Merge pull request #1098 from stencila/comments-in-reference

add decode for reference comments and update snapshots
stencila · Feb 11, 2025 · bb9d3e9 · bb9d3e9
2 parents 8fec866 + 753a047
commit bb9d3e9
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diff --git a/src/codecs/jats/__file_snapshots__/ijm-00202.yaml b/src/codecs/jats/__file_snapshots__/ijm-00202.yaml
@@ -706,6 +706,9 @@ references:
           - Grown
         givenNames:
           - Valodia
+    comments:
+      - type: Comment
+        commentAspect: Chapter 1
     datePublished:
       type: Date
       value: '2010'
@@ -996,6 +999,9 @@ references:
           - Grown
         givenNames:
           - Valodia
+    comments:
+      - type: Comment
+        commentAspect: Chapter 3
     datePublished:
       type: Date
       value: '2010'

diff --git a/src/codecs/jats/__file_snapshots__/plosone-0091296.yaml b/src/codecs/jats/__file_snapshots__/plosone-0091296.yaml
@@ -178,6 +178,9 @@ references:
           - Banks
         givenNames:
           - S
+    comments:
+      - type: Comment
+        commentAspect: doi:10.1371/journal.pbio.1000606
     datePublished:
       type: Date
       value: '2011'

diff --git a/src/codecs/jats/__file_snapshots__/plosone-0178565.yaml b/src/codecs/jats/__file_snapshots__/plosone-0178565.yaml
@@ -257,6 +257,9 @@ references:
           - Steward
         givenNames:
           - GF
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1038/35088063'
     datePublished:
       type: Date
       value: '2001'
@@ -304,6 +307,9 @@ references:
           - Wangikar
         givenNames:
           - PP
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1002/bit.24882'
     datePublished:
       type: Date
       value: '2013'
@@ -563,6 +569,9 @@ references:
           - Atsumi
         givenNames:
           - S
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.3389/fbioe.2013.00007'
     datePublished:
       type: Date
       value: '2013'
@@ -586,6 +595,9 @@ references:
           - Stephanopoulos
         givenNames:
           - G
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1006/mben.1998.0101'
     datePublished:
       type: Date
       value: '1999'
@@ -638,6 +650,9 @@ references:
           - Baba
         givenNames:
           - T
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1128/JB.00740-06'
     datePublished:
       type: Date
       value: '2006'
@@ -806,6 +821,9 @@ references:
           - Veronneau
         givenNames:
           - S
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1038/nature00935'
     datePublished:
       type: Date
       value: '2002'
@@ -838,6 +856,9 @@ references:
           - Arndt
         givenNames:
           - GM
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1111/j.1440-1711.2005.01332.x'
     datePublished:
       type: Date
       value: '2005'
@@ -932,6 +953,9 @@ references:
           - Oltvai
         givenNames:
           - ZN
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1038/35075138'
     datePublished:
       type: Date
       value: '2001'
@@ -974,6 +998,9 @@ references:
           - Bond
         givenNames:
           - AT
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1093/bioinformatics/bth234'
     datePublished:
       type: Date
       value: '2004'
@@ -1118,6 +1145,9 @@ references:
           - Wangikar
         givenNames:
           - PP
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1007/s11120-013-9911-5'
     datePublished:
       type: Date
       value: '2013'
@@ -1167,6 +1197,9 @@ references:
           - Blankenship
         givenNames:
           - RE
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1126/science.1075558'
     datePublished:
       type: Date
       value: '2002'
@@ -1301,6 +1334,9 @@ references:
           - Li
         givenNames:
           - W
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1093/bioinformatics/bts565'
     datePublished:
       type: Date
       value: '2012'
@@ -1343,6 +1379,9 @@ references:
           - Wangikar
         givenNames:
           - PP
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1007/s10482-012-9813-0'
     datePublished:
       type: Date
       value: '2013'
@@ -1390,6 +1429,9 @@ references:
           - Begley
         givenNames:
           - TP
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1074/jbc.C100033200'
     datePublished:
       type: Date
       value: '2001'
@@ -1445,6 +1487,9 @@ references:
           - Ladner
         givenNames:
           - JE
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1021/bi049059z'
     datePublished:
       type: Date
       value: '2004'
@@ -1499,6 +1544,9 @@ references:
           - Bayer
         givenNames:
           - P
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1073/pnas.0407371101'
     datePublished:
       type: Date
       value: '2004'
@@ -1535,6 +1583,9 @@ references:
           - Golden
         givenNames:
           - SS
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1128/MMBR.00036-15'
     datePublished:
       type: Date
       value: '2015'
@@ -1587,6 +1638,9 @@ references:
           - Chetty
         givenNames:
           - M
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.3389/fmicb.2013.00374'
     datePublished:
       type: Date
       value: '2013'
@@ -1637,6 +1691,9 @@ references:
           - Moreno
         givenNames:
           - PA
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1023/A:1023990402346'
     datePublished:
       type: Date
       value: '2003'
@@ -1680,6 +1737,9 @@ references:
           - Meurer
         givenNames:
           - J
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1021/bi0348260'
     datePublished:
       type: Date
       value: '2004'
@@ -2053,6 +2113,9 @@ references:
           - Gatti
         givenNames:
           - DL
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1093/emboj/19.17.4838'
     datePublished:
       type: Date
       value: '2000'
@@ -2171,6 +2234,9 @@ references:
           - Bolt
         givenNames:
           - EL
+    comments:
+      - type: Comment
+        commentAspect: 'doi: 10.1042/BJ20110901'
     datePublished:
       type: Date
       value: '2011'

