@manuscripts/transform 1.5.7 → 1.5.8-LEAN-3030

package/dist/cjs/transformer/encode.js

@@ -25,6 +25,7 @@ const utils_1 = require("../lib/utils");
 const schema_1 = require("../schema");
 const builders_1 = require("./builders");
 const highlight_markers_1 = require("./highlight-markers");
+const id_1 = require("./id");
 const node_types_1 = require("./node-types");
 const section_category_1 = require("./section-category");
 const serializer = prosemirror_model_1.DOMSerializer.fromSchema(schema_1.schema);
@@ -428,34 +429,9 @@ 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: (0, section_category_1.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: (0, section_category_1.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: (0, section_category_1.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,
     }),
@@ -577,28 +553,48 @@ const modelFromNode = (node, parent, path, priority) => {
     return { model, comments };
 };
 exports.modelFromNode = modelFromNode;
-const encode = (node) => {
+const containerTypes = [
+    schema_1.schema.nodes.affiliations,
+    schema_1.schema.nodes.contributors,
+    schema_1.schema.nodes.affiliations,
+    schema_1.schema.nodes.keywords,
+    schema_1.schema.nodes.abstracts,
+    schema_1.schema.nodes.body,
+    schema_1.schema.nodes.backmatter,
+    schema_1.schema.nodes.comments,
+];
+const encode = (node, preserveWithRepeatedID = false) => {
     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 ((0, schema_1.isHighlightMarkerNode)(child)) {
             return;
         }
-        if (child.type === schema_1.schema.nodes.meta_section) {
+        if (placeholders.includes(child.type.name)) {
             return;
         }
-        if (placeholders.includes(child.type.name)) {
+        if (parent.type === schema_1.schema.nodes.paragraph) {
             return;
         }
         const { model, comments } = (0, exports.modelFromNode)(child, parent, path, priority);
-        if (models.has(model._id)) {
-            throw Error(`Encountered duplicate ids in models map while encoding: ${model._id}`);
+        const existingModel = models.get(model._id);
+        if (existingModel) {
+            if (preserveWithRepeatedID && !(0, utils_1.modelsEqual)(model, existingModel)) {
+                model._id = (0, id_1.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);
@@ -609,23 +605,36 @@ const encode = (node) => {
             }
         });
         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_1.schema.nodes.meta_section) {
-            processMetaSectionNode(cNode, models, priority);
-        }
-    });
-    node.forEach(addModel([], node));
+    node.forEach(processNode([], node));
+    if ((0, schema_1.isManuscriptNode)(node)) {
+        builders_1.auxiliaryObjectTypes.forEach((t) => {
+            const order = generateElementOrder(node, t);
+            if (order) {
+                models.set(order._id, order);
+            }
+        });
+    }
     return models;
 };
 exports.encode = encode;
-const processMetaSectionNode = (node, models, priority) => {
-    node.descendants((child) => {
-        if ((!child.content || child.content.size === 0) &&
-            node_types_1.nodeTypesMap.get(child.type)) {
-            const { model } = (0, exports.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 = node_types_1.nodeTypesMap.get(nodeType);
+    if (!type) {
+        return undefined;
+    }
+    const order = (0, builders_1.buildElementsOrder)(type);
+    order.elements = ids;
+    return order;
 };

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

@@ -15,15 +15,15 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.insertHighlightMarkers = exports.extractHighlightMarkers = exports.isHighlightableModel = void 0;
+exports.insertHighlightMarkers = exports.extractHighlightMarkers = exports.isHighlightableModel = exports.highlightableFields = void 0;
 const builders_1 = require("./builders");
-const highlightableFields = [
+exports.highlightableFields = [
     'caption',
     'contents',
     'title',
 ];
 const isHighlightableModel = (model) => {
-    for (const field of highlightableFields) {
+    for (const field of exports.highlightableFields) {
         if (field in model) {
             return true;
         }
@@ -32,7 +32,7 @@ const isHighlightableModel = (model) => {
 };
 exports.isHighlightableModel = isHighlightableModel;
 const extractHighlightMarkers = (model, commentAnnotationsMap) => {
-    for (const field of highlightableFields) {
+    for (const field of exports.highlightableFields) {
         let html = model[field];
         if (html === undefined) {
             continue;

