Add pseudonymization of groups

CHANGELOG.md

@@ -34,7 +34,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added support for `html` when parsing the arXiv identifiers. [#14451](https://github.com/JabRef/jabref/issues/14451)
 - We added the option to change the Git username and PAT in Network Preferences. [#14509](https://github.com/JabRef/jabref/pull/14509)
 - When parsing a plain text citation, we added support for recognizing and extracting arXiv identifiers. [#14455](https://github.com/JabRef/jabref/pull/14455)
-- We introduced a new "Search Engine URL Template" setting in Preferences to allow users to customize their search engine URL templates [#12268](https://github.com/JabRef/jabref/issues/12268)
+- We introduced a new "Search Engine URL Template" setting in Preferences to allow users to customize their search engine URL templates. [#12268](https://github.com/JabRef/jabref/issues/12268)
+- We added pseudonymization of groups. [#14117](https://github.com/JabRef/jabref/issues/14117)
 - We enabled CLI parameters for customizing citation key generation in JabKit, allowing users to override citation key patterns without modifying GUI settings. [#14361](https://github.com/JabRef/jabref/issues/14361)
 - We added the option to pseudonymize a library using the GUI, via the tools tab in the Main Menu. [#14118](https://github.com/JabRef/jabref/issues/14118)
 - We added export options (Markdown and JSON) for AI Summary and AI Chat. [#13868](https://github.com/JabRef/jabref/issues/13868)

jablib/src/main/java/org/jabref/logic/pseudonymization/Pseudonymization.java

@@ -5,22 +5,27 @@
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Optional;
 
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.groups.AbstractGroup;
+import org.jabref.model.groups.GroupTreeNode;
+import org.jabref.model.metadata.MetaData;
 
 import org.jspecify.annotations.NullMarked;
 
-/**
- * This class is used to anonymize a library. It is required to make private libraries available for public use.
- * <p>
- * For "just" generating large .bib files, scripts/bib-file-generator.py can be used.
- */
+/// This class is used to anonymize a library. It is required to make private libraries available for public use.
+///
+/// For "just" generating large `.bib` files, `scripts/bib-file-generator.py` can be used.
 @NullMarked
 public class Pseudonymization {
 
+    private static final String GROUPS_PSEUDONYM_PREFIX = "group";
+
     public record Result(BibDatabaseContext bibDatabaseContext, Map<String, String> valueMapping) {
     }
 
@@ -31,13 +36,18 @@ public Result pseudonymizeLibrary(BibDatabaseContext bibDatabaseContext) {
         Map<Field, Map<String, Integer>> fieldToValueToIdMap = new HashMap<>();
         List<BibEntry> newEntries = pseudonymizeEntries(bibDatabaseContext, fieldToValueToIdMap);
 
+        Optional<GroupTreeNode> newGroups = pseudonymizeGroups(bibDatabaseContext, fieldToValueToIdMap);
+
         Map<String, String> valueMapping = new HashMap<>();
         fieldToValueToIdMap.forEach((field, stringToIntMap) ->
-                stringToIntMap.forEach((value, id) -> valueMapping.put(field.getName().toLowerCase(Locale.ROOT) + "-" + id, value)));
+                stringToIntMap.forEach((value, id) -> valueMapping.put(getFieldContent(field, id), value)));
 
         BibDatabase bibDatabase = new BibDatabase(newEntries);
         BibDatabaseContext result = new BibDatabaseContext(bibDatabase);
         result.setMode(bibDatabaseContext.getMode());
+        newGroups.ifPresent(result.getMetaData()::setGroups);
+
+        bibDatabaseContext.getMetaData().getGroupSearchSyntaxVersion().ifPresent(result.getMetaData()::setGroupSearchSyntaxVersion);
 
