Merge branch 'main' into auto-relativize-file-paths

Author: subhramit

.github/ghprcomment.yml

@@ -2,12 +2,8 @@
   message: |
     Your code currently does not meet [JabRef's code guidelines](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
     We use [Checkstyle](https://checkstyle.sourceforge.io/) to identify issues.
-    The tool reviewdog already placed comments on GitHub to indicate the places. See the tab "Files" in you PR.
     Please carefully follow [the setup guide for the codestyle](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html).
     Afterwards, please [run checkstyle locally](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.html#run-checkstyle) and fix the issues.
-
-
-    You can check review dog's comments at the tab "Files changed" of your pull request.
 - jobName: OpenRewrite
   message: |
     Your code currently does not meet JabRef's code guidelines.

CHANGELOG.md

@@ -16,8 +16,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - When a search hits a file, the file icon of that entry is changed accordingly. [#11542](https://github.com/JabRef/jabref/pull/11542)
 - We added an AI-based chat for entries with linked PDF files. [#11430](https://github.com/JabRef/jabref/pull/11430)
 - We added an AI-based summarization possibility for entries with linked PDF files. [#11430](https://github.com/JabRef/jabref/pull/11430)
+- We added an AI section in JabRef's [preferences](https://docs.jabref.org/ai/preferences). [#11430](https://github.com/JabRef/jabref/pull/11430)
+- We added AI providers: OpenAI, Mistral AI, Hugging Face and Google. [#11430](https://github.com/JabRef/jabref/pull/11430), [#11736](https://github.com/JabRef/jabref/pull/11736)
+- We added AI providers: [Ollama](https://docs.jabref.org/ai/local-llm#step-by-step-guide-for-ollama) and GPT4All, which add the possibility to use local LLMs privately on your own device. [#11430](https://github.com/JabRef/jabref/pull/11430), [#11870](https://github.com/JabRef/jabref/issues/11870)
 - We added support for selecting and using CSL Styles in JabRef's OpenOffice/LibreOffice integration for inserting bibliographic and in-text citations into a document. [#2146](https://github.com/JabRef/jabref/issues/2146), [#8893](https://github.com/JabRef/jabref/issues/8893)
-- We added Tools > New library based on references in PDF file... to create a new library based on the references section in a PDF file. [#11522](https://github.com/JabRef/jabref/pull/11522)
+- We added "Tools > New library based on references in PDF file" ... to create a new library based on the references section in a PDF file. [#11522](https://github.com/JabRef/jabref/pull/11522)
 - When converting the references section of a paper (PDF file), more than the last page is treated. [#11522](https://github.com/JabRef/jabref/pull/11522)
 - Added the functionality to invoke offline reference parsing explicitly. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - The dialog for [adding an entry using reference text](https://docs.jabref.org/collect/newentryfromplaintext) is now filled with the clipboard contents as default. [#11565](https://github.com/JabRef/jabref/pull/11565)
@@ -67,7 +70,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a new CSS style class `main-table` for the main table. [#11881](https://github.com/JabRef/jabref/pull/11881)
 - When renaming a file, the old extension is now used if there is none provided in the new name. [#11903](https://github.com/JabRef/jabref/issues/11903)
 - When importing a file using "Find Unlinked Files", when one or more file directories are available, the file path will be relativized where possible [koppor#549](https://github.com/koppor/jabref/issues/549)
-- We changed the name of the library-based file directory from 'General File Directory' to 'Library-specific File Directory' per issue [#571](https://github.com/koppor/jabref/issues/571)
+- We added minimum window sizing for windows dedicated to creating new entries [#11944](https://github.com/JabRef/jabref/issues/11944)
+- We changed the name of the library-based file directory from 'General File Directory' to 'Library-specific File Directory' per issue. [#571](https://github.com/koppor/jabref/issues/571)
 - The CitationKey column is now a default shown column for the entry table. [#10510](https://github.com/JabRef/jabref/issues/10510)
 
 ### Fixed
@@ -102,6 +106,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where recently opened files were not displayed in the main menu properly. [#9042](https://github.com/JabRef/jabref/issues/9042)
 - We fixed an issue where the DOI lookup would show an error when a DOI was found for an entry. [#11850](https://github.com/JabRef/jabref/issues/11850)
 - We fixed an issue where <kbd>Tab</kbd> cannot be used to jump to next field in some single-line fields. [#11785](https://github.com/JabRef/jabref/issues/11785)
+- We fixed an issue where the "Do not ask again" checkbox was not working, when asking for permission to use Grobid [koppor#556](https://github.com/koppor/jabref/issues/566).
 - We fixed an issue where we display warning message for moving attached open files. [#10121](https://github.com/JabRef/jabref/issues/10121)
 - We fixed an issue where it was not possible to select selecting content of other user's comments.[#11106](https://github.com/JabRef/jabref/issues/11106)
 - We fixed an issue where web search preferences "Custom API key" table modifications not discarded. [#11925](https://github.com/JabRef/jabref/issues/11925)

build.gradle

@@ -385,6 +385,7 @@ dependencies {
     testImplementation "org.testfx:testfx-core:4.0.16-alpha"
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:3.0"
+    testImplementation "com.github.javaparser:javaparser-symbol-solver-core:3.26.2"
 
