@manuscripts/transform 3.0.65 → 3.0.67

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

@@ -25,6 +25,7 @@ const debug_1 = __importDefault(require("debug"));
 const prosemirror_model_1 = require("prosemirror-model");
 const prosemirror_utils_1 = require("prosemirror-utils");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
+const credit_roles_1 = require("../../lib/credit-roles");
 const footnotes_1 = require("../../lib/footnotes");
 const html_1 = require("../../lib/html");
 const schema_1 = require("../../schema");
@@ -1135,6 +1136,20 @@ class JATSExporter {
                             contrib.appendChild(xref);
                         });
                     }
+                    if (contributor.attrs.CRediTRoles) {
+                        contributor.attrs.CRediTRoles.forEach((cr) => {
+                            const role = this.createElement('role');
+                            const creditUrl = credit_roles_1.CRediTRoleUrls.get(cr.vocabTerm);
+                            if (creditUrl) {
+                                role.setAttribute('vocab-identifier', 'http://credit.niso.org/');
+                                role.setAttribute('vocab', 'CRediT');
+                                role.setAttribute('vocab-term', cr.vocabTerm);
+                                role.setAttribute('vocab-term-identifier', creditUrl);
+                                role.innerHTML = cr.vocabTerm;
+                            }
+                            contrib.appendChild(role);
+                        });
+                    }
                     contribGroup.appendChild(contrib);
                 });
                 const affiliationRIDs = [];
@@ -1230,10 +1245,9 @@ class JATSExporter {
         };
         this.appendParagraphToElement = (paragraph, element) => {
             const parsedDoc = new DOMParser().parseFromString(paragraph.textContent, 'text/html');
-            const parsedParagraph = parsedDoc.body.querySelector('p');
-            if (parsedParagraph) {
+            if (parsedDoc.body.innerHTML.length) {
                 const paragraphEl = this.createElement('p');
-                paragraphEl.innerHTML = parsedParagraph.innerHTML;
+                paragraphEl.innerHTML = parsedDoc.body.innerHTML;
                 paragraphEl.setAttribute('id', normalizeID(paragraph.attrs.id));
                 element.appendChild(paragraphEl);
             }

package/dist/cjs/jats/importer/jats-dom-parser.js

@@ -337,6 +337,11 @@ class JATSDOMParser {
                     };
                 },
             },
+            {
+                tag: 'fn[fn-type]',
+                context: 'author_notes/',
+                ignore: true,
+            },
             {
                 tag: 'fn:not([fn-type])',
                 node: 'footnote',
@@ -402,7 +407,7 @@ class JATSDOMParser {
                         }
                     }
                     return {
-                        id: element.getAttribute('id'),
+                        id: element.getAttribute('id') || undefined,
                         role: (0, utils_1.getTrimmedTextContent)(element, 'role'),
                         affiliations,
                         corresp,
@@ -416,6 +421,7 @@ class JATSDOMParser {
                             ObjectType: json_schema_1.ObjectTypes.BibliographicName,
                         },
                         ORCIDIdentifier: (0, utils_1.getTrimmedTextContent)(element, 'contrib-id[contrib-id-type="orcid"]'),
+                        CRediTRoles: (0, utils_1.getCRediTRoleRole)(element),
                         priority: this.parsePriority(element.getAttribute('priority')),
                         email: (0, utils_1.getTrimmedTextContent)(element, 'email') || '',
                         prefix: (0, utils_1.getTrimmedTextContent)(element, 'prefix'),

package/dist/cjs/lib/credit-roles.js

@@ -0,0 +1,76 @@
+"use strict";
+/*!
+ * © 2025 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CRediTRoleUrls = void 0;
+exports.CRediTRoleUrls = new Map([
+    [
+        "Conceptualization",
+        'https://credit.niso.org/contributor-roles/conceptualization/',
+    ],
+    [
+        "Data curation",
+        'https://credit.niso.org/contributor-roles/data-curation/',
+    ],
+    [
+        "Formal analysis",
+        'https://credit.niso.org/contributor-roles/formal-analysis/',
+    ],
+    [
+        "Funding acquisition",
+        'https://credit.niso.org/contributor-roles/funding-acquisition/',
+    ],
+    [
+        "Investigation",
+        'https://credit.niso.org/contributor-roles/investigation/',
+    ],
+    [
+        "Methodology",
+        'https://credit.niso.org/contributor-roles/methodology/',
+    ],
+    [
+        "ProjectAdministration",
+        'https://credit.niso.org/contributor-roles/project-administration/',
+    ],
+    [
+        "Resources",
+        'https://credit.niso.org/contributor-roles/resources/',
+    ],
+    [
+        "Software",
+        'https://credit.niso.org/contributor-roles/software/',
+    ],
+    [
+        "Supervision",
+        'https://credit.niso.org/contributor-roles/supervision/',
+    ],
+    [
+        "Validation",
+        'https://credit.niso.org/contributor-roles/validation/',
+    ],
+    [
+        "Visualization",
+        'https://credit.niso.org/contributor-roles/visualization/',
+    ],
+    [
+        "Writing \u2013 original draft",
+        'https://credit.niso.org/contributor-roles/writing-original-draft/',
+    ],
+    [
+        "Writing \u2013 review & editing",
+        'https://credit.niso.org/contributor-roles/writing-review-editing/',
+    ],
+]);

