@manuscripts/transform 2.3.35 → 2.3.37-LEAN-3911.0

package/dist/cjs/{transformer → jats}/labels.js

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.buildTargets = void 0;
 const schema_1 = require("../schema");
-const node_names_1 = require("./node-names");
+const node_names_1 = require("../transformer/node-names");
 const labelledNodeTypes = [
     schema_1.schema.nodes.figure_element,
     schema_1.schema.nodes.table_element,
@@ -28,7 +28,7 @@ const excludedTypes = [schema_1.schema.nodes.graphical_abstract_section];
 const chooseLabel = (nodeType) => {
     return node_names_1.nodeNames.get(nodeType);
 };
-const buildTargets = (fragment) => {
+const buildTargets = (node) => {
     const counters = {};
     for (const nodeType of labelledNodeTypes) {
         counters[nodeType.name] = {
@@ -42,7 +42,7 @@ const buildTargets = (fragment) => {
         return `${counter.label} ${counter.index}`;
     };
     const targets = new Map();
-    fragment.descendants((node, pos, parent) => {
+    node.descendants((node, pos, parent) => {
         var _a;
         if (node.type.name in counters) {
             if (parent && excludedTypes.includes(parent.type)) {

package/dist/cjs/lib/utils.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
+exports.setElementAttributes = exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
 const bibliography_section_1 = require("../schema/nodes/bibliography_section");
 const graphical_abstract_section_1 = require("../schema/nodes/graphical_abstract_section");
 function* iterateChildren(node, recurse = false) {
@@ -83,3 +83,11 @@ 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();
 };
 exports.getTrimmedTextContent = getTrimmedTextContent;
+const setElementAttributes = (element, attributes) => {
+    Object.entries(attributes).forEach(([key, value]) => {
+        if (value) {
+            element.setAttribute(key, value);
+        }
+    });
+};
+exports.setElementAttributes = setElementAttributes;

package/dist/cjs/schema/index.js

@@ -43,6 +43,7 @@ const bibliography_item_1 = require("./nodes/bibliography_item");
 const bibliography_section_1 = require("./nodes/bibliography_section");
 const blockquote_element_1 = require("./nodes/blockquote_element");
 const body_1 = require("./nodes/body");
+const box_element_1 = require("./nodes/box_element");
 const caption_1 = require("./nodes/caption");
 const caption_title_1 = require("./nodes/caption_title");
 const citation_1 = require("./nodes/citation");
@@ -237,5 +238,6 @@ exports.schema = new prosemirror_model_1.Schema({
         supplement: supplement_1.supplement,
         author_notes: author_notes_1.authorNotes,
         corresp: corresp_1.corresp,
+        box_element: box_element_1.box_element,
     },
 });

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

@@ -0,0 +1,55 @@
+"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.box_element = void 0;
+exports.box_element = {
+    content: 'figcaption? section?',
+    attrs: {
+        id: { default: '' },
+        label: { default: '' },
+        dataTracked: { default: null },
+    },
+    group: 'block element',
+    selectable: false,
+    parseDOM: [
+        {
+            tag: 'div.boxed-text',
+            getAttrs: (p) => {
+                const dom = p;
+                const attrs = {
+                    id: dom.getAttribute('id') || undefined,
+                    label: dom.getAttribute('label') || undefined,
+                };
+                return attrs;
+            },
+        },
+    ],
+    toDOM: (node) => {
+        const boxElementNode = node;
+        const attrs = {};
+        if (boxElementNode.attrs.id) {
+            attrs.id = boxElementNode.attrs.id;
+        }
+        if (boxElementNode.attrs.label) {
+            attrs.label = boxElementNode.attrs.label;
+        }
+        return [
+            'div',
+            Object.assign({ class: 'boxed-text' }, attrs),
+        ];
+    },
+};

package/dist/cjs/transformer/id.js

@@ -15,14 +15,19 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateID = exports.generateNodeID = void 0;
+exports.generateNodeID = exports.generateID = exports.ExtraObjectTypes = void 0;
 const uuid_1 = require("uuid");
 const node_types_1 = require("./node-types");
-const generateNodeID = (type) => {
-    return node_types_1.nodeTypesMap.get(type) + ':' + (0, uuid_1.v4)().toUpperCase();
-};
-exports.generateNodeID = generateNodeID;
+var ExtraObjectTypes;
+(function (ExtraObjectTypes) {
+    ExtraObjectTypes["PlaceholderElement"] = "MPPlaceholderElement";
+    ExtraObjectTypes["GeneralTableFootnote"] = "MPGeneralTableFootnote";
+})(ExtraObjectTypes = exports.ExtraObjectTypes || (exports.ExtraObjectTypes = {}));
 const generateID = (objectType) => {
     return objectType + ':' + (0, uuid_1.v4)().toUpperCase();
 };
 exports.generateID = generateID;
+const generateNodeID = (type) => {
+    return node_types_1.nodeTypesMap.get(type) + ':' + (0, uuid_1.v4)().toUpperCase();
+};
+exports.generateNodeID = generateNodeID;

