@manuscripts/transform 2.0.1 → 2.0.3-LEAN-3074-0

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

@@ -265,14 +265,6 @@ exports.jatsBodyTransformations = {
             }
         });
     },
-    moveTableFooterToEnd(body) {
-        const footers = body.querySelectorAll('table-wrap-foot');
-        for (const footer of footers) {
-            if (footer.parentNode) {
-                footer.parentNode.appendChild(footer);
-            }
-        }
-    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

@@ -66,7 +66,6 @@ const parseJATSBody = (doc, body, references) => {
     jats_body_transformations_1.jatsBodyTransformations.ensureSection(body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.moveCaptionsToEnd(body);
     jats_body_transformations_1.jatsBodyTransformations.fixTables(body, createElement);
-    jats_body_transformations_1.jatsBodyTransformations.moveTableFooterToEnd(body);
     jats_body_transformations_1.jatsBodyTransformations.createBody(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createAbstracts(doc, body, createElement);
     jats_body_transformations_1.jatsBodyTransformations.createBackmatter(doc, body, createElement);
@@ -122,7 +121,7 @@ const parseJATSArticle = (doc) => {
         const type = article.getAttribute('article-type');
         manuscript.articleType = type || 'other';
     }
-    if (references) {
+    if (references && references.items.size) {
         models.push(...createBibliographyModels(references));
     }
     if (marks.length) {

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

@@ -18,8 +18,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.JATSExporter = exports.createCounter = void 0;
+exports.JATSExporter = exports.buildCitations = 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"));
@@ -115,12 +116,23 @@ 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, } = options;
+        this.serializeToJATS = async (fragment, modelMap, manuscriptID, options) => {
+            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, csl, } = 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));
@@ -462,10 +474,11 @@ class JATSExporter {
                 refList = this.document.createElement('ref-list');
             }
             back.appendChild(refList);
-            const bibliographyItems = this.models.filter((0, object_types_1.hasObjectType)(json_schema_1.ObjectTypes.BibliographyItem));
-            for (const bibliographyItem of bibliographyItems) {
+            const [meta] = this.citationProvider.makeBibliography();
+            for (const id of meta.entry_ids) {
+                const bibliographyItem = this.modelMap.get(id[0]);
                 const ref = this.document.createElement('ref');
-                ref.setAttribute('id', normalizeID(bibliographyItem._id));
+                ref.setAttribute('id', normalizeID(id[0]));
                 const updateCitationPubType = (citationEl, pubType) => {
                     if (pubType) {
                         switch (pubType) {
@@ -638,12 +651,11 @@ class JATSExporter {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'bibr');
                     xref.setAttribute('rid', normalizeID(rids.join(' ')));
-                    if (citation.attrs.contents) {
-                        const text = (0, html_1.textFromHTML)(node.attrs.contents);
-                        if (text !== null && text.length) {
-                            xref.textContent = text;
-                        }
+                    const citationTextContent = this.citationTexts.get(node.attrs.id);
+                    if (!citationTextContent) {
+                        throw new Error(`No citation text found for ${node.attrs.id}`);
                     }
+                    xref.textContent = (0, html_1.textFromHTML)(citationTextContent);
                     return xref;
                 },
                 cross_reference: (node) => {
@@ -1554,6 +1566,27 @@ 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/table_element.js

@@ -17,7 +17,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.tableElement = void 0;
 exports.tableElement = {
-    content: '(table | placeholder) figcaption? table_element_footer? (listing | placeholder)',
+    content: '(table | placeholder) table_element_footer? figcaption? (listing | placeholder)',
     attrs: {
         id: { default: '' },
         paragraphStyle: { default: '' },

package/dist/cjs/transformer/decode.js

@@ -564,7 +564,7 @@ class Decoder {
                 const comments = this.createCommentNodes(model);
                 comments.forEach((c) => this.comments.set(c.attrs.id, c));
                 const content = tableElementFooter
-                    ? [table, figcaption, tableElementFooter]
+                    ? [table, tableElementFooter, figcaption]
                     : [table, figcaption];
                 if (model.listingID) {
                     const listing = this.createListing(model.listingID);

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

@@ -262,14 +262,6 @@ export const jatsBodyTransformations = {
             }
         });
     },
-    moveTableFooterToEnd(body) {
-        const footers = body.querySelectorAll('table-wrap-foot');
-        for (const footer of footers) {
-            if (footer.parentNode) {
-                footer.parentNode.appendChild(footer);
-            }
-        }
-    },
     moveFloatsGroupToBody(doc, body, createElement) {
         const group = doc.querySelector('floats-group');
         if (group) {

