@manuscripts/transform 2.3.38-LEAN-3911.0 → 2.6.0

package/dist/cjs/index.js

@@ -15,17 +15,17 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.isSectionLabelNode = exports.migrateFor = exports.getVersion = void 0;
-__exportStar(require("./errors"), exports);
-var getVersion_1 = require("./getVersion");
-Object.defineProperty(exports, "getVersion", { enumerable: true, get: function () { return getVersion_1.getVersion; } });
-__exportStar(require("./jats"), exports);
-__exportStar(require("./jats/types"), exports);
 __exportStar(require("./lib/section-group-type"), exports);
 __exportStar(require("./lib/table-cell-styles"), exports);
 __exportStar(require("./lib/utils"), exports);
 __exportStar(require("./schema"), exports);
+__exportStar(require("./transformer"), exports);
+__exportStar(require("./jats"), exports);
+__exportStar(require("./types"), exports);
+__exportStar(require("./errors"), exports);
+var getVersion_1 = require("./getVersion");
+Object.defineProperty(exports, "getVersion", { enumerable: true, get: function () { return getVersion_1.getVersion; } });
 var migrate_1 = require("./schema/migration/migrate");
 Object.defineProperty(exports, "migrateFor", { enumerable: true, get: function () { return migrate_1.migrateFor; } });
 var section_label_1 = require("./schema/nodes/section_label");
 Object.defineProperty(exports, "isSectionLabelNode", { enumerable: true, get: function () { return section_label_1.isSectionLabelNode; } });
-__exportStar(require("./transformer"), exports);

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

@@ -0,0 +1,22 @@
+"use strict";
+/*!
+ * © 2020 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.parseJATSArticle = exports.parseJATSBody = exports.parseJATSFront = void 0;
+var parse_jats_article_1 = require("./parse-jats-article");
+Object.defineProperty(exports, "parseJATSFront", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSFront; } });
+Object.defineProperty(exports, "parseJATSBody", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSBody; } });
+Object.defineProperty(exports, "parseJATSArticle", { enumerable: true, get: function () { return parse_jats_article_1.parseJATSArticle; } });

