@manuscripts/transform 1.5.6 → 1.5.7-LEAN-3030-1

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

@@ -424,9 +424,11 @@ export class JATSExporter {
             }
         };
         this.buildBody = (fragment) => {
-            const content = this.serializeFragment(fragment);
             const body = this.document.createElement('body');
-            body.appendChild(content);
+            fragment.forEach((cFragment) => {
+                const serializedNode = this.serializeNode(cFragment);
+                body.append(...serializedNode.childNodes);
+            });
             this.fixBody(body, fragment);
             return body;
         };
@@ -593,8 +595,8 @@ export class JATSExporter {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
                 title: () => '',
-                affiliations_section: () => '',
-                contributors_section: () => '',
+                affiliations: () => '',
+                contributors: () => '',
                 table_element_footer: () => ['table-wrap-foot', 0],
                 contributor: () => '',
                 affiliation: () => '',
@@ -603,7 +605,10 @@ export class JATSExporter {
                 bibliography_element: () => '',
                 bibliography_item: () => '',
                 comment_list: () => '',
-                keywords_group: () => '',
+                keyword_group: () => '',
+                body: () => ['body', 0],
+                abstracts: () => ['abstract', 0],
+                backmatter: () => ['backmatter', 0],
                 bibliography_section: (node) => [
                     'ref-list',
                     { id: normalizeID(node.attrs.id) },
@@ -619,26 +624,15 @@ export class JATSExporter {
                     return ['title', 0];
                 },
                 citation: (node) => {
-                    if (!node.attrs.rid) {
-                        warn(`${node.attrs.id} has no rid`);
-                        return node.attrs.label;
-                    }
-                    const rids = node.attrs
-                        .embeddedCitationItems.filter((item) => {
-                        if (!this.modelMap.has(item.bibliographyItem)) {
-                            warn(`Missing ${item.bibliographyItem} referenced by ${node.attrs.rid}`);
-                            return false;
-                        }
-                        return true;
-                    });
+                    const citation = node;
+                    const rids = citation.attrs.rids;
                     if (!rids.length) {
-                        warn(`${node.attrs.rid} has no confirmed rids`);
                         return '';
                     }
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'bibr');
-                    xref.setAttribute('rid', rids.map((item) => normalizeID(item.bibliographyItem)).join(' '));
-                    if (node.attrs.contents) {
+                    xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    if (citation.attrs.contents) {
                         const text = textFromHTML(node.attrs.contents);
                         if (text !== null && text.length) {
                             xref.textContent = text;
@@ -647,41 +641,27 @@ export class JATSExporter {
                     return xref;
                 },
                 cross_reference: (node) => {
-                    var _a;
-                    if (!node.attrs.rid) {
-                        warn(`${node.attrs.id} has no rid`);
-                        return node.attrs.label;
+                    const cross = node;