     // recommended by https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
     testImplementation 'org.wiremock:wiremock-standalone:3.3.1'

src/main/java/org/jabref/gui/ai/components/privacynotice/PrivacyNoticeComponent.fxml

@@ -66,6 +66,15 @@
                   </Text>
                </children>
             </TextFlow>
+             <TextFlow fx:id="gpt4AllTextFlow">
+                 <children>
+                     <Text text="%If you have chosen %0 as an AI provider, the privacy policy of %0 applies. You find it at %1.">
+                         <font>
+                             <Font size="14.0" />
+                         </font>
+                     </Text>
+                 </children>
+             </TextFlow>
              <TextFlow>
                 <Text fx:id="embeddingModelText" text="%Additionally, we use Deep Java Library (DJL) embedding models for both chatting and summarization. The embedding model will be downloaded in background (size %0) from Deep Java Library servers anonymously.">
                    <font>

src/main/java/org/jabref/gui/ai/components/privacynotice/PrivacyNoticeComponent.java

@@ -25,6 +25,7 @@ public class PrivacyNoticeComponent extends ScrollPane {
     @FXML private TextFlow mistralAiPrivacyTextFlow;
     @FXML private TextFlow geminiPrivacyTextFlow;
     @FXML private TextFlow huggingFacePrivacyTextFlow;
+    @FXML private TextFlow gpt4AllTextFlow;
     @FXML private Text embeddingModelText;
 
     private final AiPreferences aiPreferences;
@@ -49,6 +50,7 @@ private void initialize() {
         initPrivacyHyperlink(mistralAiPrivacyTextFlow, AiProvider.MISTRAL_AI);
         initPrivacyHyperlink(geminiPrivacyTextFlow, AiProvider.GEMINI);
         initPrivacyHyperlink(huggingFacePrivacyTextFlow, AiProvider.HUGGING_FACE);
+        initPrivacyHyperlink(gpt4AllTextFlow, AiProvider.GPT4ALL);
 
         String newEmbeddingModelText = embeddingModelText.getText().replaceAll("%0", aiPreferences.getEmbeddingModel().sizeInfo());
         embeddingModelText.setText(newEmbeddingModelText);

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

@@ -37,7 +37,7 @@
 import org.jabref.gui.entryeditor.fileannotationtab.FulltextSearchResultsTab;
 import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
 import org.jabref.gui.help.HelpAction;
-import org.jabref.gui.importer.GrobidOptInDialogHelper;
+import org.jabref.gui.importer.GrobidUseDialogHelper;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.menus.ChangeEntryTypeMenu;
@@ -423,7 +423,7 @@ private void setupToolBar() {
             if (fetcher instanceof PdfMergeMetadataImporter.EntryBasedFetcherWrapper) {
                 // Handle Grobid Opt-In in case of the PdfMergeMetadataImporter
                 fetcherMenuItem.setOnAction(event -> {
-                    GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences());
+                    GrobidUseDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences());
                     PdfMergeMetadataImporter.EntryBasedFetcherWrapper pdfMergeMetadataImporter =
                             new PdfMergeMetadataImporter.EntryBasedFetcherWrapper(
                                     preferences.getImportFormatPreferences(),

src/main/java/org/jabref/gui/entrytype/EntryTypeView.java

@@ -16,6 +16,7 @@
 import javafx.scene.control.Tooltip;
 import javafx.scene.layout.FlowPane;
 import javafx.stage.Screen;
+import javafx.stage.Stage;
 
 import org.jabref.gui.DialogService;
 import org.jabref.gui.LibraryTab;
@@ -87,6 +88,10 @@ public EntryTypeView(LibraryTab libraryTab, DialogService dialogService, GuiPref
                   .load()
                   .setAsDialogPane(this);
 
+        Stage stage = (Stage) getDialogPane().getScene().getWindow();
+        stage.setMinHeight(400);
+        stage.setMinWidth(500);
+
         ControlHelper.setAction(generateButton, this.getDialogPane(), event -> viewModel.runFetcherWorker());
         setOnCloseRequest(e -> viewModel.cancelFetcherWorker());
 

