[IMP] Add re-distribution of numeric CSL citations (#11712)

* Initial commit

* Semi-fix: 0-based index

* add method for getting multiple citations

* Use XTextRangeCompare

* Fix update order

* Remove dead code, undo ai refactor changes

* Fix remaining order issues, Remove dead code, undo ai refactor changes

* Restore exceptions: UpdateCSLBibliography

* Refine

* Fix checkstyle

* Remove experiment

* Fix OOBibBase.java exceptions

* Fix OpenOfficePanel.java exceptions

* Fix adapter exception indent

* Fix adapter exception order

* Restore javadoc

* Restore javadoc, remove dead code

* Remove dead code

* Improve implementation (general changes)

* Change printStackTrace->Logger

* Fix readExistingMarks()

* Remove logs

* Finish CSLReferenceMarkManager

* openRewrite

* fix unit test (std streams -> logger)

* Redundant log

* Safety, refactoring

* Add log

* Better log

* Change log level (non-breaking)

* Add handling for multiple entries

* Better log

* Restore javadoc

* Restore javadoc

* Use list instead of singleton

* Adapt test

* Add comment

* Add stricter conditions for update

* Add stricter conditions for reading

* Make xtextcompare final

* Null handling

* Update javadoc

* Refactor

* Remove redundant condition

* Fix non-numeric side effect

* Enhance implementation

* Add newline

* Bug fix: no sync in refresh bibliography

* fix logger openrewrite

---------

Co-authored-by: Siedlerchr <siedlerkiller@gmail.com>

src/main/java/org/jabref/gui/openoffice/OOBibBase.java

@@ -87,8 +87,8 @@ public OOBibBase(Path loPath, DialogService dialogService)
     }
 
     private void initializeCitationAdapter(XTextDocument doc) throws WrappedTargetException, NoSuchElementException {
-            this.cslCitationOOAdapter = new CSLCitationOOAdapter(doc);
-            this.cslCitationOOAdapter.readExistingMarks();
+        this.cslCitationOOAdapter = new CSLCitationOOAdapter(doc);
+        this.cslCitationOOAdapter.readAndUpdateExistingMarks();
     }
 
     public void guiActionSelectDocument(boolean autoSelectForSingle) throws WrappedTargetException, NoSuchElementException {
@@ -161,9 +161,9 @@ void showDialog(String errorTitle, OOError err) {
 
     OOVoidResult<OOError> collectResults(String errorTitle, List<OOVoidResult<OOError>> results) {
         String msg = results.stream()
-                             .filter(OOVoidResult::isError)
-                             .map(e -> e.getError().getLocalizedMessage())
-                             .collect(Collectors.joining("\n\n"));
+                            .filter(OOVoidResult::isError)
+                            .map(e -> e.getError().getLocalizedMessage())
+                            .collect(Collectors.joining("\n\n"));
         if (msg.isEmpty()) {
             return OOVoidResult.ok();
         } else {
@@ -233,10 +233,10 @@ private static OOVoidResult<OOError> checkRangeOverlaps(XTextDocument doc, OOFro
         int maxReportedOverlaps = 10;
         try {
             return frontend.checkRangeOverlaps(doc,
-                                    new ArrayList<>(),
-                                    requireSeparation,
-                                    maxReportedOverlaps)
-                            .mapError(OOError::from);
+                                   new ArrayList<>(),
+                                   requireSeparation,
+                                   maxReportedOverlaps)
+                           .mapError(OOError::from);
         } catch (NoDocumentException ex) {
             return OOVoidResult.error(OOError.from(ex).setTitle(errorTitle));
         } catch (WrappedTargetException ex) {
@@ -322,7 +322,7 @@ OOResult<OOFrontend, OOError> getFrontend(XTextDocument doc) {
         } catch (NoDocumentException ex) {
             return OOResult.error(OOError.from(ex).setTitle(errorTitle));
         } catch (WrappedTargetException
-                | RuntimeException ex) {
+                 | RuntimeException ex) {
             return OOResult.error(OOError.fromMisc(ex).setTitle(errorTitle));
         }
     }
@@ -601,7 +601,7 @@ public void guiActionInsertEntry(List<BibEntry> entries,
                     this.cslCitationOOAdapter.insertInTextCitation(cursor.get(), citationStyle, entries, bibDatabaseContext, bibEntryTypesManager);
                 } else if (citationType == CitationType.INVISIBLE_CIT) {
                     // "Insert empty citation"
-                    this.cslCitationOOAdapter.insertEmpty(cursor.get(), entries);
+                    this.cslCitationOOAdapter.insertEmpty(cursor.get(), citationStyle, entries);
                 }
 
