@manuscripts/transform 2.0.1-LEAN-3092 → 2.0.2

package/dist/es/mathjax/tex-to-svg.js

@@ -0,0 +1,55 @@
+/*!
+ * © 2019 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.
+ */
+import 'mathjax-full/js/util/entities/all';
+import { HTMLAdaptor } from 'mathjax-full/js/adaptors/HTMLAdaptor';
+import { HTMLDocument } from 'mathjax-full/js/handlers/html/HTMLDocument';
+import { TeX } from 'mathjax-full/js/input/tex';
+import { SVG } from 'mathjax-full/js/output/svg';
+import { xmlSerializer } from '../transformer';
+import { packages } from './mathjax-packages';
+class ManuscriptsHTMLAdaptor extends HTMLAdaptor {
+    setAttribute(node, name, value, ns) {
+        if (name !== 'xmlns') {
+            ns ? node.setAttributeNS(ns, name, value) : node.setAttribute(name, value);
+        }
+    }
+}
+const InputJax = new TeX({
+    packages,
+});
+const OutputJax = new SVG({
+    fontCache: 'none',
+});
+const adaptor = new ManuscriptsHTMLAdaptor(window);
+const doc = new HTMLDocument(document, adaptor, {
+    InputJax,
+    OutputJax,
+});
+doc.addStyleSheet();
+export const convertTeXToSVG = (tex, display) => {
+    const item = doc.convert(tex, {
+        display,
+        em: 16,
+        ex: 8,
+        containerWidth: 1000000,
+        lineWidth: 1000000,
+        scale: 1,
+    });
+    if (!item || !item.firstChild) {
+        return null;
+    }
+    return xmlSerializer.serializeToString(item.firstChild);
+};

package/dist/es/schema/index.js

@@ -98,6 +98,7 @@ export * from './nodes/footnotes_section';
 export * from './nodes/graphical_abstract_section';
 export * from './nodes/hard_break';
 export * from './nodes/highlight_marker';
+export * from './nodes/inline_equation';
 export * from './nodes/inline_footnote';
 export * from './nodes/keyword';
 export * from './nodes/keywords_element';

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

@@ -1,5 +1,5 @@
 /*!
- * © 2023 Atypon Systems LLC
+ * © 2019 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.
@@ -17,8 +17,9 @@ import { ObjectTypes } from '@manuscripts/json-schema';
 export const equation = {
     attrs: {
         id: { default: '' },
-        contents: { default: '' },
-        format: { default: '' },
+        MathMLStringRepresentation: { default: '' },
+        SVGStringRepresentation: { default: '' },
+        TeXRepresentation: { default: '' },
         dataTracked: { default: null },
     },
     group: 'block',
@@ -26,25 +27,26 @@ export const equation = {
         {
             tag: `div.${ObjectTypes.Equation}`,
             getAttrs: (p) => {
-                const htmlEl = p;
+                const dom = p;
                 return {
-                    id: htmlEl.getAttribute('id'),
-                    format: htmlEl.getAttribute('data-equation-format'),
-                    contents: htmlEl.innerHTML,
+                    id: dom.getAttribute('id'),
+                    MathMLStringRepresentation: dom.getAttribute('data-mathml-string-representation'),
+                    SVGStringRepresentation: dom.innerHTML,
+                    TeXRepresentation: dom.getAttribute('data-tex-representation'),
                 };
             },
         },
     ],
     toDOM: (node) => {
         const equationNode = node;
-        const { id, contents, format } = equationNode.attrs;
         const dom = document.createElement('div');
+        dom.setAttribute('id', equationNode.attrs.id);
         dom.classList.add(ObjectTypes.Equation);
-        dom.setAttribute('id', id);
-        if (format) {
-            dom.setAttribute('data-equation-format', format);
+        if (equationNode.attrs.MathMLStringRepresentation) {
+            dom.setAttribute('data-mathml-string-representation', equationNode.attrs.MathMLStringRepresentation);
         }
-        dom.innerHTML = contents;
+        dom.setAttribute('data-tex-representation', equationNode.attrs.TeXRepresentation);
+        dom.innerHTML = equationNode.attrs.SVGStringRepresentation;
         return dom;
     },
 };

