@manuscripts/transform 1.5.8 → 2.0.0

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

@@ -16,34 +16,27 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.jatsBodyTransformations = void 0;
+const section_group_type_1 = require("../../lib/section-group-type");
 const transformer_1 = require("../../transformer");
 const removeNodeFromParent = (node) => node.parentNode && node.parentNode.removeChild(node);
 const capitalizeFirstLetter = (str) => str.charAt(0).toUpperCase() + str.slice(1);
-const createSectionContainer = (type, createElement) => {
-    const sectionContainer = createElement('sec');
-    const sectionCategory = (0, transformer_1.chooseSectionCategoryByType)(type);
-    sectionContainer.setAttribute('sec-type', sectionCategory ? (0, transformer_1.chooseSecType)(sectionCategory) : '');
+const createSectionGroup = (type, createElement) => {
+    const sec = createElement('sec');
+    sec.setAttribute('sec-type', type._id);
     const title = createElement('title');
-    title.textContent = sectionCategory
-        ? (0, transformer_1.getCoreSectionTitles)(sectionCategory)[0]
-        : ' ';
-    sectionContainer.appendChild(title);
-    return sectionContainer;
+    title.textContent = type.title;
+    sec.appendChild(title);
+    return sec;
 };
 exports.jatsBodyTransformations = {
     ensureSection(body, createElement) {
-        let section = createElement('sec');
-        const title = section.querySelector('title');
-        if (!title) {
-            const title = createElement('title');
-            title.textContent = '';
-            section.appendChild(title);
-        }
-        const { firstElementChild } = body;
-        if (firstElementChild && firstElementChild.tagName === 'sec') {
-            section = firstElementChild;
+        let section;
+        const element = body.firstElementChild;
+        if (element && element.tagName === 'sec') {
+            section = element;
         }
         else {
+            section = createElement('sec');
             body.insertBefore(section, body.firstChild);
         }
         body.childNodes.forEach((child) => {
@@ -58,7 +51,7 @@ exports.jatsBodyTransformations = {
             }
         });
     },
-    createAbstract(abstractNode, createElement) {
+    createAbstractSection(abstractNode, createElement) {
         const abstractType = abstractNode.getAttribute('abstract-type');
         const section = createElement('sec');
         const sectionType = abstractType ? `abstract-${abstractType}` : 'abstract';
@@ -75,7 +68,7 @@ exports.jatsBodyTransformations = {
         }
         return section;
     },
-    createAcknowledgments(ackNode, createElement) {
+    createAcknowledgmentsSection(ackNode, createElement) {
         const section = createElement('sec');
         section.setAttribute('sec-type', 'acknowledgments');
         const titleNode = ackNode.querySelector('title');
@@ -92,40 +85,7 @@ exports.jatsBodyTransformations = {
         }
         return section;
     },
-    createBibliography(doc, references, createElement) {
-        const bibSec = doc.createElement('sec');
-        bibSec.setAttribute('sec-type', 'bibliography');
-        const titleNode = doc.querySelector('back > ref-list > title');
-        if (titleNode) {
-            bibSec.appendChild(titleNode);
-        }
-        else {
-            const title = createElement('title');
-            title.textContent = 'References';
-            bibSec.appendChild(title);
-        }
-        const refList = doc.createElement('ref-list');
-        for (const ref of references) {
-            const item = doc.createElement('ref');
-            item.setAttribute('id', ref._id);
-            item.setAttribute('type', ref.type);
-            item.setAttribute('author', JSON.stringify(ref.author));
-            item.setAttribute('issued', JSON.stringify(ref.issued));
-            ref['container-title'] &&
-                item.setAttribute('container-title', ref['container-title']);
-            ref.DOI && item.setAttribute('doi', ref.DOI);
-            ref.volume && item.setAttribute('volume', ref.volume.toString());
-            ref.issue && item.setAttribute('issue', ref.issue.toString());
-            ref.supplement && item.setAttribute('supplement', ref.supplement);
