@manuscripts/transform 1.2.4-LEAN-2357 → 1.2.4

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

@@ -19,17 +19,6 @@ exports.jatsBodyTransformations = void 0;
 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 title = createElement('title');
-    title.textContent = sectionCategory
-        ? (0, transformer_1.getSectionTitles)(sectionCategory)[0]
-        : ' ';
-    sectionContainer.appendChild(title);
-    return sectionContainer;
-};
 exports.jatsBodyTransformations = {
     ensureSection(body, createElement) {
         let section = createElement('sec');
@@ -157,64 +146,34 @@ exports.jatsBodyTransformations = {
         section.append(...floatsGroup.children);
         return section;
     },
-    moveAbstractsIntoContainer(doc, abstractsContainer, createElement) {
+    moveSectionsToBody(doc, body, references, createElement) {
         const abstractNodes = doc.querySelectorAll('front > article-meta > abstract');
-        abstractNodes.forEach((abstractNode) => {
+        for (const abstractNode of abstractNodes) {
             const abstract = this.createAbstract(abstractNode, createElement);
             removeNodeFromParent(abstractNode);
-            abstractsContainer.appendChild(abstract);
-        });
-    },
-    wrapBodySections(doc, bodyContainer) {
-        const bodySections = doc.querySelectorAll('body > sec:not([sec-type="backmatter"]), body > sec:not([sec-type])');
-        bodySections.forEach((section) => {
-            removeNodeFromParent(section);
-            bodyContainer.appendChild(section);
-        });
-    },
-    moveBackSectionsIntoContainer(doc, backmatterContainer) {
+            body.insertBefore(abstract, body.firstChild);
+        }
         for (const section of doc.querySelectorAll('back > sec')) {
             removeNodeFromParent(section);
-            backmatterContainer.appendChild(section);
+            body.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);
+            body.appendChild(acknowledgements);
         }
-    },
-    moveAppendicesIntoContainer(doc, backmatterContainer, createElement) {
         const appGroup = doc.querySelectorAll('back > app-group > app');
         for (const app of appGroup) {
             const appendix = this.createAppendixSection(app, createElement);
             removeNodeFromParent(app);
-            backmatterContainer.appendChild(appendix);
+            body.appendChild(appendix);
         }
-    },
-    moveBibliographyIntoContainer(doc, backmatterContainer, references, createElement) {
         if (references) {
-            backmatterContainer.appendChild(this.createBibliography(doc, references, createElement));
+            body.appendChild(this.createBibliography(doc, references, createElement));
         }
     },
-    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);
-    },
-    mapFootnotesToSections(doc, backmatterContainer, createElement) {
+    mapFootnotesToSections(doc, body, createElement) {
         const footnoteGroups = [...doc.querySelectorAll('fn[fn-type]')];
         for (const footnote of footnoteGroups) {
             const type = footnote.getAttribute('fn-type') || '';
@@ -231,7 +190,7 @@ exports.jatsBodyTransformations = {
                 section.append(...footnote.children);
                 removeNodeFromParent(footnote);
                 section.setAttribute('sec-type', (0, transformer_1.chooseSecType)(category));
-                backmatterContainer.append(section);
+                body.append(section);
             }
         }
         const footnotes = [...doc.querySelectorAll('fn')];
@@ -246,7 +205,7 @@ exports.jatsBodyTransformations = {
         }
         if (!footnotesSection && containingGroup.innerHTML) {
             const section = this.createFootnotes([containingGroup], createElement);
-            backmatterContainer.append(section);
+            body.append(section);
         }
         let regularFootnoteGroups = [
             ...doc.querySelectorAll('back > fn-group:not([fn-type])'),
@@ -259,7 +218,7 @@ exports.jatsBodyTransformations = {
         if (regularFootnoteGroups.length > 0) {
             regularFootnoteGroups.map((g) => removeNodeFromParent(g));
             const footnotes = this.createFootnotes(regularFootnoteGroups, createElement);
-            backmatterContainer.appendChild(footnotes);
+            body.appendChild(footnotes);
         }
     },
     moveCaptionsToEnd(body) {

