fix(JATS): Decode <fig> elements as a Table if label starts wit…

…h 'Table'

Closes elifesciences/enhanced-preprints-issues#345

src/codecs/jats/index.ts

@@ -205,7 +205,7 @@ async function encodePrepare(node: stencila.Node): Promise<stencila.Node> {
  * An alternative approach would be to make the functions
  * methods of a class (e.g. the `JatsCodec` class).
  */
-interface DecodeState {
+export interface DecodeState {
   /**
    * The current `<article>` element. Used for
    * getting the target of internal references.
@@ -2257,11 +2257,15 @@ function encodeFigGroup(
 
 /**
  * Decode a JATS `<fig>` element to a Stencila `Figure` node.
+ *
+ * Sometimes the <fig> element is used for tables (where the table is represented
+ * as an image). So, if the <label> starts with 'Table', this function will return
+ * a table with the image(s) in the `content` property.
  */
-function decodeFigure(
+export function decodeFigure(
   elem: xml.Element,
   state: DecodeState
-): [stencila.Figure] {
+): [stencila.Figure | stencila.Table] {
   state = { ...state, ancestorElem: elem }
 
   const id = decodeInternalId(attr(elem, 'id'))
@@ -2296,7 +2300,11 @@ function decodeFigure(
     }
   }
 
-  return [stencila.figure({ id, label, caption, content, licenses })]
+  return [
+    label?.startsWith('Table')
+      ? stencila.table({ id, label, caption, content, licenses, rows: [] })
+      : stencila.figure({ id, label, caption, content, licenses }),
+  ]
 }
 
 /**

src/codecs/jats/jats.test.ts

@@ -1,5 +1,5 @@
 import path from 'path'
-import { decodeAff, JatsCodec } from '.'
+import { decodeAff, decodeFigure, DecodeState, JatsCodec } from '.'
 import { fixture, snapshot } from '../../__tests__/helpers'
 import {
   asciimathFragment,
@@ -97,6 +97,48 @@ test('decode: affiliation retains content not in <institution> or address elemen
   })
 })
 
+test('decode: <fig> element that is actually a table', () => {
+  const fig = xml.load(`
+    <fig id="tbl1" orientation="portrait" position="float">
+      <label>Table 1.</label>
+      <caption><p>Descriptive statistics of the adolescent lifestyle-related variables in all twins and in the subsample of twins with information on biological aging.</p></caption>
+      <graphic xlink:href="22275761v1_tbl1.tif"/>
+      <graphic xlink:href="22275761v1_tbl1a.tif"/>
+    </fig>
+`).elements?.[0]!
+
+  expect(decodeFigure(fig, {} as DecodeState)[0]).toEqual({
+    type: 'Table',
+    id: 'tbl1',
+    label: 'Table 1.',
+    caption: [
+      {
+        type: 'Paragraph',
+        content: [
+          'Descriptive statistics of the adolescent lifestyle-related variables in all twins and in the subsample of twins with information on biological aging.',
+        ],
+      },
+    ],
+    content: [
+      {
+        type: 'ImageObject',
+        contentUrl: '22275761v1_tbl1.tif',
+        meta: {
+          inline: false,
+        },
+      },
+      {
+        type: 'ImageObject',
+        contentUrl: '22275761v1_tbl1a.tif',
+        meta: {
+          inline: false,
+        },
+      },
+    ],
+    rows: [],
+  })
+})
+
 test.each([
   'fig.xml',
   'statement.xml',