@manuscripts/transform 1.5.8 → 2.0.0

package/dist/es/transformer/encode.js

@@ -15,11 +15,10 @@
  */
 import { DOMSerializer } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
-import { iterateChildren, modelsEqual } from '../lib/utils';
-import { hasGroup, isHighlightMarkerNode, isSectionNode, schema, } from '../schema';
-import { buildAttribution } from './builders';
-import { extractHighlightMarkers, isHighlightableModel, } from './highlight-markers';
-import { generateID } from './id';
+import { iterateChildren } from '../lib/utils';
+import { hasGroup, isHighlightMarkerNode, isManuscriptNode, isSectionNode, schema, } from '../schema';
+import { auxiliaryObjectTypes, buildAttribution, buildElementsOrder, } from './builders';
+import { extractCommentMarkers } from './highlight-markers';
 import { nodeTypesMap } from './node-types';
 import { buildSectionCategory } from './section-category';
 const serializer = DOMSerializer.fromSchema(schema);
@@ -421,34 +420,9 @@ const encoders = {
         elementType: 'div',
         paragraphStyle: node.attrs.paragraphStyle || undefined,
     }),
-    keywords_group: (node) => ({
+    keyword_group: (node) => ({
         type: node.attrs.type,
     }),
-    keywords_section: (node, parent, path, priority) => ({
-        category: buildSectionCategory(node),
-        priority: priority.value++,
-        title: inlineContentsOfNodeType(node, node.type.schema.nodes.section_title),
-        path: path.concat([node.attrs.id]),
-        elementIDs: childElements(node)
-            .map((childNode) => childNode.attrs.id)
-            .filter((id) => id),
-    }),
-    affiliations_section: (node, parent, path, priority) => ({
-        category: buildSectionCategory(node),
-        priority: priority.value++,
-        path: path.concat([node.attrs.id]),
-        elementIDs: childElements(node)
-            .map((childNode) => childNode.attrs.id)
-            .filter((id) => id),
-    }),
-    contributors_section: (node, parent, path, priority) => ({
-        category: buildSectionCategory(node),
-        priority: priority.value++,
-        path: path.concat([node.attrs.id]),
-        elementIDs: childElements(node)
-            .map((childNode) => childNode.attrs.id)
-            .filter((id) => id),
-    }),
     missing_figure: (node) => ({
         position: node.attrs.position || undefined,
     }),
@@ -552,7 +526,6 @@ const modelData = (node, parent, path, priority) => {
     return encoder(node, parent, path, priority);
 };
 export const modelFromNode = (node, parent, path, priority) => {
-    const commentAnnotationsMap = new Map();
     const objectType = nodeTypesMap.get(node.type);
     if (!objectType) {
         throw new Error(`No objectType is defined for ${node.type.name}`);
@@ -563,66 +536,92 @@ export const modelFromNode = (node, parent, path, priority) => {
     }
     const data = Object.assign(Object.assign({}, modelData(node, parent, path, priority)), { _id: id, objectType: objectType });
     const model = data;
-    if (isHighlightableModel(model)) {
-        extractHighlightMarkers(model, commentAnnotationsMap);
-    }
-    const comments = [...commentAnnotationsMap.values()];
-    return { model, comments };
+    const markers = extractCommentMarkers(model);
+    return { model, markers };
 };
-export const encode = (node, preserveWithRepeatedID = false) => {
+const containerTypes = [
+    schema.nodes.affiliations,
+    schema.nodes.contributors,
+    schema.nodes.affiliations,
+    schema.nodes.keywords,
+    schema.nodes.abstracts,
+    schema.nodes.body,
+    schema.nodes.backmatter,
+];
+const placeholderTypes = [
+    schema.nodes.placeholder,
+    schema.nodes.placeholder_element,
+];
+export const encode = (node) => {
