@manuscripts/transform 2.1.5 → 2.1.6-hotfix.1

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

@@ -202,7 +202,9 @@ exports.jatsBodyTransformations = {
         }
     },
     moveFootnotes(doc, group, createElement) {
-        const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot fn)')];
+        const footnotes = [
+            ...doc.querySelectorAll('fn:not(table-wrap-foot fn, author-notes fn)'),
+        ];
         const footnotesSection = doc.querySelector('sec[sec-type="endnotes"]');
         const footnotesSectionGroup = footnotesSection === null || footnotesSection === void 0 ? void 0 : footnotesSection.querySelector('fn-group');
         const containingGroup = footnotesSectionGroup || createElement('fn-group');

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

@@ -179,7 +179,45 @@ exports.jatsFrontParser = {
             affiliationIDs,
         };
     },
-    parseAuthorNotes(elements) {
+    parseAuthorNotes(element) {
+        if (!element) {
+            return {
+                footnotes: [],
+                footnoteIDs: new Map(),
+                authorNotes: [],
+                authorNotesParagraphs: [],
+                correspondingIDs: new Map(),
+                correspondingList: [],
+            };
+        }
+        const { footnotes, footnoteIDs } = this.parseFootnotes([
+            ...element.querySelectorAll('fn:not([fn-type])'),
+        ]);
+        const authorNotesParagraphs = this.parseParagraphs([
+            ...element.querySelectorAll(':scope > p'),
+        ]);
+        const { correspondingList, correspondingIDs } = this.parseCorresp([
+            ...element.querySelectorAll('corresp'),
+        ]);
+        const authorNotes = [
+            (0, transformer_1.buildAuthorNotes)([
+                ...footnoteIDs.values(),
+                ...authorNotesParagraphs.map((p) => p._id),
+            ]),
+        ];
+        return {
+            footnotes,
+            footnoteIDs,
+            authorNotesParagraphs,
+            authorNotes,
+            correspondingIDs,
+            correspondingList,
+        };
+    },
+    parseParagraphs(elements) {
+        return elements.map((p) => (0, transformer_1.buildParagraph)(p.innerHTML));
+    },
+    parseFootnotes(elements) {
         const footnoteIDs = new Map();
         const footnotes = elements.map((element) => {
             const fn = (0, transformer_1.buildFootnote)('', element.innerHTML);

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

@@ -35,12 +35,7 @@ const parseJATSFront = (doc, front) => {
     const { affiliations, affiliationIDs } = jats_front_parser_1.jatsFrontParser.parseAffiliations([
         ...front.querySelectorAll('article-meta > contrib-group > aff'),
     ]);
-    const { footnotes, footnoteIDs } = jats_front_parser_1.jatsFrontParser.parseAuthorNotes([
-        ...front.querySelectorAll('article-meta > author-notes > fn:not([fn-type])'),
-    ]);
-    const { correspondingList, correspondingIDs } = jats_front_parser_1.jatsFrontParser.parseCorresp([
-        ...front.querySelectorAll('article-meta > author-notes > corresp'),
-    ]);
+    const { footnotes, footnoteIDs, authorNotes, authorNotesParagraphs, correspondingIDs, correspondingList, } = jats_front_parser_1.jatsFrontParser.parseAuthorNotes(front.querySelector('article-meta > author-notes'));
     const authors = jats_front_parser_1.jatsFrontParser.parseContributors([
         ...front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]'),
     ], affiliationIDs, footnoteIDs, correspondingIDs);
@@ -51,6 +46,8 @@ const parseJATSFront = (doc, front) => {
         manuscript,
         titles,
         journal,
+        ...authorNotesParagraphs,
+        ...authorNotes,
         ...footnotes,
         ...authors,
         ...affiliations,

