Merge branch 'main' into postgresql

.github/workflows/pr-comment.yml

@@ -43,7 +43,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
       - name: jbang
         if: ${{ steps.read-pr_number.outputs.pr_number != '' }}
-        uses: jbangdev/jbang-action@v0.118.0
+        uses: jbangdev/jbang-action@v0.119.0
         with:
           script: ghprcomment@koppor/ghprcomment
           scriptargs: "-r JabRef/jabref -p ${{ steps.read-pr_number.outputs.pr_number }} -w ${{ github.event.workflow_run.id }}"

CHANGELOG.md

@@ -47,10 +47,12 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - ⚠️ Renamed command line parameters `embeddBibfileInPdf` to `embedBibFileInPdf`, `writeMetadatatoPdf` to `writeMetadataToPdf`, and `writeXMPtoPdf` to `writeXmpToPdf`. [#11575](https://github.com/JabRef/jabref/pull/11575)
 - The browse button for a Custom theme now opens in the directory of the current used CSS file. [#11597](https://github.com/JabRef/jabref/pull/11597)
 - The browse button for a Custom exporter now opens in the directory of the current used exporter file. [#11717](https://github.com/JabRef/jabref/pull/11717)
+- JabRef now uses TLS 1.2 for all HTTPS connections. [#11852](https://github.com/JabRef/jabref/pull/11852)
 - We improved the display of long messages in the integrity check dialog. [#11619](https://github.com/JabRef/jabref/pull/11619)
 - We improved the undo/redo buttons in the main toolbar and main menu to be disabled when there is nothing to undo/redo. [#8807](https://github.com/JabRef/jabref/issues/8807)
 - We improved the DOI detection in PDF imports. [#11782](https://github.com/JabRef/jabref/pull/11782)
 - We improved the performance when pasting and importing entries in an existing library. [#11843](https://github.com/JabRef/jabref/pull/11843)
+- When fulltext search is selected but indexing is deactivated, a dialog is now shown asking if the user wants to enable indexing now [#9491](https://github.com/JabRef/jabref/issues/9491)
 
 ### Fixed
 
@@ -73,6 +75,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where search result highlighting was incorrectly highlighting the boolean operators. [#11595](https://github.com/JabRef/jabref/issues/11595)
 - We fixed an issue where search result highlighting was broken at complex searches. [#8067](https://github.com/JabRef/jabref/issues/8067)
 - We fixed an exception when searching for unlinked files. [#11731](https://github.com/JabRef/jabref/issues/11731)
+- We fixed an issue with the link to the full text at the BVB fetcher. [#11852](https://github.com/JabRef/jabref/pull/11852)
 - We fixed an issue where two contradicting notifications were shown when cutting an entry in the main table. [#11724](https://github.com/JabRef/jabref/pull/11724)
 - We fixed an issue where unescaped braces in the arXiv fetcher were not treated. [#11704](https://github.com/JabRef/jabref/issues/11704)
 - We fixed an issue where HTML instead of the fulltext pdf was downloaded when importing arXiv entries. [#4913](https://github.com/JabRef/jabref/issues/4913)

build.gradle

@@ -262,7 +262,7 @@ dependencies {
     implementation 'org.jsoup:jsoup:1.18.1'
     implementation 'com.konghq:unirest-java-core:4.4.4'
     implementation 'com.konghq:unirest-modules-gson:4.4.4'
-    implementation 'org.apache.httpcomponents.client5:httpclient5:5.3.1'
+    implementation 'org.apache.httpcomponents.client5:httpclient5:5.4'
     // endregion
 