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

@@ -116,6 +116,7 @@ const parseJATSBody = (document, body, bibliographyItems, refModels, referenceId
     const orderedFootnotesIDs = (0, footnotes_order_1.createOrderedFootnotesIDs)(document);
     jats_body_transformations_1.jatsBodyTransformations.moveFloatsGroupToBody(document, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.ensureSection(body, createElement);
+    jats_body_transformations_1.jatsBodyTransformations.mapFootnotesToSections(document, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.moveSectionsToBody(document, body, bibliographyItems, createElement);
     jats_body_transformations_1.jatsBodyTransformations.moveCaptionsToEnd(body);
     jats_body_transformations_1.jatsBodyTransformations.moveTableFooterToEnd(body);

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

@@ -136,10 +136,8 @@ class JATSExporter {
                 article.appendChild(body);
                 const back = this.buildBack(body);
                 article.appendChild(back);
-                this.unwrapBody(body);
                 this.moveAbstracts(front, body);
                 this.moveFloatsGroup(body, article);
-                this.removeBackContainer(body);
             }
             await this.rewriteIDs(idGenerator);
             if (mediaPathGenerator) {
@@ -1394,49 +1392,21 @@ class JATSExporter {
                 table.insertBefore(tfoot, tbody);
             }
         };
-        this.unwrapBody = (body) => {
-            const container = body.querySelector(':scope > sec[sec-type="body"]');
-            if (!container) {
-                return;
-            }
-            const sections = container.querySelectorAll(':scope > sec');
-            sections.forEach((section) => {
-                body.appendChild(section.cloneNode(true));
-            });
-            body.removeChild(container);
-        };
-        this.removeBackContainer = (body) => {
-            const container = body.querySelector(':scope > sec[sec-type="backmatter"]');
-            if (!container) {
-                return;
-            }
-            const isContainerEmpty = container.children.length === 0;
-            if (!isContainerEmpty) {
-                warn('Backmatter section is not empty.');
-            }
-            body.removeChild(container);
-        };
         this.moveAbstracts = (front, body) => {
-            const container = body.querySelector(':scope > sec[sec-type="abstracts"]');
-            let abstractSections;
-            if (container) {
-                abstractSections = Array.from(container.querySelectorAll(':scope > sec'));
-            }
-            else {
-                abstractSections = Array.from(body.querySelectorAll(':scope > sec')).filter((section) => {
-                    const sectionType = section.getAttribute('sec-type');
-                    if (sectionType === 'abstract' ||
-                        sectionType === 'abstract-teaser' ||
-                        sectionType === 'abstract-graphical') {
-                        return true;
-                    }
-                    const sectionTitle = section.querySelector(':scope > title');
-                    if (!sectionTitle) {
-                        return false;
-                    }
-                    return sectionTitle.textContent === 'Abstract';
-                });
-            }
+            const sections = body.querySelectorAll(':scope > sec');
+            const abstractSections = Array.from(sections).filter((section) => {
+                const sectionType = section.getAttribute('sec-type');
+                if (sectionType === 'abstract' ||
+                    sectionType === 'abstract-teaser' ||
+                    sectionType === 'abstract-graphical') {
+                    return true;
+                }
+                const sectionTitle = section.querySelector(':scope > title');
+                if (!sectionTitle) {
+                    return false;
+                }
+                return sectionTitle.textContent === 'Abstract';
+            });
             if (abstractSections.length) {
                 for (const abstractSection of abstractSections) {
                     const abstractNode = this.document.createElement('abstract');
@@ -1457,9 +1427,6 @@ class JATSExporter {
                     }
                 }
             }
-            if (container) {
-                body.removeChild(container);
-            }
         };
         this.moveSectionsToBack = (back, body) => {
             const availabilitySection = body.querySelector('sec[sec-type="availability"]');