     const models = new Map();
     const priority = {
         value: 1,
     };
-    const placeholders = ['placeholder', 'placeholder_element'];
-    const addModel = (path, parent) => (child) => {
+    const processNode = (path, parent) => (child) => {
+        if (containerTypes.includes(child.type)) {
+            child.forEach(processNode([], child));
+            return;
+        }
         if (!child.attrs.id) {
             return;
         }
         if (isHighlightMarkerNode(child)) {
             return;
         }
-        if (child.type === schema.nodes.meta_section) {
+        if (placeholderTypes.includes(child.type)) {
             return;
         }
-        if (placeholders.includes(child.type.name)) {
+        if (parent.type === schema.nodes.paragraph &&
+            child.type !== schema.nodes.inline_equation) {
             return;
         }
-        const { model, comments } = modelFromNode(child, parent, path, priority);
-        const existingModel = models.get(model._id);
-        if (existingModel) {
-            if (preserveWithRepeatedID && !modelsEqual(model, existingModel)) {
-                model._id = generateID(model.objectType);
-            }
-            else {
-                throw Error(`Encountered duplicate ids in models map while encoding: ${model._id}`);
-            }
-        }
-        comments.forEach((comment) => {
-            const proseMirrorComment = models.get(comment._id);
-            if (proseMirrorComment) {
-                ;
-                proseMirrorComment.selector = comment.selector;
-                models.set(comment._id, proseMirrorComment);
+        const { model, markers } = modelFromNode(child, parent, path, priority);
+        markers.forEach((marker) => {
+            const comment = models.get(marker._id);
+            if (comment) {
+                comment.selector = {
+                    from: marker.from,
+                    to: marker.to,
+                };
             }
         });
+        if (models.has(model._id)) {
+            throw Error(`Duplicate ids in encode: ${model._id}`);
+        }
         models.set(model._id, model);
-        child.forEach(addModel(path.concat(child.attrs.id), child));
+        child.forEach(processNode(path.concat(child.attrs.id), child));
     };
-    node.forEach((cNode) => {
-        if (cNode.type === schema.nodes.meta_section) {
-            processMetaSectionNode(cNode, models, priority);
-        }
-    });
-    node.forEach(addModel([], node));
+    const comments = node.lastChild;
+    if (comments && comments.type === schema.nodes.comments) {
+        comments.forEach(processNode([], comments));
+    }
+    node.forEach(processNode([], node));
+    if (isManuscriptNode(node)) {
+        auxiliaryObjectTypes.forEach((t) => {
+            const order = generateElementOrder(node, t);
+            if (order) {
+                models.set(order._id, order);
+            }
+        });
+    }
     return models;
 };
-const processMetaSectionNode = (node, models, priority) => {
-    node.descendants((child) => {
-        if ((!child.content || child.content.size === 0) &&
-            nodeTypesMap.get(child.type)) {
-            const { model } = modelFromNode(child, node, [], priority);
-            models.set(model._id, model);
+const generateElementOrder = (node, nodeType) => {
+    const ids = [];
+    node.descendants((n) => {
+        if (n.type === nodeType) {
+            ids.push(n.attrs.id);
         }
+        return true;
     });
+    if (!ids.length) {
+        return undefined;
+    }
+    const type = nodeTypesMap.get(nodeType);
+    if (!type) {
+        return undefined;
+    }
+    const order = buildElementsOrder(type);
+    order.elements = ids;
+    return order;
 };