     implementation 'org.slf4j:slf4j-api:2.0.16'
@@ -336,7 +336,7 @@ dependencies {
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
     }
-    implementation('dev.langchain4j:langchain4j-mistral-ai:0.34.0') {
+    implementation('dev.langchain4j:langchain4j-mistral-ai:0.35.0') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
@@ -345,7 +345,7 @@ dependencies {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
     }
-    implementation('dev.langchain4j:langchain4j-hugging-face:0.34.0') {
+    implementation('dev.langchain4j:langchain4j-hugging-face:0.35.0') {
         exclude group: 'com.squareup.okhttp3'
         exclude group: 'com.squareup.retrofit2', module: 'retrofit'
         exclude group: 'org.jetbrains.kotlin'
@@ -373,11 +373,11 @@ dependencies {
     implementation 'io.zonky.test:embedded-postgres:2.0.7'
     implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:17.0.0')
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.175'
+    testImplementation 'io.github.classgraph:classgraph:4.8.176'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.11.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.3'
 
-    testImplementation 'org.mockito:mockito-core:5.13.0'
+    testImplementation 'org.mockito:mockito-core:5.14.1'
     testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
     testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'

rewrite.yml

@@ -102,6 +102,8 @@ recipeList:
   - org.openrewrite.java.migrate.io.ReplaceFileInOrOutputStreamFinalizeWithClose
   - org.openrewrite.java.migrate.net.JavaNetAPIs
   - org.openrewrite.java.migrate.net.URLConstructorsToURIRecipes
+  - org.openrewrite.java.migrate.util.OptionalNotEmptyToIsPresent
+  - org.openrewrite.java.migrate.util.OptionalNotPresentToIsEmpty
   - org.openrewrite.java.migrate.util.SequencedCollection
   - org.openrewrite.java.migrate.lang.StringFormatted
 

src/main/java/org/jabref/Launcher.java

@@ -172,26 +172,29 @@ private static void initLogging(String[] args) {
     /**
      * @return true if JabRef should continue starting up, false if it should quit.
      */
-    private static boolean handleMultipleAppInstances(String[] args, RemotePreferences remotePreferences) {
+    private static boolean handleMultipleAppInstances(String[] args, RemotePreferences remotePreferences) throws InterruptedException {
         LOGGER.trace("Checking for remote handling...");
         if (remotePreferences.useRemoteServer()) {
             // Try to contact already running JabRef
             RemoteClient remoteClient = new RemoteClient(remotePreferences.getPort());
             if (remoteClient.ping()) {
                 LOGGER.debug("Pinging other instance succeeded.");
-                // We are not alone, there is already a server out there, send command line
-                // arguments to other instance
-                LOGGER.debug("Passing arguments passed on to running JabRef...");
-                if (remoteClient.sendCommandLineArguments(args)) {
-                    // So we assume it's all taken care of, and quit.
-                    // Output to both to the log and the screen. Therefore, we do not have an additional System.out.println.
-                    LOGGER.info("Arguments passed on to running JabRef instance. Shutting down.");
-                    return false;
+                if (args.length == 0) {
+                    // There is already a server out there, avoid showing log "Passing arguments" while no arguments are provided.
+                    LOGGER.warn("This JabRef instance is already running. Please switch to that instance.");
                 } else {
-                    LOGGER.warn("Could not communicate with other running JabRef instance.");
-                    // We do not launch a new instance in presence of an error
-                    return false;
+                    // We are not alone, there is already a server out there, send command line arguments to other instance
+                    LOGGER.debug("Passing arguments passed on to running JabRef...");
+                    if (remoteClient.sendCommandLineArguments(args)) {
+                        // So we assume it's all taken care of, and quit.
+                        // Output to both to the log and the screen. Therefore, we do not have an additional System.out.println.
+                        LOGGER.info("Arguments passed on to running JabRef instance. Shutting down.");
+                    } else {
+                        LOGGER.warn("Could not communicate with other running JabRef instance.");
+                    }
                 }
+                // We do not launch a new instance in presence if there is another instance running
+                return false;
             } else {
                 LOGGER.debug("Could not ping JabRef instance.");
             }