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

@@ -14,10 +14,11 @@
  * limitations under the License.
  */
 export const equationElement = {
-    content: '(equation | placeholder)',
+    content: '(equation | placeholder) figcaption',
     attrs: {
         id: { default: '' },
-        label: { default: '' },
+        suppressCaption: { default: true },
+        suppressTitle: { default: undefined },
         dataTracked: { default: null },
         comments: { default: null },
     },
@@ -25,7 +26,7 @@ export const equationElement = {
     group: 'block element',
     parseDOM: [
         {
-            tag: 'div.equation',
+            tag: 'figure.equation',
             getAttrs: (p) => {
                 const dom = p;
                 return {
@@ -37,7 +38,7 @@ export const equationElement = {
     toDOM: (node) => {
         const equationElementNode = node;
         return [
-            'div',
+            'figure',
             {
                 class: 'equation',
                 id: equationElementNode.attrs.id,

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

@@ -13,39 +13,43 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import { ObjectTypes } from '@manuscripts/json-schema';
 export const inlineEquation = {
     attrs: {
+        id: { default: '' },
+        MathMLRepresentation: { default: '' },
+        SVGRepresentation: { default: '' },
+        TeXRepresentation: { default: '' },
         dataTracked: { default: null },
-        comments: { default: null },
-        contents: { default: '' },
-        format: { default: '' },
     },
-    selectable: false,
     atom: true,
     inline: true,
     draggable: true,
     group: 'inline',
     parseDOM: [
         {
-            tag: `span.MPInlineMathFragment`,
+            tag: `span.${ObjectTypes.InlineMathFragment}`,
             getAttrs: (p) => {
                 const dom = p;
                 return {
-                    format: dom.getAttribute('data-equation-format'),
-                    contents: dom.innerHTML,
+                    id: dom.getAttribute('id'),
+                    MathMLRepresentation: dom.getAttribute('data-mathml-representation') || '',
+                    SVGRepresentation: dom.innerHTML || '',
+                    TeXRepresentation: dom.getAttribute('data-tex-representation') || '',
                 };
             },
         },
     ],
     toDOM: (node) => {
         const inlineEquationNode = node;
-        const { contents, format } = inlineEquationNode.attrs;
         const dom = document.createElement('span');
-        dom.classList.add('MPInlineMathFragment');
-        if (format) {
-            dom.setAttribute('data-equation-format', format);
+        dom.classList.add(ObjectTypes.InlineMathFragment);
+        dom.setAttribute('id', inlineEquationNode.attrs.id);
+        dom.setAttribute('data-tex-representation', inlineEquationNode.attrs.TeXRepresentation);
+        if (inlineEquationNode.attrs.MathMLRepresentation) {
+            dom.setAttribute('data-mathml-representation', inlineEquationNode.attrs.MathMLRepresentation);
         }
-        dom.innerHTML = contents;
+        dom.innerHTML = inlineEquationNode.attrs.SVGRepresentation;
         return dom;
     },
 };

package/dist/es/transformer/builders.js

@@ -95,6 +95,12 @@ export const buildNote = (target, source, contents = '') => ({
     source,
     contents,
 });
+export const buildInlineMathFragment = (containingObject, TeXRepresentation) => ({
+    _id: generateID(ObjectTypes.InlineMathFragment),
+    objectType: ObjectTypes.InlineMathFragment,
+    containingObject: containingObject || undefined,
+    TeXRepresentation,
+});
 export const buildFootnote = (containingObject, contents, kind = 'footnote') => ({
     _id: generateID(ObjectTypes.Footnote),
     objectType: ObjectTypes.Footnote,

package/dist/es/transformer/decode.js

@@ -262,8 +262,9 @@ export class Decoder {
                 const model = data;
                 return schema.nodes.equation.createChecked({
                     id: model._id,
-                    contents: model.contents,
-                    format: model.format,
+                    MathMLStringRepresentation: model.MathMLStringRepresentation,
+                    SVGStringRepresentation: model.SVGStringRepresentation,
+                    TeXRepresentation: model.TeXRepresentation,
                 });
             },
             [ObjectTypes.EquationElement]: (data) => {
@@ -282,10 +283,12 @@ export class Decoder {
                 else {
                     throw new MissingElement(model.containedObjectID);
                 }
+                const figcaption = this.getFigcaption(model);
                 return schema.nodes.equation_element.createChecked({
                     id: model._id,
-                    label: model.label,
-                }, [equation]);
+                    suppressCaption: Boolean(model.suppressCaption),
+                    suppressTitle: Boolean(model.suppressTitle === undefined ? true : model.suppressTitle),
+                }, [equation, figcaption]);
             },
             [ObjectTypes.FootnotesElement]: (data) => {
                 const foonotesElementModel = data;