                 // If "Automatically sync bibliography when inserting citations" is enabled
@@ -813,7 +813,7 @@ public Optional<BibDatabase> exportCitedHelper(List<BibDatabase> databases, bool
         } catch (DisposedException ex) {
             OOError.from(ex).setTitle(errorTitle).showErrorDialog(dialogService);
         } catch (WrappedTargetException
-                | com.sun.star.lang.IllegalArgumentException ex) {
+                 | com.sun.star.lang.IllegalArgumentException ex) {
             LOGGER.warn("Problem generating new database.", ex);
             OOError.fromMisc(ex).setTitle(errorTitle).showErrorDialog(dialogService);
         }
@@ -881,8 +881,8 @@ public void guiActionUpdateDocument(List<BibDatabase> databases, OOStyle style)
             } catch (DisposedException ex) {
                 OOError.from(ex).setTitle(errorTitle).showErrorDialog(dialogService);
             } catch (CreationException
-                    | WrappedTargetException
-                    | com.sun.star.lang.IllegalArgumentException ex) {
+                     | WrappedTargetException
+                     | com.sun.star.lang.IllegalArgumentException ex) {
                 LOGGER.warn("Could not update JStyle bibliography", ex);
                 OOError.fromMisc(ex).setTitle(errorTitle).showErrorDialog(dialogService);
             }

src/main/java/org/jabref/gui/preview/CopyCitationAction.java

@@ -88,7 +88,7 @@ private List<String> generateCitations() throws IOException {
         }
 
         if (styleSource != null) {
-            return CitationStyleGenerator.generateCitations(
+            return CitationStyleGenerator.generateBibliographies(
                     selectedEntries,
                     styleSource,
                     outputFormat,

src/main/java/org/jabref/logic/citationstyle/CSLAdapter.java

@@ -17,12 +17,12 @@
 /**
  * Provides an adapter class to CSL. It holds a CSL instance under the hood that is only recreated when
  * the style changes.
- *
+ * <p>
  * Note on the API: The first call to {@link #makeBibliography} is expensive since the
  * CSL instance will be created. As long as the style stays the same, we can reuse this instance. On style-change, the
  * engine is re-instantiated. Therefore, the use-case of this class is many calls to {@link #makeBibliography} with the
  * same style. Changing the output format is cheap.
- *
+ * <p>
  * Note on the implementation:
  * The main function {@link #makeBibliography} will enforce
  * synchronized calling. The main CSL engine under the hood is not thread-safe. Since this class is usually called from
@@ -51,7 +51,7 @@ public synchronized List<String> makeBibliography(List<BibEntry> bibEntries, Str
         return Arrays.asList(bibliography.getEntries());
     }
 
-    public synchronized Citation makeInText(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) throws IOException {
+    public synchronized Citation makeCitation(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) throws IOException {
         dataProvider.setData(bibEntries, databaseContext, entryTypesManager);
         initialize(style, outputFormat);
         cslInstance.registerCitationItems(dataProvider.getIds());

src/main/java/org/jabref/logic/citationstyle/CitationStyleGenerator.java

@@ -31,38 +31,38 @@ private CitationStyleGenerator() {
      *
      * @implNote the citation is generated using JavaScript which may take some time, better call it from outside the main Thread
      */
-    protected static String generateCitation(List<BibEntry> bibEntries, CitationStyle style, BibEntryTypesManager entryTypesManager) {
-        return generateCitation(bibEntries, style.getSource(), entryTypesManager);
+    protected static String generateBibliography(List<BibEntry> bibEntries, CitationStyle style, BibEntryTypesManager entryTypesManager) {
+        return generateBibliography(bibEntries, style.getSource(), entryTypesManager);
     }
 