package/dist/cjs/lib/utils.js

@@ -15,7 +15,8 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.findParentNodeClosestToPos = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
+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) {
     for (let i = 0; i < node.childCount; i++) {
@@ -50,6 +51,16 @@ const isInGraphicalAbstractSection = ($pos) => {
     return false;
 };
 exports.isInGraphicalAbstractSection = isInGraphicalAbstractSection;
+const isInBibliographySection = ($pos) => {
+    for (let i = $pos.depth; i > 0; i--) {
+        const node = $pos.node(i);
+        if ((0, bibliography_section_1.isBibliographySectionNode)(node)) {
+            return true;
+        }
+    }
+    return false;
+};
+exports.isInBibliographySection = isInBibliographySection;
 const findParentNodeClosestToPos = ($pos, predicate) => {
     for (let i = $pos.depth; i > 0; i--) {
         const node = $pos.node(i);

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

@@ -35,7 +35,7 @@ const choosePageBreakStyle = (element) => {
     return exports.PAGE_BREAK_NONE;
 };
 exports.section = {
-    content: 'section_label? section_title (paragraph | element)* sections*',
+    content: 'section_label? section_title (paragraph | element)* section*',
     attrs: {
         id: { default: '' },
         category: { default: '' },

package/dist/cjs/transformer/encode.js

@@ -162,15 +162,6 @@ const childElements = (node) => {
     });
     return nodes;
 };
-const sectionChildElementIds = (node) => {
-    const nodes = [];
-    node.forEach((childNode) => {
-        if (!(0, schema_1.hasGroup)(childNode.type, 'sections')) {
-            nodes.push(childNode);
-        }
-    });
-    return nodes.map((childNode) => childNode.attrs.id).filter((id) => id);
-};
 const attributeOfNodeType = (node, type, attribute) => {
     for (const child of (0, utils_1.iterateChildren)(node)) {
         if (child.type.name === type) {
@@ -458,7 +449,9 @@ const encoders = {
         label: inlineContentsOfNodeType(node, node.type.schema.nodes.section_label) ||
             undefined,
         path: path.concat([node.attrs.id]),
-        elementIDs: sectionChildElementIds(node),
+        elementIDs: childElements(node)
+            .map((childNode) => childNode.attrs.id)
+            .filter((id) => id),
         titleSuppressed: node.attrs.titleSuppressed || undefined,
         generatedLabel: node.attrs.generatedLabel || undefined,
         pageBreakStyle: node.attrs.pageBreakStyle || undefined,

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

@@ -14,12 +14,8 @@
  * 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 };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.chooseSectionCategoryFromTitle = exports.chooseSectionCategory = exports.chooseSectionCategoryByType = exports.chooseSecType = exports.buildSectionCategory = exports.guessSectionCategory = exports.chooseSectionLableName = exports.chooseSectionNodeType = exports.isAnySectionNode = exports.getSectionTitles = void 0;
-const section_categories_json_1 = __importDefault(require("@manuscripts/data/dist/shared/section-categories.json"));
+exports.chooseSectionCategoryFromTitle = exports.chooseSectionCategory = exports.chooseSectionCategoryByType = exports.chooseSecType = exports.buildSectionCategory = exports.guessSectionCategory = exports.chooseSectionLableName = exports.chooseSectionNodeType = exports.isAnySectionNode = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 const schema_1 = require("../schema");
 const sectionNodeTypes = [
@@ -29,18 +25,6 @@ const sectionNodeTypes = [
     schema_1.schema.nodes.section,
     schema_1.schema.nodes.toc_section,
 ];
-const sectionCategoriesMap = new Map(section_categories_json_1.default.map((section) => [
-    section._id,
-    section,
-]));
-const getSectionTitles = (sectionCategory) => {
-    const category = sectionCategoriesMap.get(sectionCategory);
-    if (category) {
-        return category.titles.length ? category.titles : [' '];
-    }
-    throw new Error(`${sectionCategory} not found in section categories`);
-};
-exports.getSectionTitles = getSectionTitles;
 const isAnySectionNode = (node) => sectionNodeTypes.includes(node.type);
 exports.isAnySectionNode = isAnySectionNode;
 const chooseSectionNodeType = (category) => {
@@ -177,12 +161,6 @@ const chooseSectionCategoryByType = (secType) => {
             return 'MPSectionCategory:supported-by';
         case 'ethics-statement':
             return 'MPSectionCategory:ethics-statement';
-        case 'body':
-            return 'MPSectionCategory:body';
-        case 'backmatter':
-            return 'MPSectionCategory:backmatter';
-        case 'abstracts':
-            return 'MPSectionCategory:abstracts';
         default:
             return undefined;
     }

