WIP Restapi

build.gradle

@@ -42,6 +42,7 @@ version = project.findProperty('projVersion') ?: '100.0.0'
 java {
     sourceCompatibility = JavaVersion.VERSION_19
     targetCompatibility = JavaVersion.VERSION_19
+
     // Workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
     // Should be removed as soon as Gradle 7.0.1 is released ( https://github.com/gradle/gradle/issues/16922#issuecomment-828217060 )
     modularity.inferModulePath.set(false)
@@ -142,9 +143,6 @@ dependencies {
 
     implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.4.0.202211300538-r'
 
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.14.2'
-    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.14.2'
-
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.7'
 
     implementation 'org.postgresql:postgresql:42.5.4'
@@ -161,7 +159,7 @@ dependencies {
 
     implementation 'jakarta.annotation:jakarta.annotation-api:2.1.1'
     implementation 'jakarta.inject:jakarta.inject-api:2.0.1'
-
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.1'
 
     implementation 'com.github.JabRef:afterburner.fx:testmoduleinfo-SNAPSHOT'
     implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
@@ -184,10 +182,26 @@ dependencies {
 
     implementation 'de.undercouch:citeproc-java:3.0.0-alpha.6'
 
-    // jakarta.activation is already dependency of glassfish
+    // Data mapping
     implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '3.0.1'
+    // Data mapping provider for JAXB annotated classes (e.g., MedlineImporter)
     implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
+    // JSON mapping
+    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.14.2'
+    // YML mapping
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.14.2'
+
+    // JAX-WS
+    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:3.1.0'
+
+    // http sever
+    // "Starting a Grizzly server to run a JAX-RS or Jersey application is one of the most lightweight and easy ways how to expose a functional RESTful services application."
+    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.1'
+
+    implementation group: 'org.glassfish.jersey.media', name: 'jersey-media-jaxb', version: '3.1.1'
+    implementation group: 'org.glassfish.jersey.media', name: 'jersey-media-json-jackson', version: '3.1.1'
+
     implementation ('com.github.tomtung:latex2unicode_2.13:0.3.2') {
         exclude module: 'fastparse_2.13'
     }
@@ -198,8 +212,6 @@ dependencies {
     }
 
     implementation 'com.vladsch.flexmark:flexmark:0.64.0'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.64.0'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.64.0'
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 

src/main/java/module-info.java

@@ -46,12 +46,28 @@
     with org.jabref.gui.logging.GuiWriter,
          org.jabref.gui.logging.ApplicationInsightsWriter;
 
-    // Preferences and XML
     requires java.prefs;
+
+    // XML, YAML, JSON
+    requires jdk.xml.dom;
+    // Enable JAXB annotations
     requires jakarta.xml.bind;
-    // needs to be loaded here as it's otherwise not found at runtime
+
+    // Enable YAML and JSON parsing by Jackson
+    requires com.fasterxml.jackson.databind;
+    requires com.fasterxml.jackson.dataformat.yaml;
+    requires com.fasterxml.jackson.datatype.jsr310;
+    // Enable JSON mapping at the REST server using Jackson2
+    // requires resteasy.jackson2.provider;
+    // Enable JAXB using the standard implementation by Glassfish
     requires org.glassfish.jaxb.runtime;
-    requires jdk.xml.dom;
+
+    requires jersey.common;
+    requires jersey.server;
+    requires jersey.media.jaxb;
+    requires jersey.media.json.jackson;
+    requires jersey.container.grizzly2.http;
+    requires jersey.hk2;
 
     // Annotations (@PostConstruct)
     requires jakarta.annotation;
@@ -94,10 +110,9 @@
     requires com.ibm.icu;
 
     requires flexmark;
-    requires flexmark.ext.gfm.strikethrough;
-    requires flexmark.ext.gfm.tasklist;
     requires flexmark.util.ast;
     requires flexmark.util.data;
+
     requires com.h2database.mvstore;
 
     // fulltext search
@@ -110,14 +125,12 @@
     requires org.apache.lucene.analysis.common;
     requires org.apache.lucene.highlighter;
 