package/dist/es/transformer/highlight-markers.js

@@ -13,8 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { buildComment } from './builders';
-const highlightableFields = [
+export const highlightableFields = [
     'caption',
     'contents',
     'title',
@@ -27,52 +26,65 @@ export const isHighlightableModel = (model) => {
     }
     return false;
 };
-export const extractHighlightMarkers = (model, commentAnnotationsMap) => {
+export const extractCommentMarkers = (model) => {
+    if (!isHighlightableModel(model)) {
+        return [];
+    }
+    const comments = new Map();
     for (const field of highlightableFields) {
         let html = model[field];
-        if (html === undefined) {
+        if (!html || !html.includes('highlight-marker')) {
             continue;
         }
         const template = document.createElement('template');
         template.innerHTML = `<div>${html}</div>`;
         const element = template.content.firstChild;
-        if (!(element instanceof Element)) {
+        if (!element) {
             continue;
         }
         const markers = element.querySelectorAll('span.highlight-marker');
-        if (markers.length) {
-            for (const marker of markers) {
-                const markerHTML = marker.outerHTML;
-                const offset = html.indexOf(markerHTML);
-                if (offset === -1) {
-                    continue;
+        if (!markers.length) {
+            continue;
+        }
+        for (const marker of markers) {
+            const markerHTML = marker.outerHTML;
+            const offset = html.indexOf(markerHTML);
+            if (offset === -1) {
+                continue;
+            }
+            const id = marker.getAttribute('id');
+            const target = marker.getAttribute('data-target-id');
+            if (id && target) {
+                const position = marker.getAttribute('data-position');
+                if (position === 'start') {
+                    const comment = {
+                        _id: id,
+                        from: offset,
+                        to: -1,
+                    };
+                    comments.set(id, comment);
                 }
-                const _id = marker.getAttribute('id');
-                const target = marker.getAttribute('data-target-id');
-                if (_id && target) {
-                    const position = marker.getAttribute('data-position');
-                    const commentAnnotation = Object.assign(Object.assign({}, buildComment(target, '')), { _id: _id });
-                    if (position === 'start') {
-                        commentAnnotationsMap.set(commentAnnotation._id, Object.assign(Object.assign({}, commentAnnotation), { selector: {
-                                from: offset,
-                                to: -1,
-                            } }));
-                    }
-                    else if (position === 'end') {
-                        const comment = commentAnnotationsMap.get(commentAnnotation._id);
-                        if (comment && comment.selector) {
-                            commentAnnotationsMap.set(comment._id, Object.assign(Object.assign({}, comment), { selector: Object.assign(Object.assign({}, comment.selector), { to: offset }) }));
-                        }
-                    }
-                    else if (position === 'point') {
-                        commentAnnotationsMap.set(commentAnnotation._id, Object.assign(Object.assign({}, commentAnnotation), { selector: { from: offset, to: offset } }));
+                else if (position === 'end') {
+                    const comment = comments.get(id);
+                    if (comment) {
+                        comment.to = offset;
                     }
                 }
-                html = html.substr(0, offset) + html.substr(offset + markerHTML.length);
+                else if (position === 'point') {
+                    const comment = {
+                        _id: id,
+                        from: offset,
+                        to: offset,
+                    };
+                    comments.set(id, comment);
+                }
             }
-            model[field] = html;
+            html =
+                html.substring(0, offset) + html.substring(offset + markerHTML.length);
         }
+        model[field] = html;
     }
+    return Array.from(comments.values());
 };
 export const insertHighlightMarkers = (contents, commentAnnotations) => {
     let output = contents;