src/main/java/org/jabref/gui/JabRefGUI.java

@@ -393,7 +393,9 @@ public void stopBackgroundTasks() {
 
     public static void shutdownThreadPools() {
         LOGGER.trace("Shutting down taskExecutor");
-        taskExecutor.shutdown();
+        if (taskExecutor != null) {
+            taskExecutor.shutdown();
+        }
         LOGGER.trace("Shutting down fileUpdateMonitor");
         fileUpdateMonitor.shutdown();
         LOGGER.trace("Shutting down directoryMonitor");

src/main/java/org/jabref/gui/entryeditor/DeprecatedFieldsTab.java

@@ -68,7 +68,7 @@ protected SequencedSet<Field> determineFieldsToShow(BibEntry entry) {
         BibDatabaseMode mode = databaseContext.getMode();
         Optional<BibEntryType> entryType = entryTypesManager.enrich(entry.getType(), mode);
         if (entryType.isPresent()) {
-            return entryType.get().getDeprecatedFields(mode).stream().filter(field -> !entry.getField(field).isEmpty()).collect(Collectors.toCollection(LinkedHashSet::new));
+            return entryType.get().getDeprecatedFields(mode).stream().filter(field -> entry.getField(field).isPresent()).collect(Collectors.toCollection(LinkedHashSet::new));
         } else {
             // Entry type unknown -> treat all fields as required (thus no optional fields)
             return new LinkedHashSet<>();

src/main/java/org/jabref/gui/entryeditor/citationrelationtab/semanticscholar/SemanticScholarFetcher.java

@@ -33,7 +33,7 @@ public String getAPIUrl(String entry_point, BibEntry entry) {
 
     @Override
     public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
-        if (!entry.getDOI().isPresent()) {
+        if (entry.getDOI().isEmpty()) {
             return List.of();
         }
 
@@ -59,7 +59,7 @@ public List<BibEntry> searchCitedBy(BibEntry entry) throws FetcherException {
 
     @Override
     public List<BibEntry> searchCiting(BibEntry entry) throws FetcherException {
-        if (!entry.getDOI().isPresent()) {
+        if (entry.getDOI().isEmpty()) {
             return List.of();
         }
 

src/main/java/org/jabref/gui/linkedfile/DownloadLinkedFileAction.java

@@ -10,10 +10,7 @@
 import java.util.List;
 import java.util.Optional;
 
-import javax.net.ssl.HostnameVerifier;
-import javax.net.ssl.HttpsURLConnection;
 import javax.net.ssl.SSLHandshakeException;
-import javax.net.ssl.SSLSocketFactory;
 
 import javafx.beans.property.DoubleProperty;
 import javafx.beans.property.ReadOnlyDoubleProperty;
@@ -243,8 +240,6 @@ private boolean checkSSLHandshake(URLDownload urlDownload) {
     }
 
     private BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownload urlDownload) {
-        SSLSocketFactory defaultSSLSocketFactory = HttpsURLConnection.getDefaultSSLSocketFactory();
-        HostnameVerifier defaultHostnameVerifier = HttpsURLConnection.getDefaultHostnameVerifier();
         return BackgroundTask
                 .wrap(() -> {
                     String suggestedName;
@@ -263,7 +258,6 @@ private BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownlo
                 .then(destination -> new FileDownloadTask(urlDownload.getSource(), destination))
                 .onFailure(ex -> LOGGER.error("Error in download", ex))
                 .onFinished(() -> {
-                    URLDownload.setSSLVerification(defaultSSLSocketFactory, defaultHostnameVerifier);
                     downloadProgress.unbind();
                     downloadProgress.set(1);
                 });

