Add git support

.vscode/settings.json

@@ -1,5 +1,5 @@
 {
-    "java.configuration.updateBuildConfiguration": "interactive",
+    "java.configuration.updateBuildConfiguration": "automatic",
     "java.format.settings.url": "/config/VSCode Code Style.xml",
     "java.checkstyle.configuration": "${workspaceFolder}/config/checkstyle/checkstyle_reviewdog.xml",
     "java.checkstyle.version": "10.3.4"

CHANGELOG.md

@@ -12,6 +12,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Added
 
 - When importing entries form the "Citation relations" tab, the field [cites](https://docs.jabref.org/advanced/entryeditor/entrylinks) is now filled according to the relationship between the entries. [#10572](https://github.com/JabRef/jabref/pull/10752)
+- We added git support for backing up bib files with integration to local and remote repositories and support for SSH and username/password authentication [#578](https://github.com/koppor/jabref/issues/578)
 
 ### Changed
 

build.gradle

@@ -144,6 +144,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.13.1'
     implementation 'org.antlr:antlr4-runtime:4.13.1'
 
+    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit.ssh.apache', version: '6.7.0.202309050840-r'
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.8.0.202311291450-r'
 
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.16.1'
@@ -253,6 +254,12 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
+    testImplementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit.http.server', version: '6.7.0.202309050840-r'
+    testImplementation group: 'org.eclipse.jetty', name: 'jetty-servlet', version: '9.4.51.v20230217'
+    testImplementation group: 'org.eclipse.jetty', name: 'jetty-security', version: '9.4.51.v20230217'
+
+    testCompileOnly group: 'javax.servlet', name: 'javax.servlet-api', version: '3.1.0'
+
     checkstyle 'com.puppycrawl.tools:checkstyle:10.12.5'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
@@ -722,3 +729,7 @@ jmh {
     iterations = 10
     fork = 2
 }
+
+configurations.all {
+    exclude group: "commons-logging", module: "commons-logging"
+}

src/main/java/module-info.java

@@ -133,6 +133,7 @@
     requires com.sun.jna.platform;
 
     requires org.eclipse.jgit;
+    requires org.eclipse.jgit.ssh.apache;
     uses org.eclipse.jgit.transport.SshSessionFactory;
     uses org.eclipse.jgit.lib.GpgSigner;
 

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -32,6 +32,7 @@
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
 import org.jabref.logic.exporter.SaveException;
 import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
+import org.jabref.logic.git.GitHandler;
 import org.jabref.logic.l10n.Encodings;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.pdf.search.PdfIndexerManager;
@@ -45,6 +46,11 @@
 import org.jabref.model.metadata.SelfContainedSaveOrder;
 import org.jabref.preferences.PreferencesService;
 
+import org.eclipse.jgit.api.errors.CheckoutConflictException;
+import org.eclipse.jgit.api.errors.DetachedHeadException;
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.TransportException;
+import org.eclipse.jgit.errors.NoRemoteRepositoryException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -239,11 +245,23 @@ private boolean save(Path targetPath, SaveDatabaseMode mode) {
 
             boolean success = saveDatabase(targetPath, false, encoding, BibDatabaseWriter.SaveType.WITH_JABREF_META_DATA, getSaveOrder());
 