package/dist/es/transformer/encode.js

@@ -54,6 +54,12 @@ const listContents = (node) => {
     }
     return serializeToXML(output);
 };
+const svgDefs = (svg) => {
+    const template = document.createElement('template');
+    template.innerHTML = svg.trim();
+    const defs = template.content.querySelector('defs');
+    return defs ? serializeToXML(defs) : undefined;
+};
 const tableRowDisplayStyle = (tagName, parent) => {
     switch (tagName) {
         case 'thead':
@@ -339,12 +345,20 @@ const encoders = {
             : false,
     }),
     equation: (node) => ({
-        contents: node.attrs.contents,
-        format: node.attrs.format,
+        MathMLStringRepresentation: node.attrs.MathMLStringRepresentation || undefined,
+        TeXRepresentation: node.attrs.TeXRepresentation,
+        SVGStringRepresentation: node.attrs.SVGStringRepresentation,
     }),
     equation_element: (node) => ({
         containedObjectID: attributeOfNodeType(node, 'equation', 'id'),
-        label: node.attrs.label,
+        caption: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption),
+        title: inlineContentOfChildNodeType(node, node.type.schema.nodes.figcaption, node.type.schema.nodes.caption_title, false),
+        elementType: 'p',
+        suppressCaption: Boolean(node.attrs.suppressCaption) || undefined,
+        suppressTitle: node.attrs.suppressTitle === undefined ||
+            node.attrs.suppressTitle === true
+            ? undefined
+            : false,
     }),
     figure: (node) => ({
         contentType: node.attrs.contentType || undefined,
@@ -391,6 +405,12 @@ const encoders = {
             .map((childNode) => childNode.attrs.id)
             .filter((id) => id),
     }),
+    inline_equation: (node, parent) => ({
+        containingObject: parent.attrs.id,
+        TeXRepresentation: node.attrs.TeXRepresentation,
+        SVGRepresentation: node.attrs.SVGRepresentation,
+        SVGGlyphs: svgDefs(node.attrs.SVGRepresentation),
+    }),
     keyword: (node, parent) => ({
         containedGroup: parent.attrs.id,
         name: keywordContents(node),
@@ -551,7 +571,8 @@ export const encode = (node) => {
         if (placeholderTypes.includes(child.type)) {
             return;
         }
-        if (parent.type === schema.nodes.paragraph) {
+        if (parent.type === schema.nodes.paragraph &&
+            child.type !== schema.nodes.inline_equation) {
             return;
         }
         const { model, markers } = modelFromNode(child, parent, path, priority);

package/dist/es/transformer/node-types.js

@@ -36,6 +36,7 @@ export const nodeTypesMap = new Map([
     [schema.nodes.footnotes_section, ObjectTypes.Section],
     [schema.nodes.graphical_abstract_section, ObjectTypes.Section],
     [schema.nodes.highlight_marker, ObjectTypes.HighlightMarker],
+    [schema.nodes.inline_equation, ObjectTypes.InlineMathFragment],
     [schema.nodes.keyword, ObjectTypes.Keyword],
     [schema.nodes.keywords_element, ObjectTypes.KeywordsElement],
     [schema.nodes.keywords, ObjectTypes.Section],

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

@@ -35,6 +35,7 @@ export const manuscriptObjects = [
     ObjectTypes.CommentAnnotation,
     ObjectTypes.Contributor,
     ObjectTypes.Footnote,
+    ObjectTypes.InlineMathFragment,
     ObjectTypes.Section,
 ].concat(elementObjects);
 export const isManuscriptModel = (model) => {

package/dist/types/index.d.ts

@@ -1,6 +1,7 @@
 export * from './lib/section-group-type';
 export * from './lib/table-cell-styles';
 export * from './lib/utils';
+export * from './mathjax';
 export * from './schema';
 export * from './transformer';
 export * from './jats';

