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Fixes and Extends BibliographyConsistencyCheck.check to Handle Custom Entry Types #14257

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Fixes and Extends BibliographyConsistencyCheck.check to Handle Custom Entry Types #14257

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ba9446d
Modifies BibliographyConsistencyCheck.check to Allow Custom Entry Types
Hrishi-Baskaran Nov 15, 2025
c5c1b96
Merge remote-tracking branch 'upstream/main' into support-customized-…
Hrishi-Baskaran Nov 15, 2025
7941238
Adds Tests with Custom Types for Consistency Check
Hrishi-Baskaran Nov 22, 2025
94ab173
Merge remote-tracking branch 'upstream/main' into support-customized-…
Hrishi-Baskaran Nov 22, 2025
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3 changes: 1 addition & 2 deletions jabgui/src/main/java/org/jabref/gui/consistency/ConsistencyCheckAction.java
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Expand Up @@ -44,7 +44,6 @@ public ConsistencyCheckAction(Supplier<LibraryTab> tabSupplier,
this.preferences = preferences;
this.entryTypesManager = entryTypesManager;
this.taskExecutor = taskExecutor;

this.executable.bind(needsDatabase(stateManager));
}

Expand All @@ -63,7 +62,7 @@ public BibliographyConsistencyCheck.Result call() {
BibDatabaseContext bibContext = databaseContext.get();

BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
return consistencyCheck.check(bibContext, (count, total) ->
return consistencyCheck.check(bibContext, entryTypesManager, (count, total) ->
UiTaskExecutor.runInJavaFXThread(() -> {
updateProgress(count, total);
updateMessage(Localization.lang("%0/%1 entry types", count + 1, total));
Expand Down
4 changes: 3 additions & 1 deletion jabkit/src/main/java/org/jabref/toolkit/commands/CheckConsistency.java
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Expand Up @@ -14,6 +14,7 @@
import org.jabref.logic.quality.consistency.BibliographyConsistencyCheckResultTxtWriter;
import org.jabref.logic.quality.consistency.BibliographyConsistencyCheckResultWriter;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntryTypesManager;
import org.jabref.toolkit.converter.CygWinPathConverter;

import org.slf4j.Logger;
Expand Down Expand Up @@ -65,7 +66,8 @@ public Integer call() {
BibDatabaseContext databaseContext = parserResult.get().getDatabaseContext();

BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
BibliographyConsistencyCheck.Result result = consistencyCheck.check(databaseContext, (count, total) -> {
BibEntryTypesManager bibEntryTypesManager = new BibEntryTypesManager();
BibliographyConsistencyCheck.Result result = consistencyCheck.check(databaseContext, bibEntryTypesManager, (count, total) -> {
if (!sharedOptions.porcelain) {
System.out.println(Localization.lang("Checking consistency for entry type %0 of %1", count + 1, total));
}
Expand Down
12 changes: 3 additions & 9 deletions jablib/src/main/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheck.java
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Expand Up @@ -20,13 +20,12 @@
import org.jabref.model.database.BibDatabaseMode;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryType;
import org.jabref.model.entry.BibEntryTypesManager;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.InternalField;
import org.jabref.model.entry.field.SpecialField;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.field.UserSpecificCommentField;
import org.jabref.model.entry.types.BiblatexEntryTypeDefinitions;
import org.jabref.model.entry.types.BibtexEntryTypeDefinitions;
import org.jabref.model.entry.types.EntryType;

import com.google.common.annotations.VisibleForTesting;
Expand Down Expand Up @@ -102,7 +101,7 @@ public record EntryTypeResult(Collection<Field> fields, SequencedCollection<BibE
*
* @implNote This class does not implement {@link org.jabref.logic.integrity.DatabaseChecker}, because it returns a list of {@link org.jabref.logic.integrity.IntegrityMessage}, which are too fine-grained.
*/
public Result check(BibDatabaseContext bibContext, BiConsumer<Integer, Integer> entriesGroupingProgress) {
public Result check(BibDatabaseContext bibContext, BibEntryTypesManager bibEntryTypesManager, BiConsumer<Integer, Integer> entriesGroupingProgress) {
// collects fields existing in any entry, scoped by entry type
Map<EntryType, Set<Field>> entryTypeToFieldsInAnyEntryMap = new HashMap<>();
// collects fields existing in all entries, scoped by entry type
Expand All @@ -112,12 +111,7 @@ public Result check(BibDatabaseContext bibContext, BiConsumer<Integer, Integer>

collectEntriesIntoMaps(bibContext, entryTypeToFieldsInAnyEntryMap, entryTypeToFieldsInAllEntriesMap, entryTypeToEntriesMap);