package/dist/cjs/jats/importer/{jats-dom-parser.js → jats-body-dom-parser.js}

@@ -18,14 +18,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.jatsDOMParser = void 0;
-const json_schema_1 = require("@manuscripts/json-schema");
+exports.jatsBodyDOMParser = void 0;
 const mime_1 = __importDefault(require("mime"));
 const prosemirror_model_1 = require("prosemirror-model");
-const utils_1 = require("../../lib/utils");
 const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
-const jats_comments_1 = require("./jats-comments");
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
 const chooseContentType = (graphicNode) => {
     if (graphicNode) {
@@ -40,12 +37,6 @@ const chooseContentType = (graphicNode) => {
         }
     }
 };
-const parsePriority = (priority) => {
-    if (!priority) {
-        return undefined;
-    }
-    return parseInt(priority);
-};
 const getEquationContent = (p) => {
     var _a;
     const element = p;
@@ -110,224 +101,6 @@ const marks = [
     },
 ];
 const nodes = [
-    {
-        tag: 'article',
-        node: 'manuscript',
-        getAttrs: (node) => {
-            var _a, _b, _c, _d;
-            const element = node;
-            return {
-                doi: (_a = element.getAttribute('DOI')) !== null && _a !== void 0 ? _a : '',
-                articleType: (_b = element.getAttribute('article-type')) !== null && _b !== void 0 ? _b : '',
-                prototype: (_c = element.getAttribute('prototype')) !== null && _c !== void 0 ? _c : '',
-                primaryLanguageCode: (_d = element.getAttribute('primary-language-code')) !== null && _d !== void 0 ? _d : '',
-            };
-        },
-    },
-    {
-        tag: 'article-title',
-        node: 'title',
-        getAttrs: (node) => {
-            const element = node;
-            return {
-                id: element.getAttribute('id'),
-            };
-        },
-    },
-    {
-        tag: 'highlight-marker',
-        node: 'highlight_marker',
-        getAttrs: (node) => {
-            var _a;
-            const element = node;
-            const id = element.getAttribute('id');
-            return {
-                id: id,
-                position: (_a = element.getAttribute('position')) !== null && _a !== void 0 ? _a : '',
-            };
-        },
-    },
-    {
-        tag: 'comment-annotation',
-        node: 'comment',
-        getAttrs: (node) => {
-            const element = node;
-            return {
-                id: element.getAttribute('id'),
-                contents: element.textContent,
-                contributions: [
-                    {
-                        _id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.Contribution),
-                        objecType: json_schema_1.ObjectTypes.Contribution,
-                        profileID: jats_comments_1.DEFAULT_PROFILE_ID,
-                        timestamp: (0, utils_1.timestamp)(),
-                    },
-                ],
-            };
-        },
-    },
-    {
-        tag: 'author-notes',
-        node: 'author_notes',
-        getAttrs: (node) => {
-            const element = node;
-            return {
-                id: element.getAttribute('id'),
-            };
-        },
-    },
-    {
-        tag: 'fn:not([fn-type])',
-        node: 'footnote',
-        context: 'author_notes/',
-        getAttrs: (node) => {
-            const element = node;
-            return {
-                id: element.getAttribute('id'),
-                kind: 'footnote',
-            };
-        },
-    },
-    {
-        tag: 'corresp',
-        node: 'corresp',
-        getAttrs: (node) => {
-            var _a;
-            const element = node;
-            const label = element.querySelector('label');
-            if (label) {
-                label.remove();
-            }
-            return {
-                id: element.getAttribute('id'),
-                label: (_a = label === null || label === void 0 ? void 0 : label.textContent) === null || _a === void 0 ? void 0 : _a.trim(),
-            };
-        },
-        getContent: (node) => {
-            var _a;
-            const element = node;
-            return prosemirror_model_1.Fragment.from(schema_1.schema.text(((_a = element.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || ''));
-        },
-    },
-    {
-        tag: 'contrib[contrib-type="author"]',
-        node: 'contributor',
-        getAttrs: (node) => {
-            var _a, _b;
-            const element = node;
-            const footnote = [];
-            const affiliations = [];
-            const corresp = [];
-            const xrefs = element.querySelectorAll('xref');
-            for (const xref of xrefs) {
-                const rid = xref.getAttribute('rid');
-                const type = xref.getAttribute('ref-type');
-                if (!rid) {
-                    continue;
-                }
-                switch (type) {
-                    case 'fn':
-                        footnote.push({
-                            noteID: rid,
-                            noteLabel: ((_a = xref.textContent) === null || _a === void 0 ? void 0 : _a.trim()) || '',
-                        });
-                        break;
-                    case 'corresp':
-                        corresp.push({
-                            correspID: rid,
-                            correspLabel: ((_b = xref.textContent) === null || _b === void 0 ? void 0 : _b.trim()) || '',
-                        });
-                        break;
-                    case 'aff':
-                        affiliations.push(rid);
-                        break;
-                }
-            }
-            return {
-                id: element.getAttribute('id'),
-                role: 'author',
-                affiliations,
-                corresp,
-                footnote,
-                isCorresponding: element.getAttribute('corresp')
-                    ? element.getAttribute('corresp') === 'yes'
-                    : undefined,
-                bibliographicName: {
-                    given: (0, utils_1.getTrimmedTextContent)(element, 'name > given-names'),
-                    family: (0, utils_1.getTrimmedTextContent)(element, 'name > surname'),
-                    ObjectType: json_schema_1.ObjectTypes.BibliographicName,
-                    _id: (0, transformer_1.generateID)(json_schema_1.ObjectTypes.BibliographicName),
-                },
-                ORCIDIdentifier: (0, utils_1.getTrimmedTextContent)(element, 'contrib-id[contrib-id-type="orcid"]'),
-                priority: parsePriority(element.getAttribute('priority')),
-            };
-        },
-        getContent: () => {
-            return prosemirror_model_1.Fragment.from(schema_1.schema.text('_'));
-        },
-    },
-    {
-        tag: 'affiliations',
-        node: 'affiliations',
-    },
-    {
-        tag: 'aff',
-        node: 'affiliation',
-        context: 'affiliations/',
-        getAttrs: (node) => {
-            var _a, _b;
-            const element = node;
-            const getEmail = (element) => {
-                var _a, _b, _c;
-                const email = element.querySelector('email');
-                if (email) {
-                    return {
-                        href: (_a = email.getAttributeNS(XLINK_NAMESPACE, 'href')) !== null && _a !== void 0 ? _a : '',