package/dist/es/transformer/html.js

@@ -194,11 +194,9 @@ export class HTMLTransformer {
                 const citationNode = node;
                 const element = this.document.createElement('span');
                 element.setAttribute('class', 'citation');
-                const citation = getModel(citationNode.attrs.rid);
-                if (citation) {
-                    element.setAttribute('data-reference-ids', citation.embeddedCitationItems
-                        .map((item) => item.bibliographyItem)
-                        .join(' '));
+                const rids = citationNode.attrs.rids;
+                if (rids.length) {
+                    element.setAttribute('data-reference-ids', rids.join(' '));
                 }
                 if (citationNode.attrs.contents) {
                     element.innerHTML = citationNode.attrs.contents;
@@ -206,25 +204,11 @@ export class HTMLTransformer {
                 return element;
             };
             nodes.cross_reference = (node) => {
-                const crossReferenceNode = node;
+                const xref = node;
                 const element = this.document.createElement('a');
                 element.classList.add('cross-reference');
-                const auxiliaryObjectReference = getModel(crossReferenceNode.attrs.rid);
-                if (auxiliaryObjectReference &&
-                    auxiliaryObjectReference.referencedObject) {
-                    if (auxiliaryObjectReference.referencedObject.startsWith('MPFigureElement')) {
-                        const model = getModel(auxiliaryObjectReference.referencedObject);
-                        if (model && model.containedObjectIDs.length > 0) {
-                            element.setAttribute('href', `#${model.containedObjectIDs[0]}`);
-                        }
-                    }
-                    else {
-                        element.setAttribute('href', `#${auxiliaryObjectReference.referencedObject}`);
-                    }
-                    element.setAttribute('data-reference-ids', crossReferenceNode.attrs.rid);
-                }
-                element.textContent =
-                    crossReferenceNode.attrs.customLabel || crossReferenceNode.attrs.label;
+                element.setAttribute('data-reference-ids', xref.attrs.rids.join(' '));
+                element.textContent = xref.attrs.customLabel || xref.attrs.label;
                 return element;
             };
             nodes.listing = (node) => {
@@ -256,7 +240,7 @@ export class HTMLTransformer {
                 };
                 return ['span', attrs];
             };
-            nodes.meta_section = () => '';
+            nodes.comments = () => '';
             const serializer = new DOMSerializer(nodes, marks);
             return serializer.serializeFragment(fragment, { document });
         };

package/dist/es/transformer/labels.js

@@ -27,6 +27,7 @@ const labelProperties = new Map([
     [schema.nodes.equation_element, 'equationElementLabel'],
     [schema.nodes.listing_element, 'listingElementLabel'],
 ]);
+const excludedTypes = [schema.nodes.graphical_abstract_section];
 const chooseLabel = (nodeType, manuscript) => {
     const labelProperty = labelProperties.get(nodeType);
     if (labelProperty) {
@@ -51,25 +52,10 @@ export const buildTargets = (fragment, manuscript) => {
         return `${counter.label} ${counter.index}`;
     };
     const targets = new Map();
-    const figures = [];
-    fragment.forEach((node) => {
-        if (node.attrs.category === 'MPSectionCategory:abstracts') {
-            node.forEach((child) => {
-                if (child.type === node.type.schema.nodes.graphical_abstract_section) {
-                    child.forEach((item) => {
-                        if (item.type === node.type.schema.nodes.figure_element) {
-                            figures.push(item.attrs.id);
-                        }
-                    });
-                }
-            });
-        }
-    });
-    fragment.descendants((node) => {
+    fragment.descendants((node, pos, parent) => {
         var _a;
         if (node.type.name in counters) {
-            const isInGraphicalAbstract = figures.indexOf(node.attrs.id) > -1;
-            if (isInGraphicalAbstract) {
+            if (parent && excludedTypes.includes(parent.type)) {
                 return;
             }
             const label = buildLabel(node.type);

package/dist/es/transformer/node-names.js

@@ -35,6 +35,6 @@ export const nodeNames = new Map([
     [schema.nodes.table_element, 'Table'],
     [schema.nodes.blockquote_element, 'Block Quote'],
     [schema.nodes.pullquote_element, 'Pull Quote'],
-    [schema.nodes.keywords_section, 'Section'],
+    [schema.nodes.keywords, 'Section'],
     [schema.nodes.toc_section, 'Section'],
 ]);

package/dist/es/transformer/node-title.js

@@ -47,7 +47,7 @@ export const nodeTitle = (node) => {
         case nodes.section:
         case nodes.bibliography_section:
         case nodes.footnotes_section:
-        case nodes.keywords_section:
+        case nodes.keywords:
         case nodes.toc_section:
         case nodes.graphical_abstract_section:
             return snippetOfNodeType(node, nodes.section_title);