-            ref.page && item.setAttribute('page', ref.page.toString());
-            ref.title && item.setAttribute('title', ref.title);
-            ref.literal && item.setAttribute('literal', ref.literal);
-            refList.appendChild(item);
-        }
-        bibSec.appendChild(refList);
-        return bibSec;
-    },
-    createFootnotes(footnoteGroups, createElement) {
+    createFootnotesSection(footnoteGroups, createElement) {
         const section = createElement('sec');
         section.setAttribute('sec-type', 'endnotes');
         const titleNode = footnoteGroups
@@ -150,81 +110,81 @@ exports.jatsBodyTransformations = {
         section.append(...app.children);
         return section;
     },
-    createFloatsGroupSection(floatsGroup, createElement) {
+    createFloatsGroupSection(group, createElement) {
         const section = createElement('sec');
         section.setAttribute('sec-type', 'floating-element');
         const title = createElement('title');
         title.textContent = 'Floating Group';
         section.appendChild(title);
-        section.append(...floatsGroup.children);
+        section.append(...group.children);
         return section;
     },
-    moveAbstractsIntoContainer(doc, abstractsContainer, createElement) {
-        const abstractNodes = doc.querySelectorAll('front > article-meta > abstract');
-        abstractNodes.forEach((abstractNode) => {
-            const abstract = this.createAbstract(abstractNode, createElement);
-            removeNodeFromParent(abstractNode);
-            abstractsContainer.appendChild(abstract);
+    moveAbstracts(doc, group, createElement) {
+        const abstracts = doc.querySelectorAll('front > article-meta > abstract');
+        abstracts.forEach((abstract) => {
+            const sec = this.createAbstractSection(abstract, createElement);
+            removeNodeFromParent(abstract);
+            group.appendChild(sec);
         });
     },
-    wrapBodySections(doc, bodyContainer) {
+    wrapBodySections(doc, group) {
         const bodySections = doc.querySelectorAll('body > sec:not([sec-type="backmatter"]), body > sec:not([sec-type])');
         bodySections.forEach((section) => {
             removeNodeFromParent(section);
-            bodyContainer.appendChild(section);
+            group.appendChild(section);
         });
     },
-    moveBackSectionsIntoContainer(doc, backmatterContainer) {
+    moveBackSections(doc, group) {
         for (const section of doc.querySelectorAll('back > sec')) {
             removeNodeFromParent(section);
-            backmatterContainer.appendChild(section);
+            group.appendChild(section);
         }
     },
-    moveAcknowledgmentsIntoContainer(doc, backmatterContainer, createElement) {
-        const ackNode = doc.querySelector('back > ack');
-        if (ackNode) {
-            const acknowledgements = this.createAcknowledgments(ackNode, createElement);
-            removeNodeFromParent(ackNode);
-            backmatterContainer.appendChild(acknowledgements);
+    moveAcknowledgments(doc, group, createElement) {
+        const ack = doc.querySelector('back > ack');
+        if (ack) {
+            const sec = this.createAcknowledgmentsSection(ack, createElement);
+            removeNodeFromParent(ack);
+            group.appendChild(sec);
         }
     },
-    moveAppendicesIntoContainer(doc, backmatterContainer, createElement) {
-        const appGroup = doc.querySelectorAll('back > app-group > app');
-        for (const app of appGroup) {
-            const appendix = this.createAppendixSection(app, createElement);
+    moveAppendices(doc, group, createElement) {
+        const apps = doc.querySelectorAll('back > app-group > app');
+        for (const app of apps) {
+            const sec = this.createAppendixSection(app, createElement);
             removeNodeFromParent(app);
-            backmatterContainer.appendChild(appendix);
+            group.appendChild(sec);
         }
     },
-    moveBibliographyIntoContainer(doc, backmatterContainer, references, createElement) {
-        if (references && references.length) {
-            backmatterContainer.appendChild(this.createBibliography(doc, references, createElement));
-        }
+    createBody(doc, body, createElement) {
+        const group = createSectionGroup(section_group_type_1.bodyType, createElement);