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

@@ -13,20 +13,9 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { chooseSectionCategoryByType, chooseSecType, getSectionTitles, } from '../../transformer';
+import { chooseSectionCategoryByType, chooseSecType } from '../../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 = chooseSectionCategoryByType(type);
-    sectionContainer.setAttribute('sec-type', sectionCategory ? chooseSecType(sectionCategory) : '');
-    const title = createElement('title');
-    title.textContent = sectionCategory
-        ? getSectionTitles(sectionCategory)[0]
-        : ' ';
-    sectionContainer.appendChild(title);
-    return sectionContainer;
-};
 export const jatsBodyTransformations = {
     ensureSection(body, createElement) {
         let section = createElement('sec');
@@ -154,64 +143,34 @@ export const jatsBodyTransformations = {
         section.append(...floatsGroup.children);
         return section;
     },
-    moveAbstractsIntoContainer(doc, abstractsContainer, createElement) {
+    moveSectionsToBody(doc, body, references, createElement) {
         const abstractNodes = doc.querySelectorAll('front > article-meta > abstract');
-        abstractNodes.forEach((abstractNode) => {
+        for (const abstractNode of abstractNodes) {
             const abstract = this.createAbstract(abstractNode, createElement);
             removeNodeFromParent(abstractNode);
-            abstractsContainer.appendChild(abstract);
-        });
-    },
-    wrapBodySections(doc, bodyContainer) {
-        const bodySections = doc.querySelectorAll('body > sec:not([sec-type="backmatter"]), body > sec:not([sec-type])');
-        bodySections.forEach((section) => {
-            removeNodeFromParent(section);
-            bodyContainer.appendChild(section);
-        });
-    },
-    moveBackSectionsIntoContainer(doc, backmatterContainer) {
+            body.insertBefore(abstract, body.firstChild);
+        }
         for (const section of doc.querySelectorAll('back > sec')) {
             removeNodeFromParent(section);
-            backmatterContainer.appendChild(section);
+            body.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);
+            body.appendChild(acknowledgements);
         }
-    },
-    moveAppendicesIntoContainer(doc, backmatterContainer, createElement) {
         const appGroup = doc.querySelectorAll('back > app-group > app');
         for (const app of appGroup) {
             const appendix = this.createAppendixSection(app, createElement);
             removeNodeFromParent(app);
-            backmatterContainer.appendChild(appendix);
+            body.appendChild(appendix);
         }
-    },
-    moveBibliographyIntoContainer(doc, backmatterContainer, references, createElement) {
         if (references) {
-            backmatterContainer.appendChild(this.createBibliography(doc, references, createElement));
+            body.appendChild(this.createBibliography(doc, references, createElement));
         }
     },
-    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);
-    },
-    mapFootnotesToSections(doc, backmatterContainer, createElement) {
+    mapFootnotesToSections(doc, body, createElement) {
         const footnoteGroups = [...doc.querySelectorAll('fn[fn-type]')];
         for (const footnote of footnoteGroups) {
             const type = footnote.getAttribute('fn-type') || '';
@@ -228,7 +187,7 @@ export const jatsBodyTransformations = {
                 section.append(...footnote.children);
                 removeNodeFromParent(footnote);
                 section.setAttribute('sec-type', chooseSecType(category));
-                backmatterContainer.append(section);
+                body.append(section);
             }
         }
         const footnotes = [...doc.querySelectorAll('fn')];
@@ -243,7 +202,7 @@ export const jatsBodyTransformations = {
         }
         if (!footnotesSection && containingGroup.innerHTML) {
             const section = this.createFootnotes([containingGroup], createElement);
-            backmatterContainer.append(section);
+            body.append(section);
         }
         let regularFootnoteGroups = [
             ...doc.querySelectorAll('back > fn-group:not([fn-type])'),
@@ -256,7 +215,7 @@ export const jatsBodyTransformations = {
         if (regularFootnoteGroups.length > 0) {
             regularFootnoteGroups.map((g) => removeNodeFromParent(g));
             const footnotes = this.createFootnotes(regularFootnoteGroups, createElement);
-            backmatterContainer.appendChild(footnotes);
+            body.appendChild(footnotes);
         }
     },
     moveCaptionsToEnd(body) {