diff --git a/src/codecs/jats/index.ts b/src/codecs/jats/index.ts
@@ -1499,6 +1499,16 @@ export function decodeReference(
     metaEntries.label = label
   }
 
+  const comment = textOrUndefined(child(elem, 'comment'))
+  const comments: stencila.CreativeWork['comments'] = comment
+    ? [
+        {
+          type: 'Comment',
+          commentAspect: comment,
+        },
+      ]
+    : []
+
   return stencila.article({
     id,
     authors,
@@ -1510,6 +1520,7 @@ export function decodeReference(
     publisher,
     identifiers,
     url,
+    ...(comments.length ? { comments } : {}),
     meta: {
       ...(metaEntries ? { ...metaEntries } : {}),
       ...(publicationType

diff --git a/src/codecs/jats/jats.test.ts b/src/codecs/jats/jats.test.ts
@@ -287,6 +287,21 @@ test('decode: reference issue number parsed as a string', () => {
   expect((result.isPartOf as PublicationIssue)?.issueNumber).toEqual('The Issue')
 })
 
+test('decode: reference comment is parsed out', () => {
+  const reference = `
+    <mixed-citation publication-type="journal">
+      <string-name><surname>Calabrese</surname> <given-names>C</given-names></string-name>, <string-name><surname>Panuzzo</surname> <given-names>C</given-names></string-name> <etal>et al</etal> (<year>n.d.</year>)<comment>This is a comment</comment><article-title>Deferasirox-Dependent Iron Chelation Enhances Mitochondrial Dysfunction and Restores p53 Signaling by Stabilization of p53 Family Members in Leukemic Cells</article-title>. <source>International journal of molecular sciences</source>
+    </mixed-citation>
+  `
+  const citation = xml.load(reference).elements?.[0]!
+
+  const result = decodeReference(citation, null, undefined)
+  expect(result?.comments).toEqual([{
+    type: 'Comment',
+    commentAspect: 'This is a comment',
+  }]);
+})
+
 test('decode: <table-wrap> element that has more than one <graphic>', () => {
   const fig = xml.load(`
   <table-wrap id="tblS1" orientation="portrait" position="float">