Remove predatory journal checker due to false positives (#11066)

* Remove predatory journal checker due to false positives * remove * Remove all predatory stuff * checkstyle * Update CHANGELOG.md * Update CHANGELOG.md --------- Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>
JabRef · Mar 21, 2024 · 2ba3b2a · 2ba3b2a
1 parent 07fc11e
commit 2ba3b2a
Show file tree

Hide file tree

Showing 18 changed files with 30 additions and 505 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -79,6 +79,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Removed
 
+- We removed the predatory journal checks due to a high rate of false positives. [#11066](https://github.com/JabRef/jabref/pull/11066)
+
 ## [5.12] – 2023-12-24
 
 ### Added

diff --git a/build.gradle b/build.gradle
@@ -351,18 +351,8 @@ tasks.register("generateJournalListMV", JavaExec) {
     }
 }
 
-tasks.register("generatePredatoryJournalListMV", JavaExec) {
-        group = "JabRef"
-        description = "Load predatory journal information from online sources to a H2 MVStore"
-        classpath = sourceSets.main.runtimeClasspath
-        mainClass = "org.jabref.cli.PredatoryJournalsMvGenerator"
-        onlyIf {
-            !file("build/resources/main/journals/predatory-journals.mv").exists()
-        }
-}
-
-jar.dependsOn("generateJournalListMV", "generatePredatoryJournalListMV")
-compileTestJava.dependsOn("generateJournalListMV","generatePredatoryJournalListMV")
+jar.dependsOn("generateJournalListMV")
+compileTestJava.dependsOn("generateJournalListMV")
 
 tasks.register('generateCitaviSource', XjcTask) {
     group = 'JabRef'

diff --git a/src/main/java/org/jabref/Launcher.java b/src/main/java/org/jabref/Launcher.java
@@ -17,7 +17,6 @@
 import org.jabref.gui.JabRefGUI;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
-import org.jabref.logic.journals.predatory.PredatoryJournalListLoader;
 import org.jabref.logic.net.ProxyAuthenticator;
 import org.jabref.logic.net.ProxyPreferences;
 import org.jabref.logic.net.ProxyRegisterer;
@@ -188,9 +187,6 @@ private static void initGlobals(PreferencesService preferences) {
         // Read list(s) of journal names and abbreviations
         Globals.journalAbbreviationRepository = JournalAbbreviationLoader
                 .loadRepository(preferences.getJournalAbbreviationPreferences());
-        Globals.predatoryJournalRepository = PredatoryJournalListLoader
-                .loadRepository();
-
         Globals.entryTypesManager = preferences.getCustomEntryTypesRepository();
         Globals.protectedTermsLoader = new ProtectedTermsLoader(preferences.getProtectedTermsPreferences());
     }

diff --git a/src/main/java/org/jabref/cli/PredatoryJournalsMvGenerator.java b/src/main/java/org/jabref/cli/PredatoryJournalsMvGenerator.java
diff --git a/src/main/java/org/jabref/gui/Globals.java b/src/main/java/org/jabref/gui/Globals.java
@@ -8,7 +8,6 @@
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.journals.predatory.PredatoryJournalRepository;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.remote.RemotePreferences;
 import org.jabref.logic.remote.server.RemoteListenerServerManager;
@@ -51,8 +50,6 @@ public class Globals {
      * Only GUI code is allowed to access it, logic code should use dependency injection.
      */
     public static JournalAbbreviationRepository journalAbbreviationRepository;
-    public static PredatoryJournalRepository predatoryJournalRepository;
-
     /**
      * This field is initialized upon startup.
      * <p>

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -302,7 +302,6 @@ private void initLayout() {
                 taskExecutor,
                 dialogService,
                 Globals.journalAbbreviationRepository,
-                Globals.predatoryJournalRepository,
                 entryTypesManager,
                 undoManager,
                 Globals.getClipboardManager());

diff --git a/src/main/java/org/jabref/gui/JabRefGUI.java b/src/main/java/org/jabref/gui/JabRefGUI.java
@@ -102,11 +102,6 @@ public void stop() {
         OOBibBaseConnect.closeOfficeConnection();
         Globals.stopBackgroundTasks();
         Globals.shutdownThreadPools();
-        try {
-            Globals.predatoryJournalRepository.close();
-        } catch (Exception e) {
-            LOGGER.warn("Cloud not shut down predatoryJournalRepository", e);
-        }
     }
 