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

@@ -111,6 +111,7 @@ export const parseJATSBody = (document, body, bibliographyItems, refModels, refe
     const orderedFootnotesIDs = createOrderedFootnotesIDs(document);
     jatsBodyTransformations.moveFloatsGroupToBody(document, body, createElement);
     jatsBodyTransformations.ensureSection(body, createElement);
+    jatsBodyTransformations.mapFootnotesToSections(document, body, createElement);
     jatsBodyTransformations.moveSectionsToBody(document, body, bibliographyItems, createElement);
     jatsBodyTransformations.moveCaptionsToEnd(body);
     jatsBodyTransformations.moveTableFooterToEnd(body);

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

@@ -129,10 +129,8 @@ export class JATSExporter {
                 article.appendChild(body);
                 const back = this.buildBack(body);
                 article.appendChild(back);
-                this.unwrapBody(body);
                 this.moveAbstracts(front, body);
                 this.moveFloatsGroup(body, article);
-                this.removeBackContainer(body);
             }
             await this.rewriteIDs(idGenerator);
             if (mediaPathGenerator) {
@@ -1387,49 +1385,21 @@ export class JATSExporter {
                 table.insertBefore(tfoot, tbody);
             }
         };
-        this.unwrapBody = (body) => {
-            const container = body.querySelector(':scope > sec[sec-type="body"]');
-            if (!container) {
-                return;
-            }
-            const sections = container.querySelectorAll(':scope > sec');
-            sections.forEach((section) => {
-                body.appendChild(section.cloneNode(true));
-            });
-            body.removeChild(container);
-        };
-        this.removeBackContainer = (body) => {
-            const container = body.querySelector(':scope > sec[sec-type="backmatter"]');
-            if (!container) {
-                return;
-            }
-            const isContainerEmpty = container.children.length === 0;
-            if (!isContainerEmpty) {
-                warn('Backmatter section is not empty.');
-            }
-            body.removeChild(container);
-        };
         this.moveAbstracts = (front, body) => {
-            const container = body.querySelector(':scope > sec[sec-type="abstracts"]');
-            let abstractSections;
-            if (container) {
-                abstractSections = Array.from(container.querySelectorAll(':scope > sec'));
-            }
-            else {
-                abstractSections = Array.from(body.querySelectorAll(':scope > sec')).filter((section) => {
-                    const sectionType = section.getAttribute('sec-type');
-                    if (sectionType === 'abstract' ||
-                        sectionType === 'abstract-teaser' ||
-                        sectionType === 'abstract-graphical') {
-                        return true;
-                    }
-                    const sectionTitle = section.querySelector(':scope > title');
-                    if (!sectionTitle) {
-                        return false;
-                    }
-                    return sectionTitle.textContent === 'Abstract';
-                });
-            }
+            const sections = body.querySelectorAll(':scope > sec');
+            const abstractSections = Array.from(sections).filter((section) => {
+                const sectionType = section.getAttribute('sec-type');
+                if (sectionType === 'abstract' ||
+                    sectionType === 'abstract-teaser' ||
+                    sectionType === 'abstract-graphical') {
+                    return true;
+                }
+                const sectionTitle = section.querySelector(':scope > title');
+                if (!sectionTitle) {
+                    return false;
+                }
+                return sectionTitle.textContent === 'Abstract';
+            });
             if (abstractSections.length) {
                 for (const abstractSection of abstractSections) {
                     const abstractNode = this.document.createElement('abstract');
@@ -1450,9 +1420,6 @@ export class JATSExporter {
                     }
                 }
             }
-            if (container) {
-                body.removeChild(container);
-            }
         };
         this.moveSectionsToBack = (back, body) => {
             const availabilitySection = body.querySelector('sec[sec-type="availability"]');