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

@@ -615,6 +615,7 @@ class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
+                author_notes: () => ['author-notes', 0],
                 title: () => '',
                 affiliations: () => '',
                 contributors: () => '',
@@ -1035,6 +1036,7 @@ class JATSExporter {
             }
         };
         this.buildContributors = (articleMeta) => {
+            var _a;
             const contributors = this.models.filter(isContributor);
             const authorContributors = contributors
                 .filter((contributor) => contributor.role === 'author')
@@ -1253,56 +1255,61 @@ class JATSExporter {
                         }
                     });
                 }
-                const noteIDs = [];
-                for (const contributor of [...authorContributors, ...otherContributors]) {
-                    if (contributor.footnote) {
-                        const ids = contributor.footnote.map((note) => {
-                            return note.noteID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                    if (contributor.corresp) {
-                        const ids = contributor.corresp.map((corresp) => {
-                            return corresp.correspID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                }
-                const footnotes = [];
-                footnotes.push(...this.models.filter((0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Footnote)));
-                const correspodings = [];
-                correspodings.push(...this.models.filter((0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.Corresponding)));
-                if (footnotes || correspodings) {
-                    const authorNotesEl = this.document.createElement('author-notes');
-                    const usedFootnotes = footnotes.filter((footnote) => {
-                        return noteIDs.includes(footnote._id);
-                    });
-                    const usedCorrespodings = correspodings.filter((corresp) => {
-                        return noteIDs.includes(corresp._id);
-                    });
-                    usedFootnotes.forEach((footnote) => {
-                        const authorFootNote = this.document.createElement('fn');
-                        authorFootNote.setAttribute('id', normalizeID(footnote._id));
-                        authorFootNote.innerHTML = footnote.contents;
-                        authorNotesEl.appendChild(authorFootNote);
-                    });
-                    usedCorrespodings.forEach((corresponding) => {
-                        const correspondingEl = this.document.createElement('corresp');
-                        correspondingEl.setAttribute('id', normalizeID(corresponding._id));
-                        if (corresponding.label) {
-                            const labelEl = this.document.createElement('label');
-                            labelEl.textContent = corresponding.label;
-                            correspondingEl.appendChild(labelEl);
+                const authorNotesEl = this.document.createElement('author-notes');
+                const usedCorrespodings = this.getUsedCorrespondings([
+                    ...authorContributors,
+                    ...otherContributors,
+                ]);
+                usedCorrespodings.forEach((corresp) => {
+                    this.appendCorrespondingToElement(corresp, authorNotesEl);
+                });
+                const authorNotes = (_a = (0, json_schema_1.getModelsByType)(this.modelMap, json_schema_1.ObjectTypes.AuthorNotes)) === null || _a === void 0 ? void 0 : _a[0];
+                if (authorNotes) {
+                    authorNotes.containedObjectIDs.forEach((id) => {
+                        const model = this.modelMap.get(id);
+                        if (!model) {
+                            return;
+                        }
+                        if (id.startsWith('MPParagraphElement')) {
+                            this.appendParagraphToElement(model, authorNotesEl);
+                        }
+                        else if (id.startsWith('MPFootnote')) {
+                            this.appendFootnoteToElement(model, authorNotesEl);
                         }
-                        correspondingEl.append(corresponding.contents);
-                        authorNotesEl.appendChild(correspondingEl);
                     });
-                    if (authorNotesEl.childNodes.length > 0) {
-                        articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
-                    }
+                }
+                if (authorNotesEl.childNodes.length > 0) {
+                    articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
                 }
             }
         };
+        this.appendCorrespondingToElement = (corresponding, element) => {
+            const correspondingEl = this.document.createElement('corresp');
+            correspondingEl.setAttribute('id', normalizeID(corresponding._id));
+            if (corresponding.label) {
+                const labelEl = this.document.createElement('label');
+                labelEl.textContent = corresponding.label;
+                correspondingEl.appendChild(labelEl);
+            }
+            correspondingEl.append(corresponding.contents);
+            element.appendChild(correspondingEl);
+        };
+        this.appendParagraphToElement = (paragraph, element) => {
+            const parsedDoc = new DOMParser().parseFromString(paragraph.contents, 'text/html');
+            const parsedParagraph = parsedDoc.body.querySelector('p');
+            if (parsedParagraph) {
+                const paragraphEl = this.document.createElement('p');
+                paragraphEl.innerHTML = parsedParagraph.innerHTML;
+                paragraphEl.setAttribute('id', normalizeID(paragraph._id));
+                element.appendChild(paragraphEl);
+            }
+        };
+        this.appendFootnoteToElement = (footnote, element) => {
+            const footnoteEl = this.document.createElement('fn');
+            footnoteEl.setAttribute('id', normalizeID(footnote._id));
+            footnoteEl.innerHTML = footnote.contents;
+            element.appendChild(footnoteEl);
+        };
         this.fixBody = (body, fragment) => {
             fragment.descendants((node) => {
                 if (node.attrs.id) {
@@ -1605,6 +1612,12 @@ class JATSExporter {
             return mathml;
         }
     }
+    getUsedCorrespondings(contributors) {
+        return contributors
+            .flatMap((c) => { var _a; return (_a = c.corresp) !== null && _a !== void 0 ? _a : []; })
+            .map((corresp) => this.modelMap.get(corresp.correspID))
+            .filter((corresp) => !!corresp);
+    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === json_schema_1.ObjectTypes.Keyword);
         const keywordGroups = new Map();
@@ -1676,6 +1689,9 @@ class JATSExporter {
                             }
                         }
                     }
+                    if (!fnGroup.hasChildNodes()) {
+                        fnGroup.remove();
+                    }
                 }
             }
         });

package/dist/cjs/schema/index.js

@@ -36,6 +36,7 @@ const abstracts_1 = require("./nodes/abstracts");
 const affiliation_1 = require("./nodes/affiliation");
 const affiliations_1 = require("./nodes/affiliations");
 const attribution_1 = require("./nodes/attribution");
+const author_notes_1 = require("./nodes/author_notes");
 const backmatter_1 = require("./nodes/backmatter");
 const bibliography_element_1 = require("./nodes/bibliography_element");
 const bibliography_item_1 = require("./nodes/bibliography_item");
@@ -215,6 +216,7 @@ exports.schema = new prosemirror_model_1.Schema({
         table_row: table_1.tableRow,
         table_col: table_col_1.tableCol,
         table_colgroup: table_col_1.tableColGroup,
+        table_header: table_1.tableHeader,
         text: text_1.text,
         toc_element: toc_element_1.tocElement,
         toc_section: toc_section_1.tocSection,
@@ -226,6 +228,6 @@ exports.schema = new prosemirror_model_1.Schema({
         contributors: contributors_1.contributors,
         supplements: supplements_1.supplements,
         supplement: supplement_1.supplement,
-        table_header: table_1.tableHeader,
+        author_notes: author_notes_1.authorNotes,
     },
 });