List<BibEntryType> entryTypeDefinitions;
if (bibContext.getMode() == BibDatabaseMode.BIBLATEX) {
entryTypeDefinitions = BiblatexEntryTypeDefinitions.ALL;
} else {
entryTypeDefinitions = BibtexEntryTypeDefinitions.ALL;
}
List<BibEntryType> entryTypeDefinitions = bibEntryTypesManager.getAllTypes(bibContext.getMode()).stream().toList();

// Use LinkedHashMap to preserve the order of Bib(tex|latex)EntryTypeDefinitions.ALL
Map<EntryType, EntryTypeResult> resultMap = new LinkedHashMap<>();
Expand Down
41 changes: 36 additions & 5 deletions ...org/jabref/logic/quality/consistency/BibliographyConsistencyCheckResultCsvWriterTest.java
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Expand Up @@ -5,18 +5,27 @@
import java.io.Writer;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import java.util.Set;

import org.jabref.logic.importer.ImportFormatPreferences;
import org.jabref.logic.importer.fileformat.BibtexImporter;
import org.jabref.model.database.BibDatabase;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.database.BibDatabaseMode;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryType;
import org.jabref.model.entry.BibEntryTypesManager;
import org.jabref.model.entry.field.BibField;
import org.jabref.model.entry.field.FieldPriority;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.field.UnknownField;
import org.jabref.model.entry.types.EntryType;
import org.jabref.model.entry.types.StandardEntryType;
import org.jabref.model.entry.types.UnknownEntryType;
import org.jabref.model.util.DummyFileUpdateMonitor;

import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
Expand All @@ -27,8 +36,30 @@

class BibliographyConsistencyCheckResultCsvWriterTest {

private static final EntryType UNKNOWN_TYPE = new UnknownEntryType("unknownType");
private static final EntryType CUSTOM_TYPE = new UnknownEntryType("customType");

private final BibtexImporter importer = new BibtexImporter(mock(ImportFormatPreferences.class, Answers.RETURNS_DEEP_STUBS), new DummyFileUpdateMonitor());

private BibEntryType newCustomType;
private BibEntryType overwrittenStandardType;
private BibEntryTypesManager entryTypesManager;

@BeforeEach
void setUp() {
newCustomType = new BibEntryType(
CUSTOM_TYPE,
List.of(new BibField(StandardField.AUTHOR, FieldPriority.IMPORTANT)),
Set.of());

overwrittenStandardType = new BibEntryType(
StandardEntryType.Article,
List.of(new BibField(StandardField.TITLE, FieldPriority.IMPORTANT)),
Set.of());

entryTypesManager = new BibEntryTypesManager();
}

@Test
void checkSimpleLibrary(@TempDir Path tempDir) throws IOException {
BibEntry first = new BibEntry(StandardEntryType.Article, "first")
Expand All @@ -42,7 +73,7 @@ void checkSimpleLibrary(@TempDir Path tempDir) throws IOException {
database.insertEntry(second);

BibDatabaseContext bibContext = new BibDatabaseContext(database);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (count, total) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, entryTypesManager, (count, total) -> {
});

Path csvFile = tempDir.resolve("checkSimpleLibrary-result.csv");
Expand Down Expand Up @@ -73,7 +104,7 @@ void checkDifferentOutputSymbols(@TempDir Path tempDir) throws IOException {

BibDatabaseContext bibContext = new BibDatabaseContext(database);
bibContext.setMode(BibDatabaseMode.BIBTEX);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (count, total) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, entryTypesManager, (count, total) -> {
});

Path csvFile = tempDir.resolve("checkDifferentOutputSymbols-result.csv");
Expand Down Expand Up @@ -119,7 +150,7 @@ void checkComplexLibrary(@TempDir Path tempDir) throws IOException {
database.insertEntry(fifth);

BibDatabaseContext bibContext = new BibDatabaseContext(database);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (count, total) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, entryTypesManager, (count, total) -> {
});

Path csvFile = tempDir.resolve("checkSimpleLibrary-result.csv");
Expand Down Expand Up @@ -151,7 +182,7 @@ void checkLibraryWithoutIssues(@TempDir Path tempDir) throws IOException {

BibDatabaseContext bibContext = new BibDatabaseContext(database);
bibContext.setMode(BibDatabaseMode.BIBTEX);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (count, total) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, entryTypesManager, (count, total) -> {
});