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

@@ -16,6 +16,9 @@
 import { ObjectTypes } from '@manuscripts/json-schema';
 import { GROUP_ELEMENT, GROUP_EXECUTABLE, GROUP_SECTION, hasGroup, schema, } from '../schema';
 export const nodeTypesMap = new Map([
+    [schema.nodes.abstracts, ObjectTypes.Section],
+    [schema.nodes.body, ObjectTypes.Section],
+    [schema.nodes.backmatter, ObjectTypes.Section],
     [schema.nodes.comment, ObjectTypes.CommentAnnotation],
     [schema.nodes.bibliography_item, ObjectTypes.BibliographyItem],
     [schema.nodes.bibliography_element, ObjectTypes.BibliographyElement],
@@ -23,7 +26,6 @@ export const nodeTypesMap = new Map([
     [schema.nodes.blockquote_element, ObjectTypes.QuoteElement],
     [schema.nodes.bullet_list, ObjectTypes.ListElement],
     [schema.nodes.citation, ObjectTypes.Citation],
-    [schema.nodes.cross_reference, ObjectTypes.AuxiliaryObjectReference],
     [schema.nodes.equation, ObjectTypes.Equation],
     [schema.nodes.equation_element, ObjectTypes.EquationElement],
     [schema.nodes.figure, ObjectTypes.Figure],
@@ -37,8 +39,8 @@ export const nodeTypesMap = new Map([
     [schema.nodes.inline_equation, ObjectTypes.InlineMathFragment],
     [schema.nodes.keyword, ObjectTypes.Keyword],
     [schema.nodes.keywords_element, ObjectTypes.KeywordsElement],
-    [schema.nodes.keywords_section, ObjectTypes.Section],
-    [schema.nodes.keywords_group, ObjectTypes.KeywordGroup],
+    [schema.nodes.keywords, ObjectTypes.Section],
+    [schema.nodes.keyword_group, ObjectTypes.KeywordGroup],
     [schema.nodes.listing, ObjectTypes.Listing],
     [schema.nodes.listing_element, ObjectTypes.ListingElement],
     [schema.nodes.manuscript, ObjectTypes.Manuscript],
@@ -50,13 +52,12 @@ export const nodeTypesMap = new Map([
     [schema.nodes.table_element, ObjectTypes.TableElement],
     [schema.nodes.toc_element, ObjectTypes.TOCElement],
     [schema.nodes.toc_section, ObjectTypes.Section],
-    [schema.nodes.meta_section, ObjectTypes.MetaSection],
     [schema.nodes.affiliation, ObjectTypes.Affiliation],
     [schema.nodes.contributor, ObjectTypes.Contributor],
     [schema.nodes.table_element_footer, ObjectTypes.TableElementFooter],
+    [schema.nodes.contributors, ObjectTypes.Section],
+    [schema.nodes.affiliations, ObjectTypes.Section],
     [schema.nodes.title, ObjectTypes.Titles],
-    [schema.nodes.contributors_section, ObjectTypes.Section],
-    [schema.nodes.affiliations_section, ObjectTypes.Section],
 ]);
 export const isExecutableNodeType = (type) => hasGroup(type, GROUP_EXECUTABLE);
 export const isElementNodeType = (type) => hasGroup(type, GROUP_ELEMENT);

package/dist/es/transformer/object-types.js

@@ -48,6 +48,5 @@ export const hasObjectType = (objectType) => (model) => model.objectType === obj
 export const isFigure = hasObjectType(ObjectTypes.Figure);
 export const isManuscript = hasObjectType(ObjectTypes.Manuscript);
 export const isTable = hasObjectType(ObjectTypes.Table);
-export const isUserProfile = hasObjectType(ObjectTypes.UserProfile);
 export const isCommentAnnotation = hasObjectType(ObjectTypes.CommentAnnotation);
 export const isKeyword = hasObjectType(ObjectTypes.Keyword);

