moveReferencesToBackmatter = exports.createSupplementaryMaterialsSection = exports.createKeywordsSection = exports.moveCaptionsToEnd = exports.createBackmatter = exports.createAbstracts = exports.createBody = exports.createBoxedElementSection = exports.moveAbstracts = exports.moveAffiliations = exports.moveContributors = exports.moveAwards = exports.moveAuthorNotes = exports.moveTitle = exports.addMissingCaptions = void 0;
 const deafults_1 = require("../../lib/deafults");
 const jats_parser_utils_1 = require("./jats-parser-utils");
 const removeNodeFromParent = (node) => node.parentNode && node.parentNode.removeChild(node);
@@ -359,6 +359,16 @@ const orderTableFootnote = (doc, body) => {
     });
 };
 exports.orderTableFootnote = orderTableFootnote;
+const createAttachments = (doc, createElement) => {
+    const attachments = createElement('attachments');
+    doc
+        .querySelectorAll('self-uri')
+        .forEach((attachment) => attachments.appendChild(attachment));
+    if (attachments.children.length > 0) {
+        doc.documentElement.appendChild(attachments);
+    }
+};
+exports.createAttachments = createAttachments;
 const fixTables = (doc, body, createElement) => {
     const tableWraps = body.querySelectorAll('table-wrap');
     tableWraps.forEach((tableWrap) => {

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

@@ -48,6 +48,7 @@ const processJATS = (doc, sectionCategories) => {
     (0, jats_transformations_1.createKeywordsSection)(doc, body, createElement);
     (0, jats_transformations_1.fixTables)(doc, body, createElement);
     (0, jats_transformations_1.orderTableFootnote)(doc, body);
+    (0, jats_transformations_1.createAttachments)(doc, createElement);
     const back = doc.querySelector('back');
     if (!back) {
         return;

package/dist/cjs/schema/index.js

@@ -35,6 +35,8 @@ const marks_1 = require("./marks");
 const abstracts_1 = require("./nodes/abstracts");
 const affiliation_1 = require("./nodes/affiliation");
 const affiliations_1 = require("./nodes/affiliations");
+const attachment_1 = require("./nodes/attachment");
+const attachments_1 = require("./nodes/attachments");
 const attribution_1 = require("./nodes/attribution");
 const author_notes_1 = require("./nodes/author_notes");
 const award_1 = require("./nodes/award");
@@ -160,6 +162,8 @@ __exportStar(require("./nodes/table_element_footer"), exports);
 __exportStar(require("./nodes/text"), exports);
 __exportStar(require("./nodes/title"), exports);
 __exportStar(require("./types"), exports);
+__exportStar(require("./nodes/attachment"), exports);
+__exportStar(require("./nodes/attachments"), exports);
 exports.schema = new prosemirror_model_1.Schema({
     marks: {
         bold: marks_1.bold,
@@ -247,5 +251,7 @@ exports.schema = new prosemirror_model_1.Schema({
         award: award_1.award,
         embed: embed_1.embed,
         image_element: image_element_1.imageElement,
+        attachment: attachment_1.attachment,
+        attachments: attachments_1.attachments,
     },
 });

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

@@ -0,0 +1,21 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isAttachmentNode = exports.attachment = void 0;
+exports.attachment = {
+    attrs: {
+        id: { default: '' },
+        type: { default: '' },
+        href: { default: '' },
+    },
+    toDOM: (node) => {
+        return [
+            'div',
+            {
+                class: 'attachment',
+                id: node.attrs.id,
+            },
+        ];
+    },
+};
+const isAttachmentNode = (node) => node.type === node.type.schema.nodes.attachment;
+exports.isAttachmentNode = isAttachmentNode;

