@manuscripts/transform 2.0.1-LEAN-3034 → 2.0.1-LEAN-3083-2

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

@@ -18,9 +18,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.JATSExporter = exports.buildCitations = exports.createCounter = void 0;
+exports.JATSExporter = exports.createCounter = void 0;
 const json_schema_1 = require("@manuscripts/json-schema");
-const library_1 = require("@manuscripts/library");
 const debug_1 = __importDefault(require("debug"));
 const prosemirror_model_1 = require("prosemirror-model");
 const w3c_xmlserializer_1 = __importDefault(require("w3c-xmlserializer"));
@@ -116,23 +115,12 @@ const chooseRefType = (objectType) => {
     }
 };
 const sortContributors = (a, b) => Number(a.priority) - Number(b.priority);
-const buildCitations = (citations) => citations.map((citation) => ({
-    citationID: citation.attrs.id,
-    citationItems: citation.attrs.rids.map((rid) => ({
-        id: rid,
-    })),
-    properties: {
-        noteIndex: 0,
-    },
-}));
-exports.buildCitations = buildCitations;
 class JATSExporter {
     constructor() {
-        this.serializeToJATS = async (fragment, modelMap, manuscriptID, options) => {
-            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, csl, } = options;
+        this.serializeToJATS = async (fragment, modelMap, manuscriptID, options = {}) => {
+            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, } = options;
             this.modelMap = modelMap;
             this.models = Array.from(this.modelMap.values());
-            this.generateCitationTexts(fragment, csl);
             this.createSerializer();
             const versionIds = (0, jats_versions_1.selectVersionIds)(version);
             this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIds.publicId, versionIds.systemId));
@@ -474,11 +462,10 @@ class JATSExporter {
                 refList = this.document.createElement('ref-list');
             }
             back.appendChild(refList);
-            const [meta] = this.citationProvider.makeBibliography();
-            for (const id of meta.entry_ids) {
-                const bibliographyItem = this.modelMap.get(id[0]);
+            const bibliographyItems = this.models.filter((0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.BibliographyItem));
+            for (const bibliographyItem of bibliographyItems) {
                 const ref = this.document.createElement('ref');
-                ref.setAttribute('id', normalizeID(id[0]));
+                ref.setAttribute('id', normalizeID(bibliographyItem._id));
                 const updateCitationPubType = (citationEl, pubType) => {
                     if (pubType) {
                         switch (pubType) {
@@ -651,11 +638,12 @@ class JATSExporter {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'bibr');
                     xref.setAttribute('rid', normalizeID(rids.join(' ')));
-                    const citationTextContent = this.citationTexts.get(node.attrs.id);
-                    if (!citationTextContent) {
-                        throw new Error(`No citation text found for ${node.attrs.id}`);
+                    if (citation.attrs.contents) {
+                        const text = (0, html_1.textFromHTML)(node.attrs.contents);
+                        if (text !== null && text.length) {
+                            xref.textContent = text;
+                        }
                     }
-                    xref.textContent = (0, html_1.textFromHTML)(citationTextContent);
                     return xref;
                 },
                 cross_reference: (node) => {
@@ -1566,27 +1554,6 @@ class JATSExporter {
             return name;
         };
     }
-    generateCitations(fragment) {
-        const nodes = [];
-        fragment.descendants((node) => {
-            if ((0, schema_1.isCitationNode)(node)) {
-                nodes.push(node);
-            }
-        });
-        return (0, exports.buildCitations)(nodes);
-    }
-    generateCitationTexts(fragment, csl) {
-        this.citationTexts = new Map();
-        this.citationProvider = new library_1.CitationProvider({
-            getLibraryItem: (id) => this.modelMap.get(id),
-            locale: csl.locale,
-            citationStyle: csl.style,
-        });
-        const citations = this.generateCitations(fragment);
-        this.citationProvider.rebuildState(citations).forEach(([id, , output]) => {
-            this.citationTexts.set(id, output);
-        });
-    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === json_schema_1.ObjectTypes.Keyword);
         const keywordGroups = new Map();

