@manuscripts/transform 2.1.1-LEAN-3352-0 → 2.1.1-LEAN-3377-0

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

@@ -265,6 +265,16 @@ exports.jatsBodyTransformations = {
             }
         });
     },
+    orderTableFootnote(doc, body) {
+        const tableInlineFootnotesIds = new Set(Array.from(body.querySelectorAll('tbody > tr > td > xref[ref-type="fn"]').values()).map((inlineFootnote) => inlineFootnote.getAttribute('rid')));
+        const fnGroups = doc.querySelectorAll('table-wrap-foot > fn-group');
+        fnGroups.forEach((fnGroup) => {
+            const orderedFootnotes = Array.from(fnGroup.querySelectorAll('fn')).sort((fn) => tableInlineFootnotesIds.has(fn.getAttribute('id'))
+                ? -1
+                : 0);
+            fnGroup.replaceChildren(...orderedFootnotes);
+        });
+    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

@@ -45,11 +45,6 @@ exports.jatsFrontParser = {
         }
         return titles;
     },
-    parseDOI(front) {
-        var _a;
-        const doi = front === null || front === void 0 ? void 0 : front.querySelector('article-meta > article-id[pub-id-type="doi"]');
-        return (_a = doi === null || doi === void 0 ? void 0 : doi.textContent) !== null && _a !== void 0 ? _a : undefined;
-    },
     parseCounts(counts) {
         var _a, _b, _c, _d, _e;
         if (counts) {

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

@@ -31,7 +31,6 @@ const parseJATSFront = (doc, front) => {
     const createElement = createElementFn(doc);
     const journal = jats_front_parser_1.jatsFrontParser.parseJournal(front.querySelector('journal-meta'));
     const titles = jats_front_parser_1.jatsFrontParser.parseTitles(front.querySelector('article-meta > title-group'), createElement);
-    const DOI = jats_front_parser_1.jatsFrontParser.parseDOI(front);
     const { affiliations, affiliationIDs } = jats_front_parser_1.jatsFrontParser.parseAffiliations([
         ...front.querySelectorAll('article-meta > contrib-group > aff'),
     ]);
@@ -46,7 +45,7 @@ const parseJATSFront = (doc, front) => {
     ], affiliationIDs, footnoteIDs, correspondingIDs);
     const history = jats_front_parser_1.jatsFrontParser.parseDates(front.querySelector('article-meta > history'));
     const counts = jats_front_parser_1.jatsFrontParser.parseCounts(front.querySelector('article-meta counts'));
-    const manuscript = Object.assign(Object.assign(Object.assign(Object.assign({}, (0, builders_1.buildManuscript)()), counts), history), { DOI });
+    const manuscript = Object.assign(Object.assign(Object.assign({}, (0, builders_1.buildManuscript)()), counts), history);
     return generateIDs([
         manuscript,
         titles,
@@ -68,6 +67,7 @@ const parseJATSBody = (doc, body, references) => {
     jats_body_transformations_1.jatsBodyTransformations.createBackmatter(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createKeywords(doc, body, createElement);
+    jats_body_transformations_1.jatsBodyTransformations.orderTableFootnote(doc, body);
     const node = jats_body_dom_parser_1.jatsBodyDOMParser.parse(body).firstChild;
     if (!node) {
         throw new Error('No content was parsed from the JATS article body');

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

@@ -311,10 +311,10 @@ class JATSExporter {
                 articleID.textContent = id;
                 articleMeta.appendChild(articleID);
             }
-            if (doi || manuscript.DOI) {
+            if (doi) {
                 const articleID = this.document.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'doi');
-                articleID.textContent = doi !== null && doi !== void 0 ? doi : manuscript.DOI;
+                articleID.textContent = doi;
                 articleMeta.appendChild(articleID);
             }
             const titleGroup = this.document.createElement('title-group');

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

@@ -262,6 +262,16 @@ export const jatsBodyTransformations = {
             }
         });
     },
+    orderTableFootnote(doc, body) {
+        const tableInlineFootnotesIds = new Set(Array.from(body.querySelectorAll('tbody > tr > td > xref[ref-type="fn"]').values()).map((inlineFootnote) => inlineFootnote.getAttribute('rid')));
+        const fnGroups = doc.querySelectorAll('table-wrap-foot > fn-group');
+        fnGroups.forEach((fnGroup) => {
+            const orderedFootnotes = Array.from(fnGroup.querySelectorAll('fn')).sort((fn) => tableInlineFootnotesIds.has(fn.getAttribute('id'))
+                ? -1
+                : 0);
+            fnGroup.replaceChildren(...orderedFootnotes);
+        });
+    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

