Check duplicate DOI

CHANGELOG.md

@@ -17,6 +17,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added support for basic markdown in custom formatted previews [#6194](https://github.com/JabRef/jabref/issues/6194)
 - We now show the number of items found and selected to import in the online search dialog. [#6248](https://github.com/JabRef/jabref/pull/6248)
 - We created a new install screen for macOS. [#5759](https://github.com/JabRef/jabref/issues/5759)
+- We added a new integrity check for duplicate DOIs. [koppor#339](https://github.com/koppor/jabref/issues/339)
 
 ### Changed
 

src/main/java/org/jabref/gui/integrity/IntegrityCheckAction.java

@@ -54,6 +54,7 @@ protected List<IntegrityMessage> call() {
                 List<IntegrityMessage> result = new ArrayList<>();
 
                 ObservableList<BibEntry> entries = database.getDatabase().getEntries();
+                result.addAll(check.checkDatabase(database.getDatabase()));
                 for (int i = 0; i < entries.size(); i++) {
                     if (isCancelled()) {
                         break;

src/main/java/org/jabref/logic/integrity/ASCIICharacterChecker.java

@@ -4,7 +4,6 @@
 import java.util.List;
 import java.util.Map;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;

src/main/java/org/jabref/logic/integrity/BibStringChecker.java

@@ -6,7 +6,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;
@@ -17,7 +16,6 @@ public class BibStringChecker implements Checker {
     // Detect # if it doesn't have a \ in front of it or if it starts the string
     private static final Pattern UNESCAPED_HASH = Pattern.compile("(?<!\\\\)#|^#");
 
-
     /**
      * Checks, if there is an even number of unescaped #
      */

src/main/java/org/jabref/logic/integrity/BibTeXEntryTypeChecker.java

@@ -3,7 +3,6 @@
 import java.util.Collections;
 import java.util.List;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.InternalField;

src/main/java/org/jabref/logic/integrity/BibtexKeyChecker.java

@@ -4,7 +4,6 @@
 import java.util.List;
 import java.util.Optional;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.InternalField;
@@ -21,7 +20,7 @@ public List<IntegrityMessage> check(BibEntry entry) {
         Optional<String> author = entry.getField(StandardField.AUTHOR);
         Optional<String> title = entry.getField(StandardField.TITLE);
         Optional<String> year = entry.getField(StandardField.YEAR);
-        if (!author.isPresent() || !title.isPresent() || !year.isPresent()) {
+        if (author.isEmpty() || title.isEmpty() || year.isEmpty()) {
             return Collections.emptyList();
         }
 

src/main/java/org/jabref/logic/integrity/BibtexKeyDuplicationChecker.java

@@ -5,7 +5,6 @@
 import java.util.Objects;
 import java.util.Optional;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;

src/main/java/org/jabref/logic/integrity/BibtexkeyDeviationChecker.java

@@ -7,7 +7,6 @@
 
 import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternPreferences;
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -26,7 +25,7 @@ public BibtexkeyDeviationChecker(BibDatabaseContext bibDatabaseContext, BibtexKe
     @Override
     public List<IntegrityMessage> check(BibEntry entry) {
         Optional<String> valuekey = entry.getCiteKeyOptional();
-        if (!valuekey.isPresent()) {
+        if (valuekey.isEmpty()) {
             return Collections.emptyList();
         }
 

src/main/java/org/jabref/logic/integrity/Checker.java

@@ -0,0 +1,10 @@
+package org.jabref.logic.integrity;
+
+import java.util.List;
+
+import org.jabref.model.entry.BibEntry;
+
+@FunctionalInterface
+public interface Checker {
+    List<IntegrityMessage> check(BibEntry entry);
+}

src/main/java/org/jabref/logic/integrity/DatabaseChecker.java

@@ -0,0 +1,10 @@
+package org.jabref.logic.integrity;
+
+import java.util.List;
+
+import org.jabref.model.database.BibDatabase;
+
+@FunctionalInterface
+public interface DatabaseChecker {
+    List<IntegrityMessage> check(BibDatabase database);
+}