+                    const rids = cross.attrs.rids;
+                    if (!rids.length) {
+                        return cross.attrs.label;
                     }
-                    const auxiliaryObjectReference = getModel(node.attrs.rid);
-                    if (!auxiliaryObjectReference) {
-                        warn(`Missing model ${node.attrs.rid}`);
-                        return node.attrs.label;
+                    const text = cross.attrs.customLabel || cross.attrs.label;
+                    const model = getModel(rids[0]);
+                    if (!model) {
+                        warn('');
+                        return text;
                     }
                     const xref = this.document.createElement('xref');
-                    const referencedObject = getModel(auxiliaryObjectReference.referencedObject ||
-                        ((auxiliaryObjectReference === null || auxiliaryObjectReference === void 0 ? void 0 : auxiliaryObjectReference.referencedObjects) &&
-                            auxiliaryObjectReference.referencedObjects[0]));
-                    if (referencedObject) {
-                        const refType = chooseRefType(referencedObject.objectType);
-                        if (refType) {
-                            xref.setAttribute('ref-type', refType);
-                        }
-                        else {
-                            warn(`Unset ref-type for objectType ${referencedObject.objectType}`);
-                        }
+                    const type = chooseRefType(model.objectType);
+                    if (type) {
+                        xref.setAttribute('ref-type', type);
                     }
-                    const getReferencedObjectId = (referencedObject) => {
-                        return normalizeID(referencedObject);
-                    };
-                    if (auxiliaryObjectReference.referencedObjects) {
-                        const rid = (_a = auxiliaryObjectReference.referencedObjects) === null || _a === void 0 ? void 0 : _a.map((referencedObject) => getReferencedObjectId(referencedObject)).join(' ');
-                        xref.setAttribute('rid', rid);
-                    }
-                    if (auxiliaryObjectReference.referencedObject) {
-                        const rid = getReferencedObjectId(auxiliaryObjectReference.referencedObject);
-                        xref.setAttribute('rid', rid);
+                    else {
+                        warn(`Unset ref-type for objectType ${model.objectType}`);
                     }
-                    xref.textContent = node.attrs.customLabel || node.attrs.label;
+                    xref.setAttribute('rid', normalizeID(rids.join(' ')));
+                    xref.textContent = text;
                     return xref;
                 },
                 doc: () => '',
@@ -776,13 +756,13 @@ export class JATSExporter {
                 inline_footnote: (node) => {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'fn');
-                    xref.setAttribute('rid', normalizeID(node.attrs.rid));
+                    xref.setAttribute('rid', normalizeID(node.attrs.rids.join(' ')));
                     xref.textContent = node.attrs.contents;
                     return xref;
                 },
                 keyword: () => '',
                 keywords_element: () => '',
-                keywords_section: () => '',
+                keywords: () => '',
                 link: (node) => {
                     const text = node.textContent;
                     if (!text) {