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

@@ -14,22 +14,15 @@
  * limitations under the License.
  */
 import { ObjectTypes } from '@manuscripts/json-schema';
-import { coreSectionCategories } from '../lib/core-section-categories';
+import { abstractsType, backmatterType, bodyType, } from '../lib/section-group-type';
 import { schema } from '../schema';
 const sectionNodeTypes = [
     schema.nodes.bibliography_section,
     schema.nodes.footnotes_section,
-    schema.nodes.keywords_section,
+    schema.nodes.keywords,
     schema.nodes.section,
     schema.nodes.toc_section,
 ];
-export const getCoreSectionTitles = (sectionCategory) => {
-    const category = coreSectionCategories.find((section) => section._id === sectionCategory);
-    if (category) {
-        return category.titles.length ? category.titles : [' '];
-    }
-    throw new Error(`${sectionCategory} not found in core sections`);
-};
 export const isAnySectionNode = (node) => sectionNodeTypes.includes(node.type);
 export const chooseSectionNodeType = (category) => {
     switch (category) {
@@ -40,11 +33,7 @@ export const chooseSectionNodeType = (category) => {
         case 'MPSectionCategory:endnotes':
             return schema.nodes.footnotes_section;
         case 'MPSectionCategory:keywords':
-            return schema.nodes.keywords_section;
-        case 'MPSectionCategory:affiliations':
-            return schema.nodes.affiliations_section;
-        case 'MPSectionCategory:contributors':
-            return schema.nodes.contributors_section;
+            return schema.nodes.keywords;
         case 'MPSectionCategory:toc':
             return schema.nodes.toc_section;
         default:
@@ -82,16 +71,12 @@ export const buildSectionCategory = (node) => {
             return 'MPSectionCategory:bibliography';
         case schema.nodes.footnotes_section:
             return 'MPSectionCategory:endnotes';
-        case schema.nodes.keywords_section:
+        case schema.nodes.keywords:
             return 'MPSectionCategory:keywords';
         case schema.nodes.toc_section:
             return 'MPSectionCategory:toc';
         case schema.nodes.graphical_abstract_section:
             return 'MPSectionCategory:abstract-graphical';
-        case schema.nodes.affiliations_section:
-            return 'MPSectionCategory:affiliations';
-        case schema.nodes.contributors_section:
-            return 'MPSectionCategory:contributors';
         default:
             return node.attrs.category || undefined;
     }
@@ -117,6 +102,31 @@ export const chooseSecType = (sectionCategory) => {
             return suffix;
     }
 };
+export const getSectionGroupType = (category) => {
+    switch (category) {
+        case 'MPSectionCategory:abstract':
+        case 'MPSectionCategory:abstract-graphical':
+            return abstractsType;
+        case 'MPSectionCategory:competing-interests':
+        case 'MPSectionCategory:con':
+        case 'MPSectionCategory:ethics-statement':
+        case 'MPSectionCategory:financial-disclosure':
+        case 'MPSectionCategory:supplementary-material':
+        case 'MPSectionCategory:supported-by':
+        case 'MPSectionCategory:availability':
+        case 'MPSectionCategory:acknowledgement':
+        case 'MPSectionCategory:endnotes':
+        case 'MPSectionCategory:bibliography':
+        case 'MPSectionCategory:appendices':
+        case 'MPSectionCategory:deceased':
+        case 'MPSectionCategory:equal':
+        case 'MPSectionCategory:present-address':
+        case 'MPSectionCategory:presented-at':
+        case 'MPSectionCategory:previously-at':
+            return backmatterType;
+    }
+    return bodyType;
+};
 export const chooseSectionCategoryByType = (secType) => {
     switch (secType) {
         case 'abstract':
@@ -176,16 +186,6 @@ 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';
-        case 'affiliations':
-            return 'MPSectionCategory:affiliations';
-        case 'contributors':
-            return 'MPSectionCategory:contributors';
         default:
             return undefined;
     }

package/dist/types/index.d.ts

@@ -1,4 +1,4 @@
-export * from './lib/core-section-categories';
+export * from './lib/section-group-type';
 export * from './lib/table-cell-styles';
 export * from './lib/utils';
 export * from './mathjax';