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

@@ -14,8 +14,9 @@
  * limitations under the License.
  */
 import { Model } from '@manuscripts/json-schema';
+import { CitationProvider } from '@manuscripts/library';
 import { DOMSerializer } from 'prosemirror-model';
-import { ManuscriptFragment, ManuscriptNode } from '../schema';
+import { CitationNode, ManuscriptFragment, ManuscriptNode } from '../schema';
 import { Target } from '../transformer/labels';
 import { IDGenerator, MediaPathGenerator } from '../types';
 import { Version } from './jats-versions';
@@ -27,7 +28,12 @@ interface Links {
 export declare const createCounter: () => {
     increment: (field: string) => number;
 };
+export type CSLOptions = {
+    style: string;
+    locale: string;
+};
 export interface JATSExporterOptions {
+    csl: CSLOptions;
     version?: Version;
     doi?: string;
     id?: string;
@@ -37,13 +43,34 @@ export interface JATSExporterOptions {
     idGenerator?: IDGenerator;
     mediaPathGenerator?: MediaPathGenerator;
 }
+export declare const buildCitations: (citations: CitationNode[]) => {
+    citationID: string;
+    citationItems: {
+        id: string;
+    }[];
+    properties: {
+        noteIndex: number;
+    };
+}[];
 export declare class JATSExporter {
     protected document: Document;
     protected modelMap: Map<string, Model>;
     protected models: Model[];
     protected serializer: DOMSerializer;
     protected labelTargets?: Map<string, Target>;
-    serializeToJATS: (fragment: ManuscriptFragment, modelMap: Map<string, Model>, manuscriptID: string, options?: JATSExporterOptions) => Promise<string>;
+    protected citationTexts: Map<string, string>;
+    protected citationProvider: CitationProvider;
+    protected generateCitations(fragment: ManuscriptFragment): {
+        citationID: string;
+        citationItems: {
+            id: string;
+        }[];
+        properties: {
+            noteIndex: number;
+        };
+    }[];
+    protected generateCitationTexts(fragment: ManuscriptFragment, csl: CSLOptions): void;
+    serializeToJATS: (fragment: ManuscriptFragment, modelMap: Map<string, Model>, manuscriptID: string, options: JATSExporterOptions) => Promise<string>;
     private nodeFromJATS;
     protected rewriteCrossReferenceTypes: () => void;
     protected rewriteMediaPaths: (mediaPathGenerator: MediaPathGenerator) => Promise<void>;

package/dist/types/mathjax/index.d.ts

@@ -0,0 +1,3 @@
+export declare const convertMathMLToSVG: (mathml: string, display: boolean) => Promise<string | null>;
+export declare const convertTeXToMathML: (tex: string, display: boolean) => Promise<string | null>;
+export declare const convertTeXToSVG: (tex: string, display: boolean) => Promise<string | null>;

package/dist/types/mathjax/mathjax-packages.d.ts

@@ -0,0 +1,16 @@
+/*!
+ * © 2019 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 packages: string[];

package/dist/types/mathjax/mathml-to-svg.d.ts

@@ -0,0 +1,17 @@
+/*!
+ * © 2019 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.
+ */
+import 'mathjax-full/js/util/entities/all';
+export declare const convertMathMLToSVG: (mathml: string, display: boolean) => string | null;

package/dist/types/mathjax/tex-to-mathml.d.ts

@@ -0,0 +1,17 @@
+/*!
+ * © 2019 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.
+ */
+import 'mathjax-full/js/util/entities/all';
+export declare const convertTeXToMathML: (tex: string, display: boolean) => string | null;

package/dist/types/mathjax/tex-to-svg.d.ts

@@ -0,0 +1,17 @@
+/*!
+ * © 2019 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.
+ */
+import 'mathjax-full/js/util/entities/all';
+export declare const convertTeXToSVG: (tex: string, display: boolean) => string | null;

package/dist/types/schema/index.d.ts

@@ -40,6 +40,7 @@ export * from './nodes/footnotes_section';
 export * from './nodes/graphical_abstract_section';
 export * from './nodes/hard_break';
 export * from './nodes/highlight_marker';
+export * from './nodes/inline_equation';
 export * from './nodes/inline_footnote';
 export * from './nodes/keyword';
 export * from './nodes/keywords_element';