package/dist/es/lib/section-group-type.js

@@ -0,0 +1,27 @@
+/*!
+ * © 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.
+ */
+export const abstractsType = {
+    _id: 'abstracts',
+    title: 'Abstracts',
+};
+export const bodyType = {
+    _id: 'body',
+    title: 'Body',
+};
+export const backmatterType = {
+    _id: 'backmatter',
+    title: 'Backmatter',
+};

package/dist/es/lib/utils.js

@@ -84,3 +84,11 @@ 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 groupBy = (list, getKey) => list.reduce((previous, currentItem) => {
+    const group = getKey(currentItem);
+    if (!previous[group]) {
+        previous[group] = [];
+    }
+    previous[group].push(currentItem);
+    return previous;
+}, {});

package/dist/es/schema/index.js

@@ -16,7 +16,7 @@
 import { Schema } from 'prosemirror-model';
 import { bold, code, italic, smallcaps, strikethrough, styled, subscript, superscript, tracked_delete, tracked_insert, underline, } from './marks';
 import { affiliation } from './nodes/affiliation';
-import { affiliationsSection } from './nodes/affiliations_section';
+import { affiliations } from './nodes/affiliations';
 import { attribution } from './nodes/attribution';
 import { bibliographyElement } from './nodes/bibliography_element';
 import { bibliographyItem } from './nodes/bibliography_item';
@@ -28,7 +28,8 @@ import { citation } from './nodes/citation';
 import { comment } from './nodes/comment';
 import { commentList } from './nodes/comment_list';
 import { contributor } from './nodes/contributor';
-import { contributorsSection } from './nodes/contributors_section';
+import { contributors } from './nodes/contributors';
+import { coreSection } from './nodes/core_section';
 import { crossReference } from './nodes/cross_reference';
 import { doc } from './nodes/doc';
 import { equation } from './nodes/equation';
@@ -45,9 +46,9 @@ import { highlightMarker } from './nodes/highlight_marker';
 import { inlineEquation } from './nodes/inline_equation';
 import { inlineFootnote } from './nodes/inline_footnote';
 import { keyword } from './nodes/keyword';
+import { keywordGroup } from './nodes/keyword_group';
+import { keywords } from './nodes/keywords';
 import { keywordsElement } from './nodes/keywords_element';
-import { keywordsGroup } from './nodes/keywords_group';
-import { keywordsSection } from './nodes/keywords_section';
 import { link } from './nodes/link';
 import { bulletList, listItem, orderedList } from './nodes/list';
 import { listing } from './nodes/listing';
@@ -100,7 +101,7 @@ export * from './nodes/inline_equation';
 export * from './nodes/inline_footnote';
 export * from './nodes/keyword';
 export * from './nodes/keywords_element';
-export * from './nodes/keywords_section';
+export * from './nodes/keywords';
 export * from './nodes/link';
 export * from './nodes/list';
 export * from './nodes/listing';
@@ -125,8 +126,8 @@ export * from './nodes/meta_section';
 export * from './nodes/contributor';
 export * from './nodes/table_element_footer';
 export * from './nodes/title';
-export * from './nodes/affiliations_section';
-export * from './nodes/contributors_section';
+export * from './nodes/affiliations';
+export * from './nodes/contributors';
 export const schema = new Schema({
     marks: {
         bold,
@@ -153,6 +154,9 @@ export const schema = new Schema({
         caption,
         caption_title: captionTitle,
         citation,
+        abstracts: coreSection,
+        body: coreSection,
+        backmatter: coreSection,
         cross_reference: crossReference,
         doc,
         equation,
@@ -170,8 +174,8 @@ export const schema = new Schema({
         inline_footnote: inlineFootnote,
         keyword,
         keywords_element: keywordsElement,
-        keywords_section: keywordsSection,
-        keywords_group: keywordsGroup,
+        keywords: keywords,
+        keyword_group: keywordGroup,
         link,
         list_item: listItem,
         listing,
@@ -202,7 +206,7 @@ export const schema = new Schema({
         contributor: contributor,
         table_element_footer: tableElementFooter,
         title: title,
-        affiliations_section: affiliationsSection,
-        contributors_section: contributorsSection,
+        affiliations: affiliations,
+        contributors: contributors,
     },
 });

package/dist/es/schema/nodes/{affiliations_section.js → affiliations.js}

@@ -1,10 +1,11 @@
-export const affiliationsSection = {
+import { schema } from '../index';
+export const affiliations = {
     content: 'section_title? affiliation*',
     attrs: {
         id: { default: 'META_SECTION_AFFILLIATIONS' },
         dataTracked: { default: null },
     },
-    group: 'block sections',
+    group: 'block',
     selectable: false,
     parseDOM: [
         {
@@ -18,15 +19,15 @@ export const affiliationsSection = {
         },
     ],
     toDOM: (node) => {
-        const affiliationsSectionNode = node;
+        const affiliations = node;
         return [
             'section',
             {
                 class: 'affiliations',
-                id: affiliationsSectionNode.attrs.id,
+                id: affiliations.attrs.id,
             },
-            0
+            0,
         ];
     },
 };
-export const isAffiliationsSectionNode = (node) => node.type === node.type.schema.nodes.affiliations_section;
+export const isAffiliationsNode = (node) => node.type === schema.nodes.affiliations;