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java

@@ -41,7 +41,7 @@
 import org.jabref.gui.copyfiles.CopySingleFileAction;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.icon.JabRefIconView;
-import org.jabref.gui.importer.GrobidOptInDialogHelper;
+import org.jabref.gui.importer.GrobidUseDialogHelper;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.linkedfile.DeleteFileAction;
 import org.jabref.gui.linkedfile.LinkedFileEditDialog;
@@ -236,7 +236,7 @@ private Node createFileDisplay(LinkedFileViewModel linkedFile) {
         parsePdfMetadata.setTooltip(new Tooltip(Localization.lang("Parse Metadata from PDF.")));
         parsePdfMetadata.visibleProperty().bind(linkedFile.isOfflinePdfProperty());
         parsePdfMetadata.setOnAction(event -> {
-            GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences());
+            GrobidUseDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences());
             linkedFile.parsePdfMetadataAndShowMergeDialog();
         });
         parsePdfMetadata.getStyleClass().setAll("icon-button");

src/main/java/org/jabref/gui/importer/GrobidOptInDialogHelper.java renamed to src/main/java/org/jabref/gui/importer/GrobidUseDialogHelper.java

@@ -7,29 +7,31 @@
 /**
  * Metadata extraction from PDFs and plaintext works very well using Grobid, but we do not want to enable it by default
  * due to data privacy concerns.
- * To make users aware of the feature, we ask each time before querying Grobid, giving the option to opt-out.
+ * To make users aware of the feature, we ask before querying for the first time Grobid, saving the users' preference
  */
-public class GrobidOptInDialogHelper {
+public class GrobidUseDialogHelper {
 
     /**
-     * If Grobid is not enabled but the user has not explicitly opted-out of Grobid, we ask for permission to send data
-     * to Grobid using a dialog and giving an opt-out option.
+     * If the user has not explicitly opted-in/out of Grobid, we ask for permission to send data to Grobid by using
+     * a dialog. The users' preference is saved.
      *
      * @param dialogService the DialogService to use
      * @return if the user enabled Grobid, either in the past or after being asked by the dialog.
      */
     public static boolean showAndWaitIfUserIsUndecided(DialogService dialogService, GrobidPreferences preferences) {
+        if (preferences.isGrobidUseAsked()) {
+            return preferences.isGrobidEnabled();
+        }
         if (preferences.isGrobidEnabled()) {
+            preferences.setGrobidUseAsked(true);
             return true;
         }
-        if (preferences.isGrobidOptOut()) {
-            return false;
-        }
-        boolean grobidEnabled = dialogService.showConfirmationDialogWithOptOutAndWait(
+        boolean grobidEnabled = dialogService.showConfirmationDialogAndWait(
                 Localization.lang("Remote services"),
                 Localization.lang("Allow sending PDF files and raw citation strings to a JabRef online service (Grobid) to determine Metadata. This produces better results."),
-                Localization.lang("Do not ask again"),
-                optOut -> preferences.setGrobidOptOut(optOut));
+                Localization.lang("Send to Grobid"),
+                Localization.lang("Do not send"));
+        preferences.setGrobidUseAsked(true);
         preferences.setGrobidEnabled(grobidEnabled);
         return grobidEnabled;
     }

src/main/java/org/jabref/gui/importer/ImportCommand.java

@@ -144,7 +144,7 @@ private ParserResult doImport(List<Path> files, Importer importFormat) throws IO
                 if (importer.isEmpty()) {
                     // Unknown format
                     UiTaskExecutor.runAndWaitInJavaFXThread(() -> {
-                        if (FileUtil.isPDFFile(filename) && GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences())) {
+                        if (FileUtil.isPDFFile(filename) && GrobidUseDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences())) {
                             importFormatReader.reset();
                         }
                         dialogService.notify(Localization.lang("Importing file %0 as unknown format", filename.getFileName().toString()));
@@ -155,7 +155,7 @@ private ParserResult doImport(List<Path> files, Importer importFormat) throws IO
                     UiTaskExecutor.runAndWaitInJavaFXThread(() -> {
                         if (((importer.get() instanceof PdfGrobidImporter)
                                 || (importer.get() instanceof PdfMergeMetadataImporter))
-                                && GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences())) {
+                                && GrobidUseDialogHelper.showAndWaitIfUserIsUndecided(dialogService, preferences.getGrobidPreferences())) {
                             importFormatReader.reset();
                         }
                         dialogService.notify(Localization.lang("Importing in %0 format", importer.get().getName()) + "...");