Add the reference published year as a string to meta to preserve any suffixes

src/codecs/jats/__file_snapshots__/c2c3813f-6c98-1014-8ba7-9ee2cd5f4386.json

@@ -5877,6 +5877,7 @@
       "pageStart": 1303,
       "title": "Structures of human Nav1.7 channel in complex with auxiliary subunits and animal toxins",
       "meta": {
+        "yearPublished": "2019a",
         "publicationType": "journal"
       }
     },
@@ -5948,6 +5949,7 @@
       },
       "title": "Structures of human Nav1.7 channel in complex with auxiliary subunits and animal toxins",
       "meta": {
+        "yearPublished": "2019b",
         "publicationType": "journal"
       }
     },

src/codecs/jats/__file_snapshots__/ca7917ff-6cb0-1014-9b19-d05ef1e56b05.json

@@ -2179,6 +2179,7 @@
       "pageStart": 5950,
       "title": "Gustatory Learning and Processing in the Drosophila Mushroom Bodies",
       "meta": {
+        "yearPublished": "2015a",
         "publicationType": "journal"
       }
     },
@@ -2229,6 +2230,7 @@
       "pageStart": 5950,
       "title": "Gustatory Learning and Processing in the Drosophila Mushroom Bodies",
       "meta": {
+        "yearPublished": "2015b",
         "publicationType": "journal"
       }
     },

src/codecs/jats/__file_snapshots__/d6f14042-6db3-1014-b228-f9da7cb8e4cc.json

@@ -3454,6 +3454,7 @@
       "title": "Mplus User’s Guide. Eight Edition",
       "url": "https://www.statmodel.com",
       "meta": {
+        "yearPublished": "1998-2018",
         "publicationType": "book"
       }
     },

src/codecs/jats/__file_snapshots__/elife-46472-v3.yaml

@@ -1592,6 +1592,7 @@ references:
       Morphine intake and the effects of naltrexone and buprenorphine on the
       acquisition of methamphetamine intake
     meta:
+      yearPublished: 2014a
       publicationType: journal
   - type: Article
     id: bib20
@@ -1630,6 +1631,7 @@ references:
       Opioid sensitivity in mice selectively bred to consume or not consume
       methamphetamine
     meta:
+      yearPublished: 2014b
       publicationType: journal
   - type: Article
     id: bib21
@@ -1698,6 +1700,7 @@ references:
       Postsynaptic D2 dopamine receptor supersensitivity in the striatum of mice
       lacking TAAR1
     meta:
+      yearPublished: 2015a
       publicationType: journal
   - type: Article
     id: bib22
@@ -1814,6 +1817,7 @@ references:
     pageStart: 2217
     title: TAAR1 modulates cortical glutamate NMDA receptor function
     meta:
+      yearPublished: 2015b
       publicationType: journal
   - type: Article
     id: bib23
@@ -3936,6 +3940,7 @@ references:
       A genetic animal model of differential sensitivity to methamphetamine
       reinforcement
     meta:
+      yearPublished: 2012a
       publicationType: journal
   - type: Article
     id: bib59
@@ -3984,6 +3989,7 @@ references:
       Profound reduction in sensitivity to the aversive effects of
       methamphetamine in mice bred for high methamphetamine intake
     meta:
+      yearPublished: 2012b
       publicationType: journal
   - type: Article
     id: bib60

