Add support for id in decodeMath for graphic or inline-graphic (#1083)

Co-authored-by: Will Byrne <will.alex.byrne@gmail.com> Co-authored-by: A. K <74007089+soggy-mushroom@users.noreply.github.com>
stencila · Oct 14, 2024 · ad06ba0 · ad06ba0
1 parent 3d3976b
commit ad06ba0
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Showing 4 changed files with 54 additions and 3 deletions.
diff --git a/src/codecs/jats/__file_snapshots__/06908fc3-73df-1014-bb56-a21daa237ef0.json b/src/codecs/jats/__file_snapshots__/06908fc3-73df-1014-bb56-a21daa237ef0.json
@@ -6141,6 +6141,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn1",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -6282,6 +6283,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn2",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -6369,6 +6371,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn3",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -6481,6 +6484,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn4",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -6493,6 +6497,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn5",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -6635,6 +6640,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn6",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -7019,6 +7025,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn7",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -7063,6 +7070,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn8",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -7166,6 +7174,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn9",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -7286,6 +7295,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn10",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -7319,6 +7329,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn11",
           "contentUrl": "",
           "meta": {
             "inline": false
@@ -7337,6 +7348,7 @@
       "content": [
         {
           "type": "ImageObject",
+          "id": "eqn12",
           "contentUrl": "",
           "meta": {
             "inline": false

diff --git a/src/codecs/jats/__file_snapshots__/plosone-0093988.yaml b/src/codecs/jats/__file_snapshots__/plosone-0093988.yaml
@@ -1813,6 +1813,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e010
         contentUrl: ''
         meta:
           inline: false
@@ -2036,6 +2037,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e032
         contentUrl: ''
         meta:
           inline: false
@@ -2292,6 +2294,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e038
         contentUrl: ''
         meta:
           inline: false
@@ -2336,6 +2339,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e044
         contentUrl: ''
         meta:
           inline: false
@@ -2626,6 +2630,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e062
         contentUrl: ''
         meta:
           inline: false
@@ -2665,6 +2670,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e068
         contentUrl: ''
         meta:
           inline: false
@@ -2675,6 +2681,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e069
         contentUrl: ''
         meta:
           inline: false
@@ -2770,6 +2777,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e082
         contentUrl: ''
         meta:
           inline: false
@@ -2795,6 +2803,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e085
         contentUrl: ''
         meta:
           inline: false
@@ -2847,6 +2856,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e091
         contentUrl: ''
         meta:
           inline: false
@@ -2875,6 +2885,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e094
         contentUrl: ''
         meta:
           inline: false
@@ -2948,6 +2959,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e103
         contentUrl: ''
         meta:
           inline: false
@@ -2958,6 +2970,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e104
         contentUrl: ''
         meta:
           inline: false
@@ -3009,6 +3022,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e111
         contentUrl: ''
         meta:
           inline: false
@@ -3236,6 +3250,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e140
         contentUrl: ''
         meta:
           inline: false
@@ -3252,6 +3267,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e142
         contentUrl: ''
         meta:
           inline: false
@@ -3264,6 +3280,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e143
         contentUrl: ''
         meta:
           inline: false
@@ -3350,6 +3367,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e155
         contentUrl: ''
         meta:
           inline: false
@@ -3366,6 +3384,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e157
         contentUrl: ''
         meta:
           inline: false
@@ -3525,6 +3544,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e180
         contentUrl: ''
         meta:
           inline: false
@@ -3541,6 +3561,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e182
         contentUrl: ''
         meta:
           inline: false
@@ -3921,6 +3942,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e232
         contentUrl: ''
         meta:
           inline: false
@@ -4047,6 +4069,7 @@ content:
   - type: Paragraph
     content:
       - type: ImageObject
+        id: pone.0093988.e249
         contentUrl: ''
         meta:
           inline: false

diff --git a/src/codecs/jats/index.ts b/src/codecs/jats/index.ts
@@ -2518,20 +2518,20 @@ function decodeSupplementaryMaterial(
  * that is not available, uses an image as an alternative (which is wrapped
  * in a paragraph for display formulas).
  */
-function decodeMath(
+export function decodeMath(
   formula: xml.Element,
 ): (stencila.Math | stencila.ImageObject | stencila.Paragraph)[] {
   const inline = formula.name === 'inline-formula'
   const mathml = first(formula, 'mml:math') ?? first(formula, 'm:math')
+  const id = attrOrUndefined(formula, 'id')
 
   if (mathml === null) {
     const graphic = first(formula, ['graphic', 'inline-graphic'])
     if (graphic === null) return []
-    const image = decodeGraphic(graphic, inline)
+    const image = [{ id, ...decodeGraphic(graphic, inline)[0] }]
     return inline ? image : [stencila.paragraph({ content: image })]
   }
 
-  const id = attrOrUndefined(formula, 'id')
   const label = textOrUndefined(child(formula, 'label'))
   const altText = attrOrUndefined(mathml, 'alttext')
   const meta = altText !== undefined ? { altText } : undefined

diff --git a/src/codecs/jats/jats.test.ts b/src/codecs/jats/jats.test.ts
@@ -4,6 +4,7 @@ import {
   decodeAff,
   decodeAuthors,
   decodeFigure,
+  decodeMath,
   decodeMetaFront,
   decodeReference,
   DecodeState,
@@ -527,3 +528,18 @@ describe('authors', () => {
     )
   })
 })
+
+describe('decode: MathML', () => {
+  test('adds the id to the alternative graphic', () => {
+    const formula = xml.load(`
+     <disp-formula id="eqn6">
+      <alternatives>
+        <graphic xlink:href="528254v1_eqn6.gif"/>
+      </alternatives>
+    </disp-formula>
+    `).elements?.[0]!
+
+    expect(decodeMath(formula)).toEqual([{"content": [{"contentUrl": "528254v1_eqn6.gif", "meta": {"inline": false}, "type": "ImageObject", "id": "eqn6"}], "type": "Paragraph"}]);
+  });
+});
+