src/main/java/org/jabref/logic/integrity/DoiDuplicationChecker.java

@@ -0,0 +1,35 @@
+package org.jabref.logic.integrity;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import javafx.collections.ObservableList;
+
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.identifier.DOI;
+
+import com.google.common.collect.BiMap;
+import com.google.common.collect.HashBiMap;
+
+public class DoiDuplicationChecker implements DatabaseChecker {
+
+    @Override
+    public List<IntegrityMessage> check(BibDatabase database) {
+        ObservableList<BibEntry> bibEntries = database.getEntries();
+        BiMap<DOI, List<BibEntry>> duplicateMap = HashBiMap.create(bibEntries.size());
+        for (BibEntry bibEntry : bibEntries) {
+            bibEntry.getDOI().ifPresent(doi ->
+                    duplicateMap.computeIfAbsent(doi, absentDoi -> new ArrayList<>()).add(bibEntry));
+        }
+
+        return duplicateMap.inverse().keySet().stream()
+                           .filter(list -> list.size() > 1)
+                           .flatMap(list -> list.stream())
+                           .map(item -> new IntegrityMessage(Localization.lang("Unique DOI used in multiple entries"), item, StandardField.DOI))
+                           .collect(Collectors.toList());
+    }
+}

src/main/java/org/jabref/logic/integrity/DOIValidityChecker.java → src/main/java/org/jabref/logic/integrity/DoiValidityChecker.java

@@ -6,8 +6,7 @@
 import org.jabref.model.entry.identifier.DOI;
 import org.jabref.model.strings.StringUtil;
 
-public class DOIValidityChecker implements ValueChecker {
-
+public class DoiValidityChecker implements ValueChecker {
     @Override
     public Optional<String> checkValue(String value) {
         if (StringUtil.isBlank(value)) {

src/main/java/org/jabref/logic/integrity/EntryLinkChecker.java

@@ -7,7 +7,6 @@
 import java.util.Objects;
 import java.util.Set;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
@@ -28,14 +27,14 @@ public List<IntegrityMessage> check(BibEntry entry) {
         for (Entry<Field, String> field : entry.getFieldMap().entrySet()) {
             Set<FieldProperty> properties = field.getKey().getProperties();
             if (properties.contains(FieldProperty.SINGLE_ENTRY_LINK)) {
-                if (!database.getEntryByKey(field.getValue()).isPresent()) {
+                if (database.getEntryByKey(field.getValue()).isEmpty()) {
                     result.add(new IntegrityMessage(Localization.lang("Referenced BibTeX key does not exist"), entry,
                             field.getKey()));
                 }
             } else if (properties.contains(FieldProperty.MULTIPLE_ENTRY_LINK)) {
                 List<String> keys = new ArrayList<>(Arrays.asList(field.getValue().split(",")));
                 for (String key : keys) {
-                    if (!database.getEntryByKey(key).isPresent()) {
+                    if (database.getEntryByKey(key).isEmpty()) {
                         result.add(new IntegrityMessage(
                                 Localization.lang("Referenced BibTeX key does not exist") + ": " + key, entry,
                                 field.getKey()));

src/main/java/org/jabref/logic/integrity/FieldChecker.java

@@ -9,7 +9,7 @@
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.util.OptionalUtil;
 
-public class FieldChecker implements IntegrityCheck.Checker {
+public class FieldChecker implements Checker {
     protected final Field field;
     private final ValueChecker checker;
 