Path csvFile = tempDir.resolve("checkLibraryWithoutIssues-result.csv");
Expand All @@ -170,7 +201,7 @@ void checkManualInput() throws IOException {
Path file = Path.of("C:\\TEMP\\JabRef\\biblio-anon.bib");
Path csvFile = file.resolveSibling("biblio-cited.csv");
BibDatabaseContext databaseContext = importer.importDatabase(file).getDatabaseContext();
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(databaseContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(databaseContext, entryTypesManager, (_, _) -> {
});
try (Writer writer = new OutputStreamWriter(Files.newOutputStream(csvFile));
BibliographyConsistencyCheckResultCsvWriter paperConsistencyCheckResultCsvWriter = new BibliographyConsistencyCheckResultCsvWriter(result, writer, true)) {
Expand Down
16 changes: 8 additions & 8 deletions ...org/jabref/logic/quality/consistency/BibliographyConsistencyCheckResultTxtWriterTest.java
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Expand Up @@ -44,7 +44,7 @@ void checkSimpleLibrary(@TempDir Path tempDir) throws IOException {

BibDatabaseContext bibContext = new BibDatabaseContext(database);
bibContext.setMode(BibDatabaseMode.BIBTEX);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (count, total) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, new BibEntryTypesManager(), (count, total) -> {
});

Path txtFile = tempDir.resolve("checkSimpleLibrary-result.txt");
Expand Down Expand Up @@ -89,7 +89,7 @@ void entriesMissingRequiredFieldsAreReported(@TempDir Path tempDir) throws Excep
bibContext.setMode(BibDatabaseMode.BIBLATEX);

BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck()
.check(bibContext, (_, _) -> {
.check(bibContext, new BibEntryTypesManager(), (_, _) -> {
});

Path txtFile = tempDir.resolve("checkSimpleLibrary-result.txt");
Expand Down Expand Up @@ -131,7 +131,7 @@ void checkDifferentOutputSymbols(@TempDir Path tempDir) throws IOException {
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);
bibContext.setMode(BibDatabaseMode.BIBTEX);

BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, new BibEntryTypesManager(), (_, _) -> {
});

Path txtFile = tempDir.resolve("checkDifferentOutputSymbols-result.txt");
Expand Down Expand Up @@ -171,7 +171,7 @@ void checkVeryLongCitationKey(@TempDir Path tempDir) throws IOException {
bibDatabase.insertEntries(bibEntriesList);
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);
bibContext.setMode(BibDatabaseMode.BIBTEX);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, new BibEntryTypesManager(), (_, _) -> {
});

Path txtFile = tempDir.resolve("checkDifferentOutputSymbols-result.txt");
Expand Down Expand Up @@ -228,7 +228,7 @@ void checkComplexLibrary(@TempDir Path tempDir) throws IOException {
bibDatabase.insertEntries(bibEntriesList);
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, new BibEntryTypesManager(), (_, _) -> {
});

Path txtFile = tempDir.resolve("checkSimpleLibrary-result.txt");
Expand Down Expand Up @@ -270,7 +270,7 @@ void checkLibraryWithoutIssuesWithOutPorcelain(@TempDir Path tempDir) throws IOE
bibDatabase.insertEntries(bibEntriesList);
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, new BibEntryTypesManager(), (_, _) -> {
});

Path txtFile = tempDir.resolve("checkLibraryWithoutIssues-result.txt");
Expand Down Expand Up @@ -298,7 +298,7 @@ void checkLibraryWithoutIssuesWithPorcelain(@TempDir Path tempDir) throws IOExce
bibDatabase.insertEntries(bibEntriesList);
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, new BibEntryTypesManager(), (_, _) -> {
});

Path txtFile = tempDir.resolve("checkLibraryWithoutIssues-result.txt");
Expand All @@ -315,7 +315,7 @@ void checkManualInput() throws IOException {
Path file = Path.of("C:\\TEMP\\JabRef\\biblio-anon.bib");
Path txtFile = file.resolveSibling("biblio-cited.txt");
BibDatabaseContext databaseContext = importer.importDatabase(file).getDatabaseContext();
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(databaseContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(databaseContext, new BibEntryTypesManager(), (_, _) -> {
});
try (Writer writer = new OutputStreamWriter(Files.newOutputStream(txtFile));
BibliographyConsistencyCheckResultTxtWriter txtWriter = new BibliographyConsistencyCheckResultTxtWriter(result, writer, true)) {
Expand Down
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