@manuscripts/transform 2.6.1-LEAN-3966.2 → 3.0.0

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

@@ -151,7 +151,6 @@ class JATSExporter {
             this.updateFootnoteTypes(front, back);
             this.fillEmptyTableFooters(article);
             this.fillEmptyFootnotes(article);
-            this.moveAwards(front, body);
             await this.rewriteIDs();
             return (0, w3c_xmlserializer_1.default)(this.document);
         };
@@ -295,10 +294,10 @@ class JATSExporter {
             let countingElements = [];
             const figureCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.figure).length;
             countingElements.push(this.buildCountingElement('fig-count', figureCount));
-            const equationCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.equation_element).length;
-            countingElements.push(this.buildCountingElement('equation-count', equationCount));
             const tableCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.table).length;
             countingElements.push(this.buildCountingElement('table-count', tableCount));
+            const equationCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.equation_element).length;
+            countingElements.push(this.buildCountingElement('equation-count', equationCount));
             const referencesCount = (0, prosemirror_utils_1.findChildrenByType)(this.manuscriptNode, schema_1.schema.nodes.bibliography_item).length;
             countingElements.push(this.buildCountingElement('ref-count', referencesCount));
             const wordCount = this.manuscriptNode.textContent.split(/\s+/).length;
@@ -512,18 +511,8 @@ class JATSExporter {
         };
         this.createSerializer = () => {
             const nodes = {
-                awards: () => ['funding-group', 0],
-                award: (node) => {
-                    const awardGroup = node;
-                    const awardGroupElement = this.document.createElement('award-group');
-                    awardGroupElement.setAttribute('id', normalizeID(awardGroup.attrs.id));
-                    appendChildIfPresent(awardGroupElement, 'funding-source', awardGroup.attrs.source);
-                    awardGroup.attrs.code
-                        .split(';')
-                        .forEach((code) => appendChildIfPresent(awardGroupElement, 'award-id', code));
-                    appendChildIfPresent(awardGroupElement, 'principal-award-recipient', awardGroup.attrs.recipient);
-                    return awardGroupElement;
-                },
+                award: () => '',
+                awards: () => '',
                 box_element: (node) => createBoxElement(node),
                 author_notes: () => '',
                 corresp: () => '',
@@ -801,14 +790,6 @@ class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new prosemirror_model_1.DOMSerializer(nodes, marks);
-            const appendChildIfPresent = (parent, tagName, textContent) => {
-                if (!textContent) {
-                    return;
-                }
-                const element = this.document.createElement(tagName);
-                element.textContent = textContent;
-                parent.appendChild(element);
-            };
             const processChildNodes = (element, node, contentNodeType) => {
                 node.forEach((childNode) => {
                     if (childNode.type === contentNodeType) {
@@ -1316,23 +1297,6 @@ class JATSExporter {
             }
             body.removeChild(container);
         };
-        this.moveAwards = (front, body) => {
-            const awardGroups = body.querySelectorAll(':scope > award-group');
-            if (!awardGroups.length) {
-                return;
-            }
-            const fundingGroup = this.document.createElement('funding-group');
-            awardGroups.forEach((award) => {
-                fundingGroup.appendChild(award);
-            });
-            const articleMeta = front.querySelector(':scope > article-meta');
-            if (articleMeta) {
-                const insertBeforeElement = articleMeta.querySelector(':scope > support-group, :scope > conference, :scope > counts, :scope > custom-meta-group');
-                insertBeforeElement
-                    ? articleMeta.insertBefore(fundingGroup, insertBeforeElement)
-                    : articleMeta.appendChild(fundingGroup);
-            }
-        };
         this.moveAbstracts = (front, body) => {
             const container = body.querySelector(':scope > sec[sec-type="abstracts"]');
             let abstractSections;

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

@@ -292,26 +292,6 @@ const nodes = [
             };
         },
     },
-    {
-        tag: 'funding-group',
-        node: 'awards',
-    },
-    {
-        tag: 'award-group',
-        node: 'award',
-        getAttrs: (node) => {
-            var _a, _b;
-            const element = node;
-            return {
-                id: element.getAttribute('id'),
-                recipient: (_a = element.querySelector('principal-award-recipient')) === null || _a === void 0 ? void 0 : _a.textContent,
-                code: Array.from(element.querySelectorAll('award-id'))
-                    .map((awardID) => awardID.textContent)
-                    .reduce((acc, text) => (acc ? `${acc};${text}` : text), ''),
-                source: (_b = element.querySelector('funding-source')) === null || _b === void 0 ? void 0 : _b.textContent,
-            };
-        },
-    },
     {
         tag: 'fn:not([fn-type])',
         node: 'footnote',