@@ -39,11 +39,6 @@ export const jatsFrontParser = {
         }
         return titles;
     },
-    parseDOI(front) {
-        var _a;
-        const doi = front === null || front === void 0 ? void 0 : front.querySelector('article-meta > article-id[pub-id-type="doi"]');
-        return (_a = doi === null || doi === void 0 ? void 0 : doi.textContent) !== null && _a !== void 0 ? _a : undefined;
-    },
     parseCounts(counts) {
         var _a, _b, _c, _d, _e;
         if (counts) {

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

@@ -28,7 +28,6 @@ export const parseJATSFront = (doc, front) => {
     const createElement = createElementFn(doc);
     const journal = jatsFrontParser.parseJournal(front.querySelector('journal-meta'));
     const titles = jatsFrontParser.parseTitles(front.querySelector('article-meta > title-group'), createElement);
-    const DOI = jatsFrontParser.parseDOI(front);
     const { affiliations, affiliationIDs } = jatsFrontParser.parseAffiliations([
         ...front.querySelectorAll('article-meta > contrib-group > aff'),
     ]);
@@ -43,7 +42,7 @@ export const parseJATSFront = (doc, front) => {
     ], affiliationIDs, footnoteIDs, correspondingIDs);
     const history = jatsFrontParser.parseDates(front.querySelector('article-meta > history'));
     const counts = jatsFrontParser.parseCounts(front.querySelector('article-meta counts'));
-    const manuscript = Object.assign(Object.assign(Object.assign(Object.assign({}, buildManuscript()), counts), history), { DOI });
+    const manuscript = Object.assign(Object.assign(Object.assign({}, buildManuscript()), counts), history);
     return generateIDs([
         manuscript,
         titles,
@@ -64,6 +63,7 @@ export const parseJATSBody = (doc, body, references) => {
     jatsBodyTransformations.createBackmatter(doc, body, createElement);
     jatsBodyTransformations.createSuppleMaterials(doc, body, createElement);
     jatsBodyTransformations.createKeywords(doc, body, createElement);
+    jatsBodyTransformations.orderTableFootnote(doc, body);
     const node = jatsBodyDOMParser.parse(body).firstChild;
     if (!node) {
         throw new Error('No content was parsed from the JATS article body');

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

@@ -303,10 +303,10 @@ export class JATSExporter {
                 articleID.textContent = id;
                 articleMeta.appendChild(articleID);
             }
-            if (doi || manuscript.DOI) {
+            if (doi) {
                 const articleID = this.document.createElement('article-id');
                 articleID.setAttribute('pub-id-type', 'doi');
-                articleID.textContent = doi !== null && doi !== void 0 ? doi : manuscript.DOI;
+                articleID.textContent = doi;
                 articleMeta.appendChild(articleID);
             }
             const titleGroup = this.document.createElement('title-group');

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

@@ -32,6 +32,7 @@ export declare const jatsBodyTransformations: {
     moveFootnotes(doc: Document, group: Element, createElement: (tagName: string) => HTMLElement): void;
     moveCaptionsToEnd(body: Element): void;
     fixTables(body: Element, createElement: (tagName: string) => HTMLElement): void;
+    orderTableFootnote(doc: Document, body: Element): void;
     moveFloatsGroupToBody(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     createKeywords(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     createSuppleMaterials(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;

package/dist/types/jats/importer/jats-front-parser.d.ts

@@ -15,7 +15,6 @@
  */
 export declare const jatsFrontParser: {
     parseTitles(element: Element | null, createElement: (tagName: string) => HTMLElement): import("../../transformer").Build<import("@manuscripts/json-schema/dist/types").Titles>;
-    parseDOI(front: Element | null): string | undefined;
     parseCounts(counts: Element | null): {
         wordCount: number | undefined;
         figureCount: number | undefined;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.1.1-LEAN-3352-0",
+  "version": "2.1.1-LEAN-3377-0",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -78,4 +78,4 @@
     "rimraf": "^3.0.2",
     "typescript": "^4.0.5"
   }
-}
+}