package/dist/cjs/lib/utils.js

@@ -15,9 +15,10 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.dateToTimestamp = exports.getHTMLContent = exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
+exports.getCRediTRoleRole = exports.dateToTimestamp = exports.getHTMLContent = exports.getTrimmedTextContent = exports.findParentNodeClosestToPos = exports.isInBibliographySection = exports.isInGraphicalAbstractSection = exports.findNodePositions = exports.iterateChildren = void 0;
 const jats_parser_utils_1 = require("../jats/importer/jats-parser-utils");
 const schema_1 = require("../schema");
+const credit_roles_1 = require("./credit-roles");
 function* iterateChildren(node, recurse = false) {
     for (let i = 0; i < node.childCount; i++) {
         const child = node.child(i);
@@ -102,3 +103,18 @@ const dateToTimestamp = (dateElement) => {
     return Date.UTC(values[0], values[1] - 1, values[2]) / 1000;
 };
 exports.dateToTimestamp = dateToTimestamp;
+function getCRediTRoleRole(elem) {
+    const sources = elem.querySelectorAll('role[vocab="CRediT"][vocab-identifier="http://credit.niso.org/"][vocab-term][vocab-term-identifier]');
+    const results = [];
+    sources.forEach((source) => {
+        if (source &&
+            credit_roles_1.CRediTRoleUrls.has(source.getAttribute('vocab-term'))) {
+            const result = {
+                vocabTerm: source.getAttribute('vocab-term'),
+            };
+            results.push(result);
+        }
+    });
+    return results;
+}
+exports.getCRediTRoleRole = getCRediTRoleRole;

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

@@ -17,6 +17,7 @@ exports.contributor = {
         isJointContributor: { default: undefined },
         ORCIDIdentifier: { default: undefined },
         priority: { default: undefined },
+        CRediTRoles: { default: [] },
         dataTracked: { default: null },
         contents: { default: '' },
         prefix: { default: '' },

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "3.0.65";
+exports.VERSION = "3.0.67";

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

@@ -19,6 +19,7 @@ import debug from 'debug';
 import { DOMParser as ProsemirrorDOMParser, DOMSerializer, } from 'prosemirror-model';
 import { findChildrenByAttr, findChildrenByType } from 'prosemirror-utils';
 import serializeToXML from 'w3c-xmlserializer';
+import { CRediTRoleUrls } from '../../lib/credit-roles';
 import { generateFootnoteLabels } from '../../lib/footnotes';
 import { nodeFromHTML, textFromHTML } from '../../lib/html';
 import { isCitationNode, isNodeOfType, schema, } from '../../schema';
@@ -1127,6 +1128,20 @@ export class JATSExporter {
                             contrib.appendChild(xref);
                         });
                     }
+                    if (contributor.attrs.CRediTRoles) {
+                        contributor.attrs.CRediTRoles.forEach((cr) => {
+                            const role = this.createElement('role');
+                            const creditUrl = CRediTRoleUrls.get(cr.vocabTerm);
+                            if (creditUrl) {
+                                role.setAttribute('vocab-identifier', 'http://credit.niso.org/');
+                                role.setAttribute('vocab', 'CRediT');
+                                role.setAttribute('vocab-term', cr.vocabTerm);
+                                role.setAttribute('vocab-term-identifier', creditUrl);
+                                role.innerHTML = cr.vocabTerm;
+                            }
+                            contrib.appendChild(role);
+                        });
+                    }
                     contribGroup.appendChild(contrib);
                 });
                 const affiliationRIDs = [];
@@ -1222,10 +1237,9 @@ export class JATSExporter {
         };
         this.appendParagraphToElement = (paragraph, element) => {
             const parsedDoc = new DOMParser().parseFromString(paragraph.textContent, 'text/html');
-            const parsedParagraph = parsedDoc.body.querySelector('p');
-            if (parsedParagraph) {
+            if (parsedDoc.body.innerHTML.length) {
                 const paragraphEl = this.createElement('p');
-                paragraphEl.innerHTML = parsedParagraph.innerHTML;
+                paragraphEl.innerHTML = parsedDoc.body.innerHTML;
                 paragraphEl.setAttribute('id', normalizeID(paragraph.attrs.id));
                 element.appendChild(paragraphEl);
             }

