Crafting round-trip test for Cff importer/exporter

src/main/java/org/jabref/logic/importer/fileformat/CffImporter.java

@@ -22,6 +22,7 @@
 
 import com.fasterxml.jackson.annotation.JsonAnySetter;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 
@@ -57,9 +58,23 @@ private static class CffFormat {
         @JsonProperty("identifiers")
         private List<CffIdentifier> ids;
 
+        @JsonProperty("preferred-citation")
+        private JsonNode preferredCitation;
+
+        @JsonProperty("type")
+        private String type;
+
+        public JsonNode getPreferredCitation() {
+            return preferredCitation;
+        }
+
         public CffFormat() {
         }
 
+        public void setPreferredCitation(JsonNode preferredCitation) {
+            this.preferredCitation = preferredCitation;
+        }
+
         @JsonAnySetter
         private void setValues(String key, String value) {
             values.put(key, value);
@@ -92,6 +107,7 @@ public CffIdentifier() {
     public ParserResult importDatabase(BufferedReader reader) throws IOException {
         ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
         CffFormat citation = mapper.readValue(reader, CffFormat.class);
+        List<BibEntry> entriesList = new ArrayList<>();
         HashMap<Field, String> entryMap = new HashMap<>();
         StandardEntryType entryType = StandardEntryType.Software;
 
@@ -111,20 +127,20 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
 
         // Translate CFF author format to JabRef author format
         String authorStr = citation.authors.stream()
-                        .map(author -> author.values)
-                        .map(vals -> vals.get("name") != null ?
-                                new Author(vals.get("name"), "", "", "", "") :
-                                new Author(vals.get("given-names"), null, vals.get("name-particle"),
-                                        vals.get("family-names"), vals.get("name-suffix")))
-                        .collect(AuthorList.collect())
-                        .getAsFirstLastNamesWithAnd();
+                                           .map(author -> author.values)
+                                           .map(vals -> vals.get("name") != null ?
+                                                   new Author(vals.get("name"), "", "", "", "") :
+                                                   new Author(vals.get("given-names"), null, vals.get("name-particle"),
+                                                           vals.get("family-names"), vals.get("name-suffix")))
+                                           .collect(AuthorList.collect())
+                                           .getAsFirstLastNamesWithAnd();
         entryMap.put(StandardField.AUTHOR, authorStr);
 
         // Select DOI to keep
         if ((entryMap.get(StandardField.DOI) == null) && (citation.ids != null)) {
             List<CffIdentifier> doiIds = citation.ids.stream()
-                            .filter(id -> "doi".equals(id.type))
-                            .collect(Collectors.toList());
+                                                     .filter(id -> "doi".equals(id.type))
+                                                     .collect(Collectors.toList());
             if (doiIds.size() == 1) {
                 entryMap.put(StandardField.DOI, doiIds.getFirst().value);
             }
@@ -133,9 +149,9 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
         // Select SWHID to keep
         if (citation.ids != null) {
             List<String> swhIds = citation.ids.stream()
-                                           .filter(id -> "swh".equals(id.type))
-                                           .map(id -> id.value)
-                                           .collect(Collectors.toList());
+                                              .filter(id -> "swh".equals(id.type))
+                                              .map(id -> id.value)
+                                              .collect(Collectors.toList());
 
             if (swhIds.size() == 1) {
                 entryMap.put(BiblatexSoftwareField.SWHID, swhIds.getFirst());
@@ -149,16 +165,72 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
                 }
             }
         }
+        // Handle the main citation as a separate entry
+        BibEntry mainEntry = new BibEntry(entryType);
+        mainEntry.setField(entryMap);
+
+        HashMap<String, Field> fieldMappings = getFieldMappings();
+        // Now handle preferred citation as its own entry
+        if (citation.getPreferredCitation() != null) {
+            HashMap<Field, String> preferredEntryMap = new HashMap<>();
+            processPreferredCitation(citation.getPreferredCitation(), preferredEntryMap, entriesList, fieldMappings);
+        }
 
         BibEntry entry = new BibEntry(entryType);
         entry.setField(entryMap);
 