+            if (preferences.getGitPreferences().getAutoSync()) {
+                success = automaticGitPull(targetPath);
+            }
+
+            if (preferences.getGitPreferences().getAutoCommit()) {
+                boolean commited = automaticGitCommit(targetPath);
+                if (commited && preferences.getGitPreferences().getAutoSync()) {
+                    automaticGitPush(targetPath);
+                }
+            }
+
             if (success) {
                 libraryTab.getUndoManager().markUnchanged();
                 libraryTab.resetChangedProperties();
             }
             dialogService.notify(Localization.lang("Library saved"));
+
             return success;
         } catch (SaveException ex) {
             LOGGER.error(String.format("A problem occurred when trying to save the file %s", targetPath), ex);
@@ -316,4 +334,67 @@ private void saveWithDifferentEncoding(Path file, boolean selectedOnly, Charset
             }
         }
     }
+
+    /**
+     * @param filePath of library
+     * @return true on successful git pull
+     */
+    public boolean automaticGitPull(Path filePath) {
+        GitHandler git = new GitHandler(filePath.getParent(), preferences.getGitPreferences());
+        try {
+            git.pullOnCurrentBranch();
+        } catch (CheckoutConflictException e) {
+            git.forceGitPull();
+            dialogService.showErrorDialogAndWait(Localization.lang("Git"), Localization.lang("Local repository is out of date, please review the library and save again"));
+            LOGGER.info("Failed to pull");
+            return false;
+        } catch (NoRemoteRepositoryException e) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Git"), Localization.lang("No remote repository detected"));
+            LOGGER.info("No remote repository detected");
+        } catch (DetachedHeadException e) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Git"), Localization.lang("Git detached head"));
+            LOGGER.info("Git detached head");
+        } catch (TransportException e) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Git"), Localization.lang("Git credentials error"));
+            LOGGER.info("Git credentials error");
+        } catch (GitAPIException e) {
+            LOGGER.info("Failed to pull");
+            throw new RuntimeException(e);
+        } catch (IOException e) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Git"), Localization.lang("Failed to open repository"));
+            LOGGER.info("Failed to open repository");
+        }
+        return true;
+    }
+
+    /**
+     * @param filePath of library
+     * @return true on successful git commit
+     */
+    public boolean automaticGitCommit(Path filePath) {
+        GitHandler git = new GitHandler(filePath.getParent(), preferences.getGitPreferences());
+        String automaticCommitMsg = "Automatic update via JabRef";
+        if (preferences.getGitPreferences().getAutoCommit()) {
+            try {
+                return git.createCommitWithSingleFileOnCurrentBranch(filePath.getFileName().toString(), automaticCommitMsg);
+            } catch (GitAPIException | IOException e) {
+                dialogService.showErrorDialogAndWait(Localization.lang("Git"), Localization.lang("Failed to open repository"));
+                LOGGER.info("Failed to open repository");
+            }
+        }
+        return false;
+    }
+
+    /**
+     * @param filePath of library
+     */
+    public void automaticGitPush(Path filePath) {
+        GitHandler git = new GitHandler(filePath.getParent(), preferences.getGitPreferences());
+        try {
+            git.pushCommitsToRemoteRepository();
+        } catch (IOException e) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Git"), Localization.lang("Failed to push file in remote repository"));
+            LOGGER.info("Failed to push file in remote repository");
+        }
+    }
 }

