@manuscripts/transform 3.0.69 → 3.1.0

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

@@ -19,7 +19,6 @@ exports.JATSDOMParser = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const prosemirror_model_1 = require("prosemirror-model");
 const utils_1 = require("../../lib/utils");
-const schema_1 = require("../../schema");
 const jats_comments_1 = require("./jats-comments");
 class JATSDOMParser {
     constructor(sectionCategories, schema) {
@@ -131,11 +130,22 @@ class JATSDOMParser {
         this.getAddressLine = (element, index) => {
             return ((0, utils_1.getTrimmedTextContent)(element, `addr-line:nth-of-type(${index})`) || '');
         };
-        this.choosePublicationType = (element) => {
-            var _a;
-            const citationElement = element.querySelector('element-citation, mixed-citation');
-            const type = citationElement === null || citationElement === void 0 ? void 0 : citationElement.getAttribute('publication-type');
-            return type ? (_a = schema_1.publicationTypeToPM[type]) !== null && _a !== void 0 ? _a : type : 'article-journal';
+        this.getRefType = (element) => {
+            const citation = element.querySelector('element-citation, mixed-citation');
+            const type = citation === null || citation === void 0 ? void 0 : citation.getAttribute('publication-type');
+            if (!type) {
+                return 'article-journal';
+            }
+            switch (type) {
+                case 'journal':
+                    return 'article-journal';
+                case 'web':
+                    return 'webpage';
+                case 'data':
+                    return 'dataset';
+                default:
+                    return type;
+            }
         };
         this.getFigContent = (node) => {
             const element = node;
@@ -154,18 +164,6 @@ class JATSDOMParser {
             }
             return prosemirror_model_1.Fragment.from(content);
         };
-        this.parseRefLiteral = (element) => {
-            var _a;
-            const mixedCitation = element.querySelector('mixed-citation');
-            const hasDirectTextNodeWithLetters = Array.from((_a = mixedCitation === null || mixedCitation === void 0 ? void 0 : mixedCitation.childNodes) !== null && _a !== void 0 ? _a : []).some((node) => {
-                var _a;
-                return node.nodeType === Node.TEXT_NODE &&
-                    ((_a = node.textContent) === null || _a === void 0 ? void 0 : _a.match(/[A-Za-z]+/g));
-            });
-            if (hasDirectTextNodeWithLetters) {
-                return (0, utils_1.getTrimmedTextContent)(mixedCitation);
-            }
-        };
         this.parseRefPages = (element) => {
             const fpage = (0, utils_1.getTrimmedTextContent)(element, 'fpage');
             const lpage = (0, utils_1.getTrimmedTextContent)(element, 'lpage');
@@ -174,10 +172,9 @@ class JATSDOMParser {
             }
         };
         this.parseRef = (element) => {
-            var _a, _b;
             return {
                 id: element.id,
-                type: this.choosePublicationType(element),
+                type: this.getRefType(element),
                 comment: (0, utils_1.getTrimmedTextContent)(element, 'comment'),
                 volume: (0, utils_1.getTrimmedTextContent)(element, 'volume'),
                 issue: (0, utils_1.getTrimmedTextContent)(element, 'issue'),
@@ -195,23 +192,13 @@ class JATSDOMParser {
                 institution: (0, utils_1.getTrimmedTextContent)(element, 'institution'),
                 locator: (0, utils_1.getTrimmedTextContent)(element, 'elocation-id'),
                 'container-title': (0, utils_1.getHTMLContent)(element, 'source'),
-                title: (_b = (_a = (0, utils_1.getHTMLContent)(element, 'article-title')) !== null && _a !== void 0 ? _a : (0, utils_1.getHTMLContent)(element, 'data-title')) !== null && _b !== void 0 ? _b : (0, utils_1.getHTMLContent)(element, 'part-title'),
-                author: this.getNameContent(element, 'person-group[person-group-type="author"] > *'),
-                editor: this.getNameContent(element, 'person-group[person-group-type="editor"] > *'),
-                literal: this.parseRefLiteral(element),