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

@@ -0,0 +1,27 @@
+"use strict";
+/*!
+ * © 2019 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.authorNotes = void 0;
+exports.authorNotes = {
+    attrs: {
+        id: { default: '' },
+        dataTracked: { default: null },
+    },
+    content: '(footnote | paragraph)+',
+    group: 'block element',
+    toDOM: () => ['author-notes', 0],
+};

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

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.contributors = void 0;
 exports.contributors = {
-    content: 'contributor*',
+    content: 'contributor* author_notes?',
     attrs: {
         id: { default: '' },
     },

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

@@ -17,8 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.link = void 0;
 exports.link = {
-    content: 'text*',
-    marks: '',
+    content: 'inline*',
     attrs: {
         href: { default: '' },
         title: { default: '' },

package/dist/cjs/transformer/builders.js

@@ -18,7 +18,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildJournal = exports.buildAttribution = exports.buildContributorRole = exports.buildContribution = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildFootnote = exports.buildNote = exports.buildComment = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildKeywordGroup = exports.buildKeyword = exports.buildBibliographyElement = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = void 0;
+exports.buildTitles = exports.buildElementsOrder = exports.auxiliaryObjectTypes = exports.buildJournal = exports.buildAttribution = exports.buildContributorRole = exports.buildContribution = exports.buildColor = exports.buildParagraph = exports.buildSection = exports.buildCorresp = exports.buildFootnotesOrder = exports.buildAuthorNotes = exports.buildFootnote = exports.buildNote = exports.buildComment = exports.buildSupplementaryMaterial = exports.buildAffiliation = exports.buildFigure = exports.buildKeywordGroup = exports.buildKeyword = exports.buildBibliographyElement = exports.buildBibliographicDate = exports.buildBibliographicName = exports.buildBibliographyItem = exports.buildContributor = exports.buildManuscript = exports.buildProject = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
 const schema_1 = require("../schema");
@@ -123,6 +123,12 @@ const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     kind,
 });
 exports.buildFootnote = buildFootnote;
+const buildAuthorNotes = (containedObjectIDs) => ({
+    _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.AuthorNotes),
+    objectType: json_schema_1.ObjectTypes.AuthorNotes,
+    containedObjectIDs: containedObjectIDs,
+});
+exports.buildAuthorNotes = buildAuthorNotes;
 const buildFootnotesOrder = (footnotesList, containedObjectID) => ({
     _id: (0, id_1.generateID)(json_schema_1.ObjectTypes.FootnotesOrder),
     objectType: json_schema_1.ObjectTypes.FootnotesOrder,
@@ -146,13 +152,12 @@ const buildSection = (priority = 0, path = []) => {
     };
 };
 exports.buildSection = buildSection;
-const buildParagraph = (placeholderInnerHTML) => {
+const buildParagraph = (innerHTML = '') => {
     const _id = (0, id_1.generateID)(json_schema_1.ObjectTypes.ParagraphElement);
-    const element = document.createElementNS('http://www.w3.org/1999/xhtml', 'p');
+    const element = document.createElementNS(null, 'p');
     element.setAttribute('id', _id);
-    element.setAttribute('class', 'MPElement');
-    if (placeholderInnerHTML) {
-        element.setAttribute('data-placeholder-text', placeholderInnerHTML);
+    if (innerHTML) {
+        element.innerHTML = innerHTML;
     }
     const contents = (0, w3c_xmlserializer_1.default)(element);
     return {
@@ -160,7 +165,6 @@ const buildParagraph = (placeholderInnerHTML) => {
         objectType: json_schema_1.ObjectTypes.ParagraphElement,
         elementType: 'p',
         contents,
-        placeholderInnerHTML,
     };
 };
 exports.buildParagraph = buildParagraph;

