Update to encoda 1.0.9 to improve reference data [elifesciences/enhan…

…ced-preprints-issues#626]

integration-tests/api.spec.ts

@@ -11,7 +11,7 @@ describe('api', () => {
           .post('/')
           .send(xml.toString())
           .expect(200)
-          .then((response) => expect(response.headers['content-type']).toBe('application/vnd.elife.encoda.v1.0.8+json; charset=utf-8'));
+          .then((response) => expect(response.headers['content-type']).toBe('application/vnd.elife.encoda.v1.0.9+json; charset=utf-8'));
       });
 
       it.each([
@@ -21,6 +21,7 @@ describe('api', () => {
         '1.0.6',
         '1.0.7',
         '1.0.8',
+        '1.0.9',
       ])('should use the specified version - %s', async (version) => {
         const mimeType = `application/vnd.elife.encoda.v${version}+json`;
         await request(app)
@@ -35,7 +36,7 @@ describe('api', () => {
         'unknown',
         '1.0.4',
         '1.0.5',
-        '1.0.9',
+        '1.0.10',
       ])('should error if you specify wrong version - %s', async (version) => {
         const mimeType = `application/vnd.elife.encoda.v${version}+json`;
         await request(app)

package.json

@@ -29,6 +29,7 @@
     "@stencila/encoda-1-0-6": "npm:@stencila/[email protected]",
     "@stencila/encoda-1-0-7": "npm:@stencila/[email protected]",
     "@stencila/encoda-1-0-8": "npm:@stencila/[email protected]",
+    "@stencila/encoda-1-0-9": "npm:@stencila/[email protected]",
     "body-parser": "^1.20.3",
     "express": "^4.21.1"
   },

src/app.ts

@@ -6,6 +6,7 @@ import { convert as convert_1_0_3 } from '@stencila/encoda-1-0-3';
 import { convert as convert_1_0_6 } from '@stencila/encoda-1-0-6';
 import { convert as convert_1_0_7 } from '@stencila/encoda-1-0-7';
 import { convert as convert_1_0_8 } from '@stencila/encoda-1-0-8';
+import { convert as convert_1_0_9 } from '@stencila/encoda-1-0-9';
 import { mkdtempSync, writeFileSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
 
@@ -38,6 +39,10 @@ app.post('/', async (req, res) => {
     const replacementPath = typeof req.query.replacementPath === 'string' ? req.query.replacementPath : '';
 
     const versionResponders = {
+      'application/vnd.elife.encoda.v1.0.9+json': async () => {
+        res.json(JSON.parse(((await convert_1_0_9(xmlFile, undefined, parameters)) ?? '{}').replaceAll(tempOutput, replacementPath)));
+        rmSync(tempOutput, { recursive: true, force: true });
+      },
       'application/vnd.elife.encoda.v1.0.8+json': async () => {
         res.json(JSON.parse(((await convert_1_0_8(xmlFile, undefined, parameters)) ?? '{}').replaceAll(tempOutput, replacementPath)));
         rmSync(tempOutput, { recursive: true, force: true });

yarn.lock

@@ -2641,6 +2641,77 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@stencila/encoda-1-0-9@npm:@stencila/[email protected]":
+  version: 1.0.9
+  resolution: "@stencila/encoda@npm:1.0.9"
+  dependencies:
+    "@stencila/jesta": ^1.10.5
+    "@stencila/logga": ^4.0.0
+    "@stencila/thema": ^2.24.4
+    appdata-path: ^1.0.0
+    asciimath2tex: "https://github.com/christianp/asciimath2tex/tarball/dedc42ddfdb80678bfb09864cfa76afb0a4b5f44"
+    async-lock: ^1.4.1
+    bin-wrapper: ^4.1.0
+    citation-js: ^0.5.7
+    collapse-whitespace: ^1.1.7
+    content-type: ^1.0.5
+    datapackage: ^1.1.10
+    escape-html: ^1.0.3
+    fastest-levenshtein: ^1.0.16
+    fp-ts: ^2.16.5
+    fs-extra: ^11.2.0
+    get-stdin: ^8.0.0
+    github-slugger: ^1.5.0
+    globby: ^11.1.0
+    hyperscript: ^2.0.2
+    is-docker: ^2.2.1
+    jimp: ^0.22.10
+    js-beautify: ^1.15.1
+    js-yaml: ^4.1.0
+    jsdom: ^22.1.0
+    json5: ^2.2.3
+    jsonld: ^8.3.2
+    mathjax-node: ^2.1.1
+    mdast-util-compact: ^3.0.0
+    mime: ^3.0.0
+    minimist: ^1.2.8
+    papaparse: ^5.4.1
+    parse-author: ^2.0.0
+    parse-full-name: ^1.2.6
+    pdf-lib: ^1.17.1
+    plotly.js-dist: ^1.58.5
+    png-chunk-text: ^1.0.0
+    png-chunks-encode: ^1.0.0
+    png-chunks-extract: ^1.0.0
+    puppeteer: ^11.0.0
+    remark-attr: ^0.11.1
+    remark-frontmatter: ^2.0.0
+    remark-generic-extensions: ^1.4.0
+    remark-math: ^3.0.1
+    remark-parse: ^8.0.3
+    remark-stringify: ^8.1.1
+    remark-sub-super: ^1.0.21
+    sentence-case: ^3.0.4
+    tar: ^6.1.15
+    temp-dir: ^2.0.0
+    tempy: ^1.0.1
+    to-vfile: ^6.1.0
+    trash: ^7.2.0
+    unified: ^9.2.2
+    unist-util-filter: ^2.0.3
+    unist-util-map: ^2.0.1
+    unist-util-select: ^3.0.4
+    vfile: ^4.2.1
+    xlsx: ^0.18.5
+    xml-js: ^1.6.11
+  peerDependencies:
+    "@stencila/schema": 1.9.0
+  bin:
+    encoda: dist/index.js
+  checksum: 08ab1d40e8dae6cadf7e346b477e7894df337eeb6407409703d5fcfb3db76d73331c659f1b0479d80d26722d44b506d9ca12c215659a5cdc69c6730aa29e3449
+  languageName: node
+  linkType: hard
+
 "@stencila/executa@npm:^1.15.7":
   version: 1.15.7
   resolution: "@stencila/executa@npm:1.15.7"
@@ -12321,6 +12392,7 @@ __metadata:
     "@stencila/encoda-1-0-6": "npm:@stencila/[email protected]"
     "@stencila/encoda-1-0-7": "npm:@stencila/[email protected]"
     "@stencila/encoda-1-0-8": "npm:@stencila/[email protected]"
+    "@stencila/encoda-1-0-9": "npm:@stencila/[email protected]"
     "@types/eslint": ^8.44.6
     "@types/express": ^4.17.17
     "@types/jest": ^29.5.6