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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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18 changes: 5 additions & 13 deletions jablib/src/main/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,17 +67,15 @@ private static Set<Field> filterExcludedFields(Collection<Field> fields) {
/// Filters the given entries to those that violate consistency:
///
/// - Fields not set (but set in other entries of the same type)
/// - Required fields not set
///
///
/// Additionally, the entries are sorted
@VisibleForTesting
List<BibEntry> filterAndSortEntriesWithFieldDifferences(Set<BibEntry> entries, Set<Field> differingFields, Set<Field> requiredFields) {
List<BibEntry> filterAndSortEntriesWithFieldDifferences(Set<BibEntry> entries, Set<Field> differingFields) {
return entries.stream()
.filter(entry ->
// This removes entries that have all differing fields set (could be confusing to the user)
!Collections.disjoint(entry.getFields(), differingFields)
// This ensures that all entries with missing required fields are included
|| !entry.getFields().containsAll(requiredFields))
!Collections.disjoint(entry.getFields(), differingFields))
.sorted(new FieldComparatorStack<>(List.of(
new BibEntryByCitationKeyComparator(),
new BibEntryByFieldsComparator()
Expand All @@ -95,7 +93,7 @@ public record EntryTypeResult(Collection<Field> fields, SequencedCollection<BibE
* Checks the consistency of the given entries by looking at the present and absent fields.
* <p>
* Computation takes place grouped by each entryType.
* Computes the fields set in all entries. In case entries of the same type has more fields defined, it is output.
* Computes the fields set in all entries. In case entries of the same type have more fields defined, they are output.
* <p>
* This class <em>does not</em> check whether all required fields are present or if the fields are valid for the entry type.
* That result can a) be retrieved by using the JabRef UI and b) by checking the CSV output of {@link BibliographyConsistencyCheckResultCsvWriter#writeFindings}
Expand Down Expand Up @@ -138,20 +136,14 @@ public Result check(BibDatabaseContext bibContext, BiConsumer<Integer, Integer>
.filter(def -> def.getType().equals(entryType))
.findFirst();

Set<Field> requiredFields = typeDefOpt.map(typeDef ->
typeDef.getRequiredFields().stream()
.flatMap(orFields -> orFields.getFields().stream())
.collect(Collectors.toSet())
).orElse(Set.of());

Set<BibEntry> entries = entryTypeToEntriesMap.get(entryType);
assert entries != null;
if (entries == null || entries.size() <= 1 || differingFields.isEmpty()) {
// entries.size == 1 can happen if there is only one entry for one type. (E.g., only one `@Book` entry)
continue;
}

List<BibEntry> sortedEntries = filterAndSortEntriesWithFieldDifferences(entries, differingFields, requiredFields);
List<BibEntry> sortedEntries = filterAndSortEntriesWithFieldDifferences(entries, differingFields);
if (!sortedEntries.isEmpty()) {
resultMap.put(entryType, new EntryTypeResult(differingFields, sortedEntries));
}
Expand Down
44 changes: 40 additions & 4 deletions .../src/test/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheckTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,19 @@
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.BibEntryTypeBuilder;
import org.jabref.model.entry.BibEntryTypesManager;
import org.jabref.model.entry.field.BibField;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.FieldPriority;
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.EntryType;
import org.jabref.model.entry.types.StandardEntryType;
import org.jabref.model.entry.types.UnknownEntryType;

import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
Expand All @@ -23,6 +30,8 @@

class BibliographyConsistencyCheckTest {

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

@Test
void checkSimpleLibrary(@TempDir Path tempDir) {
BibEntry first = new BibEntry(StandardEntryType.Article, "first")
Expand Down Expand Up @@ -232,14 +241,14 @@ void checkFieldEntriesWithFieldDifferences() {
StandardField.TITLE,
StandardField.PAGES,
new UnknownField("customField"),
StandardField.PUBLISHER
StandardField.PUBLISHER,
StandardField.PDF
);
List<BibEntry> result = new BibliographyConsistencyCheck().filterAndSortEntriesWithFieldDifferences(
Set.of(entry1, entry2, entry3, entry4, entry5),
differingFields,
Set.of(StandardField.AUTHOR, StandardField.TITLE, StandardField.PAGES, StandardField.PDF));
differingFields);

assertEquals(List.of(entry1, entry2, entry3, entry4, entry5), result);
assertEquals(List.of(entry1, entry3, entry4, entry5), result);
}

@Test
Expand Down Expand Up @@ -279,4 +288,31 @@ void checkComplexLibraryWithAdditionalEntry(@TempDir Path tempDir) {
));
assertEquals(expectedResult, actualResult);
}

@Test
void checkCustomEntryTypes() {

BibEntry first = new BibEntry(StandardEntryType.Article, "first")
.withField(StandardField.AUTHOR, "Author One")
.withField(StandardField.PAGES, "some pages");
BibEntry second = new BibEntry(StandardEntryType.Article, "second")
.withField(StandardField.AUTHOR, "Author One")
.withField(StandardField.PUBLISHER, "publisher");
BibDatabase database = new BibDatabase(List.of(first, second));
BibDatabaseContext bibContext = new BibDatabaseContext(database);
bibContext.setMode(BibDatabaseMode.BIBTEX);

BibEntryTypesManager entryTypesManager = new BibEntryTypesManager();
BibEntryType customEntryType = new BibEntryType(CUSTOM_TYPE,
List.of(new BibField(StandardField.AUTHOR, FieldPriority.IMPORTANT), new BibField(StandardField.ABSTRACT, FieldPriority.IMPORTANT)),
Set.of());
entryTypesManager.addCustomOrModifiedType(customEntryType, bibContext.getMode());

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

BibliographyConsistencyCheck.EntryTypeResult entryTypeResult = new BibliographyConsistencyCheck.EntryTypeResult(Set.of(StandardField.PAGES, StandardField.PUBLISHER), List.of(first, second));
BibliographyConsistencyCheck.Result expected = new BibliographyConsistencyCheck.Result(Map.of(StandardEntryType.Article, entryTypeResult));
assertEquals(expected, result);
}
}
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