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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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4 changes: 3 additions & 1 deletion jabgui/src/main/java/org/jabref/gui/consistency/ConsistencyCheckAction.java
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Expand Up @@ -17,6 +17,7 @@
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntryTypesManager;

import jakarta.inject.Inject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand All @@ -31,6 +32,7 @@ public class ConsistencyCheckAction extends SimpleCommand {
private final GuiPreferences preferences;
private final BibEntryTypesManager entryTypesManager;
private final UiTaskExecutor taskExecutor;
@Inject private BibEntryTypesManager bibEntryTypesManager;
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@koppor koppor Nov 20, 2025

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We don't inject - we pass by constructor

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@Hrishi-Baskaran Hrishi-Baskaran Nov 22, 2025

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update:
https://github.com/JabRef/jabref/pull/14257/files#diff-1b46713ccfa86a11ee5ea9a4e03b335425b8e5a8981b26fdb5bfb1fc32b3c544L32


public ConsistencyCheckAction(Supplier<LibraryTab> tabSupplier,
DialogService dialogService,
Expand Down Expand Up @@ -63,7 +65,7 @@ public BibliographyConsistencyCheck.Result call() {
BibDatabaseContext bibContext = databaseContext.get();

BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
return consistencyCheck.check(bibContext, (count, total) ->
return consistencyCheck.check(bibContext, bibEntryTypesManager, (count, total) ->
UiTaskExecutor.runInJavaFXThread(() -> {
updateProgress(count, total);
updateMessage(Localization.lang("%0/%1 entry types", count + 1, total));
Expand Down
3 changes: 2 additions & 1 deletion jabkit/src/main/java/org/jabref/toolkit/cli/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.cli.converter.CygWinPathConverter;

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

BibliographyConsistencyCheck consistencyCheck = new BibliographyConsistencyCheck();
BibliographyConsistencyCheck.Result result = consistencyCheck.check(databaseContext, (count, total) -> {
BibliographyConsistencyCheck.Result result = consistencyCheck.check(databaseContext, new BibEntryTypesManager(), (count, total) -> {
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@koppor koppor Nov 20, 2025

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Refactor this as variable to follow the style of Jabef

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@Hrishi-Baskaran Hrishi-Baskaran Nov 22, 2025

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view update:
https://github.com/JabRef/jabref/pull/14257/files#diff-d3050a72d09ad6b3c585cb60f5d8e92bb6b9d7539ff23103b86c8c01391e247cR69-R70

Also just curious: should I be constructing a new BibEntryTypesManager here like I've done? This basically prevents the user from using custom types when using the cli consistency check. How might we let users specify a entry types manager from the cli? Or maybe I'm missing something and this isn't what we want to do.

if (!sharedOptions.porcelain) {
System.out.println(Localization.lang("Checking consistency for entry type %0 of %1", count + 1, total));
}
Expand Down
14 changes: 4 additions & 10 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 @@ -102,22 +101,17 @@ 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
// collects fields existing in all entries, scoped by entry typed
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@koppor koppor Nov 20, 2025

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Typo - please undo

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@Hrishi-Baskaran Hrishi-Baskaran Nov 22, 2025

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update:
https://github.com/JabRef/jabref/pull/14257/files#diff-72370ff3854216f72af92bd9037b16ec26257efb4fc057a596ab1d5b79427bacL108

Map<EntryType, Set<Field>> entryTypeToFieldsInAllEntriesMap = new HashMap<>();
// collects entries of the same type
Map<EntryType, Set<BibEntry>> entryTypeToEntriesMap = new HashMap<>();

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
11 changes: 6 additions & 5 deletions ...org/jabref/logic/quality/consistency/BibliographyConsistencyCheckResultCsvWriterTest.java
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Expand Up @@ -12,6 +12,7 @@
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.database.BibDatabaseMode;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryTypesManager;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.field.UnknownField;
import org.jabref.model.entry.types.StandardEntryType;
Expand Down Expand Up @@ -42,7 +43,7 @@ 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, new BibEntryTypesManager(), (count, total) -> {
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@koppor koppor Nov 20, 2025

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Make this a variable in the test - and reuse it.

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@Hrishi-Baskaran Hrishi-Baskaran Nov 23, 2025

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update:
https://github.com/JabRef/jabref/pull/14257/files#diff-641c831afa366f64368ec5c237c128d3fd3506f92ecc2c4d4a8125e23219849dR39-R62

I also made the mocked BibEntryTypesManager for this test file have some custom and unknown types (similar to what I did for BibliographyConsistencyCheckTest.java). But for this file, I don't use the custom and unknown types. Should I add some unit tests that use these, or remove these types for the mocked BibEntryTypesManager of the CSV test file?