package/dist/es/lib/utils.js

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { isBibliographySectionNode } from '../schema/nodes/bibliography_section';
 import { isGraphicalAbstractSectionNode } from '../schema/nodes/graphical_abstract_section';
 export function* iterateChildren(node, recurse = false) {
     for (let i = 0; i < node.childCount; i++) {
@@ -44,6 +45,15 @@ export const isInGraphicalAbstractSection = ($pos) => {
     }
     return false;
 };
+export const isInBibliographySection = ($pos) => {
+    for (let i = $pos.depth; i > 0; i--) {
+        const node = $pos.node(i);
+        if (isBibliographySectionNode(node)) {
+            return true;
+        }
+    }
+    return false;
+};
 export const findParentNodeClosestToPos = ($pos, predicate) => {
     for (let i = $pos.depth; i > 0; i--) {
         const node = $pos.node(i);

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

@@ -32,7 +32,7 @@ const choosePageBreakStyle = (element) => {
     return PAGE_BREAK_NONE;
 };
 export const section = {
-    content: 'section_label? section_title (paragraph | element)* sections*',
+    content: 'section_label? section_title (paragraph | element)* section*',
     attrs: {
         id: { default: '' },
         category: { default: '' },

package/dist/es/transformer/encode.js

@@ -16,7 +16,7 @@
 import { DOMSerializer } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
 import { iterateChildren } from '../lib/utils';
-import { hasGroup, isHighlightMarkerNode, isSectionNode, schema, } from '../schema';
+import { isHighlightMarkerNode, isSectionNode, schema, } from '../schema';
 import { buildAttribution } from './builders';
 import { extractHighlightMarkers, isHighlightableModel, } from './highlight-markers';
 import { nodeTypesMap } from './node-types';
@@ -154,15 +154,6 @@ const childElements = (node) => {
     });
     return nodes;
 };
-const sectionChildElementIds = (node) => {
-    const nodes = [];
-    node.forEach((childNode) => {
-        if (!hasGroup(childNode.type, 'sections')) {
-            nodes.push(childNode);
-        }
-    });
-    return nodes.map((childNode) => childNode.attrs.id).filter((id) => id);
-};
 const attributeOfNodeType = (node, type, attribute) => {
     for (const child of iterateChildren(node)) {
         if (child.type.name === type) {
@@ -450,7 +441,9 @@ const encoders = {
         label: inlineContentsOfNodeType(node, node.type.schema.nodes.section_label) ||
             undefined,
         path: path.concat([node.attrs.id]),
-        elementIDs: sectionChildElementIds(node),
+        elementIDs: childElements(node)
+            .map((childNode) => childNode.attrs.id)
+            .filter((id) => id),
         titleSuppressed: node.attrs.titleSuppressed || undefined,
         generatedLabel: node.attrs.generatedLabel || undefined,
         pageBreakStyle: node.attrs.pageBreakStyle || undefined,