package/dist/cjs/transformer/decode.js

@@ -62,6 +62,7 @@ const sortSectionsByPriority = (a, b) => a.priority === b.priority ? 0 : Number(
 exports.sortSectionsByPriority = sortSectionsByPriority;
 const getSections = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Section).sort(exports.sortSectionsByPriority);
 const getAffiliations = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Affiliation);
+const getAuthorNotes = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.AuthorNotes);
 const getContributors = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Contributor);
 const getKeywordElements = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.KeywordsElement);
 const getSupplements = (modelMap) => (0, exports.getModelsByType)(modelMap, json_schema_1.ObjectTypes.Supplement);
@@ -91,7 +92,11 @@ class Decoder {
         const contributors = getContributors(this.modelMap)
             .map((c) => this.decode(c))
             .filter(Boolean);
-        return schema_1.schema.nodes.contributors.createAndFill({}, contributors);
+        const authorNotes = getAuthorNotes(this.modelMap)
+            .map((authorNote) => this.decode(authorNote))
+            .filter(Boolean);
+        const content = [...contributors, ...authorNotes];
+        return schema_1.schema.nodes.contributors.createAndFill({}, content);
     }
     createKeywordsNode() {
         const elements = getKeywordElements(this.modelMap)
@@ -489,6 +494,13 @@ class Decoder {
                     id: model._id,
                 }, content);
             },
+            [json_schema_1.ObjectTypes.AuthorNotes]: (data) => {
+                const model = data;
+                const content = model.containedObjectIDs.map((id) => this.decode(this.modelMap.get(id)));
+                return schema_1.schema.nodes.author_notes.create({
+                    id: model._id,
+                }, content);
+            },
             [json_schema_1.ObjectTypes.Section]: (data) => {
                 const model = data;
                 const elements = [];

package/dist/cjs/transformer/encode.js

@@ -383,6 +383,9 @@ const encoders = {
     table_element_footer: (node) => ({
         containedObjectIDs: containedObjectIDs(node),
     }),
+    author_notes: (node) => ({
+        containedObjectIDs: containedObjectIDs(node),
+    }),
     footnotes_section: (node, parent, path, priority) => ({
         category: (0, section_category_1.buildSectionCategory)(node),
         priority: priority.value++,

package/dist/cjs/transformer/node-types.js

@@ -61,6 +61,7 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.affiliations, json_schema_1.ObjectTypes.Section],
     [schema_1.schema.nodes.title, json_schema_1.ObjectTypes.Titles],
     [schema_1.schema.nodes.supplement, json_schema_1.ObjectTypes.Supplement],
+    [schema_1.schema.nodes.author_notes, json_schema_1.ObjectTypes.AuthorNotes],
 ]);
 const isExecutableNodeType = (type) => (0, schema_1.hasGroup)(type, schema_1.GROUP_EXECUTABLE);
 exports.isExecutableNodeType = isExecutableNodeType;

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

@@ -199,7 +199,9 @@ export const jatsBodyTransformations = {
         }
     },
     moveFootnotes(doc, group, createElement) {
-        const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot fn)')];
+        const footnotes = [
+            ...doc.querySelectorAll('fn:not(table-wrap-foot fn, author-notes fn)'),
+        ];
         const footnotesSection = doc.querySelector('sec[sec-type="endnotes"]');
         const footnotesSectionGroup = footnotesSection === null || footnotesSection === void 0 ? void 0 : footnotesSection.querySelector('fn-group');
         const containingGroup = footnotesSectionGroup || createElement('fn-group');

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

@@ -15,7 +15,7 @@
  */
 import debug from 'debug';
 import { getTrimmedTextContent } from '../../lib/utils';
-import { buildAffiliation, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildJournal, buildTitles, } from '../../transformer';
+import { buildAffiliation, buildAuthorNotes, buildBibliographicName, buildContributor, buildCorresp, buildFootnote, buildJournal, buildParagraph, buildTitles, } from '../../transformer';
 import { parseJournalMeta } from './jats-journal-meta-parser';
 import { htmlFromJatsNode } from './jats-parser-utils';
 const warn = debug('manuscripts-transform');
@@ -173,7 +173,45 @@ export const jatsFrontParser = {
             affiliationIDs,
         };
     },
-    parseAuthorNotes(elements) {
+    parseAuthorNotes(element) {
+        if (!element) {
+            return {
+                footnotes: [],
+                footnoteIDs: new Map(),
+                authorNotes: [],
+                authorNotesParagraphs: [],
+                correspondingIDs: new Map(),
+                correspondingList: [],
+            };
+        }
+        const { footnotes, footnoteIDs } = this.parseFootnotes([
+            ...element.querySelectorAll('fn:not([fn-type])'),
+        ]);
+        const authorNotesParagraphs = this.parseParagraphs([
+            ...element.querySelectorAll(':scope > p'),
+        ]);
+        const { correspondingList, correspondingIDs } = this.parseCorresp([
+            ...element.querySelectorAll('corresp'),
+        ]);
+        const authorNotes = [
+            buildAuthorNotes([
+                ...footnoteIDs.values(),
+                ...authorNotesParagraphs.map((p) => p._id),
+            ]),
+        ];
+        return {
+            footnotes,
+            footnoteIDs,
+            authorNotesParagraphs,
+            authorNotes,
+            correspondingIDs,
+            correspondingList,
+        };
+    },
+    parseParagraphs(elements) {
+        return elements.map((p) => buildParagraph(p.innerHTML));
+    },
+    parseFootnotes(elements) {
         const footnoteIDs = new Map();
         const footnotes = elements.map((element) => {
             const fn = buildFootnote('', element.innerHTML);