src/main/java/org/jabref/gui/git/GitCredentialsDialogView.java

@@ -0,0 +1,74 @@
+package org.jabref.gui.git;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
+import javafx.scene.control.DialogPane;
+import javafx.scene.control.Label;
+import javafx.scene.control.PasswordField;
+import javafx.scene.control.TextArea;
+import javafx.scene.control.TextField;
+import javafx.scene.layout.VBox;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.util.BaseDialog;
+import org.jabref.logic.git.GitCredential;
+import org.jabref.logic.l10n.Localization;
+
+import com.airhacks.afterburner.injection.Injector;
+
+public class GitCredentialsDialogView extends BaseDialog<Void> {
+
+    @FXML private ButtonType copyVersionButton;
+    @FXML private TextArea textAreaVersions;
+    private DialogService dialogService;
+    private DialogPane pane;
+
+    private ButtonType acceptButton;
+    private ButtonType cancelButton;
+    private TextField inputGitUsername;
+    private PasswordField inputGitPassword;
+
+    public GitCredentialsDialogView() {
+        this.setTitle(Localization.lang("Git credentials"));
+        this.dialogService = Injector.instantiateModelOrService(DialogService.class);
+
+        this.pane = new DialogPane();
+        VBox vBox = new VBox();
+        this.inputGitUsername = new TextField();
+        this.inputGitPassword = new PasswordField();
+        this.acceptButton = new ButtonType(Localization.lang("Accept"), ButtonBar.ButtonData.APPLY);
+        this.cancelButton = new ButtonType(Localization.lang("Cancel"), ButtonBar.ButtonData.CANCEL_CLOSE);
+
+        vBox.getChildren().add(new Label(Localization.lang("Git username")));
+        vBox.getChildren().add(this.inputGitUsername);
+        vBox.getChildren().add(new Label(Localization.lang("Git password")));
+        vBox.getChildren().add(this.inputGitPassword);
+
+        this.pane.setContent(vBox);
+    }
+
+    public void showGitCredentialsDialog() {
+        dialogService.showCustomDialogAndWait(Localization.lang("Git credentials"), this.pane, this.acceptButton, this.cancelButton);
+    }
+
+    public GitCredential getCredentials() {
+        dialogService.showCustomDialogAndWait(Localization.lang("Git credentials"), this.pane, this.acceptButton, this.cancelButton);
+        GitCredential gitCredentials = new GitCredential(this.inputGitUsername.getText(), this.inputGitPassword.getText());
+
+        return gitCredentials;
+    }
+
+    public String getGitPassword() {
+        return this.inputGitPassword.getText();
+    }
+
+    public String getGitUsername() {
+        return this.inputGitUsername.getText();
+    }
+
+    @FXML
+    private void initialize() {
+        this.setResizable(false);
+    }
+}

src/main/java/org/jabref/gui/preferences/PreferencesDialogViewModel.java

@@ -24,6 +24,7 @@
 import org.jabref.gui.preferences.external.ExternalTab;
 import org.jabref.gui.preferences.externalfiletypes.ExternalFileTypesTab;
 import org.jabref.gui.preferences.general.GeneralTab;
+import org.jabref.gui.preferences.git.GitTab;
 import org.jabref.gui.preferences.groups.GroupsTab;
 import org.jabref.gui.preferences.journals.JournalAbbreviationsTab;
 import org.jabref.gui.preferences.keybindings.KeyBindingsTab;
@@ -81,7 +82,8 @@ public PreferencesDialogViewModel(DialogService dialogService, PreferencesServic
                 new XmpPrivacyTab(),
                 new CustomImporterTab(),
                 new CustomExporterTab(),
-                new NetworkTab()
+                new NetworkTab(),
+                new GitTab()
         );
     }
 

src/main/java/org/jabref/gui/preferences/git/GitTab.fxml

@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?import javafx.scene.control.Label?>
+<?import javafx.scene.control.TextField?>
+<?import javafx.scene.layout.HBox?>
+<?import javafx.scene.layout.VBox?>
+<?import javafx.scene.control.PasswordField?>
+<?import javafx.scene.control.CheckBox?>
+<fx:root spacing="10.0" type="VBox"
+         xmlns="http://javafx.com/javafx" xmlns:fx="http://javafx.com/fxml"
+         fx:controller="org.jabref.gui.preferences.git.GitTab">
+    <Label styleClass="titleHeader" text="%Git"/>
+    <Label styleClass="sectionHeader" text="%Credential"/>
+    <HBox alignment="CENTER_LEFT" spacing="10.0">
+        <Label text="%Email"/>
+        <TextField fx:id="username" minWidth="150.0" HBox.hgrow="ALWAYS"/>
+        <Label text="%Password"/>
+        <PasswordField fx:id="password" minWidth="150.0" HBox.hgrow="ALWAYS"/>
+    </HBox>
+    <HBox alignment="CENTER_LEFT" spacing="10.0">
+        <CheckBox fx:id="autoCommit" text="%Enable git auto commit" />
+    </HBox>
+    <HBox alignment="CENTER_LEFT" spacing="10.0">
+        <CheckBox fx:id="autoSync" text="%Enable git auto push and merge" />
+    </HBox>
+</fx:root>