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

@@ -13,8 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import sectionCategories from '@manuscripts/data/dist/shared/section-categories.json';
-import { ObjectTypes, } from '@manuscripts/json-schema';
+import { ObjectTypes } from '@manuscripts/json-schema';
 import { schema } from '../schema';
 const sectionNodeTypes = [
     schema.nodes.bibliography_section,
@@ -23,17 +22,6 @@ const sectionNodeTypes = [
     schema.nodes.section,
     schema.nodes.toc_section,
 ];
-const sectionCategoriesMap = new Map(sectionCategories.map((section) => [
-    section._id,
-    section,
-]));
-export const getSectionTitles = (sectionCategory) => {
-    const category = sectionCategoriesMap.get(sectionCategory);
-    if (category) {
-        return category.titles.length ? category.titles : [' '];
-    }
-    throw new Error(`${sectionCategory} not found in section categories`);
-};
 export const isAnySectionNode = (node) => sectionNodeTypes.includes(node.type);
 export const chooseSectionNodeType = (category) => {
     switch (category) {
@@ -164,12 +152,6 @@ export const chooseSectionCategoryByType = (secType) => {
             return 'MPSectionCategory:supported-by';
         case 'ethics-statement':
             return 'MPSectionCategory:ethics-statement';
-        case 'body':
-            return 'MPSectionCategory:body';
-        case 'backmatter':
-            return 'MPSectionCategory:backmatter';
-        case 'abstracts':
-            return 'MPSectionCategory:abstracts';
         default:
             return undefined;
     }

package/dist/types/jats/importer/jats-body-transformations.d.ts

@@ -22,14 +22,8 @@ export declare const jatsBodyTransformations: {
     createFootnotes(footnoteGroups: Element[], createElement: (tagName: string) => HTMLElement): HTMLElement;
     createAppendixSection(app: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
     createFloatsGroupSection(floatsGroup: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
-    moveAbstractsIntoContainer(doc: Document, abstractsContainer: Element, createElement: (tagName: string) => HTMLElement): void;
-    wrapBodySections(doc: Document, bodyContainer: Element): void;
-    moveBackSectionsIntoContainer(doc: Document, backmatterContainer: Element): void;
-    moveAcknowledgmentsIntoContainer(doc: Document, backmatterContainer: Element, createElement: (tagName: string) => HTMLElement): void;
-    moveAppendicesIntoContainer(doc: Document, backmatterContainer: Element, createElement: (tagName: string) => HTMLElement): void;
-    moveBibliographyIntoContainer(doc: Document, backmatterContainer: Element, references: BibliographyItem[] | null, createElement: (tagName: string) => HTMLElement): void;
     moveSectionsToBody(doc: Document, body: Element, references: BibliographyItem[] | null, createElement: (tagName: string) => HTMLElement): void;
-    mapFootnotesToSections(doc: Document, backmatterContainer: Element, createElement: (tagName: string) => HTMLElement): void;
+    mapFootnotesToSections(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     moveCaptionsToEnd(body: Element): void;
     moveTableFooterToEnd(body: Element): void;
     moveFloatsGroupToBody(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;

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

@@ -63,8 +63,6 @@ export declare class JATSExporter {
     private fixBody;
     private changeTag;
     private fixTable;
-    private unwrapBody;
-    private removeBackContainer;
     private moveAbstracts;
     private moveSectionsToBack;
     sectionToFootnote: (section: Element, fnType: string) => HTMLElement;

package/dist/types/lib/utils.d.ts

@@ -18,6 +18,7 @@ import { ManuscriptEditorState, ManuscriptNode } from '../schema';
 export declare function iterateChildren(node: ManuscriptNode, recurse?: boolean): Iterable<ManuscriptNode>;
 export declare const findNodePositions: (state: ManuscriptEditorState, predicate: (node: ManuscriptNode) => boolean) => number[];
 export declare const isInGraphicalAbstractSection: ($pos: ResolvedPos) => boolean;
+export declare const isInBibliographySection: ($pos: ResolvedPos) => boolean;
 export declare const findParentNodeClosestToPos: ($pos: ResolvedPos, predicate: (node: ProsemirrorNode) => boolean) => {
     pos: number;
     start: number;