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

@@ -0,0 +1,35 @@
+"use strict";
+/*!
+ * © 2025 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.isAttachmentsNode = exports.attachments = void 0;
+exports.attachments = {
+    content: 'attachment*',
+    attrs: {
+        id: { default: '' },
+    },
+    toDOM: (node) => {
+        return [
+            'div',
+            {
+                class: 'attachments',
+                id: node.attrs.id,
+            },
+        ];
+    },
+};
+const isAttachmentsNode = (node) => node.type === node.type.schema.nodes.attachments;
+exports.isAttachmentsNode = isAttachmentsNode;

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

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.isManuscriptNode = exports.manuscript = void 0;
 exports.manuscript = {
-    content: 'title? contributors? affiliations? author_notes? awards? keywords? supplements? abstracts body backmatter comments',
+    content: 'title? contributors? affiliations? author_notes? awards? keywords? supplements? abstracts body backmatter comments attachments?',
     attrs: {
         id: { default: '' },
         doi: { default: '' },

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "3.0.38";
+exports.VERSION = "3.0.40";

package/dist/es/jats/exporter/jats-exporter.js

@@ -335,6 +335,16 @@ export class JATSExporter {
             if (!journalMeta.hasChildNodes()) {
                 journalMeta.remove();
             }
+            const selfUri = findChildrenByType(this.manuscriptNode, schema.nodes.attachment).find((result) => result.node.attrs.type === 'document');
+            if (selfUri) {
+                const selfUriElement = this.document.createElement('self-uri');
+                selfUriElement.setAttribute('content-type', selfUri.node.attrs.type);
+                selfUriElement.setAttributeNS(XLINK_NAMESPACE, 'href', selfUri.node.attrs.href);
+                const insertBeforeElements = articleMeta.querySelector('related-article, related-object, abstract, trans-abstract, kwd-group, funding-group, support-group, conference, counts, custom-meta-group');
+                insertBeforeElements
+                    ? articleMeta.insertBefore(selfUriElement, insertBeforeElements)
+                    : articleMeta.appendChild(selfUriElement);
+            }
             return front;
         };
         this.buildDateElement = (timestamp, type) => {
@@ -535,6 +545,8 @@ export class JATSExporter {
         };
         this.createSerializer = () => {
             const nodes = {
+                attachment: () => '',
+                attachments: () => '',
                 image_element: (node) => node.content.firstChild
                     ? createGraphic(node.content.firstChild, false)
                     : '',

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

@@ -71,9 +71,7 @@ export const markComments = (doc) => {
             });
         }
     }
-    if (comments.hasChildNodes()) {
-        doc.documentElement.appendChild(comments);
-    }
+    doc.documentElement.appendChild(comments);
 };
 const createHighlightMarkerElement = (doc, id) => {
     const highlightMarker = doc.createElement('highlight-marker');

package/dist/es/jats/importer/jats-dom-parser.js

@@ -219,6 +219,18 @@ export class JATSDOMParser {
             return attrs;
         };
         this.nodes = [
+            {
+                tag: 'attachments > self-uri',
+                node: 'attachment',
+                getAttrs: (node) => {
+                    const element = node;
+                    return {
+                        id: element.getAttribute('id'),
+                        href: element.getAttributeNS(this.XLINK_NAMESPACE, 'href') || '',
+                        type: element.getAttribute('content-type') || '',
+                    };
+                },
+            },
             {
                 tag: 'article',
                 node: 'manuscript',
@@ -252,6 +264,10 @@ export class JATSDOMParser {
                     };
                 },
             },
+            {
+                tag: 'comments',
+                node: 'comments',
+            },
             {
                 tag: 'comment',
                 node: 'comment',

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

@@ -340,6 +340,15 @@ export const orderTableFootnote = (doc, body) => {
         fnGroup.replaceChildren(...fns);
     });
 };
+export const createAttachments = (doc, createElement) => {
+    const attachments = createElement('attachments');
+    doc
+        .querySelectorAll('self-uri')
+        .forEach((attachment) => attachments.appendChild(attachment));
+    if (attachments.children.length > 0) {
+        doc.documentElement.appendChild(attachments);
+    }
+};
 export const fixTables = (doc, body, createElement) => {
     const tableWraps = body.querySelectorAll('table-wrap');
     tableWraps.forEach((tableWrap) => {