package/dist/cjs/transformer/index.js

@@ -29,26 +29,8 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createTestDoc = void 0;
-__exportStar(require("./builders"), exports);
-__exportStar(require("./decode"), exports);
-__exportStar(require("./document-object-types"), exports);
-__exportStar(require("./encode"), exports);
-__exportStar(require("./filename"), exports);
-__exportStar(require("./highlight-markers"), exports);
-__exportStar(require("./html"), exports);
 __exportStar(require("./id"), exports);
-__exportStar(require("./labels"), exports);
-__exportStar(require("./manuscript-dependencies"), exports);
-__exportStar(require("./models"), exports);
 __exportStar(require("./node-names"), exports);
 __exportStar(require("./node-title"), exports);
 __exportStar(require("./node-types"), exports);
-__exportStar(require("./object-types"), exports);
-__exportStar(require("./project-bundle"), exports);
 __exportStar(require("./section-category"), exports);
-__exportStar(require("./serializer"), exports);
-__exportStar(require("./timestamp"), exports);
-__exportStar(require("./update-identifiers"), exports);
-var doc_1 = require("./__tests__/__helpers__/doc");
-Object.defineProperty(exports, "createTestDoc", { enumerable: true, get: function () { return doc_1.createTestDoc; } });

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

@@ -62,6 +62,7 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.supplement, json_schema_1.ObjectTypes.Supplement],
     [schema_1.schema.nodes.author_notes, json_schema_1.ObjectTypes.AuthorNotes],
     [schema_1.schema.nodes.corresp, json_schema_1.ObjectTypes.Corresponding],
+    [schema_1.schema.nodes.box_element, json_schema_1.ObjectTypes.Section],
 ]);
 const isExecutableNodeType = (type) => (0, schema_1.hasGroup)(type, schema_1.GROUP_EXECUTABLE);
 exports.isExecutableNodeType = isExecutableNodeType;

package/dist/cjs/transformer/section-category.js

@@ -40,6 +40,8 @@ const chooseSectionNodeType = (category) => {
             return schema_1.schema.nodes.keywords;
         case 'MPSectionCategory:toc':
             return schema_1.schema.nodes.toc_section;
+        case 'MPSectionCategory:box-element':
+            return schema_1.schema.nodes.box_element;
         default:
             return schema_1.schema.nodes.section;
     }
@@ -84,6 +86,8 @@ const buildSectionCategory = (node) => {
             return 'MPSectionCategory:toc';
         case schema_1.schema.nodes.graphical_abstract_section:
             return 'MPSectionCategory:abstract-graphical';
+        case schema_1.schema.nodes.box_element:
+            return 'MPSectionCategory:box-element';
         default:
             return node.attrs.category || undefined;
     }
@@ -197,6 +201,8 @@ const chooseSectionCategoryByType = (secType) => {
             return 'MPSectionCategory:supported-by';
         case 'ethics-statement':
             return 'MPSectionCategory:ethics-statement';
+        case 'box-element':
+            return 'MPSectionCategory:box-element';
         default:
             return undefined;
     }
@@ -253,6 +259,8 @@ const chooseSectionCategoryFromTitle = (title) => {
         case 'financial-disclosure':
         case 'funding information':
             return 'MPSectionCategory:financial-disclosure';
+        case 'box-element':
+            return 'MPSectionCategory:box-element';
     }
 };
 exports.chooseSectionCategoryFromTitle = chooseSectionCategoryFromTitle;

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "2.3.35";
+exports.VERSION = "2.3.37-LEAN-3911.0";

package/dist/{cjs/transformer/serializer.js → es/jats/importer/create-article-node.js}