package/dist/cjs/transformer/html.js

@@ -200,11 +200,9 @@ 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;
@@ -215,20 +213,7 @@ class HTMLTransformer {
                 const crossReferenceNode = 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.setAttribute('data-reference-ids', crossReferenceNode.attrs.rids.join(' '));
                 element.textContent =
                     crossReferenceNode.attrs.customLabel || crossReferenceNode.attrs.label;
                 return element;
@@ -262,7 +247,7 @@ class HTMLTransformer {
                 };
                 return ['span', attrs];
             };
-            nodes.meta_section = () => '';
+            nodes.comments = () => '';
             const serializer = new prosemirror_model_1.DOMSerializer(nodes, marks);
             return serializer.serializeFragment(fragment, { document });
         };

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

@@ -38,6 +38,6 @@ exports.nodeNames = new Map([
     [schema_1.schema.nodes.table_element, 'Table'],
     [schema_1.schema.nodes.blockquote_element, 'Block Quote'],
     [schema_1.schema.nodes.pullquote_element, 'Pull Quote'],
-    [schema_1.schema.nodes.keywords_section, 'Section'],
+    [schema_1.schema.nodes.keywords, 'Section'],
     [schema_1.schema.nodes.toc_section, 'Section'],
 ]);

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

@@ -50,7 +50,7 @@ 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/cjs/transformer/node-types.js

@@ -19,6 +19,9 @@ exports.isNodeType = exports.isSectionNodeType = exports.isElementNodeType = exp
 const json_schema_1 = require("@manuscripts/json-schema");
 const schema_1 = require("../schema");
 exports.nodeTypesMap = new Map([
+    [schema_1.schema.nodes.abstracts, json_schema_1.ObjectTypes.Section],
+    [schema_1.schema.nodes.body, json_schema_1.ObjectTypes.Section],
+    [schema_1.schema.nodes.backmatter, json_schema_1.ObjectTypes.Section],
     [schema_1.schema.nodes.comment, json_schema_1.ObjectTypes.CommentAnnotation],
     [schema_1.schema.nodes.bibliography_item, json_schema_1.ObjectTypes.BibliographyItem],
     [schema_1.schema.nodes.bibliography_element, json_schema_1.ObjectTypes.BibliographyElement],
@@ -26,7 +29,6 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.blockquote_element, json_schema_1.ObjectTypes.QuoteElement],
     [schema_1.schema.nodes.bullet_list, json_schema_1.ObjectTypes.ListElement],
     [schema_1.schema.nodes.citation, json_schema_1.ObjectTypes.Citation],
-    [schema_1.schema.nodes.cross_reference, json_schema_1.ObjectTypes.AuxiliaryObjectReference],
     [schema_1.schema.nodes.equation, json_schema_1.ObjectTypes.Equation],
     [schema_1.schema.nodes.equation_element, json_schema_1.ObjectTypes.EquationElement],
     [schema_1.schema.nodes.figure, json_schema_1.ObjectTypes.Figure],
@@ -40,8 +42,8 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.inline_equation, json_schema_1.ObjectTypes.InlineMathFragment],
     [schema_1.schema.nodes.keyword, json_schema_1.ObjectTypes.Keyword],
     [schema_1.schema.nodes.keywords_element, json_schema_1.ObjectTypes.KeywordsElement],
-    [schema_1.schema.nodes.keywords_section, json_schema_1.ObjectTypes.Section],
-    [schema_1.schema.nodes.keywords_group, json_schema_1.ObjectTypes.KeywordGroup],
+    [schema_1.schema.nodes.keywords, json_schema_1.ObjectTypes.Section],
+    [schema_1.schema.nodes.keyword_group, json_schema_1.ObjectTypes.KeywordGroup],
     [schema_1.schema.nodes.listing, json_schema_1.ObjectTypes.Listing],
     [schema_1.schema.nodes.listing_element, json_schema_1.ObjectTypes.ListingElement],
     [schema_1.schema.nodes.manuscript, json_schema_1.ObjectTypes.Manuscript],
@@ -53,13 +55,12 @@ exports.nodeTypesMap = new Map([
     [schema_1.schema.nodes.table_element, json_schema_1.ObjectTypes.TableElement],
     [schema_1.schema.nodes.toc_element, json_schema_1.ObjectTypes.TOCElement],
     [schema_1.schema.nodes.toc_section, json_schema_1.ObjectTypes.Section],
-    [schema_1.schema.nodes.meta_section, json_schema_1.ObjectTypes.MetaSection],
     [schema_1.schema.nodes.affiliation, json_schema_1.ObjectTypes.Affiliation],
     [schema_1.schema.nodes.contributor, json_schema_1.ObjectTypes.Contributor],
     [schema_1.schema.nodes.table_element_footer, json_schema_1.ObjectTypes.TableElementFooter],
+    [schema_1.schema.nodes.contributors, json_schema_1.ObjectTypes.Section],
+    [schema_1.schema.nodes.affiliations, json_schema_1.ObjectTypes.Section],
     [schema_1.schema.nodes.title, json_schema_1.ObjectTypes.Titles],
-    [schema_1.schema.nodes.contributors_section, json_schema_1.ObjectTypes.Section],
-    [schema_1.schema.nodes.affiliations_section, json_schema_1.ObjectTypes.Section],
 ]);
 const isExecutableNodeType = (type) => (0, schema_1.hasGroup)(type, schema_1.GROUP_EXECUTABLE);
 exports.isExecutableNodeType = isExecutableNodeType;