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

@@ -1,5 +1,5 @@
 /*!
- * © 2023 Atypon Systems LLC
+ * © 2019 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.
@@ -17,8 +17,9 @@ import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
 interface Attrs {
     id: string;
-    format: string;
-    contents: string;
+    MathMLStringRepresentation: string;
+    SVGStringRepresentation: string;
+    TeXRepresentation: string;
 }
 export interface EquationNode extends ManuscriptNode {
     attrs: Attrs;

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

@@ -18,7 +18,8 @@ import { ManuscriptNode } from '../types';
 import { CommentNode } from './comment';
 interface Attrs {
     id: string;
-    label: string;
+    suppressCaption: boolean;
+    suppressTitle?: boolean;
     comments?: CommentNode[];
 }
 export interface EquationElementNode extends ManuscriptNode {

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

@@ -15,11 +15,11 @@
  */
 import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
-import { CommentNode } from './comment';
 interface Attrs {
-    contents: string;
-    format: string;
-    comments?: CommentNode[];
+    id: string;
+    MathMLRepresentation: string;
+    SVGRepresentation: string;
+    TeXRepresentation: string;
 }
 export interface InlineEquationNode extends ManuscriptNode {
     attrs: Attrs;

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

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-import { Affiliation, Attribution, BibliographicDate, BibliographicName, BibliographyElement, BibliographyItem, Color, CommentAnnotation, Contribution, Contributor, ContributorRole, Corresponding, ElementsOrder, EmbeddedModel, Figure, Footnote, FootnotesOrder, Journal, Keyword, KeywordGroup, Manuscript, ManuscriptNote, ObjectTypes, ParagraphElement, Project, Section, Supplement, Titles } from '@manuscripts/json-schema';
+import { Affiliation, Attribution, BibliographicDate, BibliographicName, BibliographyElement, BibliographyItem, Color, CommentAnnotation, Contribution, Contributor, ContributorRole, Corresponding, ElementsOrder, EmbeddedModel, Figure, Footnote, FootnotesOrder, InlineMathFragment, Journal, Keyword, KeywordGroup, Manuscript, ManuscriptNote, ObjectTypes, ParagraphElement, Project, Section, Supplement, Titles } from '@manuscripts/json-schema';
 import { FootnotesOrderIndexList } from './footnotes-order';
 import { CommentSelector, ManuscriptModel, ModelAttachment } from './models';
 export type Build<T> = Pick<T, Exclude<keyof T, keyof ManuscriptModel>> & {
@@ -44,6 +44,7 @@ export declare const buildAffiliation: (institution: string, priority?: number)
 export declare const buildSupplementaryMaterial: (title: string, href: string) => Build<Supplement>;
 export declare const buildComment: (target: string, contents?: string, selector?: CommentSelector, contributions?: Contribution[], annotationColor?: string) => Build<CommentAnnotation>;
 export declare const buildNote: (target: string, source: 'EMAIL' | 'EDITOR' | 'DASHBOARD', contents?: string) => Build<ManuscriptNote>;
+export declare const buildInlineMathFragment: (containingObject: string, TeXRepresentation: string) => Build<InlineMathFragment>;
 export declare const buildFootnote: (containingObject: string, contents: string, kind?: 'footnote' | 'endnote') => Build<Footnote>;
 export declare const buildFootnotesOrder: (footnotesList: FootnotesOrderIndexList) => Build<FootnotesOrder>;
 export declare const buildCorresp: (contents: string) => Build<Corresponding>;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.0.1-LEAN-3092",
+  "version": "2.0.2",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,9 +29,11 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "2.2.1-LEAN-3092-v2",
+    "@manuscripts/json-schema": "^2.2.2",
+    "@manuscripts/library": "^1.3.1",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
+    "mathjax-full": "^3.2.2",
     "mime": "^3.0.0",
     "prosemirror-model": "^1.18.3",
     "uuid": "^9.0.0",