+                title: (0, utils_1.getHTMLContent)(element, 'article-title, data-title, part-title'),
+                author: this.getNameContent(element, 'author'),
+                editor: this.getNameContent(element, 'editor'),
+                literal: (0, utils_1.getTrimmedTextContent)(element, 'mixed-citation'),
                 accessed: this.getDateContent(element, 'date-in-citation'),
                 'event-date': this.getDateContent(element, 'conf-date'),
-                issued: (0, utils_1.getTrimmedTextContent)(element.querySelector('element-citation, mixed-citation'), ':scope > year')
-                    ? (0, json_schema_1.buildBibliographicDate)({
-                        'date-parts': [
-                            [
-                                (0, utils_1.getTrimmedTextContent)(element.querySelector('element-citation, mixed-citation'), ':scope > year') || '',
-                                (0, utils_1.getTrimmedTextContent)(element.querySelector('element-citation, mixed-citation'), ':scope > month') || '',
-                                (0, utils_1.getTrimmedTextContent)(element.querySelector('element-citation, mixed-citation'), ':scope > day') || '',
-                            ],
-                        ],
-                    })
-                    : undefined,
+                issued: this.getIssuedDateContent(element),
                 page: this.parseRefPages(element),
             };
         };
@@ -1075,30 +1062,22 @@ class JATSDOMParser {
             }
         }
     }
-    getNameContent(element, query) {
-        const buildName = (node) => {
-            const name = (0, json_schema_1.buildBibliographicName)({});
-            const given = (0, utils_1.getTrimmedTextContent)(node, 'given-names');
-            const family = (0, utils_1.getTrimmedTextContent)(node, 'surname');
-            if (given) {
-                name.given = given;
-            }
-            if (family) {
-                name.family = family;
-            }
-            if (node.nodeName === 'collab') {
-                name.literal = (0, utils_1.getTrimmedTextContent)(node);
-            }
-            return name;
-        };
-        const personNodes = element.querySelectorAll(query);
-        if (personNodes.length) {
-            return Array.from(personNodes).map(buildName);
+    getNameContent(element, type) {
+        const query = `person-group[person-group-type="${type}"] > *`;
+        const groups = [...element.querySelectorAll(query)];
+        if (!groups.length) {
+            return;
         }
+        return groups.map((node) => ({
+            given: (0, utils_1.getTrimmedTextContent)(node, 'given-names'),
+            family: (0, utils_1.getTrimmedTextContent)(node, 'surname'),
+            literal: node.nodeName === 'collab' ? (0, utils_1.getTrimmedTextContent)(node) : undefined,
+        }));
     }
     getDateContent(element, query) {
-        const buildDate = (element) => {
-            const isoDate = element.getAttribute('iso-8601-date');
+        const date = element.querySelector(query);
+        if (date) {
+            const isoDate = date.getAttribute('iso-8601-date');
             if (!isoDate) {
                 return;
             }
@@ -1108,14 +1087,21 @@ class JATSDOMParser {
                 parsedDate.getMonth() + 1,
                 parsedDate.getDate(),
             ];
-            return (0, json_schema_1.buildBibliographicDate)({
+            return {
                 'date-parts': [parts],
-            });
-        };
-        const dateElement = element.querySelector(query);
-        if (dateElement) {
-            return buildDate(dateElement);
+            };
+        }
+    }
+    getIssuedDateContent(element) {
+        const year = (0, utils_1.getTrimmedTextContent)(element, ':scope > * > year');
+        if (!year) {
+            return;
         }
+        const month = (0, utils_1.getTrimmedTextContent)(element, ':scope > * > month');
+        const day = (0, utils_1.getTrimmedTextContent)(element, ':scope > * > day');
+        return {
+            'date-parts': [[year, month !== null && month !== void 0 ? month : '', day !== null && day !== void 0 ? day : '']],
+        };
     }
 }
 exports.JATSDOMParser = JATSDOMParser;