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

@@ -19,38 +19,33 @@ export const citation = {
     draggable: true,
     atom: true,
     attrs: {
-        rid: { default: '' },
+        id: { default: '' },
+        rids: { default: [] },
         contents: { default: '' },
         selectedText: { default: '' },
         dataTracked: { default: null },
-        embeddedCitationItems: { default: [] },
     },
     parseDOM: [
         {
             tag: 'span.citation[data-reference-id]',
             getAttrs: (p) => {
+                var _a;
                 const dom = p;
-                const attr = {
-                    rid: dom.getAttribute('data-reference-id'),
+                return {
+                    id: dom.getAttribute('data-id'),
+                    rids: ((_a = dom.getAttribute('data-reference-id')) === null || _a === void 0 ? void 0 : _a.split(/\s+/)) || [],
                     contents: dom.innerHTML,
                 };
-                const embeddedCitationAttr = dom.getAttribute('data-reference-embedded-citation');
-                if (embeddedCitationAttr) {
-                    attr['embeddedCitationItems'] = JSON.parse(embeddedCitationAttr);
-                }
-                return attr;
             },
         },
     ],
     toDOM: (node) => {
-        const citationNode = node;
+        const citation = node;
         const dom = document.createElement('span');
         dom.className = 'citation';
-        dom.setAttribute('data-reference-id', citationNode.attrs.rid);
-        if (citationNode.attrs.embeddedCitationItems) {
-            dom.setAttribute('data-reference-embedded-citation', JSON.stringify(citationNode.attrs.embeddedCitationItems));
-        }
-        dom.innerHTML = citationNode.attrs.contents;
+        dom.setAttribute('data-id', citation.attrs.id);
+        dom.setAttribute('data-reference-id', citation.attrs.rids.join(' '));
+        dom.innerHTML = node.attrs.contents;
         return dom;
     },
 };

package/dist/es/schema/nodes/{contributors_section.js → contributors.js}

@@ -1,11 +1,12 @@
-export const contributorsSection = {
+import { schema } from '../index';
+export const contributors = {
     content: 'section_title? contributor*',
     attrs: {
         id: { default: 'META_SECTION_CONTRIBUTORS' },
         dataTracked: { default: null },
         contents: { default: '' },
     },
-    group: 'block sections',
+    group: 'block',
     selectable: false,
     parseDOM: [
         {
@@ -18,15 +19,15 @@ export const contributorsSection = {
         },
     ],
     toDOM: (node) => {
-        const contributorsSectionNode = node;
+        const contributors = node;
         return [
             'section',
             {
                 class: 'contributors',
-                id: contributorsSectionNode.attrs.id,
+                id: contributors.attrs.id,
             },
             0,
         ];
     },
 };
-export const isContributorsSectionNode = (node) => node.type === node.type.schema.nodes.contributors_section;
+export const isContributorsNode = (node) => node.type === schema.nodes.contributors;

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

@@ -0,0 +1,24 @@
+/*!
+ * © 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.
+ */
+export const coreSection = {
+    content: 'sections*',
+    atom: true,
+    attrs: {
+        id: { default: '' },
+    },
+    group: 'block',
+    toDOM: () => ['section', 0],
+};

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

@@ -19,7 +19,7 @@ export const crossReference = {
     draggable: true,
     atom: true,
     attrs: {
-        rid: { default: '' },
+        rids: { default: [] },
         label: { default: '' },
         customLabel: { default: '' },
         dataTracked: { default: null },
@@ -28,9 +28,10 @@ export const crossReference = {
         {
             tag: 'span.cross-reference',
             getAttrs: (p) => {
+                var _a;
                 const dom = p;
                 return {
-                    rid: dom.getAttribute('data-reference-id'),
+                    rid: ((_a = dom.getAttribute('data-reference-id')) === null || _a === void 0 ? void 0 : _a.split(/\s+/)) || [],
                     label: dom.textContent,
                 };
             },
@@ -42,7 +43,7 @@ export const crossReference = {
             'span',
             {
                 class: 'cross-reference',
-                'data-reference-id': crossReferenceNode.attrs.rid,
+                'data-reference-id': crossReferenceNode.attrs.rids.join(' '),
             },
             [
                 'span',

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

@@ -18,6 +18,7 @@ export const graphicalAbstractSection = {
     attrs: {
         id: { default: '' },
         category: { default: '' },
+        dataTracked: { default: null },
     },
     group: 'block sections',
     selectable: false,