package/dist/es/jats/importer/jats-dom-parser.js

@@ -15,7 +15,7 @@
  */
 import { buildBibliographicDate, buildBibliographicName, buildContribution, ObjectTypes, } from '@manuscripts/json-schema';
 import { DOMParser, Fragment } from 'prosemirror-model';
-import { dateToTimestamp, getHTMLContent, getTrimmedTextContent, } from '../../lib/utils';
+import { dateToTimestamp, getCRediTRoleRole, getHTMLContent, getTrimmedTextContent, } from '../../lib/utils';
 import { publicationTypeToPM, } from '../../schema';
 import { DEFAULT_PROFILE_ID } from './jats-comments';
 export class JATSDOMParser {
@@ -334,6 +334,11 @@ export class JATSDOMParser {
                     };
                 },
             },
+            {
+                tag: 'fn[fn-type]',
+                context: 'author_notes/',
+                ignore: true,
+            },
             {
                 tag: 'fn:not([fn-type])',
                 node: 'footnote',
@@ -399,7 +404,7 @@ export class JATSDOMParser {
                         }
                     }
                     return {
-                        id: element.getAttribute('id'),
+                        id: element.getAttribute('id') || undefined,
                         role: getTrimmedTextContent(element, 'role'),
                         affiliations,
                         corresp,
@@ -413,6 +418,7 @@ export class JATSDOMParser {
                             ObjectType: ObjectTypes.BibliographicName,
                         },
                         ORCIDIdentifier: getTrimmedTextContent(element, 'contrib-id[contrib-id-type="orcid"]'),
+                        CRediTRoles: getCRediTRoleRole(element),
                         priority: this.parsePriority(element.getAttribute('priority')),
                         email: getTrimmedTextContent(element, 'email') || '',
                         prefix: getTrimmedTextContent(element, 'prefix'),

package/dist/es/lib/credit-roles.js

@@ -0,0 +1,73 @@
+/*!
+ * © 2025 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export const CRediTRoleUrls = new Map([
+    [
+        "Conceptualization",
+        'https://credit.niso.org/contributor-roles/conceptualization/',
+    ],
+    [
+        "Data curation",
+        'https://credit.niso.org/contributor-roles/data-curation/',
+    ],
+    [
+        "Formal analysis",
+        'https://credit.niso.org/contributor-roles/formal-analysis/',
+    ],
+    [
+        "Funding acquisition",
+        'https://credit.niso.org/contributor-roles/funding-acquisition/',
+    ],
+    [
+        "Investigation",
+        'https://credit.niso.org/contributor-roles/investigation/',
+    ],
+    [
+        "Methodology",
+        'https://credit.niso.org/contributor-roles/methodology/',
+    ],
+    [
+        "ProjectAdministration",
+        'https://credit.niso.org/contributor-roles/project-administration/',
+    ],
+    [
+        "Resources",
+        'https://credit.niso.org/contributor-roles/resources/',
+    ],
+    [
+        "Software",
+        'https://credit.niso.org/contributor-roles/software/',
+    ],
+    [
+        "Supervision",
+        'https://credit.niso.org/contributor-roles/supervision/',
+    ],
+    [
+        "Validation",
+        'https://credit.niso.org/contributor-roles/validation/',
+    ],
+    [
+        "Visualization",
+        'https://credit.niso.org/contributor-roles/visualization/',
+    ],
+    [
+        "Writing \u2013 original draft",
+        'https://credit.niso.org/contributor-roles/writing-original-draft/',
+    ],
+    [
+        "Writing \u2013 review & editing",
+        'https://credit.niso.org/contributor-roles/writing-review-editing/',
+    ],
+]);