+        this.wrapBodySections(doc, group);
+        this.moveFloatsGroupToBody(doc, group, createElement);
+        body.append(group);
+    },
+    createAbstracts(doc, body, createElement) {
+        const group = createSectionGroup(section_group_type_1.abstractsType, createElement);
+        this.moveAbstracts(doc, group, createElement);
+        body.insertBefore(group, body.lastElementChild);
     },
-    moveSectionsToBody(doc, body, references, createElement) {
-        const bodyContainer = createSectionContainer('body', createElement);
-        const abstractsContainer = createSectionContainer('abstracts', createElement);
-        const backmatterContainer = createSectionContainer('backmatter', createElement);
-        this.mapFootnotesToSections(doc, backmatterContainer, createElement);
-        this.wrapBodySections(doc, bodyContainer);
-        this.moveAbstractsIntoContainer(doc, abstractsContainer, createElement);
-        this.moveBackSectionsIntoContainer(doc, backmatterContainer);
-        this.moveAcknowledgmentsIntoContainer(doc, backmatterContainer, createElement);
-        this.moveAppendicesIntoContainer(doc, backmatterContainer, createElement);
-        this.moveBibliographyIntoContainer(doc, backmatterContainer, references, createElement);
-        body.insertBefore(abstractsContainer, body.firstChild);
-        body.insertBefore(bodyContainer, abstractsContainer.nextSibling);
-        body.append(backmatterContainer);
+    createBackmatter(doc, body, createElement) {
+        const group = createSectionGroup(section_group_type_1.backmatterType, createElement);
+        this.moveBackSections(doc, group);
+        this.moveAppendices(doc, group, createElement);
+        this.moveSpecialFootnotes(doc, group, createElement);
+        this.moveFootnotes(doc, group, createElement);
+        this.moveAcknowledgments(doc, group, createElement);
+        body.append(group);
     },
-    mapFootnotesToSections(doc, backmatterContainer, createElement) {
+    moveSpecialFootnotes(doc, group, createElement) {
         var _a;
-        const footnoteGroups = [...doc.querySelectorAll('fn[fn-type]')];
-        for (const footnote of footnoteGroups) {
-            const type = footnote.getAttribute('fn-type') || '';
+        const fns = [...doc.querySelectorAll('fn[fn-type]')];
+        for (const fn of fns) {
+            const type = fn.getAttribute('fn-type') || '';
             const category = (0, transformer_1.chooseSectionCategoryByType)(type);
             if (category) {
                 const section = createElement('sec');
-                const title = footnote.querySelector('p[content-type="fn-title"]');
+                const title = fn.querySelector('p[content-type="fn-title"]');
                 if (title) {
                     const sectionTitleElement = createElement('title');
                     const titleTextContent = (_a = title.textContent) === null || _a === void 0 ? void 0 : _a.trim();
@@ -234,12 +194,14 @@ exports.jatsBodyTransformations = {
                     removeNodeFromParent(title);
                     section.append(sectionTitleElement);
                 }
-                section.append(...footnote.children);
-                removeNodeFromParent(footnote);
+                section.append(...fn.children);
+                removeNodeFromParent(fn);
                 section.setAttribute('sec-type', (0, transformer_1.chooseSecType)(category));
-                backmatterContainer.append(section);
+                group.append(section);
             }
         }
+    },
+    moveFootnotes(doc, group, createElement) {
         const footnotes = [...doc.querySelectorAll('fn:not(table-wrap-foot fn)')];
         const footnotesSection = doc.querySelector('sec[sec-type="endnotes"]');
         const footnotesSectionGroup = footnotesSection === null || footnotesSection === void 0 ? void 0 : footnotesSection.querySelector('fn-group');
@@ -251,8 +213,8 @@ exports.jatsBodyTransformations = {
             }
         }
         if (!footnotesSection && containingGroup.innerHTML) {
-            const section = this.createFootnotes([containingGroup], createElement);
-            backmatterContainer.append(section);
+            const section = this.createFootnotesSection([containingGroup], createElement);