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

@@ -6,6 +6,7 @@ exports.contributor = {
     attrs: {
         id: { default: '' },
         role: { default: '' },
+        email: { default: '' },
         affiliations: { default: [] },
         footnote: { default: undefined },
         corresp: { default: undefined },
@@ -13,6 +14,7 @@ exports.contributor = {
         userID: { default: undefined },
         invitationID: { default: undefined },
         isCorresponding: { default: undefined },
+        isJointContributor: { default: undefined },
         ORCIDIdentifier: { default: undefined },
         priority: { default: undefined },
         dataTracked: { default: null },

package/dist/cjs/transformer/decode.js

@@ -91,7 +91,7 @@ class Decoder {
         const contributors = getContributors(this.modelMap)
             .map((c) => this.decode(c))
             .filter(Boolean);
-        return schema_1.schema.nodes.contributors.createAndFill({}, contributors);
+        return schema_1.schema.nodes.contributors.createAndFill({}, contributors.sort((a, b) => Number(a.attrs.priority) - Number(b.attrs.priority)));
     }
     createKeywordsNode() {
         const elements = getKeywordElements(this.modelMap)
@@ -629,6 +629,7 @@ class Decoder {
                     id: model._id,
                     role: model.role,
                     affiliations: model.affiliations,
+                    email: model.email,
                     bibliographicName: model.bibliographicName,
                     userID: model.userID,
                     invitationID: model.invitationID,

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

@@ -14,14 +14,13 @@
  * limitations under the License.
  */
 import { ObjectTypes, } from '@manuscripts/json-schema';
-import { CitationProvider } from '@manuscripts/library';
 import debug from 'debug';
 import { DOMParser, DOMSerializer } from 'prosemirror-model';
 import serializeToXML from 'w3c-xmlserializer';
 import { nodeFromHTML, textFromHTML } from '../lib/html';
 import { normalizeStyleName } from '../lib/styled-content';
 import { iterateChildren } from '../lib/utils';
-import { isCitationNode, schema, } from '../schema';
+import { schema, } from '../schema';
 import { generateAttachmentFilename } from '../transformer/filename';
 import { buildTargets } from '../transformer/labels';
 import { isExecutableNodeType, isNodeType } from '../transformer/node-types';
@@ -109,22 +108,12 @@ const chooseRefType = (objectType) => {
     }
 };
 const sortContributors = (a, b) => Number(a.priority) - Number(b.priority);
-export const buildCitations = (citations) => citations.map((citation) => ({
-    citationID: citation.attrs.id,
-    citationItems: citation.attrs.rids.map((rid) => ({
-        id: rid,
-    })),
-    properties: {
-        noteIndex: 0,
-    },
-}));
 export class JATSExporter {
     constructor() {
-        this.serializeToJATS = async (fragment, modelMap, manuscriptID, options) => {
-            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, csl, } = options;
+        this.serializeToJATS = async (fragment, modelMap, manuscriptID, options = {}) => {
+            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, } = options;
             this.modelMap = modelMap;
             this.models = Array.from(this.modelMap.values());
-            this.generateCitationTexts(fragment, csl);
             this.createSerializer();
             const versionIds = selectVersionIds(version);
             this.document = document.implementation.createDocument(null, 'article', document.implementation.createDocumentType('article', versionIds.publicId, versionIds.systemId));
@@ -466,11 +455,10 @@ export class JATSExporter {
                 refList = this.document.createElement('ref-list');
             }
             back.appendChild(refList);
-            const [meta] = this.citationProvider.makeBibliography();
-            for (const id of meta.entry_ids) {
-                const bibliographyItem = this.modelMap.get(id[0]);
+            const bibliographyItems = this.models.filter(hasObjectType(ObjectTypes.BibliographyItem));
+            for (const bibliographyItem of bibliographyItems) {
                 const ref = this.document.createElement('ref');
-                ref.setAttribute('id', normalizeID(id[0]));
+                ref.setAttribute('id', normalizeID(bibliographyItem._id));
                 const updateCitationPubType = (citationEl, pubType) => {
                     if (pubType) {
                         switch (pubType) {
@@ -643,11 +631,12 @@ export class JATSExporter {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'bibr');
                     xref.setAttribute('rid', normalizeID(rids.join(' ')));
-                    const citationTextContent = this.citationTexts.get(node.attrs.id);
-                    if (!citationTextContent) {
-                        throw new Error(`No citation text found for ${node.attrs.id}`);
+                    if (citation.attrs.contents) {
+                        const text = textFromHTML(node.attrs.contents);
+                        if (text !== null && text.length) {
+                            xref.textContent = text;
+                        }
                     }
-                    xref.textContent = textFromHTML(citationTextContent);
                     return xref;
                 },
                 cross_reference: (node) => {
@@ -1558,27 +1547,6 @@ export class JATSExporter {
             return name;
         };
     }
-    generateCitations(fragment) {
-        const nodes = [];
-        fragment.descendants((node) => {
-            if (isCitationNode(node)) {
-                nodes.push(node);
-            }
-        });
-        return buildCitations(nodes);
-    }
-    generateCitationTexts(fragment, csl) {
-        this.citationTexts = new Map();
-        this.citationProvider = new CitationProvider({
-            getLibraryItem: (id) => this.modelMap.get(id),
-            locale: csl.locale,
-            citationStyle: csl.style,
-        });
-        const citations = this.generateCitations(fragment);
-        this.citationProvider.rebuildState(citations).forEach(([id, , output]) => {
-            this.citationTexts.set(id, output);
-        });
-    }
     buildKeywords(articleMeta) {
         const keywords = [...this.modelMap.values()].filter((model) => model.objectType === ObjectTypes.Keyword);
         const keywordGroups = new Map();