});

Path csvFile = tempDir.resolve("checkSimpleLibrary-result.csv");
Expand Down Expand Up @@ -73,7 +74,7 @@ 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, new BibEntryTypesManager(), (count, total) -> {
});

Path csvFile = tempDir.resolve("checkDifferentOutputSymbols-result.csv");
Expand Down Expand Up @@ -119,7 +120,7 @@ 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, new BibEntryTypesManager(), (count, total) -> {
});

Path csvFile = tempDir.resolve("checkSimpleLibrary-result.csv");
Expand Down Expand Up @@ -151,7 +152,7 @@ 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, new BibEntryTypesManager(), (count, total) -> {
});

Path csvFile = tempDir.resolve("checkLibraryWithoutIssues-result.csv");
Expand All @@ -170,7 +171,7 @@ 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, new BibEntryTypesManager(), (_, _) -> {
});
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
28 changes: 19 additions & 9 deletions .../src/test/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheckTest.java
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Expand Up @@ -9,20 +9,30 @@
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.database.BibDatabaseMode;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.BibEntryTypesManager;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.SpecialField;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.field.UnknownField;
import org.jabref.model.entry.field.UserSpecificCommentField;
import org.jabref.model.entry.types.StandardEntryType;

import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;

import static org.junit.jupiter.api.Assertions.assertEquals;

class BibliographyConsistencyCheckTest {

private BibEntryTypesManager entryTypesManager;

@BeforeEach
void setUp() {
// TODO: add some custom entry types for this manager and test with it
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@koppor koppor Nov 20, 2025

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Yes, please :) - The issue description at #13794 should provide you with one.

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@Hrishi-Baskaran Hrishi-Baskaran Nov 23, 2025

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added two new unit tests:
https://github.com/JabRef/jabref/pull/14257/files#diff-94f45121c423b4c0c7571ccb76a7f40e23bcef1b6966003bbdf6d1a1d4f7cb75R33-R135

entryTypesManager = new BibEntryTypesManager();
}

@Test
void checkSimpleLibrary(@TempDir Path tempDir) {
BibEntry first = new BibEntry(StandardEntryType.Article, "first")
Expand All @@ -34,7 +44,7 @@ void checkSimpleLibrary(@TempDir Path tempDir) {
BibDatabase database = new BibDatabase(List.of(first, second));
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) -> {
});

BibliographyConsistencyCheck.EntryTypeResult entryTypeResult = new BibliographyConsistencyCheck.EntryTypeResult(Set.of(StandardField.PAGES, StandardField.PUBLISHER), List.of(first, second));
Expand All @@ -55,7 +65,7 @@ void checkDifferentOutputSymbols(@TempDir Path tempDir) {
BibDatabase bibDatabase = new BibDatabase(List.of(first, second));
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);
bibContext.setMode(BibDatabaseMode.BIBTEX);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, (_, _) -> {
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck().check(bibContext, entryTypesManager, (_, _) -> {
});

BibliographyConsistencyCheck.EntryTypeResult entryTypeResult = new BibliographyConsistencyCheck.EntryTypeResult(Set.of(StandardField.PAGES, StandardField.TITLE, customField), List.of(first, second));
Expand Down Expand Up @@ -88,7 +98,7 @@ void checkComplexLibrary(@TempDir Path tempDir) {
BibDatabase bibDatabase = new BibDatabase(List.of(first, second, third, fourth, fifth));
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

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

BibliographyConsistencyCheck.EntryTypeResult articleResult = new BibliographyConsistencyCheck.EntryTypeResult(Set.of(StandardField.PAGES, StandardField.PUBLISHER), List.of(first, second));
Expand All @@ -111,7 +121,7 @@ void checkLibraryWithoutIssues(@TempDir Path tempDir) {
BibDatabase bibDatabase = new BibDatabase(List.of(first, second));
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

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

BibliographyConsistencyCheck.Result expected = new BibliographyConsistencyCheck.Result(Map.of());
Expand All @@ -133,7 +143,7 @@ void filteredFieldsAreIgnored() {
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

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

assertEquals(Map.of(), result.entryTypeToResultMap(),
Expand All @@ -150,7 +160,7 @@ void nonFilteredFieldDifferenceIsReported() {
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

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

BibliographyConsistencyCheck.EntryTypeResult typeResult =
Expand All @@ -174,7 +184,7 @@ void unsetRequriedFieldsReported() {
bibContext.setMode(BibDatabaseMode.BIBLATEX);

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

BibliographyConsistencyCheck.EntryTypeResult typeResult =
Expand All @@ -198,7 +208,7 @@ void unsetFieldsReportedInBibtexMode() {
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);
bibContext.setMode(BibDatabaseMode.BIBTEX);
BibliographyConsistencyCheck.Result result = new BibliographyConsistencyCheck()
.check(bibContext, (_, _) -> {
.check(bibContext, entryTypesManager, (_, _) -> {
});
BibliographyConsistencyCheck.EntryTypeResult typeResult =
result.entryTypeToResultMap().get(StandardEntryType.Online);
Expand Down Expand Up @@ -268,7 +278,7 @@ void checkComplexLibraryWithAdditionalEntry(@TempDir Path tempDir) {
BibDatabase bibDatabase = new BibDatabase(List.of(first, second, third, fourth, fifth, sixth));
BibDatabaseContext bibContext = new BibDatabaseContext(bibDatabase);

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

BibliographyConsistencyCheck.EntryTypeResult articleResult = new BibliographyConsistencyCheck.EntryTypeResult(Set.of(StandardField.PAGES, StandardField.PUBLISHER), List.of(first, second));
Expand Down
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