         return new Result(result, valueMapping);
     }
@@ -57,10 +67,80 @@ private static List<BibEntry> pseudonymizeEntries(BibDatabaseContext bibDatabase
                 // TODO: Use {@link org.jabref.model.entry.field.FieldProperty} to distinguish cases.
                 //       See {@link org.jabref.model.entry.field.StandardField} for usages.
                 String fieldContent = entry.getField(field).get();
-                Integer id = valueToIdMap.computeIfAbsent(fieldContent, k -> valueToIdMap.size() + 1);
-                newEntry.setField(field, field.getName() + "-" + id);
+
+                if (field == StandardField.GROUPS) {
+                    List<String> groups = splitGroups(fieldContent);
+                    String pseudonymizedGroups = pseudonymizeGroupValue(groups, valueToIdMap);
+                    newEntry.setField(field, pseudonymizedGroups);
+                } else {
+                    Integer id = valueToIdMap.computeIfAbsent(fieldContent, k -> valueToIdMap.size() + 1);
+                    newEntry.setField(field, getFieldContent(field, id));
+                }
             }
         }
         return newEntries;
     }
+
+    /**
+     * Pseudonymizes the root group and all subgroups.
+     * If no groups exist, returns empty.
+     */
+    private static Optional<GroupTreeNode> pseudonymizeGroups(BibDatabaseContext bibDatabaseContext, Map<Field, Map<String, Integer>> fieldToValueToIdMap) {
+        MetaData metadata = bibDatabaseContext.getMetaData();
+        Optional<GroupTreeNode> groupsOpt = metadata.getGroups();
+
+        if (groupsOpt.isEmpty()) {
+            return Optional.empty();
+        }
+
+        GroupTreeNode originalRoot = groupsOpt.get();
+        Map<String, Integer> groupValueMap = fieldToValueToIdMap.computeIfAbsent(StandardField.GROUPS, _ -> new HashMap<>());
+
+        GroupTreeNode newRoot = pseudonymizeGroupNode(originalRoot, groupValueMap);
+        return Optional.of(newRoot);
+    }
+
+    /**
+     * Recursively rewrites a group node and its children.
+     * Each original group receives a generated ID, resulting in: original -> "groups-n"
+     */
+    private static GroupTreeNode pseudonymizeGroupNode(GroupTreeNode node, Map<String, Integer> valueToIdMap) {
+        AbstractGroup originalGroup = node.getGroup();
+        AbstractGroup groupCopy = originalGroup.deepCopy();
+
+        String originalName = node.getName();
+        int id = valueToIdMap.computeIfAbsent(originalName, _ -> valueToIdMap.size() + 1);
+        groupCopy.nameProperty().setValue(getFieldContent(StandardField.GROUPS, id));
+
+        GroupTreeNode newNode = new GroupTreeNode(groupCopy);
+        for (GroupTreeNode child : node.getChildren()) {
+            GroupTreeNode childCopy = pseudonymizeGroupNode(child, valueToIdMap);
+            newNode.addChild(childCopy);
+        }
+
+        return newNode;
+    }
+
+    private static List<String> splitGroups(String content) {
+        return List.of(content.split("\\s*,\\s*"));
+    }
+
+    private static String pseudonymizeGroupValue(List<String> values, Map<String, Integer> valueToIdMap) {
+        List<String> pseudonymized = new ArrayList<>(values.size());
+
+        for (String value : values) {
+            Integer id = valueToIdMap.computeIfAbsent(value, k -> valueToIdMap.size() + 1);
+            pseudonymized.add(GROUPS_PSEUDONYM_PREFIX + "-" + id);
+        }
+
+        return String.join(", ", pseudonymized);
+    }
+
+    private static String getFieldContent(Field field, int id) {
+        String prefix = field == StandardField.GROUPS
+                        ? GROUPS_PSEUDONYM_PREFIX
+                        : field.getName().toLowerCase(Locale.ROOT);
+
+        return prefix + "-" + id;
+    }
 }

jablib/src/test/java/org/jabref/logic/pseudonymization/PseudonymizationTest.java

@@ -7,6 +7,7 @@
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Map;
+import java.util.Optional;
 
 import org.jabref.logic.bibtex.FieldPreferences;
 import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
@@ -21,6 +22,10 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.groups.AllEntriesGroup;
+import org.jabref.model.groups.ExplicitGroup;
+import org.jabref.model.groups.GroupHierarchyType;
+import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.metadata.SaveOrder;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
@@ -30,6 +35,7 @@
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.Mockito.mock;
 
@@ -129,4 +135,93 @@ void pseudonymizeLibraryFile(@TempDir Path tempDir) throws URISyntaxException, I
 