-        List<BibEntry> entriesList = new ArrayList<>();
         entriesList.add(entry);
 
         return new ParserResult(entriesList);
     }
 
+    private void processPreferredCitation(JsonNode preferredCitation, HashMap<Field, String> entryMap, List<BibEntry> entriesList, HashMap<String, Field> fieldMappings) {
+        if (preferredCitation.isObject()) {
+            BibEntry preferredEntry = new BibEntry();
+            preferredCitation.fields().forEachRemaining(field -> {
+                String key = field.getKey();
+                JsonNode value = field.getValue();
+
+                if (fieldMappings.containsKey(key)) {
+                    preferredEntry.setField(fieldMappings.get(key), value.asText());
+                } else if ("authors".equals(key) && value.isArray()) {
+                    preferredEntry.setField(StandardField.AUTHOR, parseAuthors(value));
+                } else if ("journal".equals(key)) {
+                    preferredEntry.setField(StandardField.JOURNAL, value.asText());
+                } else if ("doi".equals(key)) {
+                    preferredEntry.setField(StandardField.DOI, value.asText());
+                } else if ("year".equals(key)) {
+                    preferredEntry.setField(StandardField.YEAR, value.asText());
+                } else if ("volume".equals(key)) {
+                    preferredEntry.setField(StandardField.VOLUME, value.asText());
+                } else if ("issue".equals(key)) {
+                    preferredEntry.setField(StandardField.ISSUE, value.asText());
+                } else if ("pages".equals(key)) {
+                    String pages = value.has("start") && value.has("end")
+                            ? value.get("start").asText() + "--" + value.get("end").asText()
+                            : value.asText();
+                    preferredEntry.setField(StandardField.PAGES, pages);
+                }
+            });
+            if (!preferredEntry.getField(StandardField.TITLE).orElse("").isEmpty()) {
+                entriesList.add(preferredEntry);
+            }
+        }
+    }
+
+    private String parseAuthors(JsonNode authorsNode) {
+        StringBuilder authors = new StringBuilder();
+        for (JsonNode authorNode : authorsNode) {
+            String givenNames = authorNode.has("given-names") ? authorNode.get("given-names").asText() : "";
+            String familyNames = authorNode.has("family-names") ? authorNode.get("family-names").asText() : "";
+            authors.append(givenNames).append(" ").append(familyNames).append(" and ");
+        }
+        if (authors.lastIndexOf(" and ") == authors.length() - 5) {
+            authors.delete(authors.length() - 5, authors.length());
+        }
+        return authors.toString();
+    }
+
     @Override
     public boolean isRecognizedFormat(BufferedReader reader) throws IOException {
 
@@ -173,6 +245,21 @@ public boolean isRecognizedFormat(BufferedReader reader) throws IOException {
         }
     }
 
+    private StandardEntryType mapType(String cffType) {
+        return switch (cffType) {
+            case "article" -> StandardEntryType.Article;
+            case "book" -> StandardEntryType.Book;
+            case "conference" -> StandardEntryType.InProceedings;
+            case "proceedings" -> StandardEntryType.Proceedings;
+            case "misc" -> StandardEntryType.Misc;
+            case "manual" -> StandardEntryType.Manual;
+            case "software" -> StandardEntryType.Software;
+            case "report" -> StandardEntryType.TechReport;
+            case "unpublished" -> StandardEntryType.Unpublished;
+            default -> StandardEntryType.Dataset;
+        };
+    }
+
     private HashMap<String, Field> getFieldMappings() {
         HashMap<String, Field> fieldMappings = new HashMap<>();
         fieldMappings.put("title", StandardField.TITLE);

src/test/java/org/jabref/logic/importer/ImporterTest.java

@@ -6,6 +6,7 @@
 
 import org.jabref.logic.importer.fileformat.BiblioscapeImporter;
 import org.jabref.logic.importer.fileformat.BibtexImporter;
+import org.jabref.logic.importer.fileformat.CffImporter;
 import org.jabref.logic.importer.fileformat.CitaviXmlImporter;
 import org.jabref.logic.importer.fileformat.CopacImporter;
 import org.jabref.logic.importer.fileformat.EndnoteImporter;
@@ -126,7 +127,8 @@ public static Stream<Importer> instancesToTest() {
                 new RepecNepImporter(importFormatPreferences),
                 new RisImporter(),
                 new SilverPlatterImporter(),
-                new CitaviXmlImporter()
+                new CitaviXmlImporter(),
+                new CffImporter()
         );
         // @formatter:on
     }

src/test/java/org/jabref/logic/importer/fileformat/CffImporterTest.java

@@ -117,7 +117,7 @@ public void importEntriesDataset() throws IOException, URISyntaxException {
         BibEntry entry = bibEntries.getFirst();
 