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

@@ -16,6 +16,7 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.htmlFromJatsNode = exports.updateDocumentIDs = void 0;
+const uuid_1 = require("uuid");
 const schema_1 = require("../../schema");
 const transformer_1 = require("../../transformer");
 const updateDocumentIDs = (node) => {
@@ -34,6 +35,14 @@ const recurseDoc = (node, fn) => {
     node.descendants((n) => fn(n));
 };
 const updateNodeID = (node, replacements, warnings) => {
+    if (node.type === schema_1.schema.nodes.inline_equation) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `InlineMathFragment:${(0, uuid_1.v4)()}` });
+        return;
+    }
+    if (node.type === schema_1.schema.nodes.general_table_footnote) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `GeneralTableFootnote:${(0, uuid_1.v4)()}` });
+        return;
+    }
     if (node.type === schema_1.schema.nodes.comment ||
         node.type === schema_1.schema.nodes.highlight_marker) {
         return;
@@ -41,6 +50,11 @@ const updateNodeID = (node, replacements, warnings) => {
     if (!('id' in node.attrs)) {
         return;
     }
+    const objectType = transformer_1.nodeTypesMap.get(node.type);
+    if (!objectType) {
+        warnings.push(`Unknown object type for node type ${node.type.name}`);
+        return;
+    }
     const previousID = node.attrs.id;
     const nextID = (0, transformer_1.generateNodeID)(node.type);
     if (previousID) {

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

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fixTables = exports.orderTableFootnote = exports.moveReferencesToBackmatter = exports.createSupplementaryMaterialsSection = exports.createKeywordsSection = exports.moveCaptionsToEnd = exports.createBackmatter = exports.createAbstracts = exports.createBody = exports.createBoxedElementSection = exports.moveAbstracts = exports.moveAffiliations = exports.moveContributors = exports.moveAwards = exports.moveAuthorNotes = exports.moveTitle = exports.ensureSection = void 0;
+exports.fixTables = exports.orderTableFootnote = exports.moveReferencesToBackmatter = exports.createSupplementaryMaterialsSection = exports.createKeywordsSection = exports.moveCaptionsToEnd = exports.createBackmatter = exports.createAbstracts = exports.createBody = exports.createBoxedElementSection = exports.moveAbstracts = exports.moveAffiliations = exports.moveContributors = exports.moveAuthorNotes = exports.moveTitle = exports.ensureSection = void 0;
 const deafults_1 = require("../../lib/deafults");
 const section_group_type_1 = require("../../lib/section-group-type");
 const transformer_1 = require("../../transformer");
@@ -76,14 +76,6 @@ const moveAuthorNotes = (front, createElement) => {
     }
 };
 exports.moveAuthorNotes = moveAuthorNotes;
-const moveAwards = (front) => {
-    var _a;
-    const awards = front.querySelector('article-meta > funding-group');
-    if (awards) {
-        (_a = front.parentNode) === null || _a === void 0 ? void 0 : _a.insertBefore(awards, front);
-    }
-};
-exports.moveAwards = moveAwards;
 const moveContributors = (front, createElement) => {
     var _a;
     const contribs = front.querySelectorAll('contrib-group > contrib[contrib-type="author"]');

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

@@ -32,7 +32,6 @@ const processJATS = (doc) => {
     (0, jats_transformations_1.moveContributors)(front, createElement);
     (0, jats_transformations_1.moveAffiliations)(front, createElement);
     (0, jats_transformations_1.moveAuthorNotes)(front, createElement);
-    (0, jats_transformations_1.moveAwards)(front);
     const body = doc.querySelector('body');
     if (!body) {
         return;

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VERSION = void 0;
-exports.VERSION = "2.6.1-LEAN-3966.2";
+exports.VERSION = "3.0.0";