package/dist/types/jats/importer/index.d.ts

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

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

@@ -13,29 +13,26 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Affiliation, BibliographyItem, Contributor } from '@manuscripts/json-schema';
-import { Build } from '../../transformer';
 export declare const jatsBodyTransformations: {
     ensureSection(body: Element, createElement: (tagName: string) => HTMLElement): void;
-    createAbstract(abstractNode: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
-    createAcknowledgments(ackNode: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
-    createBibliography(doc: Document, references: BibliographyItem[], createElement: (tagName: string) => HTMLElement): HTMLElement;
-    createFootnotes(footnoteGroups: Element[], createElement: (tagName: string) => HTMLElement): HTMLElement;
+    createAbstractSection(abstractNode: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
+    createAcknowledgmentsSection(ackNode: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
+    createFootnotesSection(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;
+    createFloatsGroupSection(group: Element, createElement: (tagName: string) => HTMLElement): HTMLElement;
+    moveAbstracts(doc: Document, group: Element, createElement: (tagName: string) => HTMLElement): void;
+    wrapBodySections(doc: Document, group: Element): void;
+    moveBackSections(doc: Document, group: Element): void;
+    moveAcknowledgments(doc: Document, group: Element, createElement: (tagName: string) => HTMLElement): void;
+    moveAppendices(doc: Document, group: Element, createElement: (tagName: string) => HTMLElement): void;
+    createBody(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
+    createAbstracts(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
+    createBackmatter(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
+    moveSpecialFootnotes(doc: Document, group: Element, createElement: (tagName: string) => HTMLElement): void;
+    moveFootnotes(doc: Document, group: Element, createElement: (tagName: string) => HTMLElement): void;
     moveCaptionsToEnd(body: Element): void;
+    fixTables(body: Element, createElement: (tagName: string) => HTMLElement): void;
     moveTableFooterToEnd(body: Element): void;
-    moveAffiliationsToBody(doc: Document, affiliations: Build<Affiliation>[] | undefined, body: Element, createElement: (tagName: string) => HTMLElement): void;
-    moveAuthorsToBody(doc: Document, authors: Build<Contributor>[] | undefined, body: Element, createElement: (tagName: string) => HTMLElement): void;
     moveFloatsGroupToBody(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
-    moveBlockNodesFromParagraph(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
-    moveKeywordsToBody(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
+    createKeywords(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
 };

package/dist/types/jats/importer/jats-comments.d.ts

@@ -13,14 +13,18 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { BibliographyItem, CommentAnnotation, Model } from '@manuscripts/json-schema';
-import { Build } from '../../transformer';
-type ProcessingInstruction = {
+import { CommentAnnotation, Model } from '@manuscripts/json-schema';
+import { References } from './jats-references';
+export type JATSComment = {
     id: string;
-    queryText: string;
+    text: string;
 };
-export declare const parseProcessingInstruction: (node: Node) => ProcessingInstruction | undefined;
-export declare const markProcessingInstructions: (doc: Document) => Map<string, string>;
-export declare const createComments: (authorQueriesMap: Map<string, string>, manuscriptModels: Array<Model>) => Build<CommentAnnotation>[];
-export declare const createReferenceComments: (referenceQueriesMap: Map<string, string[]>, references: Array<BibliographyItem>) => Build<CommentAnnotation>[];
-export {};
+export type JATSCommentMark = {
+    token: string;
+    comment: JATSComment;
+};
+export declare const isJATSComment: (node: Node) => boolean;
+export declare const parseJATSComment: (node: Node) => JATSComment | undefined;
+export declare const markComments: (doc: Document) => JATSCommentMark[];
+export declare const createComments: (models: Model[], marks: JATSCommentMark[]) => CommentAnnotation[];
+export declare const createReferenceComments: (references: References) => CommentAnnotation[];