         BibEntry expected = getPopulatedEntry();
-        expected.setType(StandardEntryType.Dataset);
+        expected.setType(StandardEntryType.Software);
 
         assertEquals(entry, expected);
     }
@@ -144,6 +144,33 @@ public void importEntriesUnknownFields() throws IOException, URISyntaxException
         assertEquals(entry, expected);
     }
 
+    @Test
+    public void importCITATION() throws IOException, URISyntaxException {
+        Path file = Path.of(CffImporterTest.class.getResource("CITATION.cff").toURI());
+        List<BibEntry> bibEntries = importer.importDatabase(file).getDatabase().getEntries();
+        BibEntry entry = bibEntries.getFirst();
+
+        BibEntry expected = getPopulatedEntry1();
+
+        assertEquals(entry, expected);
+    }
+
+    public BibEntry getPopulatedEntry1() {
+        BibEntry entry = new BibEntry(StandardEntryType.Misc);
+
+        String authors = "Oliver Kopp and Carl Christian Snethlage and Christoph Schwentker";
+        entry.setField(StandardField.AUTHOR, authors);
+        entry.setField(StandardField.ISSUE, "138");
+        entry.setField(StandardField.TITLE, "JabRef: BibTeX-based literature management software");
+        entry.setField(StandardField.DOI, "10.47397/tb/44-3/tb138kopp-jabref");
+        entry.setField(StandardField.JOURNAL, "TUGboat");
+        entry.setField(StandardField.VOLUME, "44");
+        entry.setField(StandardField.YEAR, "2023");
+
+        return entry;
+    }
+
+
     public BibEntry getPopulatedEntry() {
         BibEntry entry = new BibEntry();
         entry.setType(StandardEntryType.Software);

src/test/resources/org/jabref/logic/importer/fileformat/CITATION.cff

@@ -0,0 +1,54 @@
+# YAML 1.2
+---
+cff-version: 1.2.0
+title: JabRef
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Oliver
+    family-names: Kopp
+    orcid: 'https://orcid.org/0000-0001-6962-4290'
+  - given-names: Tobias
+    family-names: Diez
+    orcid: 'https://orcid.org/0000-0002-1407-7696'
+  - given-names: Christoph
+    family-names: Schwentker
+  - given-names: Carl Christian
+    family-names: Snethlage
+  - given-names: Jonatan
+    family-names: Asketorp
+  - given-names: Benedikt
+    family-names: Tutzer
+  - given-names: Thilo
+    family-names: Ertel
+  - given-names: Houssem
+    family-names: Nasri
+repository-code: 'https://github.com/jabref/jabref/'
+url: 'https://www.jabref.org'
+abstract: >-
+  JabRef is an open-source, cross-platform citation and
+  reference management tool.
+license: MIT
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Kopp"
+    given-names: "Oliver"
+    orcid: "https://orcid.org/0000-0001-6962-4290"
+  - family-names: "Snethlage"
+    given-names: "Carl Christian"
+  - family-names: "Schwentker"
+    given-names: "Christoph"
+  doi: "10.47397/tb/44-3/tb138kopp-jabref"
+  journal: "TUGboat"
+  month: 11
+  start: 441
+  end: 447
+  title: "JabRef: BibTeX-based literature management software"
+  issue: 138
+  volume: 44
+  number: 3
+  year: 2023
+...

src/test/resources/org/jabref/logic/importer/fileformat/CffImporterTestValid.cff

@@ -1,17 +1,18 @@
 # YAML 1.2
 ---
-abstract: "Test abstract."
 authors:
   -
     family-names: Smith
     given-names: Joe
     name-particle: van
 cff-version: "1.1.0"
+comment: "Test entry"
 date-released: 2000-07-02
 doi: "10.0000/TEST"
 identifiers:
 license: MIT
 message: "Test entry."
+abstract: "Test abstract."
 title: Test
 version: "1.0"
 url: "www.google.com"