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

@@ -15,7 +15,7 @@
  */
 export const inlineFootnote = {
     attrs: {
-        rid: { default: '' },
+        rids: { default: [] },
         contents: { default: '' },
         dataTracked: { default: null },
     },
@@ -27,20 +27,21 @@ export const inlineFootnote = {
         {
             tag: 'span.footnote',
             getAttrs: (p) => {
+                var _a;
                 const dom = p;
                 return {
-                    rid: dom.getAttribute('data-reference-id'),
+                    rids: ((_a = dom.getAttribute('data-reference-id')) === null || _a === void 0 ? void 0 : _a.split(/\s+/)) || [],
                     contents: dom.textContent,
                 };
             },
         },
     ],
     toDOM: (node) => {
-        const inlineFootnoteNode = node;
+        const footnoteNode = node;
         const dom = document.createElement('span');
         dom.className = 'footnote';
-        dom.setAttribute('data-reference-id', inlineFootnoteNode.attrs.rid);
-        dom.textContent = inlineFootnoteNode.attrs.contents;
+        dom.setAttribute('data-reference-id', footnoteNode.attrs.rids.join(''));
+        dom.textContent = footnoteNode.attrs.contents;
         return dom;
     },
 };

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

@@ -18,7 +18,6 @@ export const keyword = {
     content: 'inline*',
     attrs: {
         id: { default: '' },
-        contents: { default: '' },
         dataTracked: { default: null },
         comments: { default: null },
     },

package/dist/es/schema/nodes/{keywords_group.js → keyword_group.js}

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export const keywordsGroup = {
+export const keywordGroup = {
     content: 'keyword*',
     attrs: {
         id: { default: '' },
@@ -28,11 +28,11 @@ export const keywordsGroup = {
         },
     ],
     toDOM: (node) => {
-        const keywordsGroupNode = node;
+        const keywordGroupNode = node;
         return [
             'div',
             {
-                id: keywordsGroupNode.attrs.id,
+                id: keywordGroupNode.attrs.id,
                 class: 'keywords',
                 spellcheck: 'false',
                 contenteditable: false,
@@ -41,4 +41,4 @@ export const keywordsGroup = {
         ];
     },
 };
-export const isKeywordsGroupNode = (node) => node.type === node.type.schema.nodes.keywords_group;
+export const isKeywordGroupNode = (node) => node.type === node.type.schema.nodes.keywords_group;

package/dist/es/schema/nodes/{keywords_section.js → keywords.js}

@@ -13,13 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export const keywordsSection = {
+export const keywords = {
     content: 'section_title (keywords_element | placeholder_element)',
     attrs: {
         id: { default: '' },
         dataTracked: { default: null },
     },
-    group: 'block sections',
+    group: 'block',
     selectable: false,
     parseDOM: [
         {
@@ -27,11 +27,11 @@ export const keywordsSection = {
         },
     ],
     toDOM: (node) => {
-        const keywordsSectionNode = node;
+        const keywords = node;
         return [
             'div',
             {
-                id: keywordsSectionNode.attrs.id,
+                id: keywords.attrs.id,
                 class: 'keywords',
                 spellcheck: 'false',
                 contenteditable: false,
@@ -40,4 +40,4 @@ export const keywordsSection = {
         ];
     },
 };
-export const isKeywordsSectionNode = (node) => node.type === node.type.schema.nodes.keywords_section;
+export const isKeywordsNode = (node) => node.type === node.type.schema.nodes.keywords;

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

@@ -15,7 +15,7 @@
  */
 export const keywordsElement = {
     atom: true,
-    content: 'keywords_group*',
+    content: 'keyword_group*',
     attrs: {
         id: { default: '' },
         contents: { default: '' },

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const manuscript = {
-    content: 'title* (section | sections)+ meta_section',
+    content: 'title? contributors? affiliations? keywords? abstracts body backmatter meta_section',
     attrs: {
         id: { default: '' },
     },