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

@@ -18,7 +18,7 @@ import { markComments } from './jats-comments';
 import { JATSDOMParser } from './jats-dom-parser';
 import { parseJournal } from './jats-journal-meta-parser';
 import { updateDocumentIDs } from './jats-parser-utils';
-import { addMissingCaptions, createAbstracts, createBackmatter, createBody, createBoxedElementSection, createKeywordsSection, createSupplementaryMaterialsSection, fixTables, moveAffiliations, moveAuthorNotes, moveAwards, moveCaptionsToEnd, moveContributors, moveReferencesToBackmatter, moveTitle, orderTableFootnote, } from './jats-transformations';
+import { addMissingCaptions, createAbstracts, createAttachments, createBackmatter, createBody, createBoxedElementSection, createKeywordsSection, createSupplementaryMaterialsSection, fixTables, moveAffiliations, moveAuthorNotes, moveAwards, moveCaptionsToEnd, moveContributors, moveReferencesToBackmatter, moveTitle, orderTableFootnote, } from './jats-transformations';
 const processJATS = (doc, sectionCategories) => {
     const createElement = createElementFn(doc);
     markComments(doc);
@@ -45,6 +45,7 @@ const processJATS = (doc, sectionCategories) => {
     createKeywordsSection(doc, body, createElement);
     fixTables(doc, body, createElement);
     orderTableFootnote(doc, body);
+    createAttachments(doc, createElement);
     const back = doc.querySelector('back');
     if (!back) {
         return;

package/dist/es/schema/index.js

@@ -18,6 +18,8 @@ import { bold, code, italic, smallcaps, strikethrough, styled, subscript, supers
 import { abstracts } from './nodes/abstracts';
 import { affiliation } from './nodes/affiliation';
 import { affiliations } from './nodes/affiliations';
+import { attachment } from './nodes/attachment';
+import { attachments } from './nodes/attachments';
 import { attribution } from './nodes/attribution';
 import { authorNotes } from './nodes/author_notes';
 import { award } from './nodes/award';
@@ -143,6 +145,8 @@ export * from './nodes/table_element_footer';
 export * from './nodes/text';
 export * from './nodes/title';
 export * from './types';
+export * from './nodes/attachment';
+export * from './nodes/attachments';
 export const schema = new Schema({
     marks: {
         bold,
@@ -230,5 +234,7 @@ export const schema = new Schema({
         award,
         embed,
         image_element: imageElement,
+        attachment,
+        attachments,
     },
 });

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

@@ -0,0 +1,17 @@
+export const attachment = {
+    attrs: {
+        id: { default: '' },
+        type: { default: '' },
+        href: { default: '' },
+    },
+    toDOM: (node) => {
+        return [
+            'div',
+            {
+                class: 'attachment',
+                id: node.attrs.id,
+            },
+        ];
+    },
+};
+export const isAttachmentNode = (node) => node.type === node.type.schema.nodes.attachment;

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

@@ -0,0 +1,31 @@
+/*!
+ * © 2025 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 const attachments = {
+    content: 'attachment*',
+    attrs: {
+        id: { default: '' },
+    },
+    toDOM: (node) => {
+        return [
+            'div',
+            {
+                class: 'attachments',
+                id: node.attrs.id,
+            },
+        ];
+    },
+};
+export const isAttachmentsNode = (node) => node.type === node.type.schema.nodes.attachments;

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const manuscript = {
-    content: 'title? contributors? affiliations? author_notes? awards? keywords? supplements? abstracts body backmatter comments',
+    content: 'title? contributors? affiliations? author_notes? awards? keywords? supplements? abstracts body backmatter comments attachments?',
     attrs: {
         id: { default: '' },
         doi: { default: '' },

package/dist/es/version.js

@@ -1 +1 @@
-export const VERSION = "3.0.38";
+export const VERSION = "3.0.40";