+            group.append(section);
         }
         let regularFootnoteGroups = [
             ...doc.querySelectorAll('back > fn-group:not([fn-type])'),
@@ -264,8 +226,8 @@ exports.jatsBodyTransformations = {
         });
         if (regularFootnoteGroups.length > 0) {
             regularFootnoteGroups.map((g) => removeNodeFromParent(g));
-            const footnotes = this.createFootnotes(regularFootnoteGroups, createElement);
-            backmatterContainer.appendChild(footnotes);
+            const footnotes = this.createFootnotesSection(regularFootnoteGroups, createElement);
+            group.appendChild(footnotes);
         }
     },
     moveCaptionsToEnd(body) {
@@ -276,103 +238,50 @@ exports.jatsBodyTransformations = {
             }
         }
     },
-    moveTableFooterToEnd(body) {
-        const tableFooters = body.querySelectorAll('table-wrap-foot');
-        for (const tableFooter of tableFooters) {
-            if (tableFooter.parentNode) {
-                tableFooter.parentNode.appendChild(tableFooter);
+    fixTables(body, createElement) {
+        const tables = body.querySelectorAll('table-wrap > table');
+        tables.forEach((table) => {
+            const colgroup = table.querySelector('colgroup');
+            const cols = table.querySelectorAll('col');
+            if (!colgroup && table.firstChild && cols.length > 0) {
+                const colgroup = createElement('colgroup');
+                for (const col of cols) {
+                    colgroup.appendChild(col);
+                }
+                table.insertBefore(colgroup, table.firstChild);
             }
-        }
-    },
-    moveAffiliationsToBody(doc, affiliations, body, createElement) {
-        if (affiliations === null || affiliations === void 0 ? void 0 : affiliations.length) {
-            const section = createElement('sec');
-            section.setAttribute('sec-type', 'affiliations');
-            affiliations.forEach((affiliation) => {
-                const item = doc.createElement('aff');
-                item.setAttribute('id', affiliation._id);
-                affiliation.institution &&
-                    item.setAttribute('institution', affiliation.institution);
-                affiliation.email &&
-                    item.setAttribute('email', JSON.stringify(affiliation.email));
-                affiliation.department &&
-                    item.setAttribute('department', affiliation.department);
-                affiliation.addressLine1 &&
-                    item.setAttribute('addressLine1', affiliation.addressLine1);
-                affiliation.addressLine2 &&
-                    item.setAttribute('addressLine2', affiliation.addressLine2);
-                affiliation.addressLine3 &&
-                    item.setAttribute('addressLine3', affiliation.addressLine3);
-                affiliation.postCode &&
-                    item.setAttribute('postCode', affiliation.postCode);
-                affiliation.country && item.setAttribute('country', affiliation.country);
-                (affiliation.priority === 0 || affiliation.priority) &&
-                    item.setAttribute('priority', affiliation.priority.toString());
-                section.appendChild(item);
-            });
-            body.prepend(section);
-        }
+            const tbody = table.querySelector('tbody');
+            if (tbody) {
+                const headerRow = table.querySelector('thead > tr');
+                if (!headerRow) {
+                    const tr = createElement('tr');
+                    tbody.insertBefore(tr, tbody.firstElementChild);
+                }
+                const footerRow = table.querySelector('tfoot > tr');
+                if (!footerRow) {
+                    const tr = createElement('tr');
+                    tbody.appendChild(tr);
+                }
+            }
+        });
     },
-    moveAuthorsToBody(doc, authors, body, createElement) {
-        if (authors === null || authors === void 0 ? void 0 : authors.length) {
-            const section = createElement('sec');
-            section.setAttribute('sec-type', 'contributors');
-            authors.forEach((author) => {
-                const item = doc.createElement('contrib');