src/main/java/org/jabref/gui/preferences/git/GitTab.java

@@ -0,0 +1,41 @@
+package org.jabref.gui.preferences.git;
+
+import javafx.fxml.FXML;
+import javafx.scene.control.CheckBox;
+import javafx.scene.control.PasswordField;
+import javafx.scene.control.TextField;
+
+import org.jabref.gui.preferences.AbstractPreferenceTabView;
+import org.jabref.logic.l10n.Localization;
+
+import com.airhacks.afterburner.views.ViewLoader;
+
+public class GitTab extends AbstractPreferenceTabView<GitTabViewModel> {
+
+    @FXML private TextField username;
+    @FXML private PasswordField password;
+    @FXML private CheckBox autoCommit;
+    @FXML private CheckBox autoSync;
+
+    public GitTab() {
+        ViewLoader.view(this)
+                  .root(this)
+                  .load();
+        initialize();
+    }
+
+    @Override
+    public String getTabName() {
+        return Localization.lang("Git");
+    }
+
+    @FXML
+    private void initialize() {
+        viewModel = new GitTabViewModel(preferencesService.getGitPreferences());
+
+        username.textProperty().bindBidirectional(viewModel.getUsernameProperty());
+        password.textProperty().bindBidirectional(viewModel.getPasswordProperty());
+        autoCommit.selectedProperty().bindBidirectional(viewModel.getAutoCommitProperty());
+        autoSync.selectedProperty().bindBidirectional(viewModel.getAutoSyncProperty());
+    }
+}

src/main/java/org/jabref/gui/preferences/git/GitTabViewModel.java

@@ -0,0 +1,71 @@
+package org.jabref.gui.preferences.git;
+
+import java.util.List;
+
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.StringProperty;
+
+import org.jabref.gui.preferences.PreferenceTabViewModel;
+import org.jabref.logic.git.GitPreferences;
+
+public class GitTabViewModel implements PreferenceTabViewModel {
+    private final StringProperty username;
+    private final StringProperty password;
+    private final BooleanProperty autoCommit;
+    private final BooleanProperty autoSync;
+    private final GitPreferences gitPreferences;
+
+    public GitTabViewModel(GitPreferences gitPreferences) {
+        this.gitPreferences = gitPreferences;
+        this.autoCommit = gitPreferences.getAutoCommitProperty();
+        this.autoSync = gitPreferences.getAutoSyncProperty();
+        this.username = gitPreferences.getUsernameProperty();
+        this.password = gitPreferences.getPasswordProperty();
+    }
+
+    @Override
+    public void setValues() {
+        this.username.setValue(this.gitPreferences.getUsername());
+        this.password.setValue(this.gitPreferences.getPassword());
+        this.autoCommit.setValue(this.gitPreferences.getAutoCommit() || this.gitPreferences.getAutoSync());
+        this.autoSync.setValue(this.gitPreferences.getAutoSync());
+    }
+
+    @Override
+    public void storeSettings() {
+    }
+
+    @Override
+    public boolean validateSettings() {
+        return PreferenceTabViewModel.super.validateSettings();
+    }
+
+    @Override
+    public List<String> getRestartWarnings() {
+        return PreferenceTabViewModel.super.getRestartWarnings();
+    }
+
+    public String getUsername() {
+        return this.username.get();
+    }
+
+    public StringProperty getUsernameProperty() {
+        return this.username;
+    }
+
+    public String getPassword() {
+        return this.password.get();
+    }
+
+    public StringProperty getPasswordProperty() {
+        return this.password;
+    }
+
+    public BooleanProperty getAutoCommitProperty() {
+        return this.autoCommit;
+    }
+
+    public BooleanProperty getAutoSyncProperty() {
+        return this.autoSync;
+    }
+}