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

@@ -32,12 +32,7 @@ export const parseJATSFront = (doc, front) => {
     const { affiliations, affiliationIDs } = jatsFrontParser.parseAffiliations([
         ...front.querySelectorAll('article-meta > contrib-group > aff'),
     ]);
-    const { footnotes, footnoteIDs } = jatsFrontParser.parseAuthorNotes([
-        ...front.querySelectorAll('article-meta > author-notes > fn:not([fn-type])'),
-    ]);
-    const { correspondingList, correspondingIDs } = jatsFrontParser.parseCorresp([
-        ...front.querySelectorAll('article-meta > author-notes > corresp'),
-    ]);
+    const { footnotes, footnoteIDs, authorNotes, authorNotesParagraphs, correspondingIDs, correspondingList, } = jatsFrontParser.parseAuthorNotes(front.querySelector('article-meta > author-notes'));
     const authors = jatsFrontParser.parseContributors([
         ...front.querySelectorAll('article-meta > contrib-group > contrib[contrib-type="author"]'),
     ], affiliationIDs, footnoteIDs, correspondingIDs);
@@ -48,6 +43,8 @@ export const parseJATSFront = (doc, front) => {
         manuscript,
         titles,
         journal,
+        ...authorNotesParagraphs,
+        ...authorNotes,
         ...footnotes,
         ...authors,
         ...affiliations,

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

@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { ObjectTypes, } from '@manuscripts/json-schema';
+import { getModelsByType, ObjectTypes, } from '@manuscripts/json-schema';
 import { CitationProvider } from '@manuscripts/library';
 import debug from 'debug';
-import { DOMParser, DOMSerializer } from 'prosemirror-model';
+import { DOMParser as ProseMirrorDOMParser, DOMSerializer, } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
 import { nodeFromHTML, textFromHTML } from '../lib/html';
 import { normalizeStyleName } from '../lib/styled-content';
@@ -32,7 +32,7 @@ import { selectVersionIds } from './jats-versions';
 const warn = debug('manuscripts-transform');
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const normalizeID = (id) => id.replace(/:/g, '_');
-const parser = DOMParser.fromSchema(schema);
+const parser = ProseMirrorDOMParser.fromSchema(schema);
 const findChildNodeOfType = (node, nodeType) => {
     for (const child of iterateChildren(node)) {
         if (child.type === nodeType) {
@@ -607,6 +607,7 @@ export class JATSExporter {
         this.createSerializer = () => {
             const getModel = (id) => id ? this.modelMap.get(id) : undefined;
             const nodes = {
+                author_notes: () => ['author-notes', 0],
                 title: () => '',
                 affiliations: () => '',
                 contributors: () => '',
@@ -1027,6 +1028,7 @@ export class JATSExporter {
             }
         };
         this.buildContributors = (articleMeta) => {
+            var _a;
             const contributors = this.models.filter(isContributor);
             const authorContributors = contributors
                 .filter((contributor) => contributor.role === 'author')
@@ -1245,56 +1247,61 @@ export class JATSExporter {
                         }
                     });
                 }
-                const noteIDs = [];
-                for (const contributor of [...authorContributors, ...otherContributors]) {
-                    if (contributor.footnote) {
-                        const ids = contributor.footnote.map((note) => {
-                            return note.noteID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                    if (contributor.corresp) {
-                        const ids = contributor.corresp.map((corresp) => {
-                            return corresp.correspID;
-                        });
-                        noteIDs.push(...ids);
-                    }
-                }
-                const footnotes = [];
-                footnotes.push(...this.models.filter(hasObjectType(ObjectTypes.Footnote)));
-                const correspodings = [];
-                correspodings.push(...this.models.filter(hasObjectType(ObjectTypes.Corresponding)));
-                if (footnotes || correspodings) {
-                    const authorNotesEl = this.document.createElement('author-notes');
-                    const usedFootnotes = footnotes.filter((footnote) => {
-                        return noteIDs.includes(footnote._id);
-                    });
-                    const usedCorrespodings = correspodings.filter((corresp) => {
-                        return noteIDs.includes(corresp._id);
-                    });
-                    usedFootnotes.forEach((footnote) => {
-                        const authorFootNote = this.document.createElement('fn');
-                        authorFootNote.setAttribute('id', normalizeID(footnote._id));
-                        authorFootNote.innerHTML = footnote.contents;
-                        authorNotesEl.appendChild(authorFootNote);
-                    });
-                    usedCorrespodings.forEach((corresponding) => {
-                        const correspondingEl = this.document.createElement('corresp');
-                        correspondingEl.setAttribute('id', normalizeID(corresponding._id));
-                        if (corresponding.label) {
-                            const labelEl = this.document.createElement('label');
-                            labelEl.textContent = corresponding.label;
-                            correspondingEl.appendChild(labelEl);
+                const authorNotesEl = this.document.createElement('author-notes');
+                const usedCorrespodings = this.getUsedCorrespondings([
+                    ...authorContributors,
+                    ...otherContributors,
+                ]);
+                usedCorrespodings.forEach((corresp) => {
+                    this.appendCorrespondingToElement(corresp, authorNotesEl);
+                });
+                const authorNotes = (_a = getModelsByType(this.modelMap, ObjectTypes.AuthorNotes)) === null || _a === void 0 ? void 0 : _a[0];
+                if (authorNotes) {
+                    authorNotes.containedObjectIDs.forEach((id) => {
+                        const model = this.modelMap.get(id);
+                        if (!model) {
+                            return;
+                        }
+                        if (id.startsWith('MPParagraphElement')) {
+                            this.appendParagraphToElement(model, authorNotesEl);
+                        }
+                        else if (id.startsWith('MPFootnote')) {
+                            this.appendFootnoteToElement(model, authorNotesEl);
                         }
-                        correspondingEl.append(corresponding.contents);
-                        authorNotesEl.appendChild(correspondingEl);
                     });
-                    if (authorNotesEl.childNodes.length > 0) {
-                        articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
-                    }
+                }
+                if (authorNotesEl.childNodes.length > 0) {
+                    articleMeta.insertBefore(authorNotesEl, contribGroup.nextSibling);
                 }
             }
         };
+        this.appendCorrespondingToElement = (corresponding, element) => {
+            const correspondingEl = this.document.createElement('corresp');
+            correspondingEl.setAttribute('id', normalizeID(corresponding._id));
+            if (corresponding.label) {
+                const labelEl = this.document.createElement('label');
+                labelEl.textContent = corresponding.label;
+                correspondingEl.appendChild(labelEl);
+            }
+            correspondingEl.append(corresponding.contents);
+            element.appendChild(correspondingEl);
+        };
+        this.appendParagraphToElement = (paragraph, element) => {
+            const parsedDoc = new DOMParser().parseFromString(paragraph.contents, 'text/html');
+            const parsedParagraph = parsedDoc.body.querySelector('p');
+            if (parsedParagraph) {
+                const paragraphEl = this.document.createElement('p');
+                paragraphEl.innerHTML = parsedParagraph.innerHTML;
+                paragraphEl.setAttribute('id', normalizeID(paragraph._id));
+                element.appendChild(paragraphEl);
+            }
+        };
+        this.appendFootnoteToElement = (footnote, element) => {
+            const footnoteEl = this.document.createElement('fn');
+            footnoteEl.setAttribute('id', normalizeID(footnote._id));
+            footnoteEl.innerHTML = footnote.contents;
+            element.appendChild(footnoteEl);
+        };
         this.fixBody = (body, fragment) => {
             fragment.descendants((node) => {
                 if (node.attrs.id) {
@@ -1597,6 +1604,12 @@ export class JATSExporter {
             return mathml;
         }
     }
+    getUsedCorrespondings(contributors) {
+        return contributors
+            .flatMap((c) => { var _a; return (_a = c.corresp) !== null && _a !== void 0 ? _a : []; })
+            .map((corresp) => this.modelMap.get(corresp.correspID))
+            .filter((corresp) => !!corresp);
+    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === ObjectTypes.Keyword);
         const keywordGroups = new Map();
@@ -1668,6 +1681,9 @@ export class JATSExporter {
                             }
                         }
                     }
+                    if (!fnGroup.hasChildNodes()) {
+                        fnGroup.remove();
+                    }
                 }
             }
         });