src/main/java/org/jabref/gui/preferences/websearch/WebSearchTabViewModel.java

@@ -5,10 +5,6 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
-import javax.net.ssl.HostnameVerifier;
-import javax.net.ssl.HttpsURLConnection;
-import javax.net.ssl.SSLSocketFactory;
-
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.ListProperty;
 import javafx.beans.property.ObjectProperty;
@@ -217,15 +213,10 @@ public void checkCustomApiKey() {
         if (!apiKey.isEmpty()) {
             URLDownload urlDownload;
             try {
-                SSLSocketFactory defaultSslSocketFactory = HttpsURLConnection.getDefaultSSLSocketFactory();
-                HostnameVerifier defaultHostnameVerifier = HttpsURLConnection.getDefaultHostnameVerifier();
-
                 urlDownload = new URLDownload(testUrlWithoutApiKey + apiKey);
                 // The HEAD request cannot be used because its response is not 200 (maybe 404 or 596...).
                 int statusCode = ((HttpURLConnection) urlDownload.getSource().openConnection()).getResponseCode();
                 keyValid = (statusCode >= 200) && (statusCode < 300);
-
-                URLDownload.setSSLVerification(defaultSslSocketFactory, defaultHostnameVerifier);
             } catch (IOException | UnirestException e) {
                 keyValid = false;
             }

src/main/java/org/jabref/gui/search/GlobalSearchBar.java

@@ -44,6 +44,7 @@
 import org.jabref.architecture.AllowedToUseClassGetResource;
 import org.jabref.gui.ClipBoardManager;
 import org.jabref.gui.DialogService;
+import org.jabref.gui.LibraryTab;
 import org.jabref.gui.LibraryTabContainer;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.autocompleter.AppendPersonNamesStrategy;
@@ -57,6 +58,7 @@
 import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.TooltipTextUtil;
 import org.jabref.gui.util.UiTaskExecutor;
+import org.jabref.logic.FilePreferences;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.AutoCompleteFirstNameMode;
 import org.jabref.logic.search.SearchPreferences;
@@ -96,6 +98,7 @@ public class GlobalSearchBar extends HBox {
     private final DialogService dialogService;
     private final BooleanProperty globalSearchActive = new SimpleBooleanProperty(false);
     private final BooleanProperty illegalSearch = new SimpleBooleanProperty(false);
+    private final FilePreferences filePreferences;
     private GlobalSearchResultDialog globalSearchResultDialog;
     private final SearchType searchType;
 
@@ -109,6 +112,7 @@ public GlobalSearchBar(LibraryTabContainer tabContainer,
         this.stateManager = stateManager;
         this.preferences = preferences;
         this.searchPreferences = preferences.getSearchPreferences();
+        this.filePreferences = preferences.getFilePreferences();
         this.undoManager = undoManager;
         this.dialogService = dialogService;
         this.tabContainer = tabContainer;
@@ -151,7 +155,10 @@ public GlobalSearchBar(LibraryTabContainer tabContainer,
             if (keyBindingRepository.matches(event, KeyBinding.CLEAR_SEARCH)) {
                 searchField.clear();
                 if (searchType == SearchType.NORMAL_SEARCH) {
-                    tabContainer.getCurrentLibraryTab().getMainTable().requestFocus();
+                    LibraryTab currentLibraryTab = tabContainer.getCurrentLibraryTab();
+                    if (currentLibraryTab != null) {
+                        currentLibraryTab.getMainTable().requestFocus();
+                    }
                 }
                 event.consume();
             }
@@ -231,32 +238,59 @@ public GlobalSearchBar(LibraryTabContainer tabContainer,
     }
 