@@ -1,6 +1,5 @@
-"use strict";
 /*!
- * © 2019 Atypon Systems LLC
+ * © 2024 Atypon Systems LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -14,10 +13,15 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
+import { schema } from '../../schema';
+import { defaultTitle } from './jats-front-transformations';
+export const createArticleNode = (manuscript) => {
+    const title = schema.nodes.title.createChecked({}, schema.text(defaultTitle));
+    return schema.nodes.manuscript.createAndFill({
+        id: manuscript._id,
+        doi: manuscript.DOI,
+        articleType: manuscript.articleType,
+        prototype: manuscript.prototype,
+        primaryLanguageCode: manuscript.primaryLanguageCode,
+    }, title);
 };
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.xmlSerializer = void 0;
-const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
-exports.xmlSerializer = { serializeToString: w3c_xmlserializer_1.default };

package/dist/es/jats/importer/index.js

@@ -13,4 +13,5 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-export { parseJATSFront, parseJATSBody, parseJATSArticle, } from './parse-jats-article';
+export { createArticleNode } from './create-article-node';
+export { parseJATSArticle } from './parse-jats-article';

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

@@ -299,4 +299,74 @@ export const jatsBodyTransformations = {
             body.prepend(section);
         }
     },
+    moveReferencesToBackmatter(body, references, createElement) {
+        const backmatter = body.querySelector('sec[sec-type="backmatter"]');
+        if (!references || !references.items.size || !backmatter) {
+            return;
+        }
+        const bibliographySection = this.createBibliographySection(createElement);
+        const bibliographyElement = createElement('bibliography-element');
+        references.getBibliographyItems().forEach((item) => {
+            const bibliographyItem = this.createBibliographyItem(item, createElement);
+            bibliographyElement.appendChild(bibliographyItem);
+        });
+        bibliographySection.appendChild(bibliographyElement);
+        backmatter.appendChild(bibliographySection);
+    },
+    createBibliographySection(createElement) {
+        const section = createElement('sec');
+        section.setAttribute('sec-type', 'bibliography_section');
+        const title = createElement('title');
+        title.textContent = 'References';
+        section.appendChild(title);
+        return section;
+    },
+    createBibliographyItem(item, createElement) {
+        var _a, _b, _c;
+        const bibliographyItem = createElement('bibliography-item');
+        bibliographyItem.setAttribute('id', item.id);
+        bibliographyItem.setAttribute('type', item.type);
+        (_a = item.author) === null || _a === void 0 ? void 0 : _a.forEach((author) => {
+            const authorElement = createElement('author');
+            authorElement.setAttribute('id', author._id);
+            authorElement.setAttribute('family', author.family || '');
+            authorElement.setAttribute('given', author.given || '');
+            bibliographyItem.appendChild(authorElement);
+        });
+        if (item.issued) {
+            const issuedEl = createElement('issued');
+            issuedEl.setAttribute('id', ((_b = item.issued) === null || _b === void 0 ? void 0 : _b._id) || '');
+            const dateParts = item.issued['date-parts'];
+            const year = (_c = dateParts === null || dateParts === void 0 ? void 0 : dateParts[0]) === null || _c === void 0 ? void 0 : _c[0];
+            if (year) {
+                issuedEl.setAttribute('year', year.toString());
+            }
+            bibliographyItem.appendChild(issuedEl);
+        }
+        if (item.containerTitle) {
+            bibliographyItem.setAttribute('containerTitle', item.containerTitle);
+        }
+        if (item.volume) {
+            bibliographyItem.setAttribute('volume', item.volume.toString());
+        }
+        if (item.issue) {
+            bibliographyItem.setAttribute('issue', item.issue.toString());
+        }
+        if (item.supplement) {
+            bibliographyItem.setAttribute('supplement', item.supplement);
+        }
+        if (item.page) {
+            bibliographyItem.setAttribute('page', item.page.toString());
+        }
+        if (item.title) {
+            bibliographyItem.setAttribute('title', item.title);
+        }
+        if (item.literal) {
+            bibliographyItem.setAttribute('literal', item.literal);
+        }
+        if (item.doi) {
+            bibliographyItem.setAttribute('DOI', item.doi);
+        }
+        return bibliographyItem;
+    },
 };