package/dist/cjs/lib/citeproc.js

@@ -0,0 +1,13 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.buildCiteprocCitation = void 0;
+const buildCiteprocCitation = (citation) => ({
+    citationID: citation.id,
+    citationItems: citation.rids.map((rid) => ({
+        id: rid,
+    })),
+    properties: {
+        noteIndex: 0,
+    },
+});
+exports.buildCiteprocCitation = buildCiteprocCitation;

package/dist/cjs/schema/index.js

@@ -160,6 +160,7 @@ __exportStar(require("./nodes/placeholder_element"), exports);
 __exportStar(require("./nodes/pullquote_element"), exports);
 __exportStar(require("./nodes/section"), exports);
 __exportStar(require("./nodes/section_title"), exports);
+__exportStar(require("./nodes/section_label"), exports);
 __exportStar(require("./nodes/supplement"), exports);
 __exportStar(require("./nodes/supplements"), exports);
 __exportStar(require("./nodes/table"), exports);

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

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.bibliographyElement = void 0;
+exports.isBibliographyElementNode = exports.bibliographyElement = void 0;
 exports.bibliographyElement = {
     content: 'bibliography_item*',
     attrs: {
@@ -41,3 +41,5 @@ exports.bibliographyElement = {
         return dom;
     },
 };
+const isBibliographyElementNode = (node) => node.type === node.type.schema.nodes.bibliography_element;
+exports.isBibliographyElementNode = isBibliographyElementNode;

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

@@ -15,13 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.bibliographyItem = exports.publicationTypeToPM = void 0;
-exports.publicationTypeToPM = {
-    journal: 'article-journal',
-    web: 'webpage',
-    data: 'dataset',
-    preprint: 'article-journal',
-};
+exports.isBibliographyItemNode = exports.bibliographyItem = void 0;
 exports.bibliographyItem = {
     content: 'inline{0}',
     attrs: {
@@ -58,3 +52,5 @@ exports.bibliographyItem = {
     selectable: false,
     group: 'block',
 };
+const isBibliographyItemNode = (node) => node.type === node.type.schema.nodes.bibliography_item;
+exports.isBibliographyItemNode = isBibliographyItemNode;

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

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.comment = void 0;
+exports.isCommentNode = exports.comment = void 0;
 exports.comment = {
     attrs: {
         id: { default: '' },
@@ -27,3 +27,5 @@ exports.comment = {
         originalText: { default: '' },
     },
 };
+const isCommentNode = (node) => node.type === node.type.schema.nodes.comment;
+exports.isCommentNode = isCommentNode;

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

@@ -1,55 +1,14 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isListNode = exports.listItem = exports.list = exports.getListType = exports.getJatsListType = void 0;
+exports.isListNode = exports.listItem = exports.list = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
-const getJatsListType = (cssStyle) => {
-    switch (cssStyle) {
-        case 'disc':
-            return 'bullet';
-        case 'decimal':
-            return 'order';
-        case 'lower-alpha':
-            return 'alpha-lower';
-        case 'upper-alpha':
-            return 'alpha-upper';
-        case 'lower-roman':
-            return 'roman-lower';
-        case 'upper-roman':
-            return 'roman-upper';
-        case 'simple':
-            return 'none';
-        default:
-            return 'none';
-    }
-};
-exports.getJatsListType = getJatsListType;
-const getListType = (style) => {
-    switch (style) {
-        case 'bullet':
-            return { type: 'ul', style: 'disc' };
-        case 'order':
-            return { type: 'ul', style: 'decimal' };
-        case 'alpha-lower':
-            return { type: 'ul', style: 'lower-alpha' };
-        case 'alpha-upper':
-            return { type: 'ul', style: 'upper-alpha' };
-        case 'roman-lower':
-            return { type: 'ul', style: 'lower-roman' };
-        case 'roman-upper':
-            return { type: 'ul', style: 'upper-roman' };
-        case 'simple':
-        default:
-            return { type: 'ul', style: 'none' };
-    }
-};
-exports.getListType = getListType;
 exports.list = {
     content: 'list_item+',
     group: 'block list element',
     attrs: {
         id: { default: '' },
-        dataTracked: { default: null },
         listStyleType: { default: null },
+        dataTracked: { default: null },
     },
     parseDOM: [
         {
@@ -75,9 +34,8 @@ exports.list = {
     ],
     toDOM: (node) => {
         const list = node;
-        const { type } = (0, exports.getListType)(list.attrs.listStyleType);
         return [
-            type,
+            'ul',
             {
                 id: list.attrs.id,
                 'list-type': list.attrs.listStyleType,