-    requires com.fasterxml.jackson.databind;
-    requires com.fasterxml.jackson.dataformat.yaml;
-    requires com.fasterxml.jackson.datatype.jsr310;
     requires net.harawata.appdirs;
     requires com.sun.jna;
     requires com.sun.jna.platform;
 
     requires org.eclipse.jgit;
+    requires jakarta.ws.rs;
     uses org.eclipse.jgit.transport.SshSessionFactory;
     uses org.eclipse.jgit.lib.GpgSigner;
 }

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

@@ -3,6 +3,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.Authenticator;
+import java.net.URI;
 import java.nio.file.DirectoryStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -21,13 +22,15 @@
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.remote.RemotePreferences;
 import org.jabref.logic.remote.client.RemoteClient;
+import org.jabref.logic.shared.restserver.rest.Root;
 import org.jabref.logic.util.BuildInfo;
 import org.jabref.migrations.PreferencesMigrations;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreferencesService;
 
+import jakarta.ws.rs.SeBootstrap;
 import net.harawata.appdirs.AppDirsFactory;
 import org.apache.commons.cli.ParseException;
 import org.slf4j.Logger;
@@ -42,13 +45,15 @@
  * - Start the JavaFX application (if not in cli mode)
  */
 public class Launcher {
-    private static Logger LOGGER;
-    private static String[] ARGUMENTS;
+    // initialized after reading the preferences (which configure log directory, ...)
+    static Logger LOGGER;
 
     public static void main(String[] args) {
-        ARGUMENTS = args;
         addLogToDisk();
         try {
+            // we need a copy of the original arguments
+            String[] arguments = args;
+
             // Init preferences
             final JabRefPreferences preferences = JabRefPreferences.getInstance();
             Globals.prefs = preferences;
@@ -73,8 +78,9 @@ public static void main(String[] args) {
                     LOGGER.debug("JabRef shut down after processing command line arguments");
                     return;
                 }
+                startServer();
 
-                MainApplication.main(argumentProcessor.getParserResults(), argumentProcessor.isBlank(), preferences, ARGUMENTS);
+                MainApplication.main(argumentProcessor.getParserResults(), argumentProcessor.isBlank(), preferences, arguments);
             } catch (ParseException e) {
                 LOGGER.error("Problem parsing arguments", e);
                 JabRefCLI.printUsage(preferences);
@@ -84,6 +90,28 @@ public static void main(String[] args) {
         }
     }
 
+    static void startServer() {
+        SeBootstrap.Configuration.Builder configBuilder = SeBootstrap.Configuration.builder();
+        configBuilder.property(SeBootstrap.Configuration.PROTOCOL, "HTTP")
+                     .property(SeBootstrap.Configuration.HOST, "localhost")
+                     .property(SeBootstrap.Configuration.PORT, 2005);
+        SeBootstrap.start(new Root(), configBuilder.build()).thenAccept(instance -> {
+            instance.stopOnShutdown(stopResult ->
+                    System.out.printf("JabRef REST server stop result: %s [Native stop result: %s].%n", stopResult, stopResult.unwrap(Object.class)));
+            URI uri = instance.configuration().baseUri();
+            System.out.printf("JabRef REST server %s running at %s [Native handle: %s].%n", instance, uri, instance.unwrap(Object.class));
+        }).exceptionally(ex -> {
+            LOGGER.error("Error starting server", ex);
+            return null;
+       });
+
+        try {
+            Thread.currentThread().join();
+        } catch (InterruptedException e) {
+            LOGGER.error("could not join on current thread", e);
+        }
+    }
+
     /**
      * This needs to be called as early as possible. After the first log write, it
      * is not possible to alter

src/main/java/org/jabref/logic/layout/format/MarkdownFormatter.java

@@ -1,32 +1,21 @@
 package org.jabref.logic.layout.format;
 
-import java.util.List;
 import java.util.Objects;
 
 import org.jabref.logic.layout.LayoutFormatter;
 