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

@@ -13,9 +13,9 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { v4 as uuidv4 } from 'uuid';
-import { buildComment, buildContribution, highlightableFields, isHighlightableModel, isKeyword, } from '../../transformer';
-const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
+import { ObjectTypes } from '@manuscripts/json-schema';
+import { generateID } from '../../transformer';
+export const DEFAULT_PROFILE_ID = 'MPUserProfile:0000000000000000000000000000000000000001';
 export const isJATSComment = (node) => {
     return (node.nodeType === node.PROCESSING_INSTRUCTION_NODE &&
         node.nodeName === 'AuthorQuery');
@@ -23,34 +23,33 @@ export const isJATSComment = (node) => {
 export const parseJATSComment = (node) => {
     const text = node.textContent;
     if (text) {
-        const id = /id="(.+)"/.exec(text);
         const queryText = /queryText="(.+)"/.exec(text);
-        if (id && queryText) {
+        if (queryText) {
+            const parentNode = node.parentNode;
+            const index = parentNode.outerHTML.indexOf(queryText[1]);
             return {
-                id: id[1],
+                id: generateID(ObjectTypes.CommentAnnotation),
                 text: queryText[1],
+                index,
             };
         }
     }
 };
 export const markComments = (doc) => {
-    const marks = [];
+    var _a;
     const root = doc.getRootNode();
     const queue = [root];
+    const commentsElement = doc.createElement('comments-annotations');
     while (queue.length !== 0) {
         const node = queue.shift();
         if (node) {
             if (isJATSComment(node)) {
                 const comment = parseJATSComment(node);
                 if (comment) {
-                    const token = addMark(doc, node);
-                    if (token) {
-                        const mark = {
-                            token,
-                            comment,
-                        };
-                        marks.push(mark);
-                    }
+                    const highlightMarker = createHighlightMarkerElement(doc, comment.id);
+                    (_a = node.parentNode) === null || _a === void 0 ? void 0 : _a.insertBefore(highlightMarker, node);
+                    const commentElement = createCommentElement(doc, comment);
+                    commentsElement.appendChild(commentElement);
                 }
             }
             node.childNodes.forEach((child) => {
@@ -58,93 +57,19 @@ export const markComments = (doc) => {
             });
         }
     }
-    return marks;
-};
-const addMark = (doc, node) => {
-    const parent = node.parentElement;
-    if (parent) {
-        const token = uuidv4();
-        const tokenNode = doc.createTextNode(token);
-        parent.insertBefore(tokenNode, node);
-        return token;
-    }
-};
-export const createComments = (models, marks) => {
-    const comments = [];
-    for (const model of models) {
-        if (isHighlightableModel(model)) {
-            comments.push(...processModel(model, marks));
-        }
-        else if (isKeyword(model)) {
-            comments.push(...processKeyword(model, marks));
-        }
+    if (commentsElement.hasChildNodes()) {
+        doc.documentElement.appendChild(commentsElement);
     }
-    return comments;
-};
-const getFieldMarks = (content, marks) => {
-    return marks
-        .filter((m) => content.indexOf(m.token) >= 0)
-        .sort((a, b) => content.indexOf(a.token) - content.indexOf(b.token));
 };
-const processModel = (model, marks) => {
-    const comments = [];
-    for (const field of highlightableFields) {
-        const content = model[field];
-        if (!content) {
-            continue;
-        }
-        const results = processContent(model, content, getFieldMarks(content, marks));
-        model[field] = results.content;
-        comments.push(...results.comments);
-    }
-    return comments;
+const createHighlightMarkerElement = (doc, id) => {
+    const highlightMarker = doc.createElement('highlight-marker');
+    highlightMarker.setAttribute('id', id);
+    highlightMarker.setAttribute('position', 'point');
+    return highlightMarker;
 };
-const processKeyword = (model, marks) => {
-    const comments = [];
-    const name = model.name;
-    let content = name;
-    for (const mark of getFieldMarks(name, marks)) {
-        content = name.replace(mark.token, '');
-        const target = model.containedGroup;
-        if (!target) {
-            continue;
-        }
-        const contributions = [buildContribution(DEFAULT_PROFILE_ID)];
-        const comment = buildComment(target, mark.comment.text, undefined, contributions);
-        model.name = content;
-        comments.push(comment);
-    }
-    return comments;
-};
-const processContent = (model, content, marks) => {
-    const comments = [];
-    let result = content;
-    for (const mark of marks) {
-        const token = mark.token;
-        const index = result.indexOf(token);
-        result = result.replace(token, '');
-        const contributions = [buildContribution(DEFAULT_PROFILE_ID)];
-        const selector = {
-            from: index,
-            to: index,
-        };
-        const comment = buildComment(model._id, mark.comment.text, selector, contributions);
-        comments.push(comment);
-    }
-    return {
-        content: result,
-        comments,
-    };
-};
-export const createReferenceComments = (references) => {
-    const comments = [];
-    for (const item of references.getBibliographyItems()) {
-        const id = item._id;
-        for (const comment of references.getComments(id)) {
-            const contributions = [buildContribution(DEFAULT_PROFILE_ID)];
-            const c = buildComment(id, comment.text, undefined, contributions);
-            comments.push(c);
-        }
-    }
-    return comments;
+const createCommentElement = (doc, comment) => {
+    const commentElement = doc.createElement('comment-annotation');
+    commentElement.setAttribute('id', comment.id);
+    commentElement.textContent = comment.text;
+    return commentElement;
 };