@manuscripts/transform 1.3.4 → 1.3.5-LIT-528106

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

@@ -135,11 +135,13 @@ class JATSExporter {
                 const body = this.buildBody(fragment);
                 article.appendChild(body);
                 const back = this.buildBack(body);
+                this.moveCoiStatementToAuthorNotes(back, front);
                 article.appendChild(back);
                 this.unwrapBody(body);
                 this.moveAbstracts(front, body);
                 this.moveFloatsGroup(body, article);
                 this.removeBackContainer(body);
+                this.updateFootnoteTypes(front, back);
             }
             await this.rewriteIDs(idGenerator);
             if (mediaPathGenerator) {
@@ -1575,5 +1577,37 @@ class JATSExporter {
             articleMeta.appendChild(kwdGroup);
         }
     }
+    moveCoiStatementToAuthorNotes(back, front) {
+        const fnGroups = back.querySelectorAll('fn-group');
+        fnGroups.forEach((fnGroup) => {
+            if (fnGroup) {
+                const coiStatement = fnGroup.querySelector('fn[fn-type="competing-interests"]');
+                if (coiStatement) {
+                    const authorNotes = this.document.createElement('author-notes');
+                    authorNotes.append(coiStatement);
+                    const articleMeta = front.querySelector('article-meta');
+                    if (articleMeta) {
+                        const authorNoteEl = articleMeta.querySelector('author-notes');
+                        if (authorNoteEl) {
+                            authorNoteEl.append(...authorNotes.childNodes);
+                        }
+                        else {
+                            articleMeta.appendChild(authorNotes);
+                        }
+                    }
+                }
+            }
+        });
+    }
+    updateFootnoteTypes(front, body) {
+        const footnotes = [...front.querySelectorAll('fn').values()];
+        footnotes.push(...body.querySelectorAll('fn'));
+        footnotes.forEach((fn) => {
+            const fnType = fn.getAttribute('fn-type');
+            if (fnType) {
+                fn.setAttribute('fn-type', (0, section_category_1.chooseJatsFnType)(fnType));
+            }
+        });
+    }
 }
 exports.JATSExporter = JATSExporter;

package/dist/cjs/lib/utils.js

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
+exports.modelsEqual = exports.getTrimmedTextContent = 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) {
@@ -83,3 +83,16 @@ const getTrimmedTextContent = (node, querySelector) => {
     return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
 };
 exports.getTrimmedTextContent = getTrimmedTextContent;
+function modelsEqual(model, model2) {
+    for (const v in model) {
+        for (const v2 in model2) {
+            const prepV = typeof v == 'object' ? JSON.stringify(v) : v;
+            const prepV2 = typeof v2 == 'object' ? JSON.stringify(v2) : v2;
+            if (prepV !== prepV2) {
+                return false;
+            }
+        }
+    }
+    return true;
+}
+exports.modelsEqual = modelsEqual;

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);
@@ -526,7 +527,7 @@ const modelFromNode = (node, parent, path, priority) => {
     return { model, commentAnnotationsMap };
 };
 exports.modelFromNode = modelFromNode;
-const encode = (node) => {
+const encode = (node, preserveWithRepeatedID = false) => {
     const models = new Map();
     const priority = {
         value: 1,
@@ -546,8 +547,14 @@ const encode = (node) => {
             return;
         }
         const { model } = (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}`);
+            }
         }
         models.set(model._id, model);
         child.forEach(addModel(path.concat(child.attrs.id), child));

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

@@ -18,7 +18,7 @@ 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;
+exports.chooseSectionCategoryFromTitle = exports.chooseSectionCategory = exports.chooseSectionCategoryByType = exports.chooseSecType = exports.chooseJatsFnType = 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"));
 const json_schema_1 = require("@manuscripts/json-schema");
 const schema_1 = require("../schema");
@@ -104,6 +104,15 @@ const buildSectionCategory = (node) => {
     }
 };
 exports.buildSectionCategory = buildSectionCategory;
+const chooseJatsFnType = (footnoteType) => {
+    switch (footnoteType) {
+        case 'competing-interests':
+            return 'coi-statement';
+        default:
+            return footnoteType;
+    }
+};
+exports.chooseJatsFnType = chooseJatsFnType;
 const chooseSecType = (sectionCategory) => {
     const [, suffix] = sectionCategory.split(':', 2);
     switch (suffix) {

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

@@ -26,7 +26,7 @@ import { buildTargets } from '../transformer/labels';
 import { isExecutableNodeType, isNodeType } from '../transformer/node-types';
 import { hasObjectType } from '../transformer/object-types';
 import { findManuscript, findManuscriptById, } from '../transformer/project-bundle';
-import { chooseSecType } from '../transformer/section-category';
+import { chooseJatsFnType, chooseSecType, } from '../transformer/section-category';
 import { selectVersionIds } from './jats-versions';
 const warn = debug('manuscripts-transform');
 const XLINK_NAMESPACE = 'http://www.w3.org/1999/xlink';
@@ -128,11 +128,13 @@ export class JATSExporter {
                 const body = this.buildBody(fragment);
                 article.appendChild(body);
                 const back = this.buildBack(body);
+                this.moveCoiStatementToAuthorNotes(back, front);
                 article.appendChild(back);
                 this.unwrapBody(body);
                 this.moveAbstracts(front, body);
                 this.moveFloatsGroup(body, article);
                 this.removeBackContainer(body);
+                this.updateFootnoteTypes(front, back);
             }
             await this.rewriteIDs(idGenerator);
             if (mediaPathGenerator) {
@@ -1568,4 +1570,36 @@ export class JATSExporter {
             articleMeta.appendChild(kwdGroup);
         }
     }
+    moveCoiStatementToAuthorNotes(back, front) {
+        const fnGroups = back.querySelectorAll('fn-group');
+        fnGroups.forEach((fnGroup) => {
+            if (fnGroup) {
+                const coiStatement = fnGroup.querySelector('fn[fn-type="competing-interests"]');
+                if (coiStatement) {
+                    const authorNotes = this.document.createElement('author-notes');
+                    authorNotes.append(coiStatement);
+                    const articleMeta = front.querySelector('article-meta');
+                    if (articleMeta) {
+                        const authorNoteEl = articleMeta.querySelector('author-notes');
+                        if (authorNoteEl) {
+                            authorNoteEl.append(...authorNotes.childNodes);
+                        }
+                        else {
+                            articleMeta.appendChild(authorNotes);
+                        }
+                    }
+                }
+            }
+        });
+    }
+    updateFootnoteTypes(front, body) {
+        const footnotes = [...front.querySelectorAll('fn').values()];
+        footnotes.push(...body.querySelectorAll('fn'));
+        footnotes.forEach((fn) => {
+            const fnType = fn.getAttribute('fn-type');
+            if (fnType) {
+                fn.setAttribute('fn-type', chooseJatsFnType(fnType));
+            }
+        });
+    }
 }