src/codecs/jats/__file_snapshots__/elife-46793-v1.yaml

@@ -1848,6 +1848,7 @@ references:
       Bortezomib as the first proteasome inhibitor anticancer drug: current
       status and future perspectives
     meta:
+      yearPublished: 2011a
       publicationType: journal
   - type: Article
     id: bib26
@@ -1926,6 +1927,7 @@ references:
       Selective and cell-active inhibitors of the USP1/ UAF1 deubiquitinase
       complex reverse cisplatin resistance in non-small cell lung cancer cells
     meta:
+      yearPublished: 2011b
       publicationType: journal
   - type: Article
     id: bib27
@@ -2451,6 +2453,7 @@ references:
       Reevaluation of telomerase inhibition by quadruplex ligands and their
       mechanisms of action
     meta:
+      yearPublished: 2007a
       publicationType: journal
   - type: Article
     id: bib35
@@ -2503,6 +2506,7 @@ references:
     pageStart: 1856
     title: Highly efficient G-quadruplex recognition by bisquinolinium compounds
     meta:
+      yearPublished: 2007b
       publicationType: journal
   - type: Article
     id: bib36
@@ -4058,6 +4062,7 @@ references:
       Systematic and integrative analysis of large gene lists using DAVID
       bioinformatics resources
     meta:
+      yearPublished: 2009a
       publicationType: journal
   - type: Article
     id: bib60
@@ -4101,6 +4106,7 @@ references:
       Bioinformatics enrichment tools: paths toward the comprehensive functional
       analysis of large gene lists
     meta:
+      yearPublished: 2009b
       publicationType: journal
   - type: Article
     id: bib61
@@ -4836,6 +4842,7 @@ references:
     pageStart: 50
     title: Targeting the ubiquitin pathway for cancer treatment
     meta:
+      yearPublished: 2015a
       publicationType: journal
   - type: Article
     id: bib75
@@ -4880,6 +4887,7 @@ references:
       associations between human diseases, genes, drugs, metabolites, toxins and
       more
     meta:
+      yearPublished: 2015b
       publicationType: journal
   - type: Article
     id: bib76

src/codecs/jats/__file_snapshots__/elife-52882-v2.yaml

@@ -1544,6 +1544,7 @@ references:
     title: Programs closed-loop phototaxis
     url: https://gitlab.com/Phiasso/programs_closed-loop_phototaxis.git
     meta:
+      yearPublished: 2019a
       publicationType: software
   - type: Article
     id: bib30
@@ -1562,6 +1563,7 @@ references:
     title: Analysis behavioral phototaxis
     url: https://gitlab.com/Phiasso/analysis.git
     meta:
+      yearPublished: 2019b
       publicationType: software
   - type: Article
     id: bib31

src/codecs/jats/index.ts

@@ -1493,7 +1493,16 @@ export function decodeReference(
   ]
   if (identifiers.length === 0) identifiers = undefined
 
-  const meta = typeof label === 'string' ? { label } : undefined
+  const metaEntries: Record<string, string> = {}
+  if (
+    datePublishedString !== undefined &&
+    (datePublishedString.length > 4 || datePublished === undefined)
+  ) {
+    metaEntries.yearPublished = datePublishedString
+  }
+  if (typeof label === 'string') {
+    metaEntries.label = label
+  }
 
   return stencila.article({
     id,
@@ -1507,7 +1516,7 @@ export function decodeReference(
     identifiers,
     url,
     meta: {
-      ...meta,
+      ...(metaEntries ? { ...metaEntries } : {}),
       ...(publicationType
         ? {
             publicationType,

src/codecs/jats/jats.test.ts

@@ -240,6 +240,30 @@ test.each([
   expect(decodeReference(citation, null, undefined)).toEqual(expected)
 })
 
+test('decode: reference datePublished is added to meta.yearPublished to preserve suffixes', () => {
+  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>2020a</year>) <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> <fpage>21</fpage>
+    </mixed-citation>
+  `  
+  const citation = xml.load(reference).elements?.[0]!
+
+  const result = decodeReference(citation, null, undefined);
+  expect(result.meta?.yearPublished).toEqual('2020a');
+});
+
+test('decode: reference n.d. is parsed out of date published', () => {
+  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>) <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> <fpage>21</fpage>
+    </mixed-citation>
+  `  
+  const citation = xml.load(reference).elements?.[0]!
+
+  const result = decodeReference(citation, null, undefined);
+  expect(result.meta?.yearPublished).toEqual('n.d.');
+});
+
 test('decode: <table-wrap> element that has more than one <graphic>', () => {
   const fig = xml.load(`
   <table-wrap id="tblS1" orientation="portrait" position="float">