-                        text: (_c = (_b = email.textContent) === null || _b === void 0 ? void 0 : _b.trim()) !== null && _c !== void 0 ? _c : '',
-                    };
-                }
-            };
-            const getInstitutionDetails = (element) => {
-                var _a;
-                let department = '';
-                let institution = '';
-                for (const node of element.querySelectorAll('institution')) {
-                    const content = (_a = node.textContent) === null || _a === void 0 ? void 0 : _a.trim();
-                    if (!content) {
-                        continue;
-                    }
-                    const type = node.getAttribute('content-type');
-                    if (type === 'dept') {
-                        department = content;
-                    }
-                    else {
-                        institution = content;
-                    }
-                }
-                return { department, institution };
-            };
-            const getAddressLine = (element, index) => {
-                return ((0, utils_1.getTrimmedTextContent)(element, `addr-line:nth-of-type(${index})`) ||
-                    '');
-            };
-            const { department, institution } = getInstitutionDetails(element);
-            return {
-                id: element.getAttribute('id'),
-                institution: institution !== null && institution !== void 0 ? institution : '',
-                department: department !== null && department !== void 0 ? department : '',
-                addressLine1: getAddressLine(element, 1),
-                addressLine2: getAddressLine(element, 2),
-                addressLine3: getAddressLine(element, 3),
-                postCode: (_a = (0, utils_1.getTrimmedTextContent)(element, 'postal-code')) !== null && _a !== void 0 ? _a : '',
-                country: (_b = (0, utils_1.getTrimmedTextContent)(element, 'country')) !== null && _b !== void 0 ? _b : '',
-                email: getEmail(element),
-                priority: parsePriority(element.getAttribute('priority')),
-            };
-        },
-        getContent: () => {
-            return prosemirror_model_1.Fragment.from(schema_1.schema.text('_'));
-        },
-    },
     {
         tag: 'attrib',
         node: 'attribution',
@@ -336,6 +109,10 @@ const nodes = [
         tag: 'back',
         ignore: true,
     },
+    {
+        tag: 'body',
+        node: 'manuscript',
+    },
     {
         tag: 'break',
         node: 'hard_break',
@@ -355,13 +132,13 @@ const nodes = [
             const title = element.querySelector('title');
             if (title) {
                 const captionTitle = schema.nodes.caption_title.create();
-                content.push(exports.jatsDOMParser.parse(title, { topNode: captionTitle }));
+                content.push(exports.jatsBodyDOMParser.parse(title, { topNode: captionTitle }));
             }
             const paragraphs = element.querySelectorAll('p');
             if (paragraphs.length) {
                 const figcaption = schema.nodes.caption.create();
                 for (const paragraph of paragraphs) {
-                    content.push(exports.jatsDOMParser.parse(paragraph, { topNode: figcaption }));
+                    content.push(exports.jatsBodyDOMParser.parse(paragraph, { topNode: figcaption }));
                 }
             }
             return prosemirror_model_1.Fragment.from(content);
@@ -372,6 +149,17 @@ const nodes = [
         node: 'figcaption',
         context: 'table_element/',
     },
+    {
+        tag: 'caption',
+        node: 'figcaption',
+        context: 'box_element/',
+        getAttrs: (node) => {
+            const element = node;
+            return {
+                id: element.getAttribute('id'),
+            };
+        },
+    },
     {
         tag: 'code',
         node: 'listing',
@@ -552,7 +340,7 @@ const nodes = [
             const paragraphs = [];
             node.childNodes.forEach((p) => {
                 const paragraph = schema_1.schema.nodes.paragraph.create();
-                const content = exports.jatsDOMParser.parse(p, {
+                const content = exports.jatsBodyDOMParser.parse(p, {
                     topNode: paragraph,
                 });
                 paragraphs.push(content);
@@ -652,50 +440,14 @@ const nodes = [
         node: 'backmatter',
     },
     {
-        tag: 'bibliography-element',
-        node: 'bibliography_element',
-        getAttrs: (node) => {
-            const element = node;
-            return {
-                id: element.getAttribute('id'),
-            };
-        },
-    },
-    {
-        tag: 'bibliography-item',
-        node: 'bibliography_item',
+        tag: 'sec[sec-type="box-element"]',
+        node: 'box_element',
         getAttrs: (node) => {
+            var _a;
             const element = node;
-            const authors = [];
-            element.querySelectorAll('author').forEach((author) => {
-                authors.push({
-                    _id: author.getAttribute('id') || '',
-                    given: author.getAttribute('given') || '',
-                    family: author.getAttribute('family') || '',
-                    objectType: 'MPBibliographicName',
-                });
-            });
-            const issuedEl = element.querySelector('issued');
-            const issued = issuedEl
-                ? {
-                    objectType: 'MPBibliographicDate',
-                    _id: issuedEl.getAttribute('id'),
-                    'date-parts': [[issuedEl.getAttribute('year')]],
-                }
-                : undefined;
             return {
                 id: element.getAttribute('id'),
-                type: element.getAttribute('type'),
-                containerTitle: element.getAttribute('container-title'),
-                volume: element.getAttribute('volume'),
-                issue: element.getAttribute('issue'),
-                supplement: element.getAttribute('supplement'),
-                page: element.getAttribute('page'),
-                title: element.getAttribute('title'),
-                literal: element.getAttribute('literal'),
-                author: authors,
-                issued,
-                DOI: element.getAttribute('DOI'),
+                label: (_a = element.querySelector('label')) === null || _a === void 0 ? void 0 : _a.textContent,
             };
         },
     },
@@ -731,6 +483,15 @@ const nodes = [
         context: 'keyword_group//',
         node: 'keyword',
     },
+    {
+        tag: 'label',
+        context: 'box_element/',
+        ignore: true,
+    },
+    {
+        tag: 'boxed-text',
+        ignore: true,
+    },
     {
         tag: 'label',
         context: 'section/',
@@ -769,7 +530,7 @@ const nodes = [
     {
         tag: 'title',
         node: 'section_title',
-        context: 'section/|footnotes_section/|bibliography_section/|keywords/|supplements/|author_notes/',
+        context: 'section/|footnotes_section/|bibliography_section/|keywords/|supplements/',
     },
     {
         tag: 'title',
@@ -851,4 +612,4 @@ const nodes = [
         },
     },
 ];
-exports.jatsDOMParser = new prosemirror_model_1.DOMParser(schema_1.schema, [...marks, ...nodes]);
+exports.jatsBodyDOMParser = new prosemirror_model_1.DOMParser(schema_1.schema, [...marks, ...nodes]);