@@ -21,7 +21,7 @@ public FieldChecker(Field field, ValueChecker checker) {
     @Override
     public List<IntegrityMessage> check(BibEntry entry) {
         Optional<String> value = entry.getField(field);
-        if (!value.isPresent()) {
+        if (value.isEmpty()) {
             return Collections.emptyList();
         }
 

src/main/java/org/jabref/logic/integrity/FieldCheckers.java

@@ -40,7 +40,7 @@ private static Multimap<Field, ValueChecker> getAllMap(BibDatabaseContext databa
         fieldCheckers.put(StandardField.BOOKTITLE, new BooktitleChecker());
         fieldCheckers.put(StandardField.TITLE, new BracketChecker());
         fieldCheckers.put(StandardField.TITLE, new TitleChecker(databaseContext));
-        fieldCheckers.put(StandardField.DOI, new DOIValidityChecker());
+        fieldCheckers.put(StandardField.DOI, new DoiValidityChecker());
         fieldCheckers.put(StandardField.EDITION, new EditionChecker(databaseContext, allowIntegerEdition));
         fieldCheckers.put(StandardField.FILE, new FileChecker(databaseContext, filePreferences));
         fieldCheckers.put(StandardField.HOWPUBLISHED, new HowPublishedChecker(databaseContext));

src/main/java/org/jabref/logic/integrity/HTMLCharacterChecker.java

@@ -6,7 +6,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;

src/main/java/org/jabref/logic/integrity/IntegrityCheck.java

@@ -1,11 +1,12 @@
 package org.jabref.logic.integrity;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
-import java.util.Objects;
 
 import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternPreferences;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
+import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
@@ -14,75 +15,77 @@
 public class IntegrityCheck {
 
     private final BibDatabaseContext bibDatabaseContext;
-    private final FilePreferences filePreferences;
-    private final BibtexKeyPatternPreferences bibtexKeyPatternPreferences;
-    private final JournalAbbreviationRepository journalAbbreviationRepository;
-    private final boolean enforceLegalKey;
-    private final boolean allowIntegerEdition;
+    private final FieldCheckers fieldCheckers;
+    private final List<Checker> entryCheckers;
 
     public IntegrityCheck(BibDatabaseContext bibDatabaseContext,
                           FilePreferences filePreferences,
                           BibtexKeyPatternPreferences bibtexKeyPatternPreferences,
                           JournalAbbreviationRepository journalAbbreviationRepository,
                           boolean enforceLegalKey,
                           boolean allowIntegerEdition) {
-        this.bibDatabaseContext = Objects.requireNonNull(bibDatabaseContext);
-        this.filePreferences = Objects.requireNonNull(filePreferences);
-        this.bibtexKeyPatternPreferences = Objects.requireNonNull(bibtexKeyPatternPreferences);
-        this.journalAbbreviationRepository = Objects.requireNonNull(journalAbbreviationRepository);
-        this.enforceLegalKey = enforceLegalKey;
-        this.allowIntegerEdition = allowIntegerEdition;
+        this.bibDatabaseContext = bibDatabaseContext;
+
+        fieldCheckers = new FieldCheckers(bibDatabaseContext,
+                filePreferences,
+                journalAbbreviationRepository,
+                enforceLegalKey,
+                allowIntegerEdition);
+
+        entryCheckers = new ArrayList<>(List.of(
+                new BibtexKeyChecker(),
+                new TypeChecker(),
+                new BibStringChecker(),
+                new HTMLCharacterChecker(),
+                new EntryLinkChecker(bibDatabaseContext.getDatabase()),
+                new BibtexkeyDeviationChecker(bibDatabaseContext, bibtexKeyPatternPreferences),
+                new BibtexKeyDuplicationChecker(bibDatabaseContext.getDatabase())
+        ));
+
+        if (!bibDatabaseContext.isBiblatexMode()) {
+            entryCheckers.add(new JournalInAbbreviationListChecker(StandardField.JOURNALTITLE, journalAbbreviationRepository));
+        } else {
+            entryCheckers.addAll(List.of(
+                    new JournalInAbbreviationListChecker(StandardField.JOURNAL, journalAbbreviationRepository),
+                    new ASCIICharacterChecker(),
+                    new NoBibtexFieldChecker(),
+                    new BibTeXEntryTypeChecker())
+            );
+        }
     }
 