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

@@ -143,7 +143,6 @@ export class JATSExporter {
             this.updateFootnoteTypes(front, back);
             this.fillEmptyTableFooters(article);
             this.fillEmptyFootnotes(article);
-            this.moveAwards(front, body);
             await this.rewriteIDs();
             return serializeToXML(this.document);
         };
@@ -287,10 +286,10 @@ export class JATSExporter {
             let countingElements = [];
             const figureCount = findChildrenByType(this.manuscriptNode, schema.nodes.figure).length;
             countingElements.push(this.buildCountingElement('fig-count', figureCount));
-            const equationCount = findChildrenByType(this.manuscriptNode, schema.nodes.equation_element).length;
-            countingElements.push(this.buildCountingElement('equation-count', equationCount));
             const tableCount = findChildrenByType(this.manuscriptNode, schema.nodes.table).length;
             countingElements.push(this.buildCountingElement('table-count', tableCount));
+            const equationCount = findChildrenByType(this.manuscriptNode, schema.nodes.equation_element).length;
+            countingElements.push(this.buildCountingElement('equation-count', equationCount));
             const referencesCount = findChildrenByType(this.manuscriptNode, schema.nodes.bibliography_item).length;
             countingElements.push(this.buildCountingElement('ref-count', referencesCount));
             const wordCount = this.manuscriptNode.textContent.split(/\s+/).length;
@@ -504,18 +503,8 @@ export class JATSExporter {
         };
         this.createSerializer = () => {
             const nodes = {
-                awards: () => ['funding-group', 0],
-                award: (node) => {
-                    const awardGroup = node;
-                    const awardGroupElement = this.document.createElement('award-group');
-                    awardGroupElement.setAttribute('id', normalizeID(awardGroup.attrs.id));
-                    appendChildIfPresent(awardGroupElement, 'funding-source', awardGroup.attrs.source);
-                    awardGroup.attrs.code
-                        .split(';')
-                        .forEach((code) => appendChildIfPresent(awardGroupElement, 'award-id', code));
-                    appendChildIfPresent(awardGroupElement, 'principal-award-recipient', awardGroup.attrs.recipient);
-                    return awardGroupElement;
-                },
+                award: () => '',
+                awards: () => '',
                 box_element: (node) => createBoxElement(node),
                 author_notes: () => '',
                 corresp: () => '',
@@ -793,14 +782,6 @@ export class JATSExporter {
                 tracked_delete: () => ['del'],
             };
             this.serializer = new DOMSerializer(nodes, marks);
-            const appendChildIfPresent = (parent, tagName, textContent) => {
-                if (!textContent) {
-                    return;
-                }
-                const element = this.document.createElement(tagName);
-                element.textContent = textContent;
-                parent.appendChild(element);
-            };
             const processChildNodes = (element, node, contentNodeType) => {
                 node.forEach((childNode) => {
                     if (childNode.type === contentNodeType) {
@@ -1308,23 +1289,6 @@ export class JATSExporter {
             }
             body.removeChild(container);
         };
-        this.moveAwards = (front, body) => {
-            const awardGroups = body.querySelectorAll(':scope > award-group');
-            if (!awardGroups.length) {
-                return;
-            }
-            const fundingGroup = this.document.createElement('funding-group');
-            awardGroups.forEach((award) => {
-                fundingGroup.appendChild(award);
-            });
-            const articleMeta = front.querySelector(':scope > article-meta');
-            if (articleMeta) {
-                const insertBeforeElement = articleMeta.querySelector(':scope > support-group, :scope > conference, :scope > counts, :scope > custom-meta-group');
-                insertBeforeElement
-                    ? articleMeta.insertBefore(fundingGroup, insertBeforeElement)
-                    : articleMeta.appendChild(fundingGroup);
-            }
-        };
         this.moveAbstracts = (front, body) => {
             const container = body.querySelector(':scope > sec[sec-type="abstracts"]');
             let abstractSections;

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

@@ -286,26 +286,6 @@ const nodes = [
             };
         },
     },
-    {
-        tag: 'funding-group',
-        node: 'awards',
-    },
-    {
-        tag: 'award-group',
-        node: 'award',
-        getAttrs: (node) => {
-            var _a, _b;
-            const element = node;
-            return {
-                id: element.getAttribute('id'),
-                recipient: (_a = element.querySelector('principal-award-recipient')) === null || _a === void 0 ? void 0 : _a.textContent,
-                code: Array.from(element.querySelectorAll('award-id'))
-                    .map((awardID) => awardID.textContent)
-                    .reduce((acc, text) => (acc ? `${acc};${text}` : text), ''),
-                source: (_b = element.querySelector('funding-source')) === null || _b === void 0 ? void 0 : _b.textContent,
-            };
-        },
-    },
     {
         tag: 'fn:not([fn-type])',
         node: 'footnote',