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

@@ -156,6 +156,25 @@ exports.jatsBodyTransformations = {
             group.appendChild(sec);
         }
     },
+    createBoxedElementSection(doc, body, createElement) {
+        const boxedTexts = body.querySelectorAll('boxed-text');
+        for (const boxedText of boxedTexts) {
+            const boxElementSec = createElement('sec');
+            boxElementSec.setAttribute('sec-type', 'box-element');
+            const title = createElement('title');
+            title.textContent = 'BoxElement';
+            boxElementSec.append(title);
+            for (const element of [...boxedText.children]) {
+                if ((element === null || element === void 0 ? void 0 : element.tagName) === 'label' || (element === null || element === void 0 ? void 0 : element.tagName) === 'caption') {
+                    boxElementSec.append(element);
+                }
+            }
+            const containerSection = createElement('sec');
+            containerSection.append(...boxedText.children);
+            boxElementSec.append(containerSection);
+            boxedText.replaceWith(boxElementSec);
+        }
+    },
     createBody(doc, body, createElement) {
         const group = createSectionGroup(section_group_type_1.bodyType, createElement);
         this.wrapBodySections(doc, group);
@@ -221,7 +240,9 @@ exports.jatsBodyTransformations = {
     moveCaptionsToEnd(body) {
         const captions = body.querySelectorAll('caption');
         for (const caption of captions) {
-            if (caption.parentNode && caption.parentNode.nodeName !== 'table-wrap') {
+            if (caption.parentNode &&
+                caption.parentNode.nodeName !== 'table-wrap' &&
+                caption.parentNode.nodeName !== 'boxed-text') {
                 caption.parentNode.appendChild(caption);
             }
         }
@@ -302,77 +323,4 @@ exports.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);
-        }
-        if (item.literal) {
-            bibliographyItem.setAttribute('literal', item.literal);
-        }
-        return bibliographyItem;
-    },
 };