-                item.setAttribute('id', author._id);
-                author.role && item.setAttribute('role', author.role);
-                author.affiliations &&
-                    item.setAttribute('affiliations', JSON.stringify(author.affiliations));
-                author.footnote &&
-                    item.setAttribute('footnote', JSON.stringify(author.footnote));
-                author.corresp &&
-                    item.setAttribute('corresp', JSON.stringify(author.corresp));
-                author.bibliographicName &&
-                    item.setAttribute('bibliographicName', JSON.stringify(author.bibliographicName));
-                author.userID && item.setAttribute('userID', author.userID);
-                author.invitationID &&
-                    item.setAttribute('invitationID', author.invitationID);
-                author.isCorresponding &&
-                    item.setAttribute('isCorresponding', JSON.stringify(author.isCorresponding));
-                author.ORCIDIdentifier &&
-                    item.setAttribute('ORCIDIdentifier', author.ORCIDIdentifier);
-                (author.priority === 0 || author.priority) &&
-                    item.setAttribute('priority', author.priority.toString());
-                section.appendChild(item);
-            });
-            body.prepend(section);
+    moveTableFooterToEnd(body) {
+        const footers = body.querySelectorAll('table-wrap-foot');
+        for (const footer of footers) {
+            if (footer.parentNode) {
+                footer.parentNode.appendChild(footer);
+            }
         }
     },
     moveFloatsGroupToBody(doc, body, createElement) {
-        const floatsGroup = doc.querySelector('floats-group');
-        if (floatsGroup) {
-            const floatsGroupSection = this.createFloatsGroupSection(floatsGroup, createElement);
-            removeNodeFromParent(floatsGroup);
-            body.appendChild(floatsGroupSection);
+        const group = doc.querySelector('floats-group');
+        if (group) {
+            const sec = this.createFloatsGroupSection(group, createElement);
+            removeNodeFromParent(group);
+            body.appendChild(sec);
         }
     },
-    moveBlockNodesFromParagraph(doc, body, createElement) {
-        const blockNodes = ['disp-formula'];
-        const paragraphs = [...body.querySelectorAll('sec > p')].filter((node) => blockNodes.find((node_name) => node.querySelector(`:scope > ${node_name}`)));
-        paragraphs.map((paragraph) => {
-            let newParagraph = createElement('p');
-            const parent = doc.createDocumentFragment();
-            while (paragraph === null || paragraph === void 0 ? void 0 : paragraph.firstChild) {
-                if (blockNodes.includes(paragraph === null || paragraph === void 0 ? void 0 : paragraph.firstChild.nodeName)) {
-                    if (newParagraph.innerHTML.trim().length > 0) {
-                        parent.append(newParagraph);
-                        newParagraph = createElement('p');
-                    }
-                    parent.append(paragraph === null || paragraph === void 0 ? void 0 : paragraph.firstChild);
-                }
-                else {
-                    newParagraph.append(paragraph === null || paragraph === void 0 ? void 0 : paragraph.firstChild);
-                }
-            }
-            paragraph === null || paragraph === void 0 ? void 0 : paragraph.replaceWith(parent);
-        });
-    },
-    moveKeywordsToBody(document, body, createElement) {
+    createKeywords(document, body, createElement) {
         const keywordGroups = [...document.querySelectorAll('kwd-group')];
         if (keywordGroups.length > 0) {
             const section = createElement('sec');
@@ -380,9 +289,9 @@ exports.jatsBodyTransformations = {
             const title = createElement('title');
             title.textContent = 'Keywords';
             section.append(title);
-            const kwdGroupsEl = createElement('kwd-group-list');
-            kwdGroupsEl.append(keywordGroups[0]);
-            section.append(kwdGroupsEl);
+            const keywordsElement = createElement('kwd-group-list');
+            keywordsElement.append(keywordGroups[0]);
+            section.append(keywordsElement);
             body.prepend(section);
         }
     },