package/dist/es/schema/index.js

@@ -19,6 +19,7 @@ import { abstracts } from './nodes/abstracts';
 import { affiliation } from './nodes/affiliation';
 import { affiliations } from './nodes/affiliations';
 import { attribution } from './nodes/attribution';
+import { authorNotes } from './nodes/author_notes';
 import { backmatter } from './nodes/backmatter';
 import { bibliographyElement } from './nodes/bibliography_element';
 import { bibliographyItem } from './nodes/bibliography_item';
@@ -198,6 +199,7 @@ export const schema = new Schema({
         table_row: tableRow,
         table_col: tableCol,
         table_colgroup: tableColGroup,
+        table_header: tableHeader,
         text,
         toc_element: tocElement,
         toc_section: tocSection,
@@ -209,6 +211,6 @@ export const schema = new Schema({
         contributors,
         supplements,
         supplement,
-        table_header: tableHeader,
+        author_notes: authorNotes,
     },
 });

package/dist/es/schema/nodes/author_notes.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 authorNotes = {
+    attrs: {
+        id: { default: '' },
+        dataTracked: { default: null },
+    },
+    content: '(footnote | paragraph)+',
+    group: 'block element',
+    toDOM: () => ['author-notes', 0],
+};

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const contributors = {
-    content: 'contributor*',
+    content: 'contributor* author_notes?',
     attrs: {
         id: { default: '' },
     },