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

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isKeyword = exports.isCommentAnnotation = exports.isUserProfile = exports.isTable = exports.isManuscript = exports.isFigure = exports.hasObjectType = exports.isManuscriptModel = exports.manuscriptObjects = exports.elementObjects = exports.ExtraObjectTypes = void 0;
+exports.isKeyword = exports.isCommentAnnotation = exports.isTable = exports.isManuscript = exports.isFigure = exports.hasObjectType = exports.isManuscriptModel = exports.manuscriptObjects = exports.elementObjects = exports.ExtraObjectTypes = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
 var ExtraObjectTypes;
 (function (ExtraObjectTypes) {
@@ -53,6 +53,5 @@ exports.hasObjectType = hasObjectType;
 exports.isFigure = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Figure);
 exports.isManuscript = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Manuscript);
 exports.isTable = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Table);
-exports.isUserProfile = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.UserProfile);
 exports.isCommentAnnotation = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.CommentAnnotation);
 exports.isKeyword = (0, exports.hasObjectType)(json_schema_1.ObjectTypes.Keyword);

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

@@ -15,25 +15,16 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.chooseSectionCategoryFromTitle = exports.chooseSectionCategory = exports.chooseSectionCategoryByType = exports.chooseSecType = exports.chooseJatsFnType = exports.buildSectionCategory = exports.guessSectionCategory = exports.chooseSectionLableName = exports.chooseSectionNodeType = exports.isAnySectionNode = exports.getCoreSectionTitles = void 0;
+exports.chooseSectionCategoryFromTitle = exports.chooseSectionCategory = exports.chooseSectionCategoryByType = exports.chooseCoreSectionBySection = exports.chooseSecType = exports.chooseJatsFnType = exports.buildSectionCategory = exports.guessSectionCategory = exports.chooseSectionLableName = exports.chooseSectionNodeType = exports.isAnySectionNode = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
-const core_section_categories_1 = require("../lib/core-section-categories");
 const schema_1 = require("../schema");
 const sectionNodeTypes = [
     schema_1.schema.nodes.bibliography_section,
     schema_1.schema.nodes.footnotes_section,
-    schema_1.schema.nodes.keywords_section,
+    schema_1.schema.nodes.keywords,
     schema_1.schema.nodes.section,
     schema_1.schema.nodes.toc_section,
 ];
-const getCoreSectionTitles = (sectionCategory) => {
-    const category = core_section_categories_1.coreSectionCategories.find((section) => section._id === sectionCategory);
-    if (category) {
-        return category.titles.length ? category.titles : [' '];
-    }
-    throw new Error(`${sectionCategory} not found in core sections`);
-};
-exports.getCoreSectionTitles = getCoreSectionTitles;
 const isAnySectionNode = (node) => sectionNodeTypes.includes(node.type);
 exports.isAnySectionNode = isAnySectionNode;
 const chooseSectionNodeType = (category) => {
@@ -45,11 +36,11 @@ const chooseSectionNodeType = (category) => {
         case 'MPSectionCategory:endnotes':