package/dist/es/lib/utils.js

@@ -74,3 +74,15 @@ export const getTrimmedTextContent = (node, querySelector) => {
     }
     return (_b = (_a = node.querySelector(querySelector)) === null || _a === void 0 ? void 0 : _a.textContent) === null || _b === void 0 ? void 0 : _b.trim();
 };
+export function modelsEqual(model, model2) {
+    for (const v in model) {
+        for (const v2 in model2) {
+            const prepV = typeof v == 'object' ? JSON.stringify(v) : v;
+            const prepV2 = typeof v2 == 'object' ? JSON.stringify(v2) : v2;
+            if (prepV !== prepV2) {
+                return false;
+            }
+        }
+    }
+    return true;
+}

package/dist/es/transformer/encode.js

@@ -15,10 +15,11 @@
  */
 import { DOMSerializer } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
-import { iterateChildren } from '../lib/utils';
+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 { nodeTypesMap } from './node-types';
 import { buildSectionCategory } from './section-category';
 const serializer = DOMSerializer.fromSchema(schema);
@@ -517,7 +518,7 @@ export const modelFromNode = (node, parent, path, priority) => {
     }
     return { model, commentAnnotationsMap };
 };
-export const encode = (node) => {
+export const encode = (node, preserveWithRepeatedID = false) => {
     const models = new Map();
     const priority = {
         value: 1,
@@ -537,8 +538,14 @@ export const encode = (node) => {
             return;
         }
         const { model } = 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 && !modelsEqual(model, existingModel)) {
+                model._id = generateID(model.objectType);
+            }
+            else {
+                throw Error(`Encountered duplicate ids in models map while encoding: ${model._id}`);
+            }
         }
         models.set(model._id, model);
         child.forEach(addModel(path.concat(child.attrs.id), child));

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

@@ -92,6 +92,14 @@ export const buildSectionCategory = (node) => {
             return node.attrs.category || undefined;
     }
 };
+export const chooseJatsFnType = (footnoteType) => {
+    switch (footnoteType) {
+        case 'competing-interests':
+            return 'coi-statement';
+        default:
+            return footnoteType;
+    }
+};
 export const chooseSecType = (sectionCategory) => {
     const [, suffix] = sectionCategory.split(':', 2);
     switch (suffix) {

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

@@ -70,5 +70,7 @@ export declare class JATSExporter {
     sectionToFootnote: (section: Element, fnType: string) => HTMLElement;
     private moveFloatsGroup;
     private buildContributorName;
+    private moveCoiStatementToAuthorNotes;
+    private updateFootnoteTypes;
 }
 export {};

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

@@ -13,6 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { Model } from '@manuscripts/json-schema';
 import { Node as ProsemirrorNode, ResolvedPos } from 'prosemirror-model';
 import { ManuscriptEditorState, ManuscriptNode } from '../schema';
 export declare function iterateChildren(node: ManuscriptNode, recurse?: boolean): Iterable<ManuscriptNode>;
@@ -26,3 +27,4 @@ export declare const findParentNodeClosestToPos: ($pos: ResolvedPos, predicate:
     node: ProsemirrorNode;
 } | undefined;
 export declare const getTrimmedTextContent: (node: Element | Document, querySelector: string) => string | null | undefined;
+export declare function modelsEqual(model: Model, model2: Model): boolean;

package/dist/types/transformer/encode.d.ts

@@ -25,5 +25,5 @@ export declare const modelFromNode: (node: ManuscriptNode, parent: ManuscriptNod
 interface PrioritizedValue {
     value: number;
 }
-export declare const encode: (node: ManuscriptNode) => Map<string, Model>;
+export declare const encode: (node: ManuscriptNode, preserveWithRepeatedID?: boolean) => Map<string, Model>;
 export {};

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

@@ -23,6 +23,7 @@ export declare const chooseSectionNodeType: (category?: SectionCategory) => Manu
 export declare const chooseSectionLableName: (type?: SecType) => string;
 export declare const guessSectionCategory: (elements: Element[]) => SectionCategory | undefined;
 export declare const buildSectionCategory: (node: ManuscriptNode) => SectionCategory | undefined;
+export declare const chooseJatsFnType: (footnoteType: string) => string;
 export declare const chooseSecType: (sectionCategory: SectionCategory) => SecType;
 export declare const chooseSectionCategoryByType: (secType: string) => SectionCategory | undefined;
 export declare const chooseSectionCategory: (section: HTMLElement) => SectionCategory | undefined;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "1.3.4",
+  "version": "1.3.5-LIT-528106",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",