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

@@ -14,8 +14,7 @@
  * limitations under the License.
  */
 export const link = {
-    content: 'text*',
-    marks: '',
+    content: 'inline*',
     attrs: {
         href: { default: '' },
         title: { default: '' },

package/dist/es/transformer/builders.js

@@ -102,6 +102,11 @@ export const buildFootnote = (containingObject, contents, kind = 'footnote') =>
     contents,
     kind,
 });
+export const buildAuthorNotes = (containedObjectIDs) => ({
+    _id: generateID(ObjectTypes.AuthorNotes),
+    objectType: ObjectTypes.AuthorNotes,
+    containedObjectIDs: containedObjectIDs,
+});
 export const buildFootnotesOrder = (footnotesList, containedObjectID) => ({
     _id: generateID(ObjectTypes.FootnotesOrder),
     objectType: ObjectTypes.FootnotesOrder,
@@ -122,13 +127,12 @@ export const buildSection = (priority = 0, path = []) => {
         path: path.concat(id),
     };
 };
-export const buildParagraph = (placeholderInnerHTML) => {
+export const buildParagraph = (innerHTML = '') => {
     const _id = generateID(ObjectTypes.ParagraphElement);
-    const element = document.createElementNS('http://www.w3.org/1999/xhtml', 'p');
+    const element = document.createElementNS(null, 'p');
     element.setAttribute('id', _id);
-    element.setAttribute('class', 'MPElement');
-    if (placeholderInnerHTML) {
-        element.setAttribute('data-placeholder-text', placeholderInnerHTML);
+    if (innerHTML) {
+        element.innerHTML = innerHTML;
     }
     const contents = serializeToXML(element);
     return {
@@ -136,7 +140,6 @@ export const buildParagraph = (placeholderInnerHTML) => {
         objectType: ObjectTypes.ParagraphElement,
         elementType: 'p',
         contents,
-        placeholderInnerHTML,
     };
 };
 export const buildColor = (value, priority) => ({

package/dist/es/transformer/decode.js

@@ -53,6 +53,7 @@ export const getModelsByType = (modelMap, objectType) => {
 export const sortSectionsByPriority = (a, b) => a.priority === b.priority ? 0 : Number(a.priority) - Number(b.priority);
 const getSections = (modelMap) => getModelsByType(modelMap, ObjectTypes.Section).sort(sortSectionsByPriority);
 const getAffiliations = (modelMap) => getModelsByType(modelMap, ObjectTypes.Affiliation);
+const getAuthorNotes = (modelMap) => getModelsByType(modelMap, ObjectTypes.AuthorNotes);
 const getContributors = (modelMap) => getModelsByType(modelMap, ObjectTypes.Contributor);
 const getKeywordElements = (modelMap) => getModelsByType(modelMap, ObjectTypes.KeywordsElement);
 const getSupplements = (modelMap) => getModelsByType(modelMap, ObjectTypes.Supplement);
@@ -82,7 +83,11 @@ export class Decoder {
         const contributors = getContributors(this.modelMap)
             .map((c) => this.decode(c))
             .filter(Boolean);
-        return schema.nodes.contributors.createAndFill({}, contributors);
+        const authorNotes = getAuthorNotes(this.modelMap)
+            .map((authorNote) => this.decode(authorNote))
+            .filter(Boolean);
+        const content = [...contributors, ...authorNotes];
+        return schema.nodes.contributors.createAndFill({}, content);
     }
     createKeywordsNode() {
         const elements = getKeywordElements(this.modelMap)
@@ -480,6 +485,13 @@ export class Decoder {
                     id: model._id,
                 }, content);
             },
+            [ObjectTypes.AuthorNotes]: (data) => {
+                const model = data;
+                const content = model.containedObjectIDs.map((id) => this.decode(this.modelMap.get(id)));
+                return schema.nodes.author_notes.create({
+                    id: model._id,
+                }, content);
+            },
             [ObjectTypes.Section]: (data) => {
                 const model = data;
                 const elements = [];

package/dist/es/transformer/encode.js

@@ -375,6 +375,9 @@ const encoders = {
     table_element_footer: (node) => ({
         containedObjectIDs: containedObjectIDs(node),
     }),
+    author_notes: (node) => ({
+        containedObjectIDs: containedObjectIDs(node),
+    }),
     footnotes_section: (node, parent, path, priority) => ({
         category: buildSectionCategory(node),
         priority: priority.value++,

package/dist/es/transformer/node-types.js

@@ -58,6 +58,7 @@ export const nodeTypesMap = new Map([
     [schema.nodes.affiliations, ObjectTypes.Section],
     [schema.nodes.title, ObjectTypes.Titles],
     [schema.nodes.supplement, ObjectTypes.Supplement],
+    [schema.nodes.author_notes, ObjectTypes.AuthorNotes],
 ]);
 export const isExecutableNodeType = (type) => hasGroup(type, GROUP_EXECUTABLE);
 export const isElementNodeType = (type) => hasGroup(type, GROUP_ELEMENT);