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

@@ -13,8 +13,9 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { v4 as uuidv4 } from 'uuid';
 import { schema, } from '../../schema';
-import { generateNodeID } from '../../transformer';
+import { generateNodeID, nodeTypesMap } from '../../transformer';
 export const updateDocumentIDs = (node) => {
     const replacements = new Map();
     const warnings = [];
@@ -30,6 +31,14 @@ const recurseDoc = (node, fn) => {
     node.descendants((n) => fn(n));
 };
 const updateNodeID = (node, replacements, warnings) => {
+    if (node.type === schema.nodes.inline_equation) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `InlineMathFragment:${uuidv4()}` });
+        return;
+    }
+    if (node.type === schema.nodes.general_table_footnote) {
+        node.attrs = Object.assign(Object.assign({}, node.attrs), { id: `GeneralTableFootnote:${uuidv4()}` });
+        return;
+    }
     if (node.type === schema.nodes.comment ||
         node.type === schema.nodes.highlight_marker) {
         return;
@@ -37,6 +46,11 @@ const updateNodeID = (node, replacements, warnings) => {
     if (!('id' in node.attrs)) {
         return;
     }
+    const objectType = nodeTypesMap.get(node.type);
+    if (!objectType) {
+        warnings.push(`Unknown object type for node type ${node.type.name}`);
+        return;
+    }
     const previousID = node.attrs.id;
     const nextID = generateNodeID(node.type);
     if (previousID) {

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

@@ -70,13 +70,6 @@ export const moveAuthorNotes = (front, createElement) => {
         (_a = front.parentNode) === null || _a === void 0 ? void 0 : _a.insertBefore(authorNotes, front);
     }
 };
-export const moveAwards = (front) => {
-    var _a;
-    const awards = front.querySelector('article-meta > funding-group');
-    if (awards) {
-        (_a = front.parentNode) === null || _a === void 0 ? void 0 : _a.insertBefore(awards, front);
-    }
-};
 export const moveContributors = (front, createElement) => {
     var _a;
     const contribs = front.querySelectorAll('contrib-group > contrib[contrib-type="author"]');

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

@@ -17,7 +17,7 @@ import { markComments } from './jats-comments';
 import { jatsDOMParser } from './jats-dom-parser';
 import { parseJournal } from './jats-journal-meta-parser';
 import { updateDocumentIDs } from './jats-parser-utils';
-import { createAbstracts, createBackmatter, createBody, createBoxedElementSection, createKeywordsSection, createSupplementaryMaterialsSection, ensureSection, fixTables, moveAffiliations, moveAuthorNotes, moveAwards, moveCaptionsToEnd, moveContributors, moveReferencesToBackmatter, moveTitle, orderTableFootnote, } from './jats-transformations';
+import { createAbstracts, createBackmatter, createBody, createBoxedElementSection, createKeywordsSection, createSupplementaryMaterialsSection, ensureSection, fixTables, moveAffiliations, moveAuthorNotes, moveCaptionsToEnd, moveContributors, moveReferencesToBackmatter, moveTitle, orderTableFootnote, } from './jats-transformations';
 const processJATS = (doc) => {
     const createElement = createElementFn(doc);
     markComments(doc);
@@ -29,7 +29,6 @@ const processJATS = (doc) => {
     moveContributors(front, createElement);
     moveAffiliations(front, createElement);
     moveAuthorNotes(front, createElement);
-    moveAwards(front);
     const body = doc.querySelector('body');
     if (!body) {
         return;

package/dist/es/version.js

@@ -1 +1 @@
-export const VERSION = "2.6.1-LEAN-3966.2";
+export const VERSION = "3.0.0";

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

@@ -85,7 +85,6 @@ export declare class JATSExporter {
     private fixTable;
     private unwrapBody;
     private removeBackContainer;
-    private moveAwards;
     private moveAbstracts;
     private moveSectionsToBack;
     sectionToFootnote: (section: Element, fnType: string) => HTMLElement;

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

@@ -17,7 +17,6 @@ export type CreateElement = (tagName: string) => HTMLElement;
 export declare const ensureSection: (body: Element, createElement: CreateElement) => void;
 export declare const moveTitle: (front: Element, createElement: CreateElement) => void;
 export declare const moveAuthorNotes: (front: Element, createElement: CreateElement) => void;
-export declare const moveAwards: (front: Element) => void;
 export declare const moveContributors: (front: Element, createElement: CreateElement) => void;
 export declare const moveAffiliations: (front: Element, createElement: CreateElement) => void;
 export declare const moveAbstracts: (doc: Document, group: Element, createElement: CreateElement) => void;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const VERSION = "2.6.1-LEAN-3966.2";
+export declare const VERSION = "3.0.0";

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.6.1-LEAN-3966.2",
+  "version": "3.0.0",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",