-    public List<IntegrityMessage> checkDatabase() {
+    List<IntegrityMessage> executeAllCheckers() {
         List<IntegrityMessage> result = new ArrayList<>();
 
-        for (BibEntry entry : bibDatabaseContext.getDatabase().getEntries()) {
+        BibDatabase database = bibDatabaseContext.getDatabase();
+
+        for (BibEntry entry : database.getEntries()) {
             result.addAll(checkEntry(entry));
         }
 
+        result.addAll(checkDatabase(database));
+
         return result;
     }
 
     public List<IntegrityMessage> checkEntry(BibEntry entry) {
         List<IntegrityMessage> result = new ArrayList<>();
-
         if (entry == null) {
             return result;
         }
 
-        FieldCheckers fieldCheckers = new FieldCheckers(bibDatabaseContext,
-                                                        filePreferences,
-                                                        journalAbbreviationRepository,
-                                                        enforceLegalKey,
-                                                        allowIntegerEdition);
-        for (FieldChecker checker : fieldCheckers.getAll()) {
-            result.addAll(checker.check(entry));
+        for (FieldChecker fieldChecker : fieldCheckers.getAll()) {
+            result.addAll(fieldChecker.check(entry));
         }
 
-        if (!bibDatabaseContext.isBiblatexMode()) {
-            // BibTeX only checkers
-            result.addAll(new ASCIICharacterChecker().check(entry));
-            result.addAll(new NoBibtexFieldChecker().check(entry));
-            result.addAll(new BibTeXEntryTypeChecker().check(entry));
-            result.addAll(new JournalInAbbreviationListChecker(StandardField.JOURNAL, journalAbbreviationRepository).check(entry));
-        } else {
-            result.addAll(new JournalInAbbreviationListChecker(StandardField.JOURNALTITLE, journalAbbreviationRepository).check(entry));
+        for (Checker entryChecker : entryCheckers) {
+            result.addAll(entryChecker.check(entry));
         }
 
-        result.addAll(new BibtexKeyChecker().check(entry));
-        result.addAll(new TypeChecker().check(entry));
-        result.addAll(new BibStringChecker().check(entry));
-        result.addAll(new HTMLCharacterChecker().check(entry));
-        result.addAll(new EntryLinkChecker(bibDatabaseContext.getDatabase()).check(entry));
-        result.addAll(new BibtexkeyDeviationChecker(bibDatabaseContext, bibtexKeyPatternPreferences).check(entry));
-        result.addAll(new BibtexKeyDuplicationChecker(bibDatabaseContext.getDatabase()).check(entry));
-
         return result;
     }
 
-    @FunctionalInterface
-    public interface Checker {
-        List<IntegrityMessage> check(BibEntry entry);
+    public List<IntegrityMessage> checkDatabase(BibDatabase database) {
+        return new DoiDuplicationChecker().check(database);
     }
 }

src/main/java/org/jabref/logic/integrity/IntegrityMessage.java

@@ -6,9 +6,7 @@
 import org.jabref.model.entry.field.Field;
 
 public final class IntegrityMessage implements Cloneable {
-
     private final BibEntry entry;
-
     private final Field field;
     private final String message;
 

src/main/java/org/jabref/logic/integrity/JournalInAbbreviationListChecker.java

@@ -5,7 +5,6 @@
 import java.util.Objects;
 import java.util.Optional;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
@@ -24,7 +23,7 @@ public JournalInAbbreviationListChecker(Field field, JournalAbbreviationReposito
     @Override
     public List<IntegrityMessage> check(BibEntry entry) {
         Optional<String> value = entry.getField(field);
-        if (!value.isPresent()) {
+        if (value.isEmpty()) {
             return Collections.emptyList();
         }
 

src/main/java/org/jabref/logic/integrity/NoBibtexFieldChecker.java

@@ -4,7 +4,6 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import org.jabref.logic.integrity.IntegrityCheck.Checker;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.BibField;