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

@@ -63,7 +63,16 @@ export declare const jatsFrontParser: {
         affiliations: import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").Affiliation>[];
         affiliationIDs: Map<string, string>;
     };
-    parseAuthorNotes(elements: Element[]): {
+    parseAuthorNotes(element: Element | null): {
+        footnotes: import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").Footnote>[];
+        footnoteIDs: Map<string, string>;
+        authorNotesParagraphs: import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").ParagraphElement>[];
+        authorNotes: import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").AuthorNotes>[];
+        correspondingIDs: Map<string, string>;
+        correspondingList: import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").Corresponding>[];
+    };
+    parseParagraphs(elements: Element[]): import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").ParagraphElement>[];
+    parseFootnotes(elements: Element[]): {
         footnotes: import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").Footnote>[];
         footnoteIDs: Map<string, string>;
     };

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

@@ -87,6 +87,10 @@ export declare class JATSExporter {
     protected serializeNode: (node: ManuscriptNode) => Node;
     private validateContributor;
     private buildContributors;
+    private appendCorrespondingToElement;
+    private getUsedCorrespondings;
+    private appendParagraphToElement;
+    private appendFootnoteToElement;
     private buildKeywords;
     private fixBody;
     private changeTag;

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

@@ -0,0 +1,25 @@
+/*!
+ * © 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.
+ */
+import { NodeSpec } from 'prosemirror-model';
+import { ManuscriptNode } from '../types';
+interface Attrs {
+    id: string;
+}
+export interface AuthorNotesNode extends ManuscriptNode {
+    attrs: Attrs;
+}
+export declare const authorNotes: NodeSpec;
+export {};

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' | 'bullet_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' | 'ordered_list' | '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' | 'text' | 'toc_element' | 'toc_section' | 'affiliation' | 'contributor' | 'table_element_footer' | 'title' | 'affiliations' | 'contributors' | 'supplements' | 'supplement' | 'table_header';
+export type Nodes = 'attribution' | 'bibliography_item' | 'bibliography_element' | 'bibliography_section' | 'blockquote_element' | 'bullet_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' | 'ordered_list' | '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' | 'toc_element' | 'toc_section' | 'affiliation' | 'contributor' | 'table_element_footer' | 'title' | 'affiliations' | 'contributors' | 'supplements' | 'supplement' | 'author_notes';
 export type ManuscriptSchema = Schema<Nodes, Marks>;
 export type ManuscriptEditorState = EditorState;
 export type ManuscriptEditorView = EditorView;

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

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Affiliation, Attribution, BibliographicDate, BibliographicName, BibliographyElement, BibliographyItem, Color, CommentAnnotation, Contribution, Contributor, ContributorRole, Corresponding, ElementsOrder, EmbeddedModel, Figure, Footnote, FootnotesOrder, Journal, Keyword, KeywordGroup, Manuscript, ManuscriptNote, ObjectTypes, ParagraphElement, Project, Section, Supplement, Titles } from '@manuscripts/json-schema';
+import { Affiliation, Attribution, AuthorNotes, BibliographicDate, BibliographicName, BibliographyElement, BibliographyItem, Color, CommentAnnotation, Contribution, Contributor, ContributorRole, Corresponding, ElementsOrder, EmbeddedModel, Figure, Footnote, FootnotesOrder, Journal, Keyword, KeywordGroup, Manuscript, ManuscriptNote, ObjectTypes, ParagraphElement, Project, Section, Supplement, Titles } from '@manuscripts/json-schema';
 import { FootnotesOrderIndexList } from './footnotes-order';
 import { CommentSelector, ManuscriptModel, ModelAttachment } from './models';
 export type Build<T> = Pick<T, Exclude<keyof T, keyof ManuscriptModel>> & {
@@ -45,10 +45,11 @@ export declare const buildSupplementaryMaterial: (title: string, href: string) =
 export declare const buildComment: (target: string, contents?: string, selector?: CommentSelector, contributions?: Contribution[], annotationColor?: string) => Build<CommentAnnotation>;
 export declare const buildNote: (target: string, source: 'EMAIL' | 'EDITOR' | 'DASHBOARD', contents?: string) => Build<ManuscriptNote>;
 export declare const buildFootnote: (containingObject: string, contents: string, kind?: 'footnote' | 'endnote') => Build<Footnote>;
+export declare const buildAuthorNotes: (containedObjectIDs: string[]) => Build<AuthorNotes>;
 export declare const buildFootnotesOrder: (footnotesList: FootnotesOrderIndexList, containedObjectID: string) => Build<FootnotesOrder>;
 export declare const buildCorresp: (contents: string) => Build<Corresponding>;
 export declare const buildSection: (priority?: number, path?: string[]) => Build<Section>;
-export declare const buildParagraph: (placeholderInnerHTML: string) => Build<ParagraphElement>;
+export declare const buildParagraph: (innerHTML?: string) => Build<ParagraphElement>;
 export declare const buildColor: (value: string, priority: number) => Build<Color>;
 export declare const buildContribution: (profileID: string) => Contribution;
 export declare const buildContributorRole: (name: string) => Build<ContributorRole>;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.1.5",
+  "version": "2.1.6-hotfix.1",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,8 +29,8 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "^2.2.5",
-    "@manuscripts/library": "^1.3.4",
+    "@manuscripts/json-schema": "^2.2.6",
+    "@manuscripts/library": "^1.3.5",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
     "mime": "^3.0.0",