     private void setupProxy() {

diff --git a/src/main/java/org/jabref/gui/MainMenu.java b/src/main/java/org/jabref/gui/MainMenu.java
@@ -66,7 +66,6 @@
 import org.jabref.logic.importer.IdFetcher;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.journals.predatory.PredatoryJournalRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -84,7 +83,6 @@ public class MainMenu extends MenuBar {
     private final TaskExecutor taskExecutor;
     private final DialogService dialogService;
     private final JournalAbbreviationRepository abbreviationRepository;
-    private final PredatoryJournalRepository predatoryJournalRepository;
     private final BibEntryTypesManager entryTypesManager;
     private final UndoManager undoManager;
     private final ClipBoardManager clipBoardManager;
@@ -98,7 +96,6 @@ public MainMenu(JabRefFrame frame,
                     TaskExecutor taskExecutor,
                     DialogService dialogService,
                     JournalAbbreviationRepository abbreviationRepository,
-                    PredatoryJournalRepository predatoryJournalRepository,
                     BibEntryTypesManager entryTypesManager,
                     UndoManager undoManager,
                     ClipBoardManager clipBoardManager) {
@@ -111,7 +108,6 @@ public MainMenu(JabRefFrame frame,
         this.taskExecutor = taskExecutor;
         this.dialogService = dialogService;
         this.abbreviationRepository = abbreviationRepository;
-        this.predatoryJournalRepository = predatoryJournalRepository;
         this.entryTypesManager = entryTypesManager;
         this.undoManager = undoManager;
         this.clipBoardManager = clipBoardManager;
@@ -229,7 +225,7 @@ private void createMenu() {
         quality.getItems().addAll(
                 factory.createMenuItem(StandardActions.FIND_DUPLICATES, new DuplicateSearch(frame::getCurrentLibraryTab, dialogService, stateManager, preferencesService, entryTypesManager, taskExecutor)),
                 factory.createMenuItem(StandardActions.MERGE_ENTRIES, new MergeEntriesAction(dialogService, stateManager, preferencesService)),
-                factory.createMenuItem(StandardActions.CHECK_INTEGRITY, new IntegrityCheckAction(frame::getCurrentLibraryTab, preferencesService, dialogService, stateManager, taskExecutor, abbreviationRepository, predatoryJournalRepository)),
+                factory.createMenuItem(StandardActions.CHECK_INTEGRITY, new IntegrityCheckAction(frame::getCurrentLibraryTab, preferencesService, dialogService, stateManager, taskExecutor, abbreviationRepository)),
                 factory.createMenuItem(StandardActions.CLEANUP_ENTRIES, new CleanupAction(frame::getCurrentLibraryTab, preferencesService, dialogService, stateManager, taskExecutor, undoManager)),
 
                 new SeparatorMenuItem(),

diff --git a/src/main/java/org/jabref/gui/integrity/IntegrityCheckAction.java b/src/main/java/org/jabref/gui/integrity/IntegrityCheckAction.java
@@ -15,7 +15,6 @@
 import org.jabref.logic.integrity.IntegrityCheck;
 import org.jabref.logic.integrity.IntegrityMessage;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.journals.predatory.PredatoryJournalRepository;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -31,23 +30,19 @@ public class IntegrityCheckAction extends SimpleCommand {
     private final PreferencesService preferencesService;
     private final StateManager stateManager;
     private final JournalAbbreviationRepository abbreviationRepository;
-    private final PredatoryJournalRepository predatoryJournalRepository;
 
     public IntegrityCheckAction(Supplier<LibraryTab> tabSupplier,
                                 PreferencesService preferencesService,
                                 DialogService dialogService,
                                 StateManager stateManager,
                                 TaskExecutor taskExecutor,
-                                JournalAbbreviationRepository abbreviationRepository,
-                                PredatoryJournalRepository predatoryJournalRepository) {
+                                JournalAbbreviationRepository abbreviationRepository) {
         this.tabSupplier = tabSupplier;
         this.stateManager = stateManager;
         this.taskExecutor = taskExecutor;
         this.preferencesService = preferencesService;
         this.dialogService = dialogService;
         this.abbreviationRepository = abbreviationRepository;
-        this.predatoryJournalRepository = predatoryJournalRepository;
-
         this.executable.bind(needsDatabase(this.stateManager));
     }
 
@@ -58,7 +53,6 @@ public void execute() {
                 preferencesService.getFilePreferences(),
                 preferencesService.getCitationKeyPatternPreferences(),
                 abbreviationRepository,
-                predatoryJournalRepository,
                 preferencesService.getEntryEditorPreferences().shouldAllowIntegerEditionBibtex());
 
         Task<List<IntegrityMessage>> task = new Task<>() {

diff --git a/src/main/java/org/jabref/logic/integrity/IntegrityCheck.java b/src/main/java/org/jabref/logic/integrity/IntegrityCheck.java
@@ -6,7 +6,6 @@
 
 import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
-import org.jabref.logic.journals.predatory.PredatoryJournalRepository;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -23,7 +22,6 @@ public IntegrityCheck(BibDatabaseContext bibDatabaseContext,
                           FilePreferences filePreferences,
                           CitationKeyPatternPreferences citationKeyPatternPreferences,
                           JournalAbbreviationRepository journalAbbreviationRepository,
-                          PredatoryJournalRepository predatoryJournalRepository,
                           boolean allowIntegerEdition) {
         this.bibDatabaseContext = bibDatabaseContext;
 
@@ -42,10 +40,8 @@ public IntegrityCheck(BibDatabaseContext bibDatabaseContext,
                 new CitationKeyDuplicationChecker(bibDatabaseContext.getDatabase()),
                 new AmpersandChecker(),
                 new LatexIntegrityChecker(),
-                new JournalInAbbreviationListChecker(StandardField.JOURNAL, journalAbbreviationRepository),
-                new PredatoryJournalChecker(predatoryJournalRepository,
-                        List.of(StandardField.JOURNAL, StandardField.PUBLISHER, StandardField.BOOKTITLE))
-                ));
+                new JournalInAbbreviationListChecker(StandardField.JOURNAL, journalAbbreviationRepository)));
+
         if (bibDatabaseContext.isBiblatexMode()) {
             entryCheckers.add(new UTF8Checker(bibDatabaseContext.getMetaData().getEncoding().orElse(StandardCharsets.UTF_8)));
         } else {

diff --git a/src/main/java/org/jabref/logic/integrity/PredatoryJournalChecker.java b/src/main/java/org/jabref/logic/integrity/PredatoryJournalChecker.java
diff --git a/src/main/java/org/jabref/logic/journals/predatory/PredatoryJournalInformation.java b/src/main/java/org/jabref/logic/journals/predatory/PredatoryJournalInformation.java