     /**
      * Generates a Citation based on a given list of entries and a style with a default {@link BibDatabaseContext}
      *
      * @implNote the citation is generated using JavaScript which may take some time, better call it from outside the main Thread
      */
-    protected static String generateCitation(List<BibEntry> bibEntries, String style, BibEntryTypesManager entryTypesManager) {
-        return generateCitation(bibEntries, style, CitationStyleOutputFormat.HTML, new BibDatabaseContext(), entryTypesManager).getFirst();
+    protected static String generateBibliography(List<BibEntry> bibEntries, String style, BibEntryTypesManager entryTypesManager) {
+        return generateBibliography(bibEntries, style, CitationStyleOutputFormat.HTML, new BibDatabaseContext(), entryTypesManager).getFirst();
     }
 
     /**
      * Generates a Citation based on a given list of entries, style, and output format
      *
      * @implNote the citation is generated using JavaScript which may take some time, better call it from outside the main Thread
      */
-    public static List<String> generateCitation(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) {
-        return generateCitations(bibEntries, style, outputFormat, databaseContext, entryTypesManager);
+    public static List<String> generateBibliography(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) {
+        return generateBibliographies(bibEntries, style, outputFormat, databaseContext, entryTypesManager);
     }
 
-    public static Citation generateInText(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) throws IOException {
-        return CSL_ADAPTER.makeInText(bibEntries, style, outputFormat, databaseContext, entryTypesManager);
+    public static Citation generateCitation(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) throws IOException {
+        return CSL_ADAPTER.makeCitation(bibEntries, style, outputFormat, databaseContext, entryTypesManager);
     }
 
     /**
      * Generates the citation for multiple entries at once.
      *
      * @implNote The citations are generated using JavaScript which may take some time, better call it from outside the main thread.
      */
-    public static List<String> generateCitations(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) {
+    public static List<String> generateBibliographies(List<BibEntry> bibEntries, String style, CitationStyleOutputFormat outputFormat, BibDatabaseContext databaseContext, BibEntryTypesManager entryTypesManager) {
         try {
             return CSL_ADAPTER.makeBibliography(bibEntries, style, outputFormat, databaseContext, entryTypesManager);
         } catch (IllegalArgumentException e) {

src/main/java/org/jabref/logic/citationstyle/CitationStylePreviewLayout.java

@@ -18,7 +18,7 @@ public CitationStylePreviewLayout(CitationStyle citationStyle, BibEntryTypesMana
 
     @Override
     public String generatePreview(BibEntry entry, BibDatabaseContext databaseContext) {
-        return CitationStyleGenerator.generateCitation(List.of(entry), citationStyle.getSource(), CitationStyleOutputFormat.HTML, databaseContext, bibEntryTypesManager).getFirst();
+        return CitationStyleGenerator.generateBibliography(List.of(entry), citationStyle.getSource(), CitationStyleOutputFormat.HTML, databaseContext, bibEntryTypesManager).getFirst();
     }
 
     @Override

src/main/java/org/jabref/logic/openoffice/ReferenceMark.java

@@ -1,5 +1,7 @@
 package org.jabref.logic.openoffice;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -9,77 +11,85 @@
 import org.slf4j.LoggerFactory;
 
 public class ReferenceMark {
+    public static final String[] PREFIXES = {"JABREF_", "CID_"};
+
     private static final Logger LOGGER = LoggerFactory.getLogger(ReferenceMark.class);
 
-    private static final Pattern REFERENCE_MARK_FORMAT = Pattern.compile("^JABREF_(\\w+) CID_(\\w+) (\\w+)$");
-    private final String name;
+    private static final Pattern REFERENCE_MARK_FORMAT = Pattern.compile("^((?:JABREF_\\w+ CID_\\w+(?:,\\s*)?)+)(\\s*\\w+)?$");
+    private static final Pattern ENTRY_PATTERN = Pattern.compile("JABREF_(\\w+) CID_(\\w+)");
 
-    private String citationKey;
-    private Integer citationNumber;
+    private final String name;
+    private List<String> citationKeys;
+    private List<Integer> citationNumbers;
     private String uniqueId;
 