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "3.0.69";
+exports.VERSION = "3.1.0";

package/dist/es/index.js

@@ -5,8 +5,8 @@ export * from './jats/types';
 export * from './lib/footnotes';
 export * from './lib/utils';
 export * from './lib/section-categories';
+export * from './lib/citeproc';
 export * from './schema';
 export { migrateFor } from './schema/migration/migrate';
-export { isSectionLabelNode } from './schema/nodes/section_label';
 export * from './transformer';
 export * from './types';

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

@@ -0,0 +1,156 @@
+/*!
+ * © 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 Citeproc from 'citeproc';
+const normalizeID = (id) => id.replace(/:/g, '_');
+const labelOnly = /^<label>.+<\/label>$/;
+export const initJats = () => {
+    if (Citeproc.Output.Formats.jats) {
+        return;
+    }
+    Citeproc.Output.Formats.jats = Object.assign(Object.assign({}, Citeproc.Output.Formats.html), { text_escape: function (text) {
+            return text !== null && text !== void 0 ? text : '';
+        }, bibstart: '<ref-list>', bibend: '</ref-list>', '@font-style/italic': '<italic>%%STRING%%</italic>', '@font-style/oblique': '<italic>%%STRING%%</italic>', '@font-style/normal': false, '@font-variant/small-caps': '<smallcaps>%%STRING%%</smallcaps>', '@font-variant/normal': false, '@font-weight/bold': '<bold>%%STRING%%</bold>', '@font-weight/normal': false, '@font-weight/light': false, '@text-decoration/none': false, '@text-decoration/underline': '<underline>%%STRING%%</underline>', '@vertical-align/sup': '<sup>%%STRING%%</sup>', '@vertical-align/sub': '<sub>%%STRING%%</sub>', '@vertical-align/baseline': false, '@bibliography/entry': function (state, str) {
+            const id = this.system_id;
+            const item = state.registry.registry[id].ref;
+            const type = getPublicationType(item);
+            str = str.trim();
+            if (labelOnly.test(str)) {
+                return `<ref id="${normalizeID(id)}">${str}<mixed-citation publication-type="${type}">${item.literal}</mixed-citation></ref>`;
+            }
+            else if (str.includes('mixed-citation')) {
+                return `<ref id="${normalizeID(id)}">${str.replace('%%TYPE%%', type)}</ref>`;
+            }
+            else {
+                return `<ref id="${normalizeID(id)}"><mixed-citation publication-type="${type}">${str}</mixed-citation></ref>`;
+            }
+        }, '@display/block': false, '@display/left-margin': function (state, str) {
+            return `<label>${str}</label>`;
+        }, '@display/right-inline': function (state, str) {
+            return `<mixed-citation publication-type="%%TYPE%%">${str}</mixed-citation>`;
+        }, '@display/indent': false, '@URL/true': false, '@DOI/true': false });
+    const name = Citeproc.NameOutput.prototype._renderOnePersonalName;
+    Citeproc.NameOutput.prototype._renderOnePersonalName = function (...args) {
+        const area = this.state.tmp.area;
+        const blob = name.call(this, ...args);
+        if (blob && area === 'bibliography') {
+            blob.strings.prefix = '<string-name>';
+            blob.strings.suffix = '</string-name>';
+        }
+        return blob;
+    };
+    const given = Citeproc.NameOutput.prototype._givenName;
+    Citeproc.NameOutput.prototype._givenName = function (...args) {
+        const area = this.state.tmp.area;
+        const info = given.call(this, ...args);
+        if (info.blob && area === 'bibliography') {
+            info.blob.strings.prefix = '<given-names>';
+            info.blob.strings.suffix = '</given-names>';
+        }
+        return info;
+    };