         assertTrue(Files.exists(target));
     }
+
+    @Test
+    void pseudonymizeGroups() {
+        // given
+        GroupTreeNode root = new GroupTreeNode(new AllEntriesGroup("Root"));
+        GroupTreeNode used = root.addSubgroup(new ExplicitGroup("Used", GroupHierarchyType.INDEPENDENT, ','));
+        used.addSubgroup(new ExplicitGroup("Sub", GroupHierarchyType.INDEPENDENT, ','));
+
+        BibDatabaseContext databaseContext = new BibDatabaseContext(new BibDatabase());
+        databaseContext.getMetaData().setGroups(root);
+
+        Pseudonymization pseudonymization = new Pseudonymization();
+
+        // when
+        Pseudonymization.Result result = pseudonymization.pseudonymizeLibrary(databaseContext);
+        GroupTreeNode newRoot = result.bibDatabaseContext().getMetaData().getGroups().orElseThrow();
+
+        // then
+        assertEquals("group-1", newRoot.getName());
+        assertTrue(newRoot.getFirstChild().isPresent());
+
+        GroupTreeNode newUsed = newRoot.getFirstChild().orElseThrow();
+        assertEquals("group-2", newUsed.getName());
+        assertTrue(newUsed.getFirstChild().isPresent());
+
+        GroupTreeNode newSub = newUsed.getFirstChild().orElseThrow();
+        assertEquals("group-3", newSub.getName());
+
+        Map<String, String> mapping = result.valueMapping();
+        assertEquals("Root", mapping.get("group-1"));
+        assertEquals("Used", mapping.get("group-2"));
+        assertEquals("Sub", mapping.get("group-3"));
+    }
+
+    @Test
+    void pseudonymizeEntriesWithGroup() {
+        // given
+        BibDatabaseContext databaseContext = new BibDatabaseContext(new BibDatabase(List.of(
+                new BibEntry("first").withField(StandardField.GROUPS, "MyGroup"),
+                new BibEntry("second").withField(StandardField.GROUPS, "MyGroup, OtherGroup"),
+                new BibEntry("third").withField(StandardField.GROUPS, "OtherGroup")
+        )));
+
+        Pseudonymization pseudonymization = new Pseudonymization();
+
+        // when
+        Pseudonymization.Result result = pseudonymization.pseudonymizeLibrary(databaseContext);
+
+        // then
+        List<BibEntry> entries = result.bibDatabaseContext().getEntries();
+        assertEquals(3, entries.size());
+
+        assertEquals(Optional.of("group-1"), entries.getFirst().getField(StandardField.GROUPS));
+        assertEquals(Optional.of("group-1, group-2"), entries.get(1).getField(StandardField.GROUPS));
+        assertEquals(Optional.of("group-2"), entries.get(2).getField(StandardField.GROUPS));
+
+        Map<String, String> mapping = result.valueMapping();
+        assertEquals("MyGroup", mapping.get("group-1"));
+        assertEquals("OtherGroup", mapping.get("group-2"));
+    }
+
+    @Test
+    void pseudonymizeEntryWithMultipleGroups() {
+        // given
+        BibDatabaseContext databaseContext = new BibDatabaseContext(new BibDatabase(List.of(
+                new BibEntry("first").withField(StandardField.GROUPS, "one, two, three")
+        )));
+
+        Pseudonymization pseudonymization = new Pseudonymization();
+
+        // when
+        Pseudonymization.Result result = pseudonymization.pseudonymizeLibrary(databaseContext);
+
+        // then
+        BibEntry pseudonymizedEntry = result.bibDatabaseContext().getEntries().getFirst();
+        String pseudonymizedGroups = pseudonymizedEntry.getField(StandardField.GROUPS).orElseThrow();
+
+        String[] groups = pseudonymizedGroups.split(", ");
+        assertEquals(3, groups.length);
+
+        assertEquals("group-1", groups[0]);
+        assertEquals("group-2", groups[1]);
+        assertEquals("group-3", groups[2]);
+
+        Map<String, String> mapping = result.valueMapping();
+        assertEquals("one", mapping.get(groups[0]));
+        assertEquals("two", mapping.get(groups[1]));
+        assertEquals("three", mapping.get(groups[2]));
+    }
 }

jablib/src/test/resources/org/jabref/logic/pseudonymization/Chocolate-pseudnomyized.bib

@@ -77,7 +77,7 @@ @Article{citationkey-6
   number       = {number-4},
   pages        = {pages-5},
   volume       = {volume-6},
-  groups       = {groups-1},
+  groups       = {group-1},
   publisher    = {publisher-6},
   readstatus   = {readstatus-2},
 }
@@ -93,7 +93,7 @@ @Article{citationkey-7
   pages        = {pages-6},
   volume       = {volume-7},
   file         = {file-5},
-  groups       = {groups-1},
+  groups       = {group-1},
   publisher    = {publisher-7},
   readstatus   = {readstatus-2},
 }
@@ -123,7 +123,7 @@ @Article{citationkey-9
   number       = {number-6},
   pages        = {pages-8},
   volume       = {volume-9},
-  groups       = {groups-1},
+  groups       = {group-1},
   publisher    = {publisher-6},
   readstatus   = {readstatus-2},
 }
@@ -177,7 +177,7 @@ @Article{citationkey-13
   number       = {number-1},
   pages        = {pages-11},
   volume       = {volume-13},
-  groups       = {groups-1},
+  groups       = {group-1},
   publisher    = {publisher-4},
   readstatus   = {readstatus-2},
 }
@@ -190,7 +190,7 @@ @Article{citationkey-14
   doi          = {doi-14},
   issn         = {issn-14},
   volume       = {volume-14},
-  groups       = {groups-1},
+  groups       = {group-1},
   publisher    = {publisher-10},
   readstatus   = {readstatus-2},
 }
@@ -211,3 +211,16 @@ @Article{citationkey-15
 }
 
 @Comment{jabref-meta: databaseType:biblatex;}
+
+@Comment{jabref-meta: grouping:
+0 AllEntriesGroup:;
+1 SearchGroup:group-3\;0\;groups !=~ .+\;0\;1\;1\;\;\;\;;
+1 SearchGroup:group-4\;0\;file !=~ .+\;0\;1\;1\;\;\;\;;
+1 StaticGroup:group-5\;0\;1\;\;\;\;;
+1 SearchGroup:group-6\;0\;groups !=~ .+ and readstatus !=~ .+\;0\;1\;1\;\;\;\;;
+1 KeywordGroup:group-7\;0\;readstatus\;skimmed\;0\;0\;1\;\;\;\;;
+1 KeywordGroup:group-8\;0\;readstatus\;read\;0\;0\;1\;\;\;\;;
+1 StaticGroup:group-1\;0\;1\;\;\;\;;
+}
+
+@Comment{jabref-meta: groups-search-syntax-version:6.0-alpha_1}