     /**
      * @param name Format: <code>JABREF_{citationKey} CID_{citationNumber} {uniqueId}</code>
      */
     public ReferenceMark(String name) {
         this.name = name;
+        parse(name);
+    }
 
-        Matcher matcher = getMatcher(name);
+    public ReferenceMark(String name, List<String> citationKeys, List<Integer> citationNumbers, String uniqueId) {
+        this.name = name;
+        this.citationKeys = citationKeys;
+        this.citationNumbers = citationNumbers;
+        this.uniqueId = uniqueId;
+    }
+
+    private void parse(String name) {
+        Matcher matcher = REFERENCE_MARK_FORMAT.matcher(name);
         if (!matcher.matches()) {
             LOGGER.warn("CSLReferenceMark: name={} does not match pattern. Assuming random values", name);
-            this.citationKey = CUID.randomCUID2(8).toString();
-            this.citationNumber = 0;
-            this.uniqueId = this.citationKey;
+            this.citationKeys = List.of(CUID.randomCUID2(8).toString());
+            this.citationNumbers = List.of(0);
+            this.uniqueId = this.citationKeys.getFirst();
             return;
         }
 
-        this.citationKey = matcher.group(1);
-        this.citationNumber = Integer.parseInt(matcher.group(2));
-        this.uniqueId = matcher.group(3);
+        String entriesString = matcher.group(1).trim();
+        this.uniqueId = matcher.group(2) != null ? matcher.group(2).trim() : CUID.randomCUID2(8).toString();
 
-        LOGGER.debug("CSLReferenceMark: citationKey={} citationNumber={} uniqueId={}", getCitationKey(), getCitationNumber(), getUniqueId());
-    }
+        this.citationKeys = new ArrayList<>();
+        this.citationNumbers = new ArrayList<>();
 
-    public ReferenceMark(String name, String citationKey, Integer citationNumber, String uniqueId) {
-        this.name = name;
-        this.citationKey = citationKey;
-        this.citationNumber = citationNumber;
-        this.uniqueId = uniqueId;
-    }
+        Matcher entryMatcher = ENTRY_PATTERN.matcher(entriesString);
+        while (entryMatcher.find()) {
+            this.citationKeys.add(entryMatcher.group(1));
+            this.citationNumbers.add(Integer.parseInt(entryMatcher.group(2)));
+        }
 
-    private ReferenceMark(String name, String citationKey, String citationNumber, String uniqueId) {
-        this(name, citationKey, Integer.parseInt(citationNumber), uniqueId);
-    }
+        if (this.citationKeys.isEmpty() || this.citationNumbers.isEmpty()) {
+            LOGGER.warn("CSLReferenceMark: Failed to parse any entries from name={}. Assuming random values", name);
+            this.citationKeys = List.of(CUID.randomCUID2(8).toString());
+            this.citationNumbers = List.of(0);
+        }
 
-    private static Matcher getMatcher(String name) {
-        return REFERENCE_MARK_FORMAT.matcher(name);
+        LOGGER.debug("CSLReferenceMark: citationKeys={} citationNumbers={} uniqueId={}", getCitationKeys(), getCitationNumbers(), getUniqueId());
     }
 
     public String getName() {
         return name;
     }
 
     /**
-     * The BibTeX citation key
+     * The BibTeX citation keys
      */
-    public String getCitationKey() {
-        return citationKey;
+    public List<String> getCitationKeys() {
+        return citationKeys;
     }
 
-    public int getCitationNumber() {
-        return citationNumber;
+    public List<Integer> getCitationNumbers() {
+        return citationNumbers;
     }
 
     public String getUniqueId() {
         return uniqueId;
     }
 
     public static Optional<ReferenceMark> of(String name) {
-        Matcher matcher = getMatcher(name);
-        if (!matcher.matches()) {
-            return Optional.empty();
-        }
-
-        return Optional.of(new ReferenceMark(name, matcher.group(1), matcher.group(2), matcher.group(3)));
+        ReferenceMark mark = new ReferenceMark(name);
+        return mark.citationKeys.isEmpty() ? Optional.empty() : Optional.of(mark);
     }
 }