             return schema_1.schema.nodes.footnotes_section;
         case 'MPSectionCategory:keywords':
-            return schema_1.schema.nodes.keywords_section;
+            return schema_1.schema.nodes.keywords;
         case 'MPSectionCategory:affiliations':
-            return schema_1.schema.nodes.affiliations_section;
+            return schema_1.schema.nodes.affiliations;
         case 'MPSectionCategory:contributors':
-            return schema_1.schema.nodes.contributors_section;
+            return schema_1.schema.nodes.contributors;
         case 'MPSectionCategory:toc':
             return schema_1.schema.nodes.toc_section;
         default:
@@ -90,15 +81,15 @@ const buildSectionCategory = (node) => {
             return 'MPSectionCategory:bibliography';
         case schema_1.schema.nodes.footnotes_section:
             return 'MPSectionCategory:endnotes';
-        case schema_1.schema.nodes.keywords_section:
+        case schema_1.schema.nodes.keywords:
             return 'MPSectionCategory:keywords';
         case schema_1.schema.nodes.toc_section:
             return 'MPSectionCategory:toc';
         case schema_1.schema.nodes.graphical_abstract_section:
             return 'MPSectionCategory:abstract-graphical';
-        case schema_1.schema.nodes.affiliations_section:
+        case schema_1.schema.nodes.affiliations:
             return 'MPSectionCategory:affiliations';
-        case schema_1.schema.nodes.contributors_section:
+        case schema_1.schema.nodes.contributors:
             return 'MPSectionCategory:contributors';
         default:
             return node.attrs.category || undefined;
@@ -128,6 +119,33 @@ const chooseSecType = (sectionCategory) => {
     }
 };
 exports.chooseSecType = chooseSecType;
+const chooseCoreSectionBySection = (section) => {
+    switch (section) {
+        case 'MPSectionCategory:abstract':
+        case 'MPSectionCategory:abstract-teaser':
+        case 'MPSectionCategory:abstract-graphical':
+            return 'MPSectionCategory:abstracts';
+        case 'MPSectionCategory:acknowledgement':
+        case 'MPSectionCategory:availability':
+        case 'MPSectionCategory:conclusions':
+        case 'MPSectionCategory:bibliography':
+        case 'MPSectionCategory:discussion':
+        case 'MPSectionCategory:endnotes':
+        case 'MPSectionCategory:appendices':
+        case 'MPSectionCategory:competing-interests':
+        case 'MPSectionCategory:con':
+        case 'MPSectionCategory:deceased':
+        case 'MPSectionCategory:ethics-statement':
+        case 'MPSectionCategory:financial-disclosure':
+        case 'MPSectionCategory:supplementary-material':
+        case 'MPSectionCategory:supported-by':
+        case 'MPSectionCategory:abbreviations':
+        case 'MPSectionCategory:results':
+            return 'MPSectionCategory:backmatter';
+    }
+    return 'MPSectionCategory:body';
+};
+exports.chooseCoreSectionBySection = chooseCoreSectionBySection;
 const chooseSectionCategoryByType = (secType) => {
     switch (secType) {
         case 'abstract':

package/dist/es/index.js

@@ -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/es/jats/importer/index.js

@@ -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';