package/dist/types/transformer/section-category.d.ts

@@ -15,10 +15,9 @@
  */
 import { Element } from '@manuscripts/json-schema';
 import { ManuscriptNode, ManuscriptNodeType } from '../schema';
-export declare const getSectionTitles: (sectionCategory: SectionCategory) => string[];
 export declare const isAnySectionNode: (node: ManuscriptNode) => boolean;
-export type SectionCategory = 'MPSectionCategory:abstract' | 'MPSectionCategory:abstract-teaser' | 'MPSectionCategory:abstract-graphical' | 'MPSectionCategory:acknowledgement' | 'MPSectionCategory:availability' | 'MPSectionCategory:bibliography' | 'MPSectionCategory:conclusions' | 'MPSectionCategory:discussion' | 'MPSectionCategory:endnotes' | 'MPSectionCategory:introduction' | 'MPSectionCategory:keywords' | 'MPSectionCategory:materials-method' | 'MPSectionCategory:results' | 'MPSectionCategory:toc' | 'MPSectionCategory:floating-element' | 'MPSectionCategory:appendices' | 'MPSectionCategory:competing-interests' | 'MPSectionCategory:financial-disclosure' | 'MPSectionCategory:con' | 'MPSectionCategory:deceased' | 'MPSectionCategory:equal' | 'MPSectionCategory:present-address' | 'MPSectionCategory:presented-at' | 'MPSectionCategory:previously-at' | 'MPSectionCategory:supplementary-material' | 'MPSectionCategory:supported-by' | 'MPSectionCategory:ethics-statement' | 'MPSectionCategory:body' | 'MPSectionCategory:abstracts' | 'MPSectionCategory:backmatter';
-export type SecType = 'abstract' | 'abstract-teaser' | 'abstract-graphical' | 'acknowledgments' | 'availability' | 'bibliography' | 'conclusions' | 'data-availability' | 'discussion' | 'endnotes' | 'intro' | 'keywords' | 'materials' | 'methods' | 'results' | 'toc' | 'floating-element' | 'appendices' | 'competing-interests' | 'financial-disclosure' | 'con' | 'deceased' | 'equal' | 'present-address' | 'presented-at' | 'previously-at' | 'supplementary-material' | 'supported-by' | 'ethics-statement' | 'abstracts' | 'body' | 'backmatter';
+export type SectionCategory = 'MPSectionCategory:abstract' | 'MPSectionCategory:abstract-teaser' | 'MPSectionCategory:abstract-graphical' | 'MPSectionCategory:acknowledgement' | 'MPSectionCategory:availability' | 'MPSectionCategory:bibliography' | 'MPSectionCategory:conclusions' | 'MPSectionCategory:discussion' | 'MPSectionCategory:endnotes' | 'MPSectionCategory:introduction' | 'MPSectionCategory:keywords' | 'MPSectionCategory:materials-method' | 'MPSectionCategory:results' | 'MPSectionCategory:toc' | 'MPSectionCategory:floating-element' | 'MPSectionCategory:appendices' | 'MPSectionCategory:competing-interests' | 'MPSectionCategory:financial-disclosure' | 'MPSectionCategory:con' | 'MPSectionCategory:deceased' | 'MPSectionCategory:equal' | 'MPSectionCategory:present-address' | 'MPSectionCategory:presented-at' | 'MPSectionCategory:previously-at' | 'MPSectionCategory:supplementary-material' | 'MPSectionCategory:supported-by' | 'MPSectionCategory:ethics-statement';
+export type SecType = 'abstract' | 'abstract-teaser' | 'abstract-graphical' | 'acknowledgments' | 'availability' | 'bibliography' | 'conclusions' | 'data-availability' | 'discussion' | 'endnotes' | 'intro' | 'keywords' | 'materials' | 'methods' | 'results' | 'toc' | 'floating-element' | 'appendices' | 'competing-interests' | 'financial-disclosure' | 'con' | 'deceased' | 'equal' | 'present-address' | 'presented-at' | 'previously-at' | 'supplementary-material' | 'supported-by' | 'ethics-statement';
 export declare const chooseSectionNodeType: (category?: SectionCategory) => ManuscriptNodeType;
 export declare const chooseSectionLableName: (type?: SecType) => string;
 export declare const guessSectionCategory: (elements: Element[]) => SectionCategory | undefined;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "1.2.4-LEAN-2357",
+  "version": "1.2.4",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,7 +29,7 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "^2.0.1-LEAN-2416",
+    "@manuscripts/json-schema": "^2.0.1",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
     "mathjax-full": "^3.2.2",