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

@@ -31,4 +31,5 @@ export declare const createKeywordsSection: (document: Document, body: Element,
 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 createAttachments: (doc: Document, createElement: CreateElement) => void;
 export declare const fixTables: (doc: Document, body: Element, createElement: CreateElement) => void;

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

@@ -78,4 +78,6 @@ export * from './nodes/table_element_footer';
 export * from './nodes/text';
 export * from './nodes/title';
 export * from './types';
+export * from './nodes/attachment';
+export * from './nodes/attachments';
 export declare const schema: Schema<Nodes, Marks>;

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

@@ -0,0 +1,12 @@
+import { NodeSpec } from 'prosemirror-model';
+import { ManuscriptNode } from '../types';
+export interface AttachmentAttrs {
+    id: string;
+    href: string;
+    type: string;
+}
+export interface AttachmentNode extends ManuscriptNode {
+    attrs: AttachmentAttrs;
+}
+export declare const attachment: NodeSpec;
+export declare const isAttachmentNode: (node: ManuscriptNode) => node is AttachmentNode;

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

@@ -0,0 +1,25 @@
+/*!
+ * © 2025 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 { NodeSpec } from 'prosemirror-model';
+import { ManuscriptNode } from '../types';
+export interface AttachmentsAttrs {
+    id: string;
+}
+export interface AttachmentsNode extends ManuscriptNode {
+    attrs: AttachmentsAttrs;
+}
+export declare const attachments: NodeSpec;
+export declare const isAttachmentsNode: (node: ManuscriptNode) => node is AttachmentsNode;

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

@@ -17,7 +17,7 @@ import { Fragment, Mark as ProsemirrorMark, MarkType, Node as ProsemirrorNode, N
 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';
-export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'list' | 'caption' | 'caption_title' | 'comment' | 'comments' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figcaption' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keyword_group' | 'keywords' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'abstracts' | 'body' | 'backmatter' | 'missing_figure' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'table_header' | 'text' | 'text_block' | 'affiliation' | 'contributor' | 'table_element_footer' | 'title' | 'affiliations' | 'contributors' | 'supplements' | 'supplement' | 'author_notes' | 'corresp' | 'general_table_footnote' | 'box_element' | 'awards' | 'award' | 'embed' | 'image_element';
+export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'list' | 'caption' | 'caption_title' | 'comment' | 'comments' | 'citation' | 'cross_reference' | 'doc' | 'equation' | 'equation_element' | 'figcaption' | 'figure' | 'graphical_abstract_section' | 'figure_element' | 'footnote' | 'footnotes_element' | 'footnotes_section' | 'hard_break' | 'highlight_marker' | 'inline_equation' | 'inline_footnote' | 'keyword' | 'keywords_element' | 'keyword_group' | 'keywords' | 'link' | 'list_item' | 'listing' | 'listing_element' | 'manuscript' | 'abstracts' | 'body' | 'backmatter' | 'missing_figure' | 'paragraph' | 'placeholder' | 'placeholder_element' | 'pullquote_element' | 'section' | 'section_label' | 'section_title' | 'section_title_plain' | 'table' | 'table_cell' | 'table_element' | 'table_row' | 'table_colgroup' | 'table_col' | 'table_header' | 'text' | 'text_block' | 'affiliation' | 'contributor' | 'table_element_footer' | 'title' | 'affiliations' | 'contributors' | 'supplements' | 'supplement' | 'author_notes' | 'corresp' | 'general_table_footnote' | 'box_element' | 'awards' | 'award' | 'embed' | 'image_element' | 'attachment' | 'attachments';
 export type ManuscriptSchema = Schema<Nodes, Marks>;
 export type ManuscriptEditorState = EditorState;
 export type ManuscriptEditorView = EditorView;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const VERSION = "3.0.38";
+export declare const VERSION = "3.0.40";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "3.0.38",
+  "version": "3.0.40",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",