-import com.vladsch.flexmark.ext.gfm.strikethrough.StrikethroughExtension;
-import com.vladsch.flexmark.ext.gfm.tasklist.TaskListExtension;
 import com.vladsch.flexmark.html.HtmlRenderer;
 import com.vladsch.flexmark.parser.Parser;
 import com.vladsch.flexmark.util.ast.Node;
-import com.vladsch.flexmark.util.data.MutableDataSet;
 
 public class MarkdownFormatter implements LayoutFormatter {
 
     private final Parser parser;
     private final HtmlRenderer renderer;
 
     public MarkdownFormatter() {
-        MutableDataSet options = new MutableDataSet();
-        // in case a new extension is added here, the depedency has to be added to build.gradle, too.
-        options.set(Parser.EXTENSIONS, List.of(
-                StrikethroughExtension.create(),
-                TaskListExtension.create()
-        ));
-
-        parser = Parser.builder(options).build();
-        renderer = HtmlRenderer.builder(options).build();
+        parser = Parser.builder().build();
+        renderer = HtmlRenderer.builder().build();
     }
 
     @Override

src/main/java/org/jabref/logic/shared/restserver/core/properties/ServerPropertyService.java

@@ -0,0 +1,49 @@
+package org.jabref.logic.shared.restserver.core.properties;
+
+import java.nio.file.Path;
+
+import org.jabref.gui.desktop.JabRefDesktop;
+import org.jabref.gui.desktop.os.NativeDesktop;
+import org.jabref.model.strings.StringUtil;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ServerPropertyService {
+    private static final Logger LOGGER = LoggerFactory.getLogger(ServerPropertyService.class);
+    private static ServerPropertyService instance;
+    private Path workingDirectory;
+
+    private ServerPropertyService() {
+        workingDirectory = determineWorkingDirectory();
+    }
+
+    public static ServerPropertyService getInstance() {
+        if (instance == null) {
+            instance = new ServerPropertyService();
+        }
+        return instance;
+    }
+
+    /**
+     * Tries to determine the working directory of the library.
+     * Uses the first path it finds when resolving in this order:
+     * 1. Environment variable LIBRARY_WORKSPACE
+     * 2. Default User home (via {@link NativeDesktop#getDefaultFileChooserDirectory()}) with a new directory for the library
+     */
+    private Path determineWorkingDirectory() {
+        String libraryWorkspaceEnvironmentVariable = System.getenv("LIBRARY_WORKSPACE");
+        if (!StringUtil.isNullOrEmpty(libraryWorkspaceEnvironmentVariable)) {
+            LOGGER.info("Environment Variable found, using defined directory: {}", libraryWorkspaceEnvironmentVariable);
+            return Path.of(libraryWorkspaceEnvironmentVariable);
+        } else {
+            Path fallbackDirectory = JabRefDesktop.getNativeDesktop().getDefaultFileChooserDirectory().resolve("planqk-library");
+            LOGGER.info("Working directory was not found in either the properties or the environment variables, falling back to default location: {}", fallbackDirectory);
+            return fallbackDirectory;
+        }
+    }
+
+    public Path getWorkingDirectory() {
+        return workingDirectory;
+    }
+}

src/main/java/org/jabref/logic/shared/restserver/core/repository/CrawlTask.java

@@ -0,0 +1,33 @@
+package org.jabref.logic.shared.restserver.core.repository;
+
+import java.io.IOException;
+
+import org.jabref.logic.crawler.Crawler;
+import org.jabref.logic.exporter.SaveException;
+
+import org.eclipse.jgit.api.errors.GitAPIException;
+
+public class CrawlTask implements Runnable {
+    private final Crawler crawler;
+    private TaskStatus status;
+
+    public CrawlTask(Crawler crawler) {
+        this.crawler = crawler;
+    }
+
+    public TaskStatus getStatus() {
+        return status;
+    }
+
+    @Override
+    public void run() {
+        status = TaskStatus.RUNNING;
+        try {
+            crawler.performCrawl();
+        } catch (IOException | GitAPIException | SaveException e) {
+            status = TaskStatus.FAILED;
+            throw new RuntimeException(e);
+        }
+        status = TaskStatus.DONE;
+    }
+}