+    const family = Citeproc.NameOutput.prototype._familyName;
+    Citeproc.NameOutput.prototype._familyName = function (...args) {
+        const area = this.state.tmp.area;
+        const blob = family.call(this, ...args);
+        if (blob && area === 'bibliography') {
+            blob.strings.prefix = '<surname>';
+            blob.strings.suffix = '</surname>';
+        }
+        return blob;
+    };
+};
+const namesWrapper = (type) => (str) => `<person-group person-group-type="${type}">${str}</person-group>`;
+const formatDate = (date) => {
+    let output = date.year;
+    if (date.month) {
+        output += '-' + String(date.month).padStart(2, '0');
+        if (date.day) {
+            output += '-' + String(date.day).padStart(2, '0');
+        }
+    }
+    return output;
+};
+const getPublicationType = (item) => {
+    switch (item.type) {
+        case 'article-journal':
+            return 'journal';
+        case 'webpage':
+            return 'page';
+        case 'dataset':
+            return 'data';
+        default:
+            return item.type;
+    }
+};
+const wrappers = {
+    author: namesWrapper('author'),
+    issued: (str, item) => str.replace(item.issued.year, `<year>${item.issued.year}</year>`),
+    'container-title': (str) => `<source>${str}</source>`,
+    volume: (str) => `<volume>${str}</volume>`,
+    issue: (str) => `<issue>${str}</issue>`,
+    supplement: (str) => `<supplement>${str}</supplement>`,
+    page: (str) => {
+        let fpage = str;
+        let lpage;
+        const parts = str.split('-');
+        if (parts.length === 2) {
+            fpage = parts[0];
+            lpage = parts[1];
+        }
+        str = str.replace(fpage, `<fpage>${fpage}</fpage>`);
+        if (lpage) {
+            str = str.replace(lpage, `<lpage>${lpage}</lpage>`);
+        }
+        return str;
+    },
+    title: (str, item) => {
+        const type = item.type;
+        switch (type) {
+            case 'dataset':
+                return `<data-title>${str}</data-title>`;
+            case 'article-journal':
+            case 'preprint':
+                return `<article-title>${str}</article-title>`;
+            default:
+                return `<part-title>${str}</part-title>`;
+        }
+    },
+    std: (str) => `<pub-id pub-id-type="std-designation">${str}</pub-id>`,
+    'collection-title': (str) => `<series>${str}</series>`,
+    edition: (str) => `<edition>${str}</edition>`,
+    publisher: (str) => `<publisher-name>${str}</publisher-name>`,
+    'publisher-place': (str) => `<publisher-loc>${str}</publisher-loc>`,
+    event: (str) => `<conf-name>${str}</conf-name>`,
+    'event-place': (str) => `<conf-loc>${str}</conf-loc>`,
+    'number-of-pages': (str) => `<size units="pages">${str}</size>`,
+    institution: (str) => `<institution>${str}</institution>`,
+    locator: (str) => `<elocation-id>${str}</elocation-id>`,
+    editor: namesWrapper('editor'),
+    accessed: (str, item) => `<date-in-citation content-type="access-date" iso-8601-date="${formatDate(item.accessed)}">${str}</date-in-citation>`,
+    'event-date': (str, item) => `<conf-date iso-8601-date="${formatDate(item['event-date'])}">${str}</conf-date>`,
+    DOI: (str) => `<pub-id pub-id-type="doi">${str}</pub-id>`,
+    URL: (str) => `<ext-link ext-link-type="uri" xlink:href="${str}">${str}</ext-link>`,
+};
+export const jatsVariableWrapper = (params, pre, str, post) => {
+    if (str && params.context === 'bibliography') {
+        const name = params.variableNames[0];
+        const fn = wrappers[name];
+        if (fn) {
+            str = fn(str, params.itemData);
+        }
+    }
+    return `${pre}${str !== null && str !== void 0 ? str : ''}${post}`;
+};