     private void initSearchModifierButtons() {
-        fulltextButton.setSelected(searchPreferences.isFulltext());
         fulltextButton.setTooltip(new Tooltip(Localization.lang("Fulltext search")));
         initSearchModifierButton(fulltextButton);
+
+        EasyBind.subscribe(filePreferences.fulltextIndexLinkedFilesProperty(), enabled -> {
+            if (!enabled) {
+                fulltextButton.setSelected(false);
+            } else if (searchPreferences.isFulltext()) {
+                fulltextButton.setSelected(true);
+            }
+        });
+
         fulltextButton.selectedProperty().addListener((obs, oldVal, newVal) -> {
-            searchPreferences.setSearchFlag(SearchFlags.FULLTEXT, newVal);
+            if (!filePreferences.shouldFulltextIndexLinkedFiles() && newVal) {
+                boolean enableFulltextSearch = dialogService.showConfirmationDialogAndWait(Localization.lang("Fulltext search"), Localization.lang("Fulltext search requires the setting 'Automatically index all linked files for fulltext search' to be enabled. Do you want to enable indexing now?"), Localization.lang("Enable indexing"), Localization.lang("Keep disabled"));
+
+                LibraryTab libraryTab = tabContainer.getCurrentLibraryTab();
+                if (libraryTab != null && enableFulltextSearch) {
+                    filePreferences.setFulltextIndexLinkedFiles(true);
+                    searchPreferences.setSearchFlag(SearchFlags.FULLTEXT, true);
+                }
+                if (!enableFulltextSearch) {
+                    fulltextButton.setSelected(false);
+                    searchPreferences.setSearchFlag(SearchFlags.FULLTEXT, false);
+                }
+            } else {
+                searchPreferences.setSearchFlag(SearchFlags.FULLTEXT, newVal);
+            }
+            searchField.requestFocus();
             updateSearchQuery();
         });
 
         keepSearchString.setSelected(searchPreferences.shouldKeepSearchString());
         keepSearchString.setTooltip(new Tooltip(Localization.lang("Keep search string across libraries")));
         initSearchModifierButton(keepSearchString);
-        keepSearchString.selectedProperty().addListener((obs, oldVal, newVal) -> searchPreferences.setKeepSearchString(newVal));
+        keepSearchString.selectedProperty().addListener((obs, oldVal, newVal) -> {
+            searchPreferences.setKeepSearchString(newVal);
+            searchField.requestFocus();
+        });
 
         filterModeButton.setSelected(searchPreferences.getSearchDisplayMode() == SearchDisplayMode.FILTER);
         filterModeButton.setTooltip(new Tooltip(Localization.lang("Filter search results")));
         initSearchModifierButton(filterModeButton);
-        filterModeButton.setOnAction(event -> searchPreferences.setSearchDisplayMode(filterModeButton.isSelected() ? SearchDisplayMode.FILTER : SearchDisplayMode.FLOAT));
+        filterModeButton.setOnAction(event -> {
+            searchPreferences.setSearchDisplayMode(filterModeButton.isSelected() ? SearchDisplayMode.FILTER : SearchDisplayMode.FLOAT);
+            searchField.requestFocus();
+        });
 
         openGlobalSearchButton.disableProperty().bindBidirectional(globalSearchActive);
         openGlobalSearchButton.setTooltip(new Tooltip(Localization.lang("Search across libraries in a new window")));
         initSearchModifierButton(openGlobalSearchButton);
         openGlobalSearchButton.setOnAction(evt -> openGlobalSearchDialog());
 
-        searchPreferences.getObservableSearchFlags().addListener((SetChangeListener.Change<? extends SearchFlags> change) -> {
-            fulltextButton.setSelected(searchPreferences.isFulltext());
-        });
+        searchPreferences.getObservableSearchFlags().addListener((SetChangeListener.Change<? extends SearchFlags> change) -> fulltextButton.setSelected(searchPreferences.isFulltext()));
     }
 
     public void openGlobalSearchDialog() {
@@ -268,7 +302,7 @@ public void openGlobalSearchDialog() {
             globalSearchResultDialog = new GlobalSearchResultDialog(undoManager, tabContainer);
         }
         stateManager.activeSearchQuery(SearchType.NORMAL_SEARCH).get().ifPresent(query ->
-                    stateManager.activeSearchQuery(SearchType.GLOBAL_SEARCH).set(Optional.of(query)));
+                stateManager.activeSearchQuery(SearchType.GLOBAL_SEARCH).set(Optional.of(query)));
         updateSearchQuery();
         dialogService.showCustomDialogAndWait(globalSearchResultDialog);
         globalSearchActive.setValue(false);