package/dist/es/lib/utils.js

@@ -15,6 +15,7 @@
  */
 import { htmlFromJatsNode } from '../jats/importer/jats-parser-utils';
 import { isBibliographySectionNode, isGraphicalAbstractSectionNode, } from '../schema';
+import { CRediTRoleUrls } from './credit-roles';
 export function* iterateChildren(node, recurse = false) {
     for (let i = 0; i < node.childCount; i++) {
         const child = node.child(i);
@@ -91,3 +92,17 @@ export const dateToTimestamp = (dateElement) => {
     }
     return Date.UTC(values[0], values[1] - 1, values[2]) / 1000;
 };
+export function getCRediTRoleRole(elem) {
+    const sources = elem.querySelectorAll('role[vocab="CRediT"][vocab-identifier="http://credit.niso.org/"][vocab-term][vocab-term-identifier]');
+    const results = [];
+    sources.forEach((source) => {
+        if (source &&
+            CRediTRoleUrls.has(source.getAttribute('vocab-term'))) {
+            const result = {
+                vocabTerm: source.getAttribute('vocab-term'),
+            };
+            results.push(result);
+        }
+    });
+    return results;
+}

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

@@ -14,6 +14,7 @@ export const contributor = {
         isJointContributor: { default: undefined },
         ORCIDIdentifier: { default: undefined },
         priority: { default: undefined },
+        CRediTRoles: { default: [] },
         dataTracked: { default: null },
         contents: { default: '' },
         prefix: { default: '' },

package/dist/es/version.js

@@ -1 +1 @@
-export const VERSION = "3.0.65";
+export const VERSION = "3.0.67";

package/dist/types/lib/credit-roles.d.ts

@@ -0,0 +1,32 @@
+/*!
+ * © 2025 Atypon Systems LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+export declare const enum CreditVocabTerm {
+    Conceptualization = "Conceptualization",
+    DataCuration = "Data curation",
+    FormalAnalysis = "Formal analysis",
+    FundingAcquisition = "Funding acquisition",
+    Investigation = "Investigation",
+    Methodology = "Methodology",
+    ProjectAdministration = "ProjectAdministration",
+    Resources = "Resources",
+    Software = "Software",
+    Supervision = "Supervision",
+    Validation = "Validation",
+    Visualization = "Visualization",
+    WritingOriginalDraft = "Writing \u2013 original draft",
+    WritingReviewEditing = "Writing \u2013 review & editing"
+}
+export declare const CRediTRoleUrls: Map<CreditVocabTerm, string>;

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 import { Node as ProsemirrorNode, ResolvedPos } from 'prosemirror-model';
-import { ManuscriptEditorState, ManuscriptNode } from '../schema';
+import { CRediTRole, 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: ($pos: ResolvedPos) => boolean;
@@ -28,3 +28,4 @@ export declare const findParentNodeClosestToPos: ($pos: ResolvedPos, predicate:
 export declare const getTrimmedTextContent: (node: Element | Document | null, selector?: string) => string | undefined;
 export declare const getHTMLContent: (node: Element, querySelector: string) => string | undefined;
 export declare const dateToTimestamp: (dateElement: Element) => number | undefined;
+export declare function getCRediTRoleRole(elem: Element): CRediTRole[];

package/dist/types/schema/nodes/contributor.d.ts

@@ -1,5 +1,6 @@
 import { BibliographicName } from '@manuscripts/json-schema';
 import { NodeSpec } from 'prosemirror-model';
+import { CreditVocabTerm } from '../../lib/credit-roles';
 import { ManuscriptNode } from '../types';
 export type ContributorCorresp = {
     correspID: string;
@@ -9,6 +10,10 @@ export type ContributorFootnote = {
     noteID: string;
     noteLabel: string;
 };
+export type CRediTRole = {
+    vocabTerm: CreditVocabTerm;
+    degreeContribution?: string;
+};
 interface Attrs {
     id: string;
     role: string;
@@ -24,6 +29,7 @@ interface Attrs {
     isJointContributor: boolean;
     footnote: ContributorFootnote[];
     prefix: string;
+    CRediTRoles?: CRediTRole[];
 }
 export interface ContributorNode extends ManuscriptNode {
     attrs: Attrs;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const VERSION = "3.0.65";
+export declare const VERSION = "3.0.67";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "3.0.65",
+  "version": "3.0.67",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -30,7 +30,7 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "2.2.11",
+    "@manuscripts/json-schema": "2.2.12",
     "@manuscripts/library": "1.3.14",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",