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

@@ -3,6 +3,7 @@ export const contributor = {
     attrs: {
         id: { default: '' },
         role: { default: '' },
+        email: { default: '' },
         affiliations: { default: [] },
         footnote: { default: undefined },
         corresp: { default: undefined },
@@ -10,6 +11,7 @@ export const contributor = {
         userID: { default: undefined },
         invitationID: { default: undefined },
         isCorresponding: { default: undefined },
+        isJointContributor: { default: undefined },
         ORCIDIdentifier: { default: undefined },
         priority: { default: undefined },
         dataTracked: { default: null },

package/dist/es/transformer/decode.js

@@ -82,7 +82,7 @@ export class Decoder {
         const contributors = getContributors(this.modelMap)
             .map((c) => this.decode(c))
             .filter(Boolean);
-        return schema.nodes.contributors.createAndFill({}, contributors);
+        return schema.nodes.contributors.createAndFill({}, contributors.sort((a, b) => Number(a.attrs.priority) - Number(b.attrs.priority)));
     }
     createKeywordsNode() {
         const elements = getKeywordElements(this.modelMap)
@@ -620,6 +620,7 @@ export class Decoder {
                     id: model._id,
                     role: model.role,
                     affiliations: model.affiliations,
+                    email: model.email,
                     bibliographicName: model.bibliographicName,
                     userID: model.userID,
                     invitationID: model.invitationID,

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

@@ -14,9 +14,8 @@
  * limitations under the License.
  */
 import { Model } from '@manuscripts/json-schema';
-import { CitationProvider } from '@manuscripts/library';
 import { DOMSerializer } from 'prosemirror-model';
-import { CitationNode, ManuscriptFragment, ManuscriptNode } from '../schema';
+import { ManuscriptFragment, ManuscriptNode } from '../schema';
 import { Target } from '../transformer/labels';
 import { IDGenerator, MediaPathGenerator } from '../types';
 import { Version } from './jats-versions';
@@ -28,12 +27,7 @@ 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;
@@ -43,34 +37,13 @@ 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>;
-    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>;
+    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/schema/nodes/contributor.d.ts

@@ -1,12 +1,13 @@
-import { Affiliation, BibliographicName } from '@manuscripts/json-schema';
+import { BibliographicName } from '@manuscripts/json-schema';
 import { NodeSpec } from 'prosemirror-model';
 import { ManuscriptNode } from '../types';
 interface Attrs {
     id: string;
     role: string;
-    affiliations: Affiliation[];
+    affiliations: string[];
     bibliographicName: BibliographicName;
     userID: string;
+    email: string;
     invitationID: string;
     isCorresponding: boolean;
     ORCIDIdentifier: string;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.0.1-LEAN-3034",
+  "version": "2.0.1-LEAN-3083-2",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,8 +29,7 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "2.2.1-LEAN-3034",
-    "@manuscripts/library": "1.3.0-LEAN-3034",
+    "@manuscripts/json-schema": "2.2.1",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
     "mathjax-full": "^3.2.2",