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

@@ -62,7 +62,6 @@ export const parseJATSBody = (doc, body, references) => {
     jatsBodyTransformations.ensureSection(body, createElement);
     jatsBodyTransformations.moveCaptionsToEnd(body);
     jatsBodyTransformations.fixTables(body, createElement);
-    jatsBodyTransformations.moveTableFooterToEnd(body);
     jatsBodyTransformations.createBody(doc, body, createElement);
     jatsBodyTransformations.createAbstracts(doc, body, createElement);
     jatsBodyTransformations.createBackmatter(doc, body, createElement);
@@ -117,7 +116,7 @@ export const parseJATSArticle = (doc) => {
         const type = article.getAttribute('article-type');
         manuscript.articleType = type || 'other';
     }
-    if (references) {
+    if (references && references.items.size) {
         models.push(...createBibliographyModels(references));
     }
     if (marks.length) {

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

@@ -14,13 +14,14 @@
  * 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 { schema, } from '../schema';
+import { isCitationNode, schema, } from '../schema';
 import { generateAttachmentFilename } from '../transformer/filename';
 import { buildTargets } from '../transformer/labels';
 import { isExecutableNodeType, isNodeType } from '../transformer/node-types';
@@ -108,12 +109,22 @@ 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, } = options;
+        this.serializeToJATS = async (fragment, modelMap, manuscriptID, options) => {
+            const { version = '1.2', doi, id, frontMatterOnly = false, links, idGenerator, mediaPathGenerator, csl, } = 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));
@@ -455,10 +466,11 @@ export class JATSExporter {
                 refList = this.document.createElement('ref-list');
             }
             back.appendChild(refList);
-            const bibliographyItems = this.models.filter(hasObjectType(ObjectTypes.BibliographyItem));
-            for (const bibliographyItem of bibliographyItems) {
+            const [meta] = this.citationProvider.makeBibliography();
+            for (const id of meta.entry_ids) {
+                const bibliographyItem = this.modelMap.get(id[0]);
                 const ref = this.document.createElement('ref');
-                ref.setAttribute('id', normalizeID(bibliographyItem._id));
+                ref.setAttribute('id', normalizeID(id[0]));
                 const updateCitationPubType = (citationEl, pubType) => {
                     if (pubType) {
                         switch (pubType) {
@@ -631,12 +643,11 @@ export class JATSExporter {
                     const xref = this.document.createElement('xref');
                     xref.setAttribute('ref-type', 'bibr');
                     xref.setAttribute('rid', normalizeID(rids.join(' ')));
-                    if (citation.attrs.contents) {
-                        const text = textFromHTML(node.attrs.contents);
-                        if (text !== null && text.length) {
-                            xref.textContent = text;
-                        }
+                    const citationTextContent = this.citationTexts.get(node.attrs.id);
+                    if (!citationTextContent) {
+                        throw new Error(`No citation text found for ${node.attrs.id}`);
                     }
+                    xref.textContent = textFromHTML(citationTextContent);
                     return xref;
                 },
                 cross_reference: (node) => {
@@ -1547,6 +1558,27 @@ 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/table_element.js

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 export const tableElement = {
-    content: '(table | placeholder) figcaption? table_element_footer? (listing | placeholder)',
+    content: '(table | placeholder) table_element_footer? figcaption? (listing | placeholder)',
     attrs: {
         id: { default: '' },
         paragraphStyle: { default: '' },

package/dist/es/transformer/decode.js

@@ -555,7 +555,7 @@ export class Decoder {
                 const comments = this.createCommentNodes(model);
                 comments.forEach((c) => this.comments.set(c.attrs.id, c));
                 const content = tableElementFooter
-                    ? [table, figcaption, tableElementFooter]
+                    ? [table, tableElementFooter, figcaption]
                     : [table, figcaption];
                 if (model.listingID) {
                     const listing = this.createListing(model.listingID);

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

@@ -32,7 +32,6 @@ 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;
-    moveTableFooterToEnd(body: Element): void;
     moveFloatsGroupToBody(doc: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
     createKeywords(document: Document, body: Element, createElement: (tagName: string) => HTMLElement): void;
 };

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/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@manuscripts/transform",
   "description": "ProseMirror transformer for Manuscripts applications",
-  "version": "2.0.1",
+  "version": "2.0.3-LEAN-3074-0",
   "repository": "github:Atypon-OpenSource/manuscripts-transform",
   "license": "Apache-2.0",
   "main": "dist/cjs",
@@ -29,7 +29,8 @@
     "version": "yarn build"
   },
   "dependencies": {
-    "@manuscripts/json-schema": "2.2.1",
+    "@manuscripts/json-schema": "^2.2.2",
+    "@manuscripts/library": "1.3.1-LEAN-3074-0",
     "debug": "^4.3.4",
     "jszip": "^3.10.1",
     "mathjax-full": "^3.2.2",
@@ -77,4 +78,4 @@
     "rimraf": "^3.0.2",
     "typescript": "^4.0.5"
   }
-}
+}